From d7d459e531627c9c83bfc5943c2913e79c2045ac Mon Sep 17 00:00:00 2001 From: Edric Choi Date: Tue, 18 Aug 2026 22:12:25 -0500 Subject: [PATCH 01/11] Add ShapeMapper2 public container candidate --- .../workflows/shapemapper2-container-poc.yml | 62 + containers/shapemapper2/.dockerignore | 10 + containers/shapemapper2/COMPLIANCE.md | 123 + containers/shapemapper2/Dockerfile | 87 + containers/shapemapper2/Dockerfile.reference | 43 + containers/shapemapper2/LICENSES/AGPL-3.0.txt | 661 + .../shapemapper2/LICENSES/Artistic-2.0.txt | 171 + .../shapemapper2/LICENSES/BBMap-UC-LBL.txt | 25 + containers/shapemapper2/LICENSES/GPL-3.0.txt | 674 + .../Ghostscript-bundled-COPYING-GPL-3.0.txt | 674 + .../LICENSES/Graphviz-EPL-1.0.txt | 227 + .../shapemapper2/LICENSES/Miniconda.txt | 50 + .../LICENSES/OpenJDK-Assembly-Exception.txt | 27 + .../LICENSES/OpenJDK-DISCLAIMER.txt | 47 + .../shapemapper2/LICENSES/OpenJDK-GPL-2.0.txt | 347 + .../LICENSES/OpenJDK-THIRD_PARTY_README.txt | 3600 ++ .../LICENSES/OpenJDK-source-offer-readme.txt | 18 + .../shapemapper2/LICENSES/ShapeMapper-MIT.txt | 27 + .../PUBLIC_THIRD_PARTY_NOTICES.md | 25 + containers/shapemapper2/QUEST.md | 30 + containers/shapemapper2/README.md | 132 + .../shapemapper2/THIRD_PARTY_NOTICES.md | 50 + containers/shapemapper2/build-metadata.json | 40 + containers/shapemapper2/checksums.txt | 10 + containers/shapemapper2/conda-packages.tsv | 219 + .../shapemapper2/copyleft-conda-packages.tsv | 65 + .../shapemapper2/fetch-compliance-sources.sh | 78 + containers/shapemapper2/sbom.spdx.json | 40331 ++++++++++++++++ containers/shapemapper2/source-manifest.tsv | 11 + containers/shapemapper2/test-container.sh | 35 + containers/shapemapper2/test-upstream.sh | 47 + .../shapemapper2/validate-sif-on-quest.sh | 57 + 32 files changed, 48003 insertions(+) create mode 100644 .github/workflows/shapemapper2-container-poc.yml create mode 100644 containers/shapemapper2/.dockerignore create mode 100644 containers/shapemapper2/COMPLIANCE.md create mode 100644 containers/shapemapper2/Dockerfile create mode 100644 containers/shapemapper2/Dockerfile.reference create mode 100644 containers/shapemapper2/LICENSES/AGPL-3.0.txt create mode 100644 containers/shapemapper2/LICENSES/Artistic-2.0.txt create mode 100644 containers/shapemapper2/LICENSES/BBMap-UC-LBL.txt create mode 100644 containers/shapemapper2/LICENSES/GPL-3.0.txt create mode 100644 containers/shapemapper2/LICENSES/Ghostscript-bundled-COPYING-GPL-3.0.txt create mode 100644 containers/shapemapper2/LICENSES/Graphviz-EPL-1.0.txt create mode 100644 containers/shapemapper2/LICENSES/Miniconda.txt create mode 100644 containers/shapemapper2/LICENSES/OpenJDK-Assembly-Exception.txt create mode 100644 containers/shapemapper2/LICENSES/OpenJDK-DISCLAIMER.txt create mode 100644 containers/shapemapper2/LICENSES/OpenJDK-GPL-2.0.txt create mode 100644 containers/shapemapper2/LICENSES/OpenJDK-THIRD_PARTY_README.txt create mode 100644 containers/shapemapper2/LICENSES/OpenJDK-source-offer-readme.txt create mode 100644 containers/shapemapper2/LICENSES/ShapeMapper-MIT.txt create mode 100644 containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md create mode 100644 containers/shapemapper2/QUEST.md create mode 100644 containers/shapemapper2/README.md create mode 100644 containers/shapemapper2/THIRD_PARTY_NOTICES.md create mode 100644 containers/shapemapper2/build-metadata.json create mode 100644 containers/shapemapper2/checksums.txt create mode 100644 containers/shapemapper2/conda-packages.tsv create mode 100644 containers/shapemapper2/copyleft-conda-packages.tsv create mode 100755 containers/shapemapper2/fetch-compliance-sources.sh create mode 100644 containers/shapemapper2/sbom.spdx.json create mode 100644 containers/shapemapper2/source-manifest.tsv create mode 100755 containers/shapemapper2/test-container.sh create mode 100755 containers/shapemapper2/test-upstream.sh create mode 100755 containers/shapemapper2/validate-sif-on-quest.sh diff --git a/.github/workflows/shapemapper2-container-poc.yml b/.github/workflows/shapemapper2-container-poc.yml new file mode 100644 index 0000000..7e99357 --- /dev/null +++ b/.github/workflows/shapemapper2-container-poc.yml @@ -0,0 +1,62 @@ +name: ShapeMapper2 public candidate validation + +on: + pull_request: + paths: + - .github/workflows/shapemapper2-container-poc.yml + - containers/shapemapper2/** + workflow_dispatch: + +permissions: + contents: read + +jobs: + build-and-test: + runs-on: ubuntu-latest + timeout-minutes: 60 + steps: + - name: Check out NERD + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 + + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@bb05f3f5519dd87d3ba754cc423b652a5edd6d2c # v4.2.0 + + - name: Build amd64 image without publishing + uses: docker/build-push-action@53b7df96c91f9c12dcc8a07bcb9ccacbed38856a # v7.3.0 + with: + context: containers/shapemapper2 + platforms: linux/amd64 + load: true + push: false + tags: nerd-shapemapper2:2.3-public-candidate + + - name: Run upstream example smoke test + run: containers/shapemapper2/test-container.sh nerd-shapemapper2:2.3-public-candidate + + - name: Run complete upstream test suite + run: containers/shapemapper2/test-upstream.sh nerd-shapemapper2:2.3-public-candidate + + - name: Capture exact Debian binary and source package inventory + run: | + docker run --rm --entrypoint dpkg-query \ + nerd-shapemapper2:2.3-public-candidate \ + -W '-f=${binary:Package}\t${Version}\t${source:Package}\t${source:Version}\n' \ + | LC_ALL=C sort > shapemapper2-2.3-r0.debian-packages.tsv + + - name: Upload Debian package inventory + uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2 + with: + name: shapemapper2-2.3-r0-debian-packages + path: shapemapper2-2.3-r0.debian-packages.tsv + retention-days: 30 + if-no-files-found: error + + - name: Generate SPDX SBOM + uses: anchore/sbom-action@e22c389904149dbc22b58101806040fa8d37a610 # v0.24.0 + with: + image: nerd-shapemapper2:2.3-public-candidate + format: spdx-json + output-file: shapemapper2-2.3-r0.spdx.json + artifact-name: shapemapper2-2.3-r0.spdx.json + upload-artifact-retention: 30 + upload-release-assets: false diff --git a/containers/shapemapper2/.dockerignore b/containers/shapemapper2/.dockerignore new file mode 100644 index 0000000..3599c2c --- /dev/null +++ b/containers/shapemapper2/.dockerignore @@ -0,0 +1,10 @@ +** +!Dockerfile +!Dockerfile.reference +!LICENSES/ +!LICENSES/** +!THIRD_PARTY_NOTICES.md +!PUBLIC_THIRD_PARTY_NOTICES.md +!source-manifest.tsv +!conda-packages.tsv +!copyleft-conda-packages.tsv diff --git a/containers/shapemapper2/COMPLIANCE.md b/containers/shapemapper2/COMPLIANCE.md new file mode 100644 index 0000000..7ce0bb6 --- /dev/null +++ b/containers/shapemapper2/COMPLIANCE.md @@ -0,0 +1,123 @@ +# ShapeMapper2 container compliance checklist + +This is a working redistribution checklist, not legal advice. Public GHCR +publication remains blocked until the public-candidate checklist is complete +and the project owner gives explicit approval. + +## Public candidate (`Dockerfile`) + +The public candidate compiles the unchanged upstream v2.3 source tag and uses +Debian 12 packages. It excludes the official release archive's Miniconda +environment and old prebuilt third-party executables. That removes the exact +Azul Zulu and historical Conda source gaps described later in this document. + +- [x] Pin the upstream ShapeMapper v2.3 source archive by SHA-256. +- [x] Preserve the ShapeMapper MIT notice in the source tree and image. +- [x] Compile without patching or vendoring the upstream repository. +- [x] Use distribution packages for Bowtie2, STAR, BBMap/BBMerge, Graphviz, + Ghostscript, pv, OpenJDK, Python, Boost, zlib, and transitive dependencies. +- [x] Preserve Debian package copyright records under + `/usr/share/doc//copyright`. +- [x] Add `PUBLIC_THIRD_PARTY_NOTICES.md` as an index to those records. +- [ ] Run the upstream example and all built-in tests against the final + candidate image. +- [ ] Export the exact installed binary-to-source Debian package inventory + using `dpkg-query`, and retain it with the release record. +- [ ] Generate a fresh SPDX SBOM from the final candidate; the existing + `sbom.spdx.json` describes only the private reference image. +- [ ] Retrieve and retain the exact Debian corresponding-source packages needed + for redistributed copyleft components. Do this from the tested final package + inventory, not from the older Conda list. +- [ ] Confirm that every directly used executable is found at the expected + command name, especially Debian's BBMerge launcher. +- [ ] Record the final image digest, CI run, package inventory, SBOM, and source + bundle checksums together. +- [ ] Obtain explicit owner approval before the first GHCR push or public + visibility change. + +The first local source build produced a 508,942,308-byte amd64 image. Runtime +inspection was interrupted by host disk exhaustion immediately after the +build. A second build compiled with the final two-job limit and installed all +runtime packages, but storage failed during final layer assembly. The size is +therefore provisional evidence rather than a release result. + +## Private reference image (`Dockerfile.reference`) + +The remaining sections document the official-release wrapper. They explain why +it is retained privately as a behavioral reference rather than published. + +## Evidence already captured + +- [x] Preserve the upstream ShapeMapper MIT license in the image and in + `LICENSES/ShapeMapper-MIT.txt`. +- [x] Pin and checksum the exact upstream v2.3 release archive. +- [x] Generate an SPDX JSON SBOM from the locally built image. +- [x] Record the prominent bundled tools and their versions. +- [x] Extract and preserve the upstream archive's exact license texts for + Bowtie2, Ghostscript, Miniconda, and pv. +- [x] Extract and preserve the Conda environment's exact license texts for + BBMap, Graphviz, and OpenJDK. +- [x] Export all 218 embedded Conda package records, including exact package + URLs and available checksums, to `conda-packages.tsv`. +- [x] Isolate 64 Conda records with copyleft-related metadata into + `copyleft-conda-packages.tsv` for source/notice follow-up. +- [x] Download and checksum exact source releases for Bowtie2, STAR, + Ghostscript, BBMap, and Graphviz. +- [x] Preserve the exact Conda package archives containing the historical + build recipes for STAR, BBMap, Graphviz, and Azul Zulu OpenJDK in the source + retrieval plan. + +The current SBOM contains 168 package records. Thirty-six records have +`NOASSERTION` for at least one SPDX license field, but the Conda metadata +resolves most of those scanner omissions. Four Conda records themselves lack +a license value: `_libgcc_mutex`, `mysql-common`, `mysql-libs`, and the old +`readline` 6.2 package. The SBOM remains discovery evidence rather than a +complete redistribution determination. + +## Historical release-wrapper review + +- [ ] ShapeMapper2: retain the MIT copyright and permission notice. +- [x] Bowtie2 2.3.4.3: retain its bundled GPLv3 license and map its exact + versioned source archive and build scripts. +- [x] STAR 2.5.2a: retain GPLv3 and map the exact source plus the Conda recipe + that selected the bundled static executable. +- [ ] Ghostscript 9.25: conservatively treat the executable as AGPL and ship + the official complete 9.25 source. Keep documenting that ShapeMapper's + adjacent binary-archive `COPYING` file unexpectedly contains GPLv3 instead. +- [x] BBMap/BBMerge 37.78: retain the UC/LBNL notice. The license is permissive, + the exact source was verified, and the installed package includes Java source. +- [x] pv 1.6.20: retain Artistic License 2.0. The bundled tarball is a source + archive; the previous GPL classification was incorrect. +- [x] Graphviz 7.1.0: retain EPL-1.0 and map the exact source, Conda package, + recipe, and patches. +- [ ] OpenJDK 8.0.112: the exact Zulu binary input, license, exception, third- + party notices, source-offer identifier, Conda package, and recipe are known. + The upstream OpenJDK 8u112-b16 source is only a baseline; obtain Azul's + complete source for build `Zulu 8.19.0.1 d0cf8daf3adb` or replace this JDK + with a source-traceable runtime before public distribution. +- [ ] Miniconda and Conda packages: retain Miniconda terms; resolve the four + empty license records and map corresponding source for every remaining + copyleft package, not only the prominent tools. The focused list currently + contains 64 records, including large build/GUI stacks that ShapeMapper may + not need at runtime. +- [ ] Debian base packages: retain required copyright/license material and + document the Debian source retrieval path for the exact package versions. +- [x] Assemble a draft distributable `THIRD_PARTY_NOTICES.md`, license set, + source manifest, and checksum-verifying source fetcher. +- [ ] Retain the verified source collection as immutable release artifacts; + do not rely solely on upstream URLs. +- [ ] Optionally have the final notices/source bundle reviewed before changing + GHCR visibility to public. + +## Publication records for the public candidate + +- [ ] Save the successful CI run URL and source commit. +- [ ] Save the pushed OCI digest and generated provenance attestation. +- [ ] Attach the SPDX SBOM to the immutable release record. +- [ ] Validate the digest-pinned image after conversion to SIF on Quest. +- [ ] Record the SIF SHA-256, runtime/module version, host, date, and test log. +- [ ] Obtain explicit owner approval before making the GHCR package public. +- [ ] Verify anonymous pull only after approval and visibility change. + +Do not describe the container as compliance-complete while any review item is +unchecked. diff --git a/containers/shapemapper2/Dockerfile b/containers/shapemapper2/Dockerfile new file mode 100644 index 0000000..cc2a4da --- /dev/null +++ b/containers/shapemapper2/Dockerfile @@ -0,0 +1,87 @@ +# syntax=docker/dockerfile:1.7 + +# Public candidate: compile the unchanged upstream v2.3 source tag and use +# source-traceable Debian packages for runtime dependencies. +FROM --platform=linux/amd64 debian:bookworm-slim@sha256:362e64223cc0da95422b3b13c045186fc0a81250e765d31c025fbddf257f6143 AS build + +ARG SHAPEMAPPER_VERSION=2.3 +ARG SHAPEMAPPER_SOURCE_SHA256=1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f866b6f +ARG SHAPEMAPPER_SOURCE_URL=https://codeload.github.com/Weeks-UNC/shapemapper2/tar.gz/refs/tags/v2.3 + +RUN apt-get update \ + && apt-get install -y --no-install-recommends \ + ca-certificates \ + cmake \ + g++ \ + libboost-filesystem-dev \ + libboost-iostreams-dev \ + libboost-program-options-dev \ + libboost-system-dev \ + make \ + zlib1g-dev \ + && rm -rf /var/lib/apt/lists/* + +ADD --checksum=sha256:1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f866b6f \ + https://codeload.github.com/Weeks-UNC/shapemapper2/tar.gz/refs/tags/v2.3 \ + /tmp/shapemapper2-v2.3.tar.gz + +RUN test "${SHAPEMAPPER_VERSION}" = "2.3" \ + && test "${SHAPEMAPPER_SOURCE_SHA256}" = "1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f866b6f" \ + && test "${SHAPEMAPPER_SOURCE_URL}" = "https://codeload.github.com/Weeks-UNC/shapemapper2/tar.gz/refs/tags/v2.3" \ + && tar -xzf /tmp/shapemapper2-v2.3.tar.gz -C /opt \ + && mv /opt/shapemapper2-2.3 /opt/shapemapper2 \ + && rm /tmp/shapemapper2-v2.3.tar.gz \ + && cmake -S /opt/shapemapper2 -B /tmp/shapemapper-build -DCMAKE_BUILD_TYPE=Release \ + && cmake --build /tmp/shapemapper-build --parallel 2 + +FROM --platform=linux/amd64 debian:bookworm-slim@sha256:362e64223cc0da95422b3b13c045186fc0a81250e765d31c025fbddf257f6143 + +ARG SHAPEMAPPER_VERSION=2.3 +ARG SHAPEMAPPER_SOURCE_SHA256=1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f866b6f + +LABEL org.opencontainers.image.title="NERD ShapeMapper2" \ + org.opencontainers.image.description="ShapeMapper2 v2.3 built from the unchanged upstream source tag with Debian runtime packages" \ + org.opencontainers.image.source="https://github.com/LucksLab/nerd" \ + org.opencontainers.image.url="https://github.com/LucksLab/nerd" \ + org.opencontainers.image.version="2.3-r0-candidate" \ + org.opencontainers.image.vendor="Lucks Lab" \ + org.opencontainers.image.documentation="https://github.com/LucksLab/nerd/tree/main/containers/shapemapper2" \ + io.nerd.shapemapper.upstream="https://github.com/Weeks-UNC/shapemapper2/tree/v2.3" \ + io.nerd.shapemapper.source-sha256="1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f866b6f" \ + io.nerd.shapemapper.distribution="public-candidate" + +# Keep /usr/share/doc: Debian copyright files are part of the redistribution +# record and intentionally are not removed as a size optimization. +RUN apt-get update \ + && apt-get install -y --no-install-recommends \ + bbmap \ + bowtie2 \ + ca-certificates \ + fonts-dejavu-core \ + ghostscript \ + graphviz \ + libboost-filesystem1.74.0 \ + libboost-iostreams1.74.0 \ + libboost-program-options1.74.0 \ + libboost-system1.74.0 \ + pv \ + python3 \ + python3-matplotlib \ + python3-numpy \ + python3-scipy \ + python3-sklearn \ + rna-star \ + zlib1g \ + && rm -rf /var/lib/apt/lists/* + +COPY --from=build /opt/shapemapper2 /opt/shapemapper2 +COPY LICENSES/ShapeMapper-MIT.txt /usr/share/licenses/nerd-shapemapper2/ShapeMapper-MIT.txt +COPY PUBLIC_THIRD_PARTY_NOTICES.md /usr/share/licenses/nerd-shapemapper2/THIRD_PARTY_NOTICES.md + +ENV SHAPEMAPPER_ROOT_DIR=/opt/shapemapper2 \ + PATH=/opt/shapemapper2:/opt/shapemapper2/internals/bin:/usr/share/bbmap:${PATH} + +WORKDIR /work + +ENTRYPOINT ["/opt/shapemapper2/shapemapper"] +CMD ["--help"] diff --git a/containers/shapemapper2/Dockerfile.reference b/containers/shapemapper2/Dockerfile.reference new file mode 100644 index 0000000..71ca42a --- /dev/null +++ b/containers/shapemapper2/Dockerfile.reference @@ -0,0 +1,43 @@ +# syntax=docker/dockerfile:1.7 + +# Private reference image: this deliberately wraps the large official v2.3 +# release archive, including its historical Miniconda environment and binaries. +FROM --platform=linux/amd64 debian:bookworm-slim@sha256:362e64223cc0da95422b3b13c045186fc0a81250e765d31c025fbddf257f6143 + +ARG SHAPEMAPPER_VERSION=2.3 +ARG SHAPEMAPPER_ARCHIVE_SHA256=c3f14fdd782266522b377b1c22986b98cf9949164ec3f4d582fbe65da5e53ec6 +ARG SHAPEMAPPER_ARCHIVE_URL=https://github.com/Weeks-UNC/shapemapper2/releases/download/v2.3/shapemapper2-2.3.tar.gz + +LABEL org.opencontainers.image.title="NERD ShapeMapper2 reference" \ + org.opencontainers.image.description="Private reference wrapper around the official ShapeMapper2 v2.3 release archive" \ + org.opencontainers.image.source="https://github.com/LucksLab/nerd" \ + org.opencontainers.image.version="2.3-reference" \ + org.opencontainers.image.vendor="Lucks Lab" \ + io.nerd.shapemapper.upstream="https://github.com/Weeks-UNC/shapemapper2/releases/tag/v2.3" \ + io.nerd.shapemapper.archive-sha256="c3f14fdd782266522b377b1c22986b98cf9949164ec3f4d582fbe65da5e53ec6" \ + io.nerd.shapemapper.distribution="private-reference" + +ADD --checksum=sha256:c3f14fdd782266522b377b1c22986b98cf9949164ec3f4d582fbe65da5e53ec6 \ + https://github.com/Weeks-UNC/shapemapper2/releases/download/v2.3/shapemapper2-2.3.tar.gz \ + /tmp/shapemapper2-2.3.tar.gz + +RUN test "${SHAPEMAPPER_VERSION}" = "2.3" \ + && test "${SHAPEMAPPER_ARCHIVE_SHA256}" = "c3f14fdd782266522b377b1c22986b98cf9949164ec3f4d582fbe65da5e53ec6" \ + && test "${SHAPEMAPPER_ARCHIVE_URL}" = "https://github.com/Weeks-UNC/shapemapper2/releases/download/v2.3/shapemapper2-2.3.tar.gz" \ + && tar -xzf /tmp/shapemapper2-2.3.tar.gz -C /opt \ + && mv /opt/shapemapper2-2.3 /opt/shapemapper2 \ + && rm -f /tmp/shapemapper2-2.3.tar.gz \ + && rm -rf /opt/shapemapper2/.git + +COPY LICENSES/ /usr/share/licenses/nerd-shapemapper2/LICENSES/ +COPY THIRD_PARTY_NOTICES.md source-manifest.tsv conda-packages.tsv \ + copyleft-conda-packages.tsv \ + /usr/share/licenses/nerd-shapemapper2/ + +ENV SHAPEMAPPER_ROOT_DIR=/opt/shapemapper2 \ + PATH=/opt/shapemapper2:/opt/shapemapper2/internals/bin:/opt/shapemapper2/internals/thirdparty/miniconda/envs/shapemapper_make/bin:/opt/shapemapper2/internals/thirdparty/bowtie2:/opt/shapemapper2/internals/thirdparty/pipeviewer/bin:/opt/shapemapper2/internals/thirdparty/ghostscript:${PATH} + +WORKDIR /work + +ENTRYPOINT ["/opt/shapemapper2/shapemapper"] +CMD ["--help"] diff --git a/containers/shapemapper2/LICENSES/AGPL-3.0.txt b/containers/shapemapper2/LICENSES/AGPL-3.0.txt new file mode 100644 index 0000000..dba13ed --- /dev/null +++ b/containers/shapemapper2/LICENSES/AGPL-3.0.txt @@ -0,0 +1,661 @@ + GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +our General Public Licenses are intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + Developers that use our General Public Licenses protect your rights +with two steps: (1) assert copyright on the software, and (2) offer +you this License which gives you legal permission to copy, distribute +and/or modify the software. + + A secondary benefit of defending all users' freedom is that +improvements made in alternate versions of the program, if they +receive widespread use, become available for other developers to +incorporate. Many developers of free software are heartened and +encouraged by the resulting cooperation. However, in the case of +software used on network servers, this result may fail to come about. +The GNU General Public License permits making a modified version and +letting the public access it on a server without ever releasing its +source code to the public. + + The GNU Affero General Public License is designed specifically to +ensure that, in such cases, the modified source code becomes available +to the community. It requires the operator of a network server to +provide the source code of the modified version running there to the +users of that server. Therefore, public use of a modified version, on +a publicly accessible server, gives the public access to the source +code of the modified version. + + An older license, called the Affero General Public License and +published by Affero, was designed to accomplish similar goals. This is +a different license, not a version of the Affero GPL, but Affero has +released a new version of the Affero GPL which permits relicensing under +this license. + + The precise terms and conditions for copying, distribution and +modification follow. + + TERMS AND CONDITIONS + + 0. Definitions. + + "This License" refers to version 3 of the GNU Affero General Public License. + + "Copyright" also means copyright-like laws that apply to other kinds of +works, such as semiconductor masks. + + "The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + + To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of an +exact copy. 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Each party waives its rights + to a jury trial in any resulting litigation. diff --git a/containers/shapemapper2/LICENSES/Miniconda.txt b/containers/shapemapper2/LICENSES/Miniconda.txt new file mode 100644 index 0000000..82a4f2a --- /dev/null +++ b/containers/shapemapper2/LICENSES/Miniconda.txt @@ -0,0 +1,50 @@ +=================================== +Anaconda End User License Agreement +=================================== + +Copyright 2017, Continuum Analytics, Inc. + +All rights reserved under the 3-clause BSD License: + +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. + * Neither the name of Continuum Analytics, Inc. ("Continuum") nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL CONTINUUM ANALYTICS, INC. BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +Notice of Third Party Software Licenses +======================================= + +Anaconda contains open source software packages from third parties. These are available on an "as is" basis and subject to their individual license agreements. These licenses are available in Anaconda or at http://docs.continuum.io/anaconda/pkg-docs . Any binary packages of these third party tools you obtain via Anaconda are subject to their individual licenses as well as the Anaconda license. Continuum Analytics ("Continuum") reserves the right to change which third party tools are provided in Anaconda. + +In particular, Anaconda contains re-distributable, run-time, shared-library files from the Intel(TM) Math Kernel Library ("MKL binaries"). You are specifically authorized to use the MKL binaries with your installation of Anaconda. You are also authorized to redistribute the MKL binaries with Anaconda or in the conda package that contains them. Use and redistribution of the MKL binaries are subject to the licensing terms located at https://software.intel.com/en-us/license/intel-simplified-software-license. If needed, instructions for removing the MKL binaries after installation of Anaconda are available at http://www.continuum.io. + +Anaconda also contains cuDNN software binaries from NVIDIA Corporation ("cuDNN binaries"). You are specifically authorized to use the cuDNN binaries with your installation of Anaconda. 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IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE + LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION + OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION + WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +--- end of LICENSE --- + +-------------------------------------------------------------------------------- + +%% This notice is provided with respect to Kerberos functionality, which +which may be included with JRE 8, JDK 8, and OpenJDK 8. + +--- begin of LICENSE --- + + (C) Copyright IBM Corp. 1999 All Rights Reserved. + Copyright 1997 The Open Group Research Institute. All rights reserved. + +--- end of LICENSE --- + +------------------------------------------------------------------------------- + +%% This notice is provided with respect to Kerberos functionality from +FundsXpress, INC., which may be included with JRE 8, JDK 8, and OpenJDK 8. + +--- begin of LICENSE --- + + Copyright (C) 1998 by the FundsXpress, INC. + + All rights reserved. + + Export of this software from the United States of America may require + a specific license from the United States Government. It is the + responsibility of any person or organization contemplating export to + obtain such a license before exporting. + + WITHIN THAT CONSTRAINT, permission to use, copy, modify, and + distribute this software and its documentation for any purpose and + without fee is hereby granted, provided that the above copyright + notice appear in all copies and that both that copyright notice and + this permission notice appear in supporting documentation, and that + the name of FundsXpress. not be used in advertising or publicity pertaining + to distribution of the software without specific, written prior + permission. FundsXpress makes no representations about the suitability of + this software for any purpose. It is provided "as is" without express + or implied warranty. + + THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR + IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED + WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. + + +--- end of LICENSE --- + +------------------------------------------------------------------------------- + +%% This notice is provided with respect to Kronos OpenGL headers, which may be +included with JDK 8 and OpenJDK 8 source distributions. + +--- begin of LICENSE --- + + Copyright (c) 2007 The Khronos Group Inc. + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and/or associated documentation files (the "Materials"), to + deal in the Materials without restriction, including without limitation the + rights to use, copy, modify, merge, publish, distribute, sublicense, and/or + sell copies of the Materials, and to permit persons to whom the Materials are + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in all + copies or substantial portions of the Materials. + + THE MATERIALS ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE MATERIALS OR THE USE OR OTHER DEALINGS IN THE + MATERIALS. + +--- end of LICENSE --- + +------------------------------------------------------------------------------- + +%% Portions Copyright Eastman Kodak Company 1992 + +------------------------------------------------------------------------------- + +%% This notice is provided with respect to libpng 1.6.16, which may be +included with JRE 8, JDK 8, and OpenJDK 8. + +--- begin of LICENSE --- + +This copy of the libpng notices is provided for your convenience. In case of +any discrepancy between this copy and the notices in the file png.h that is +included in the libpng distribution, the latter shall prevail. + +COPYRIGHT NOTICE, DISCLAIMER, and LICENSE: + +If you modify libpng you may insert additional notices immediately following +this sentence. + +This code is released under the libpng license. + +libpng versions 1.2.6, August 15, 2004, through 1.6.16, December 22, 2014, are +Copyright (c) 2004, 2006-2014 Glenn Randers-Pehrson, and are +distributed according to the same disclaimer and license as libpng-1.2.5 +with the following individual added to the list of Contributing Authors + + Cosmin Truta + +libpng versions 1.0.7, July 1, 2000, through 1.2.5 - October 3, 2002, are +Copyright (c) 2000-2002 Glenn Randers-Pehrson, and are +distributed according to the same disclaimer and license as libpng-1.0.6 +with the following individuals added to the list of Contributing Authors + + Simon-Pierre Cadieux + Eric S. Raymond + Gilles Vollant + +and with the following additions to the disclaimer: + + There is no warranty against interference with your enjoyment of the + library or against infringement. There is no warranty that our + efforts or the library will fulfill any of your particular purposes + or needs. This library is provided with all faults, and the entire + risk of satisfactory quality, performance, accuracy, and effort is with + the user. + +libpng versions 0.97, January 1998, through 1.0.6, March 20, 2000, are +Copyright (c) 1998, 1999 Glenn Randers-Pehrson, and are +distributed according to the same disclaimer and license as libpng-0.96, +with the following individuals added to the list of Contributing Authors: + + Tom Lane + Glenn Randers-Pehrson + Willem van Schaik + +libpng versions 0.89, June 1996, through 0.96, May 1997, are +Copyright (c) 1996, 1997 Andreas Dilger +Distributed according to the same disclaimer and license as libpng-0.88, +with the following individuals added to the list of Contributing Authors: + + John Bowler + Kevin Bracey + Sam Bushell + Magnus Holmgren + Greg Roelofs + Tom Tanner + +libpng versions 0.5, May 1995, through 0.88, January 1996, are +Copyright (c) 1995, 1996 Guy Eric Schalnat, Group 42, Inc. + +For the purposes of this copyright and license, "Contributing Authors" +is defined as the following set of individuals: + + Andreas Dilger + Dave Martindale + Guy Eric Schalnat + Paul Schmidt + Tim Wegner + +The PNG Reference Library is supplied "AS IS". The Contributing Authors +and Group 42, Inc. disclaim all warranties, expressed or implied, +including, without limitation, the warranties of merchantability and of +fitness for any purpose. The Contributing Authors and Group 42, Inc. +assume no liability for direct, indirect, incidental, special, exemplary, +or consequential damages, which may result from the use of the PNG +Reference Library, even if advised of the possibility of such damage. + +Permission is hereby granted to use, copy, modify, and distribute this +source code, or portions hereof, for any purpose, without fee, subject +to the following restrictions: + +1. The origin of this source code must not be misrepresented. + +2. Altered versions must be plainly marked as such and must not + be misrepresented as being the original source. + +3. This Copyright notice may not be removed or altered from any + source or altered source distribution. + +The Contributing Authors and Group 42, Inc. specifically permit, without +fee, and encourage the use of this source code as a component to +supporting the PNG file format in commercial products. If you use this +source code in a product, acknowledgment is not required but would be +appreciated. + + +A "png_get_copyright" function is available, for convenient use in "about" +boxes and the like: + + printf("%s",png_get_copyright(NULL)); + +Also, the PNG logo (in PNG format, of course) is supplied in the +files "pngbar.png" and "pngbar.jpg (88x31) and "pngnow.png" (98x31). + +Libpng is OSI Certified Open Source Software. OSI Certified Open Source is a +certification mark of the Open Source Initiative. + +Glenn Randers-Pehrson +glennrp at users.sourceforge.net +December 22, 2014 + +--- end of LICENSE --- + +------------------------------------------------------------------------------- + +%% This notice is provided with respect to GIFLIB 5.1.1 & libungif 4.1.3, which may be +included with JRE 8, JDK 8, and OpenJDK 8. + +--- begin of LICENSE --- + +The GIFLIB distribution is Copyright (c) 1997 Eric S. Raymond + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. + +--- end of LICENSE --- + +------------------------------------------------------------------------------- + +%% This notice is provided with respect to Little CMS 2.7, which may be +included with JRE 8, JDK 8, and OpenJDK 8. + +--- begin of LICENSE --- + +Little CMS +Copyright (c) 1998-2015 Marti Maria Saguer + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. + +--- end of LICENSE --- + +------------------------------------------------------------------------------- + +%% Lucida is a registered trademark or trademark of Bigelow & Holmes in the +U.S. and other countries. + +------------------------------------------------------------------------------- + +%% This notice is provided with respect to Mesa 3D Graphics Library v4.1, +which may be included with JRE 8, JDK 8, and OpenJDK 8 source distributions. + +--- begin of LICENSE --- + + Mesa 3-D graphics library + Version: 4.1 + + Copyright (C) 1999-2002 Brian Paul All Rights Reserved. + + Permission is hereby granted, free of charge, to any person obtaining a + copy of this software and associated documentation files (the "Software"), + to deal in the Software without restriction, including without limitation + the rights to use, copy, modify, merge, publish, distribute, sublicense, + and/or sell copies of the Software, and to permit persons to whom the + Software is furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included + in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS + OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL + BRIAN PAUL BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN + AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +--- end of LICENSE --- + +------------------------------------------------------------------------------- + +%% This notice is provided with respect to Mozilla Network Security +Services (NSS), which is supplied with the JDK test suite in the OpenJDK +source code repository. It is licensed under Mozilla Public License (MPL), +version 2.0. + +The NSS libraries are supplied in executable form, built from unmodified +NSS source code labeled with the "NSS_3_16_RTM" HG tag. + +The NSS source code is available in the OpenJDK source code repository at: + jdk/test/sun/security/pkcs11/nss/src + +The NSS libraries are available in the OpenJDK source code repository at: + jdk/test/sun/security/pkcs11/nss/lib + +--- begin of LICENSE --- + +Mozilla Public License Version 2.0 +================================== + +1. Definitions +-------------- + +1.1. "Contributor" + means each individual or legal entity that creates, contributes to + the creation of, or owns Covered Software. + +1.2. "Contributor Version" + means the combination of the Contributions of others (if any) used + by a Contributor and that particular Contributor's Contribution. + +1.3. "Contribution" + means Covered Software of a particular Contributor. + +1.4. "Covered Software" + means Source Code Form to which the initial Contributor has attached + the notice in Exhibit A, the Executable Form of such Source Code + Form, and Modifications of such Source Code Form, in each case + including portions thereof. + +1.5. "Incompatible With Secondary Licenses" + means + + (a) that the initial Contributor has attached the notice described + in Exhibit B to the Covered Software; or + + (b) that the Covered Software was made available under the terms of + version 1.1 or earlier of the License, but not also under the + terms of a Secondary License. + +1.6. "Executable Form" + means any form of the work other than Source Code Form. + +1.7. "Larger Work" + means a work that combines Covered Software with other material, in + a separate file or files, that is not Covered Software. + +1.8. "License" + means this document. + +1.9. "Licensable" + means having the right to grant, to the maximum extent possible, + whether at the time of the initial grant or subsequently, any and + all of the rights conveyed by this License. + +1.10. "Modifications" + means any of the following: + + (a) any file in Source Code Form that results from an addition to, + deletion from, or modification of the contents of Covered + Software; or + + (b) any new file in Source Code Form that contains any Covered + Software. + +1.11. "Patent Claims" of a Contributor + means any patent claim(s), including without limitation, method, + process, and apparatus claims, in any patent Licensable by such + Contributor that would be infringed, but for the grant of the + License, by the making, using, selling, offering for sale, having + made, import, or transfer of either its Contributions or its + Contributor Version. + +1.12. "Secondary License" + means either the GNU General Public License, Version 2.0, the GNU + Lesser General Public License, Version 2.1, the GNU Affero General + Public License, Version 3.0, or any later versions of those + licenses. + +1.13. "Source Code Form" + means the form of the work preferred for making modifications. + +1.14. "You" (or "Your") + means an individual or a legal entity exercising rights under this + License. For legal entities, "You" includes any entity that + controls, is controlled by, or is under common control with You. For + purposes of this definition, "control" means (a) the power, direct + or indirect, to cause the direction or management of such entity, + whether by contract or otherwise, or (b) ownership of more than + fifty percent (50%) of the outstanding shares or beneficial + ownership of such entity. + +2. License Grants and Conditions +-------------------------------- + +2.1. Grants + +Each Contributor hereby grants You a world-wide, royalty-free, +non-exclusive license: + +(a) under intellectual property rights (other than patent or trademark) + Licensable by such Contributor to use, reproduce, make available, + modify, display, perform, distribute, and otherwise exploit its + Contributions, either on an unmodified basis, with Modifications, or + as part of a Larger Work; and + +(b) under Patent Claims of such Contributor to make, use, sell, offer + for sale, have made, import, and otherwise transfer either its + Contributions or its Contributor Version. + +2.2. Effective Date + +The licenses granted in Section 2.1 with respect to any Contribution +become effective for each Contribution on the date the Contributor first +distributes such Contribution. + +2.3. Limitations on Grant Scope + +The licenses granted in this Section 2 are the only rights granted under +this License. No additional rights or licenses will be implied from the +distribution or licensing of Covered Software under this License. +Notwithstanding Section 2.1(b) above, no patent license is granted by a +Contributor: + +(a) for any code that a Contributor has removed from Covered Software; + or + +(b) for infringements caused by: (i) Your and any other third party's + modifications of Covered Software, or (ii) the combination of its + Contributions with other software (except as part of its Contributor + Version); or + +(c) under Patent Claims infringed by Covered Software in the absence of + its Contributions. + +This License does not grant any rights in the trademarks, service marks, +or logos of any Contributor (except as may be necessary to comply with +the notice requirements in Section 3.4). + +2.4. Subsequent Licenses + +No Contributor makes additional grants as a result of Your choice to +distribute the Covered Software under a subsequent version of this +License (see Section 10.2) or under the terms of a Secondary License (if +permitted under the terms of Section 3.3). + +2.5. Representation + +Each Contributor represents that the Contributor believes its +Contributions are its original creation(s) or it has sufficient rights +to grant the rights to its Contributions conveyed by this License. + +2.6. Fair Use + +This License is not intended to limit any rights You have under +applicable copyright doctrines of fair use, fair dealing, or other +equivalents. + +2.7. Conditions + +Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted +in Section 2.1. + +3. Responsibilities +------------------- + +3.1. Distribution of Source Form + +All distribution of Covered Software in Source Code Form, including any +Modifications that You create or to which You contribute, must be under +the terms of this License. You must inform recipients that the Source +Code Form of the Covered Software is governed by the terms of this +License, and how they can obtain a copy of this License. You may not +attempt to alter or restrict the recipients' rights in the Source Code +Form. + +3.2. Distribution of Executable Form + +If You distribute Covered Software in Executable Form then: + +(a) such Covered Software must also be made available in Source Code + Form, as described in Section 3.1, and You must inform recipients of + the Executable Form how they can obtain a copy of such Source Code + Form by reasonable means in a timely manner, at a charge no more + than the cost of distribution to the recipient; and + +(b) You may distribute such Executable Form under the terms of this + License, or sublicense it under different terms, provided that the + license for the Executable Form does not attempt to limit or alter + the recipients' rights in the Source Code Form under this License. + +3.3. Distribution of a Larger Work + +You may create and distribute a Larger Work under terms of Your choice, +provided that You also comply with the requirements of this License for +the Covered Software. If the Larger Work is a combination of Covered +Software with a work governed by one or more Secondary Licenses, and the +Covered Software is not Incompatible With Secondary Licenses, this +License permits You to additionally distribute such Covered Software +under the terms of such Secondary License(s), so that the recipient of +the Larger Work may, at their option, further distribute the Covered +Software under the terms of either this License or such Secondary +License(s). + +3.4. Notices + +You may not remove or alter the substance of any license notices +(including copyright notices, patent notices, disclaimers of warranty, +or limitations of liability) contained within the Source Code Form of +the Covered Software, except that You may alter any license notices to +the extent required to remedy known factual inaccuracies. + +3.5. Application of Additional Terms + +You may choose to offer, and to charge a fee for, warranty, support, +indemnity or liability obligations to one or more recipients of Covered +Software. However, You may do so only on Your own behalf, and not on +behalf of any Contributor. You must make it absolutely clear that any +such warranty, support, indemnity, or liability obligation is offered by +You alone, and You hereby agree to indemnify every Contributor for any +liability incurred by such Contributor as a result of warranty, support, +indemnity or liability terms You offer. You may include additional +disclaimers of warranty and limitations of liability specific to any +jurisdiction. + +4. Inability to Comply Due to Statute or Regulation +--------------------------------------------------- + +If it is impossible for You to comply with any of the terms of this +License with respect to some or all of the Covered Software due to +statute, judicial order, or regulation then You must: (a) comply with +the terms of this License to the maximum extent possible; and (b) +describe the limitations and the code they affect. Such description must +be placed in a text file included with all distributions of the Covered +Software under this License. Except to the extent prohibited by statute +or regulation, such description must be sufficiently detailed for a +recipient of ordinary skill to be able to understand it. + +5. Termination +-------------- + +5.1. The rights granted under this License will terminate automatically +if You fail to comply with any of its terms. However, if You become +compliant, then the rights granted under this License from a particular +Contributor are reinstated (a) provisionally, unless and until such +Contributor explicitly and finally terminates Your grants, and (b) on an +ongoing basis, if such Contributor fails to notify You of the +non-compliance by some reasonable means prior to 60 days after You have +come back into compliance. Moreover, Your grants from a particular +Contributor are reinstated on an ongoing basis if such Contributor +notifies You of the non-compliance by some reasonable means, this is the +first time You have received notice of non-compliance with this License +from such Contributor, and You become compliant prior to 30 days after +Your receipt of the notice. + +5.2. If You initiate litigation against any entity by asserting a patent +infringement claim (excluding declaratory judgment actions, +counter-claims, and cross-claims) alleging that a Contributor Version +directly or indirectly infringes any patent, then the rights granted to +You by any and all Contributors for the Covered Software under Section +2.1 of this License shall terminate. + +5.3. In the event of termination under Sections 5.1 or 5.2 above, all +end user license agreements (excluding distributors and resellers) which +have been validly granted by You or Your distributors under this License +prior to termination shall survive termination. + +************************************************************************ +* * +* 6. Disclaimer of Warranty * +* ------------------------- * +* * +* Covered Software is provided under this License on an "as is" * +* basis, without warranty of any kind, either expressed, implied, or * +* statutory, including, without limitation, warranties that the * +* Covered Software is free of defects, merchantable, fit for a * +* particular purpose or non-infringing. The entire risk as to the * +* quality and performance of the Covered Software is with You. * +* Should any Covered Software prove defective in any respect, You * +* (not any Contributor) assume the cost of any necessary servicing, * +* repair, or correction. This disclaimer of warranty constitutes an * +* essential part of this License. No use of any Covered Software is * +* authorized under this License except under this disclaimer. * +* * +************************************************************************ + +************************************************************************ +* * +* 7. Limitation of Liability * +* -------------------------- * +* * +* Under no circumstances and under no legal theory, whether tort * +* (including negligence), contract, or otherwise, shall any * +* Contributor, or anyone who distributes Covered Software as * +* permitted above, be liable to You for any direct, indirect, * +* special, incidental, or consequential damages of any character * +* including, without limitation, damages for lost profits, loss of * +* goodwill, work stoppage, computer failure or malfunction, or any * +* and all other commercial damages or losses, even if such party * +* shall have been informed of the possibility of such damages. This * +* limitation of liability shall not apply to liability for death or * +* personal injury resulting from such party's negligence to the * +* extent applicable law prohibits such limitation. Some * +* jurisdictions do not allow the exclusion or limitation of * +* incidental or consequential damages, so this exclusion and * +* limitation may not apply to You. * +* * +************************************************************************ + +8. Litigation +------------- + +Any litigation relating to this License may be brought only in the +courts of a jurisdiction where the defendant maintains its principal +place of business and such litigation shall be governed by laws of that +jurisdiction, without reference to its conflict-of-law provisions. +Nothing in this Section shall prevent a party's ability to bring +cross-claims or counter-claims. + +9. Miscellaneous +---------------- + +This License represents the complete agreement concerning the subject +matter hereof. If any provision of this License is held to be +unenforceable, such provision shall be reformed only to the extent +necessary to make it enforceable. Any law or regulation which provides +that the language of a contract shall be construed against the drafter +shall not be used to construe this License against a Contributor. + +10. Versions of the License +--------------------------- + +10.1. New Versions + +Mozilla Foundation is the license steward. Except as provided in Section +10.3, no one other than the license steward has the right to modify or +publish new versions of this License. Each version will be given a +distinguishing version number. + +10.2. Effect of New Versions + +You may distribute the Covered Software under the terms of the version +of the License under which You originally received the Covered Software, +or under the terms of any subsequent version published by the license +steward. + +10.3. Modified Versions + +If you create software not governed by this License, and you want to +create a new license for such software, you may create and use a +modified version of this License if you rename the license and remove +any references to the name of the license steward (except to note that +such modified license differs from this License). + +10.4. Distributing Source Code Form that is Incompatible With Secondary +Licenses + +If You choose to distribute Source Code Form that is Incompatible With +Secondary Licenses under the terms of this version of the License, the +notice described in Exhibit B of this License must be attached. + +Exhibit A - Source Code Form License Notice +------------------------------------------- + + This Source Code Form is subject to the terms of the Mozilla Public + License, v. 2.0. If a copy of the MPL was not distributed with this + file, You can obtain one at http://mozilla.org/MPL/2.0/. + +If it is not possible or desirable to put the notice in a particular +file, then You may include the notice in a location (such as a LICENSE +file in a relevant directory) where a recipient would be likely to look +for such a notice. + +You may add additional accurate notices of copyright ownership. + +Exhibit B - "Incompatible With Secondary Licenses" Notice +--------------------------------------------------------- + + This Source Code Form is "Incompatible With Secondary Licenses", as + defined by the Mozilla Public License, v. 2.0. + +--- end of LICENSE --- + +------------------------------------------------------------------------------- + +%% This notice is provided with respect to PC/SC Lite for Suse Linux v.1.1.1, +which may be included with JRE 8, JDK 8, and OpenJDK 8 on Linux and Solaris. + +--- begin of LICENSE --- + +Copyright (c) 1999-2004 David Corcoran +Copyright (c) 1999-2004 Ludovic Rousseau +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions +are met: + +1. Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. +2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. +3. All advertising materials mentioning features or use of this software + must display the following acknowledgement: + This product includes software developed by: + David Corcoran + http://www.linuxnet.com (MUSCLE) +4. The name of the author may not be used to endorse or promote products + derived from this software without specific prior written permission. + +Changes to this license can be made only by the copyright author with +explicit written consent. + +THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR +IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES +OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. +IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, +INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT +NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF +THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +--- end of LICENSE --- + +------------------------------------------------------------------------------- + +%% This notice is provided with respect to PorterStemmer v4, which may be +included with JRE 8, JDK 8, and OpenJDK 8. + +--- begin of LICENSE --- + +See: http://tartarus.org/~martin/PorterStemmer + +The software is completely free for any purpose, unless notes at the head of +the program text indicates otherwise (which is rare). In any case, the notes +about licensing are never more restrictive than the BSD License. + +In every case where the software is not written by me (Martin Porter), this +licensing arrangement has been endorsed by the contributor, and it is +therefore unnecessary to ask the contributor again to confirm it. + +I have not asked any contributors (or their employers, if they have them) for +proofs that they have the right to distribute their software in this way. + +--- end of LICENSE --- + +------------------------------------------------------------------------------- + +%% This notice is provided with respect to Relax NG Object/Parser v.20050510, +which may be included with JRE 8, JDK 8, and OpenJDK 8. + +--- begin of LICENSE --- + +Copyright (c) Kohsuke Kawaguchi + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: The above copyright +notice and this permission notice shall be included in all copies or +substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. + +--- end of LICENSE --- + +------------------------------------------------------------------------------- + +%% This notice is provided with respect to RelaxNGCC v1.12, which may be +included with JRE 8, JDK 8, and OpenJDK 8. + +--- begin of LICENSE --- + +Copyright (c) 2000-2003 Daisuke Okajima and Kohsuke Kawaguchi. +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. The end-user documentation included with the redistribution, if any, must + include the following acknowledgment: + + "This product includes software developed by Daisuke Okajima + and Kohsuke Kawaguchi (http://relaxngcc.sf.net/)." + +Alternately, this acknowledgment may appear in the software itself, if and +wherever such third-party acknowledgments normally appear. + +4. The names of the copyright holders must not be used to endorse or promote + products derived from this software without prior written permission. For + written permission, please contact the copyright holders. + +5. 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All rights +reserved. + +This software was developed by the Computer Systems Engineering group at +Lawrence Berkeley Laboratory under DARPA contract BG 91-66 and contributed to +Berkeley. + +All advertising materials mentioning features or use of this software must +display the following acknowledgement: This product includes software +developed by the University of California, Lawrence Berkeley Laboratory. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + + 3. 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IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY +DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 3.2.3. The +NetBSD Foundation, Inc. + +Copyright (c) 2003 The NetBSD Foundation, Inc. All rights reserved. + +This code is derived from software contributed to The NetBSD Foundation by Ben +Collver + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + + 3. All advertising materials mentioning features or use of this software + must display the following acknowledgement: This product includes software + developed by the NetBSD Foundation, Inc. and its contributors. + + 4. Neither the name of The NetBSD Foundation nor the names of its + contributors may be used to endorse or promote products derived from this + software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE NETBSD FOUNDATION, INC. AND CONTRIBUTORS ``AS +IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE FOUNDATION OR CONTRIBUTORS BE LIABLE FOR ANY +DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 3.2.4. Theodore +Ts'o. + +Copyright Theodore Ts'o, 1994, 1995, 1996, 1997, 1998, 1999. All rights +reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, + and the entire permission notice in its entirety, including the disclaimer + of warranties. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + + 3. he name of the author may not be used to endorse or promote products + derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, +INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND +FITNESS FOR A PARTICULAR PURPOSE, ALL OF WHICH ARE HEREBY DISCLAIMED. IN NO +EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR +BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER +IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF NOT ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. 3.2.5. Theo de Raadt and Damien Miller + +Copyright (c) 1995,1999 Theo de Raadt. All rights reserved. Copyright (c) +2001-2002 Damien Miller. All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + +THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED +WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR +BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER +IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. 3.2.6. Todd C. Miller + +Copyright (c) 1998 Todd C. Miller + +Permission to use, copy, modify, and distribute this software for any purpose +with or without fee is hereby granted, provided that the above copyright +notice and this permission notice appear in all copies. + +THE SOFTWARE IS PROVIDED "AS IS" AND TODD C. MILLER DISCLAIMS ALL WARRANTIES +WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL TODD C. MILLER BE LIABLE FOR +ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES +WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION +OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN +CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. 3.2.7. Thomas +Winischhofer + +Copyright (C) 2001-2004 Thomas Winischhofer + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + + 3. The name of the author may not be used to endorse or promote products + derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESSED OR IMPLIED +WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR +BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER +IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. 3.3. NVIDIA Corp + +Copyright (c) 1996 NVIDIA, Corp. All rights reserved. + +NOTICE TO USER: The source code is copyrighted under U.S. and international +laws. NVIDIA, Corp. of Sunnyvale, California owns the copyright and as design +patents pending on the design and interface of the NV chips. Users and +possessors of this source code are hereby granted a nonexclusive, royalty-free +copyright and design patent license to use this code in individual and +commercial software. + +Any use of this source code must include, in the user documentation and +internal comments to the code, notices to the end user as follows: + +Copyright (c) 1996 NVIDIA, Corp. NVIDIA design patents pending in the U.S. and +foreign countries. + +NVIDIA, CORP. MAKES NO REPRESENTATION ABOUT THE SUITABILITY OF THIS SOURCE +CODE FOR ANY PURPOSE. IT IS PROVIDED "AS IS" WITHOUT EXPRESS OR IMPLIED +WARRANTY OF ANY KIND. NVIDIA, CORP. DISCLAIMS ALL WARRANTIES WITH REGARD TO +THIS SOURCE CODE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND +FITNESS FOR A PARTICULAR PURPOSE. IN NO EVENT SHALL NVIDIA, CORP. BE LIABLE +FOR ANY SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, OR ANY +DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN +ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN +CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOURCE CODE. 3.4. GLX Public +License + +GLX PUBLIC LICENSE (Version 1.0 (2/11/99)) ("License") + +Subject to any third party claims, Silicon Graphics, Inc. ("SGI") hereby +grants permission to Recipient (defined below), under Recipient's copyrights +in the Original Software (defined below), to use, copy, modify, merge, +publish, distribute, sublicense and/or sell copies of Subject Software +(defined below), and to permit persons to whom the Subject Software is +furnished in accordance with this License to do the same, subject to all of +the following terms and conditions, which Recipient accepts by engaging in any +such use, copying, modifying, merging, publishing, distributing, sublicensing +or selling: + +1. Definitions. + + (a) "Original Software" means source code of computer software code which + is described in Exhibit A as Original Software. + + (b) "Modifications" means any addition to or deletion from the substance + or structure of either the Original Software or any previous + Modifications. When Subject Software is released as a series of files, a + Modification means (i) any addition to or deletion from the contents of a + file containing Original Software or previous Modifications and (ii) any + new file that contains any part of the Original Code or previous + Modifications. + + (c) "Subject Software" means the Original Software or Modifications or the + combination of the Original Software and Modifications, or portions of any + of the foregoing. + + (d) "Recipient" means an individual or a legal entity exercising rights + under, and complying with all of the terms of, this License. For legal + entities, "Recipient" includes any entity which controls, is controlled + by, or is under common control with Recipient. For purposes of this + definition, "control" of an entity means (a) the power, direct or + indirect, to direct or manage such entity, or (b) ownership of fifty + percent (50%) or more of the outstanding shares or beneficial ownership of + such entity. + +2. Redistribution of Source Code Subject to These Terms. Redistributions of +Subject Software in source code form must retain the notice set forth in +Exhibit A, below, in every file. A copy of this License must be included in +any documentation for such Subject Software where the recipients' rights +relating to Subject Software are described. Recipient may distribute the +source code version of Subject Software under a license of Recipient's choice, +which may contain terms different from this License, provided that (i) +Recipient is in compliance with the terms of this License, and (ii) the +license terms include this Section 2 and Sections 3, 4, 7, 8, 10, 12 and 13 of +this License, which terms may not be modified or superseded by any other terms +of such license. If Recipient distributes the source code version under a +different license Recipient must make it absolutely clear that any terms which +differ from this License are offered by Recipient alone, not by SGI. Recipient +hereby agrees to indemnify SGI for any liability incurred by SGI as a result +of any such terms Recipient offers. + +3. Redistribution in Executable Form. The notice set forth in Exhibit A must +be conspicuously included in any notice in an executable version of Subject +Software, related documentation or collateral in which Recipient describes the +user's rights relating to the Subject Software. Recipient may distribute the +executable version of Subject Software under a license of Recipient's choice, +which may contain terms different from this License, provided that (i) +Recipient is in compliance with the terms of this License, and (ii) the +license terms include this Section 3 and Sections 4, 7, 8, 10, 12 and 13 of +this License, which terms may not be modified or superseded by any other terms +of such license. If Recipient distributes the executable version under a +different license Recipient must make it absolutely clear that any terms which +differ from this License are offered by Recipient alone, not by SGI. Recipient +hereby agrees to indemnify SGI for any liability incurred by SGI as a result +of any such terms Recipient offers. + +4. Termination. This License and the rights granted hereunder will terminate +automatically if Recipient fails to comply with terms herein and fails to cure +such breach within 30 days of the breach. Any sublicense to the Subject +Software which is properly granted shall survive any termination of this +License absent termination by the terms of such sublicense. Provisions which, +by their nature, must remain in effect beyond the termination of this License +shall survive. + +5. No Trademark Rights. This License does not grant any rights to use any +trade name, trademark or service mark whatsoever. No trade name, trademark or +service mark of SGI may be used to endorse or promote products derived from +the Subject Software without prior written permission of SGI. + +6. No Other Rights. This License does not grant any rights with respect to the +OpenGL API or to any software or hardware implementation thereof or to any +other software whatsoever, nor shall any other rights or licenses not +expressly granted hereunder arise by implication, estoppel or otherwise with +respect to the Subject Software. Title to and ownership of the Original +Software at all times remains with SGI. All rights in the Original Software +not expressly granted under this License are reserved. + +7. Compliance with Laws; Non-Infringement. Recipient shall comply with all +applicable laws and regulations in connection with use and distribution of the +Subject Software, including but not limited to, all export and import control +laws and regulations of the U.S. government and other countries. Recipient may +not distribute Subject Software that (i) in any way infringes (directly or +contributorily) the rights (including patent, copyright, trade secret, +trademark or other intellectual property rights of any kind) of any other +person or entity or (ii) breaches any representation or warranty, express, +implied or statutory, which under any applicable law it might be deemed to +have been distributed. + +8. Claims of Infringement. If Recipient at any time has knowledge of any one +or more third party claims that reproduction, modification, use, distribution, +import or sale of Subject Software (including particular functionality or code +incorporated in Subject Software) infringes the third party's intellectual +property rights, Recipient must place in a well-identified web page bearing +the title "LEGAL" a description of each such claim and a description of the +party making each such claim in sufficient detail that a user of the Subject +Software will know whom to contact regarding the claim. Also, upon gaining +such knowledge of any such claim, Recipient must conspicuously include the URL +for such web page in the Exhibit A notice required under Sections 2 and 3, +above, and in the text of any related documentation, license agreement or +collateral in which Recipient describes end user's rights relating to the +Subject Software. If Recipient obtains such knowledge after it makes Subject +Software available to any other person or entity, Recipient shall take other +steps (such as notifying appropriate mailing lists or newsgroups) reasonably +calculated to inform those who received the Subject Software that new +knowledge has been obtained. + +9. DISCLAIMER OF WARRANTY. SUBJECT SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, +WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, WITHOUT +LIMITATION, WARRANTIES THAT THE SUBJECT SOFTWARE IS FREE OF DEFECTS, +MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE OR NON- INFRINGING. SGI ASSUMES NO +RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE. SHOULD ANY SOFTWARE +PROVE DEFECTIVE IN ANY RESPECT, SGI ASSUMES NO COST OR LIABILITY FOR ANY +SERVICING, REPAIR OR CORRECTION. THIS DISCLAIMER OF WARRANTY CONSTITUTES AN +ESSENTIAL PART OF THIS LICENSE. NO USE OF ANY SUBJECT SOFTWARE IS AUTHORIZED +HEREUNDER EXCEPT UNDER THIS DISCLAIMER. + +10. LIMITATION OF LIABILITY. UNDER NO CIRCUMSTANCES AND UNDER NO LEGAL THEORY, +WHETHER TORT (INCLUDING, WITHOUT LIMITATION, NEGLIGENCE OR STRICT LIABILITY), +CONTRACT, OR OTHERWISE, SHALL SGI OR ANY SGI LICENSOR BE LIABLE FOR ANY +DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES OF ANY +CHARACTER INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL, WORK +STOPPAGE, LOSS OF DATA, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL OTHER +COMMERCIAL DAMAGES OR LOSSES, EVEN IF SUCH PARTY SHALL HAVE BEEN INFORMED OF +THE POSSIBILITY OF SUCH DAMAGES. THIS LIMITATION OF LIABILITY SHALL NOT APPLY +TO LIABILITY FOR DEATH OR PERSONAL INJURY RESULTING FROM SGI's NEGLIGENCE TO +THE EXTENT APPLICABLE LAW PROHIBITS SUCH LIMITATION. SOME JURISDICTIONS DO NOT +ALLOW THE EXCLUSION OR LIMITATION OF INCIDENTAL OR CONSEQUENTIAL DAMAGES, SO +THAT EXCLUSION AND LIMITATION MAY NOT APPLY TO RECIPIENT. + +11. Indemnity. Recipient shall be solely responsible for damages arising, +directly or indirectly, out of its utilization of rights under this License. +Recipient will defend, indemnify and hold harmless Silicon Graphics, Inc. from +and against any loss, liability, damages, costs or expenses (including the +payment of reasonable attorneys fees) arising out of Recipient's use, +modification, reproduction and distribution of the Subject Software or out of +any representation or warranty made by Recipient. + +12. U.S. Government End Users. The Subject Software is a "commercial item" +consisting of "commercial computer software" as such terms are defined in +title 48 of the Code of Federal Regulations and all U.S. Government End Users +acquire only the rights set forth in this License and are subject to the terms +of this License. + +13. Miscellaneous. This License represents the complete agreement concerning +subject matter hereof. If any provision of this License is held to be +unenforceable, such provision shall be reformed so as to achieve as nearly as +possible the same economic effect as the original provision and the remainder +of this License will remain in effect. This License shall be governed by and +construed in accordance with the laws of the United States and the State of +California as applied to agreements entered into and to be performed entirely +within California between California residents. Any litigation relating to +this License shall be subject to the exclusive jurisdiction of the Federal +Courts of the Northern District of California (or, absent subject matter +jurisdiction in such courts, the courts of the State of California), with +venue lying exclusively in Santa Clara County, California, with the losing +party responsible for costs, including without limitation, court costs and +reasonable attorneys fees and expenses. The application of the United Nations +Convention on Contracts for the International Sale of Goods is expressly +excluded. Any law or regulation which provides that the language of a contract +shall be construed against the drafter shall not apply to this License. + +Exhibit A + +The contents of this file are subject to Sections 2, 3, 4, 7, 8, 10, 12 and 13 +of the GLX Public License Version 1.0 (the "License"). You may not use this +file except in compliance with those sections of the License. You may obtain a +copy of the License at Silicon Graphics, Inc., attn: Legal Services, 2011 N. +Shoreline Blvd., Mountain View, CA 94043 or at +http://www.sgi.com/software/opensource/glx/license.html. + +Software distributed under the License is distributed on an "AS IS" basis. ALL +WARRANTIES ARE DISCLAIMED, INCLUDING, WITHOUT LIMITATION, ANY IMPLIED +WARRANTIES OF MERCHANTABILITY, OF FITNESS FOR A PARTICULAR PURPOSE OR OF NON- +INFRINGEMENT. See the License for the specific language governing rights and +limitations under the License. + +The Original Software is GLX version 1.2 source code, released February, 1999. +The developer of the Original Software is Silicon Graphics, Inc. Those +portions of the Subject Software created by Silicon Graphics, Inc. are +Copyright (c) 1991-9 Silicon Graphics, Inc. All Rights Reserved. 3.5. CID +Font Code Public License + +CID FONT CODE PUBLIC LICENSE (Version 1.0 (3/31/99))("License") + +Subject to any applicable third party claims, Silicon Graphics, Inc. ("SGI") +hereby grants permission to Recipient (defined below), under SGI's copyrights +in the Original Software (defined below), to use, copy, modify, merge, +publish, distribute, sublicense and/or sell copies of Subject Software +(defined below) in both source code and executable form, and to permit persons +to whom the Subject Software is furnished in accordance with this License to +do the same, subject to all of the following terms and conditions, which +Recipient accepts by engaging in any such use, copying, modifying, merging, +publication, distributing, sublicensing or selling: + +1. Definitions. + + a. "Original Software" means source code of computer software code that is + described in Exhibit A as Original Software. + + b. "Modifications" means any addition to or deletion from the substance or + structure of either the Original Software or any previous Modifications. + When Subject Software is released as a series of files, a Modification + means (i) any addition to or deletion from the contents of a file + containing Original Software or previous Modifications and (ii) any new + file that contains any part of the Original Code or previous + Modifications. + + c. "Subject Software" means the Original Software or Modifications or the + combination of the Original Software and Modifications, or portions of any + of the foregoing. + + d. "Recipient" means an individual or a legal entity exercising rights + under the terms of this License. For legal entities, "Recipient" includes + any entity that controls, is controlled by, or is under common control + with Recipient. For purposes of this definition, "control" of an entity + means (i) the power, direct or indirect, to direct or manage such entity, + or (ii) ownership of fifty percent (50%) or more of the outstanding shares + or beneficial ownership of such entity. + + e. "Required Notice" means the notice set forth in Exhibit A to this + License. + + f. "Accompanying Technology" means any software or other technology that + is not a Modification and that is distributed or made publicly available + by Recipient with the Subject Software. Separate software files that do + not contain any Original Software or any previous Modification shall not + be deemed a Modification, even if such software files are aggregated as + part of a product, or in any medium of storage, with any file that does + contain Original Software or any previous Modification. + +2. License Terms. All distribution of the Subject Software must be made +subject to the terms of this License. A copy of this License and the Required +Notice must be included in any documentation for Subject Software where +Recipient's rights relating to Subject Software and/or any Accompanying +Technology are described. Distributions of Subject Software in source code +form must also include the Required Notice in every file distributed. In +addition, a ReadMe file entitled "Important Legal Notice" must be distributed +with each distribution of one or more files that incorporate Subject Software. +That file must be included with distributions made in both source code and +executable form. A copy of the License and the Required Notice must be +included in that file. Recipient may distribute Accompanying Technology under +a license of Recipient's choice, which may contain terms different from this +License, provided that (i) Recipient is in compliance with the terms of this +License, (ii) such other license terms do not modify or supersede the terms of +this License as applicable to the Subject Software, (iii) Recipient hereby +indemnifies SGI for any liability incurred by SGI as a result of the +distribution of Accompanying Technology or the use of other license terms. + +3. Termination. This License and the rights granted hereunder will terminate +automatically if Recipient fails to comply with terms herein and fails to cure +such breach within 30 days of the breach. Any sublicense to the Subject +Software that is properly granted shall survive any termination of this +License absent termination by the terms of such sublicense. Provisions which, +by their nature, must remain in effect beyond the termination of this License +shall survive. + +4. Trademark Rights. This License does not grant any rights to use any trade +name, trademark or service mark whatsoever. No trade name, trademark or +service mark of SGI may be used to endorse or promote products derived from or +incorporating any Subject Software without prior written permission of SGI. + +5. No Other Rights. No rights or licenses not expressly granted hereunder +shall arise by implication, estoppel or otherwise. Title to and ownership of +the Original Software at all times remains with SGI. All rights in the +Original Software not expressly granted under this License are reserved. + +6. Compliance with Laws; Non-Infringement. Recipient shall comply with all +applicable laws and regulations in connection with use and distribution of the +Subject Software, including but not limited to, all export and import control +laws and regulations of the U.S. government and other countries. Recipient may +not distribute Subject Software that (i) in any way infringes (directly or +contributorily) the rights (including patent, copyright, trade secret, +trademark or other intellectual property rights of any kind) of any other +person or entity, or (ii) breaches any representation or warranty, express, +implied or statutory, which under any applicable law it might be deemed to +have been distributed. + +7. Claims of Infringement. If Recipient at any time has knowledge of any one +or more third party claims that reproduction, modification, use, distribution, +import or sale of Subject Software (including particular functionality or code +incorporated in Subject Software) infringes the third party's intellectual +property rights, Recipient must place in a well-identified web page bearing +the title "LEGAL" a description of each such claim and a description of the +party making each such claim in sufficient detail that a user of the Subject +Software will know whom to contact regarding the claim. Also, upon gaining +such knowledge of any such claim, Recipient must conspicuously include the URL +for such web page in the Required Notice, and in the text of any related +documentation, license agreement or collateral in which Recipient describes +end user's rights relating to the Subject Software. If Recipient obtains such +knowledge after it makes Subject Software available to any other person or +entity, Recipient shall take other steps (such as notifying appropriate +mailing lists or newsgroups) reasonably calculated to provide such knowledge +to those who received the Subject Software. + +8. DISCLAIMER OF WARRANTY. SUBJECT SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, +WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, WITHOUT +LIMITATION, WARRANTIES THAT THE SUBJECT SOFTWARE IS FREE OF DEFECTS, +MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE OR NON-INFRINGING. SGI ASSUMES NO +RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE. SHOULD ANY SOFTWARE +PROVE DEFECTIVE IN ANY RESPECT, SGI ASSUMES NO COST OR LIABILITY FOR ANY +SERVICING, REPAIR OR CORRECTION. THIS DISCLAIMER OF WARRANTY CONSTITUTES AN +ESSENTIAL PART OF THIS LICENSE. NO USE OF ANY SUBJECT SOFTWARE IS AUTHORIZED +HEREUNDER EXCEPT UNDER THIS DISCLAIMER. + +9. LIMITATION OF LIABILITY. UNDER NO CIRCUMSTANCES AND UNDER NO LEGAL THEORY, +WHETHER TORT (INCLUDING, WITHOUT LIMITATION, NEGLIGENCE OR STRICT LIABILITY), +CONTRACT, OR OTHERWISE, SHALL SGI OR ANY SGI LICENSOR BE LIABLE FOR ANY CLAIM, +DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR +OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SUBJECT SOFTWARE OR +THE USE OR OTHER DEALINGS IN THE SUBJECT SOFTWARE. SOME JURISDICTIONS DO NOT +ALLOW THE EXCLUSION OR LIMITATION OF CERTAIN DAMAGES, SO THIS EXCLUSION AND +LIMITATION MAY NOT APPLY TO RECIPIENT TO THE EXTENT SO DISALLOWED. + +10. Indemnity. Recipient shall be solely responsible for damages arising, +directly or indirectly, out of its utilization of rights under this License. +Recipient will defend, indemnify and hold SGI and its successors and assigns +harmless from and against any loss, liability, damages, costs or expenses +(including the payment of reasonable attorneys fees) arising out of +(Recipient's use, modification, reproduction and distribution of the Subject +Software or out of any representation or warranty made by Recipient. + +11. U.S. Government End Users. The Subject Software is a "commercial item" +consisting of "commercial computer software" as such terms are defined in +title 48 of the Code of Federal Regulations and all U.S. Government End Users +acquire only the rights set forth in this License and are subject to the terms +of this License. + +12. Miscellaneous. This License represents the complete agreement concerning +subject matter hereof. If any provision of this License is held to be +unenforceable by any judicial or administrative authority having proper +jurisdiction with respect thereto, such provision shall be reformed so as to +achieve as nearly as possible the same economic effect as the original +provision and the remainder of this License will remain in effect. This +License shall be governed by and construed in accordance with the laws of the +United States and the State of California as applied to agreements entered +into and to be performed entirely within California between California +residents. Any litigation relating to this License shall be subject to the +exclusive jurisdiction of the Federal Courts of the Northern District of +California (or, absent subject matter jurisdiction in such courts, the courts +of the State of California), with venue lying exclusively in Santa Clara +County, California, with the losing party responsible for costs, including +without limitation, court costs and reasonable attorneys fees and expenses. +The application of the United Nations Convention on Contracts for the +International Sale of Goods is expressly excluded. Any law or regulation that +provides that the language of a contract shall be construed against the +drafter shall not apply to this License. + +Exhibit A + +Copyright (c) 1994-1999 Silicon Graphics, Inc. + +The contents of this file are subject to the CID Font Code Public License +Version 1.0 (the "License"). You may not use this file except in compliance +with the License. You may obtain a copy of the License at Silicon Graphics, +Inc., attn: Legal Services, 2011 N. Shoreline Blvd., Mountain View, CA 94043 +or at http://www.sgi.com/software/opensource/cid/license.html + +Software distributed under the License is distributed on an "AS IS" basis. ALL +WARRANTIES ARE DISCLAIMED, INCLUDING, WITHOUT LIMITATION, ANY IMPLIED +WARRANTIES OF MERCHANTABILITY, OF FITNESS FOR A PARTICULAR PURPOSE OR OF +NON-INFRINGEMENT. See the License for the specific language governing rights +and limitations under the License. + +The Original Software (as defined in the License) is CID font code that was +developed by Silicon Graphics, Inc. Those portions of the Subject Software (as +defined in the License) that were created by Silicon Graphics, Inc. are +Copyright (c) 1994-1999 Silicon Graphics, Inc. All Rights Reserved. + +[NOTE: When using this text in connection with Subject Software delivered +solely in object code form, Recipient may replace the words "this file" with +"this software" in both the first and second sentences.] 3.6. Bitstream Vera +Fonts Copyright + +The fonts have a generous copyright, allowing derivative works (as long as +"Bitstream" or "Vera" are not in the names), and full redistribution (so long +as they are not *sold* by themselves). They can be be bundled, redistributed +and sold with any software. + +The fonts are distributed under the following copyright: + +Copyright (c) 2003 by Bitstream, Inc. All Rights Reserved. Bitstream Vera is a +trademark of Bitstream, Inc. + +Permission is hereby granted, free of charge, to any person obtaining a copy +of the fonts accompanying this license ("Fonts") and associated documentation +files (the "Font Software"), to reproduce and distribute the Font Software, +including without limitation the rights to use, copy, merge, publish, +distribute, and/or sell copies of the Font Software, and to permit persons to +whom the Font Software is furnished to do so, subject to the following +conditions: + +The above copyright and trademark notices and this permission notice shall be +included in all copies of one or more of the Font Software typefaces. + +The Font Software may be modified, altered, or added to, and in particular the +designs of glyphs or characters in the Fonts may be modified and additional +glyphs or characters may be added to the Fonts, only if the fonts are renamed +to names not containing either the words "Bitstream" or the word "Vera". + +This License becomes null and void to the extent applicable to Fonts or Font +Software that has been modified and is distributed under the "Bitstream Vera" +names. + +The Font Software may be sold as part of a larger software package but no copy +of one or more of the Font Software typefaces may be sold by itself. + +THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT OF COPYRIGHT, PATENT, +TRADEMARK, OR OTHER RIGHT. 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For a period of three years from +the date of your receipt of this software, Azul will provide upon +request, a complete machine readable copy of the source code for such +portions based on OpenJDK on a medium customarily used for software +interchange for a charge no more than the cost of physically performing +source distribution. + + + Please email azul_openjdk@azulsystems.com for further information. + + Include this version code in your email: + Zulu 8.19.0.1 d0cf8daf3adb + diff --git a/containers/shapemapper2/LICENSES/ShapeMapper-MIT.txt b/containers/shapemapper2/LICENSES/ShapeMapper-MIT.txt new file mode 100644 index 0000000..ed73c34 --- /dev/null +++ b/containers/shapemapper2/LICENSES/ShapeMapper-MIT.txt @@ -0,0 +1,27 @@ +Copyright 2024 + +Contributors +Steven Busan +Anthony Mustoe +David Mitchell III +Patrick Irving +Thomas Miller +Lucas Kearns + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. diff --git a/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md b/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md new file mode 100644 index 0000000..c84eb16 --- /dev/null +++ b/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md @@ -0,0 +1,25 @@ +# Third-party notices for the source-built public candidate + +This image compiles the unchanged ShapeMapper2 v2.3 source tag and installs +runtime dependencies as Debian 12 (bookworm) packages. It does not contain the +official ShapeMapper release archive's bundled Miniconda environment or its +historical prebuilt executables. + +ShapeMapper2 is Copyright (c) 2018 Steven Busan and is distributed under the +MIT License. The complete notice is installed beside this file and remains in +the upstream source tree at `/opt/shapemapper2/LICENSE`. + +The image includes Debian packages for BBMap/BBMerge, Bowtie2, STAR, Graphviz, +Ghostscript, pv, Python and its scientific libraries, Boost, zlib, and their +runtime dependencies. Their package-specific copyright and license notices +are retained under `/usr/share/doc//copyright`. The corresponding +Debian source packages can be located by the exact binary-package versions +reported by `dpkg-query -W` and retrieved from Debian's source archives. + +This notice is an index, not a replacement for the package-specific notices. +The CI-generated SPDX SBOM and exact `dpkg-query` inventory are release +records for a published image and must be associated with its immutable OCI +digest. + +The private reference image built with `Dockerfile.reference` has a different +dependency set and separate notices in `THIRD_PARTY_NOTICES.md`. diff --git a/containers/shapemapper2/QUEST.md b/containers/shapemapper2/QUEST.md new file mode 100644 index 0000000..c37a47d --- /dev/null +++ b/containers/shapemapper2/QUEST.md @@ -0,0 +1,30 @@ +# Quest SIF validation + +SIF is the single-file image format used by Singularity and Apptainer. The +same digest-pinned GHCR image can be downloaded once, converted to SIF, cached +in scratch storage, and executed without Docker privileges. + +Quest currently documents SingularityCE through a module such as +`singularityce/4.3.1-gcc-8.5.0`. Confirm the currently available module name at +run time. Apptainer is also supported by the validation script when its command +is available instead. + +After the image has an immutable OCI digest: + +```bash +module load singularityce/4.3.1-gcc-8.5.0 + +./containers/shapemapper2/validate-sif-on-quest.sh \ + ghcr.io/edr-choi/nerd-shapemapper2@sha256: \ + "$SCRATCH/nerd/shapemapper2" +``` + +The script refuses mutable tags. It caches the SIF by OCI digest, runs the +upstream example through a writable bind mount, and prints the SIF SHA-256. +Store its output with the CI run URL and OCI digest. + +This validation cannot be completed before an image is reachable from Quest. +For the approval-gated first release, push the image privately, authenticate +Singularity to GHCR for the test, and only then request approval to change the +package to public. Alternatively, transfer a local OCI archive to Quest for a +pre-push infrastructure check; that does not validate registry access. diff --git a/containers/shapemapper2/README.md b/containers/shapemapper2/README.md new file mode 100644 index 0000000..1486da7 --- /dev/null +++ b/containers/shapemapper2/README.md @@ -0,0 +1,132 @@ +# ShapeMapper2 v2.3 container + +This directory contains two Linux-amd64 container recipes for the unmodified +upstream ShapeMapper2 v2.3 code. Neither recipe forks ShapeMapper, and neither +image is currently published to GHCR. + +- `Dockerfile` is the smaller public candidate. It downloads the upstream v2.3 + source tag directly, verifies its SHA-256, compiles ShapeMapper, and uses + Debian packages for runtime dependencies. +- `Dockerfile.reference` is the private reference recipe. It wraps the official + upstream release archive, including its historical Miniconda environment. + This image remains useful as a behavioral comparison but is not the public + distribution candidate. + +Intended image name: + +```text +ghcr.io/edr-choi/nerd-shapemapper2:2.3-r0 +``` + +Build and test locally: + +```bash +docker build --platform linux/amd64 \ + --tag nerd-shapemapper2:2.3-public-candidate \ + containers/shapemapper2 + +containers/shapemapper2/test-container.sh nerd-shapemapper2:2.3-public-candidate +containers/shapemapper2/test-upstream.sh nerd-shapemapper2:2.3-public-candidate +``` + +The test wrappers use Docker by default. To run the same checks with Podman, +set `CONTAINER_ENGINE=podman`. + +Build the private reference image only when a comparison is needed: + +```bash +docker build --platform linux/amd64 \ + --file containers/shapemapper2/Dockerfile.reference \ + --tag nerd-shapemapper2:2.3-reference \ + containers/shapemapper2 +``` + +Both recipes pin the amd64 Debian base manifest. The public candidate pins the +upstream source-tag archive; the private reference recipe pins the official +release asset. No ShapeMapper source files are copied into this repository or +patched during either build. + +## Test levels + +- The smoke test runs `shapemapper --version` and the upstream example using a + host-mounted writable work directory. +- The full upstream suite can be run separately inside the image: + + ```bash + docker run --rm --entrypoint bash nerd-shapemapper2:2.3-public-candidate \ + /opt/shapemapper2/internals/test/run_all_tests.sh + ``` + + The `test-upstream.sh` wrapper accepts either all 208 tests passing or the + exact upstream-documented result in which one of 63 environment-dependent + module-failure injection tests fails. It does not accept failures in normal + end-to-end, unit, variant-correction, or ROC tests. + +The full suite writes beneath `/opt/shapemapper2`, so this command is intended +for Docker validation. Singularity/Apptainer validation should copy the test +tree to a writable directory or use a writable temporary overlay. + +### Private reference result + +On 2026-08-18, the image built and the upstream example completed successfully. +After adding the redistribution records, the local amd64 image size was +2,053,836,415 bytes (about 1.91 GiB), before conversion to SIF. The example +also passed while running as the host UID/GID and writing all results through +a mounted work directory. + +The complete upstream suite reported all 208 tests passing on the final beta +wrapper validation: + +- 98 of 98 C++ unit tests +- 32 of 32 normal end-to-end tests +- 63 of 63 injected component-failure tests +- 13 of 13 sequence-variant correction tests +- 2 of 2 ROC tests + +An earlier run exhibited the upstream-documented environment-sensitive +BowtieAligner failure-injection variation. The wrapper permits one such +failure-injection miss while rejecting any normal execution failure. + +### Smaller public candidate result + +On 2026-08-18, the source-based candidate compiled successfully from the +unchanged upstream v2.3 source archive. Its local amd64 image size was +508,942,308 bytes (about 485 MiB), approximately 75% smaller than the private +reference image. A second low-memory build also compiled successfully with the +recipe's two-job compiler limit and installed the full Debian runtime. Runtime +and built-in test validation is pending because the host ran out of disk space +during final layer assembly, leaving both local container stores unavailable. +This is an infrastructure failure, not a ShapeMapper compile or test failure. + +## Publication gate + +Do not push either image or change GHCR visibility until the public candidate's +built-in tests, image-size report, Debian package inventory, SBOM, and source +availability record have been presented to and approved by the project owner. +Release tags must never be overwritten; NERD should consume a published image +by OCI digest. + +The manual GitHub Actions workflow builds, runs both test levels, and retains +an SPDX SBOM. It has no package-write permission, registry login, or push step. +All third-party actions are pinned to immutable commits. + +## Licensing status + +ShapeMapper itself is MIT-licensed; its license is preserved in the upstream +tree and copied into `LICENSES/ShapeMapper-MIT.txt`. The smaller candidate +avoids the private reference image's unresolved historical Miniconda and Azul +Zulu source mapping by installing maintained Debian packages instead. Debian's +package-specific notices remain under `/usr/share/doc//copyright`. + +The private reference image carries the historical records in +`THIRD_PARTY_NOTICES.md`, `source-manifest.tsv`, and the Conda inventories. The +smaller candidate instead carries `PUBLIC_THIRD_PARTY_NOTICES.md`; its exact +Debian binary/source package inventory and new SBOM must be generated from the +tested final image before approval. + +## SIF validation + +After an OCI image exists by digest, follow `QUEST.md` and run +`validate-sif-on-quest.sh`. The script supports either Singularity or Apptainer, +refuses mutable tags, caches by OCI digest, and runs the upstream example. An +actual Quest validation is pending registry reachability and Quest access. diff --git a/containers/shapemapper2/THIRD_PARTY_NOTICES.md b/containers/shapemapper2/THIRD_PARTY_NOTICES.md new file mode 100644 index 0000000..4bb64b0 --- /dev/null +++ b/containers/shapemapper2/THIRD_PARTY_NOTICES.md @@ -0,0 +1,50 @@ +# Third-party notices for NERD ShapeMapper2 v2.3 + +This image packages the unmodified ShapeMapper2 v2.3 release together with the +third-party programs and libraries that release supplies. Each component +remains under its own license. Inclusion in one container does not replace +those licenses with the license of NERD or ShapeMapper. + +The complete machine-generated inventories are `sbom.spdx.json` and +`conda-packages.tsv`. `copyleft-conda-packages.tsv` is a focused review list +of 64 records whose metadata mentions GPL, LGPL, AGPL, EPL, MPL, Artistic, or +CDDL terms. Exact binary and source checksums for prominent components are in +`source-manifest.tsv`. + +## Prominent components + +| Component | Version | License and retained notice | +| --- | --- | --- | +| ShapeMapper2 | v2.3; runtime 2.3.0 | MIT; `LICENSES/ShapeMapper-MIT.txt` | +| Bowtie2 | 2.3.4.3 | GPLv3; `LICENSES/GPL-3.0.txt` | +| STAR | 2.5.2a | GPLv3; `LICENSES/GPL-3.0.txt` | +| Ghostscript | 9.25 | Official source is AGPLv3; `LICENSES/AGPL-3.0.txt` | +| BBMap/BBMerge | 37.78 | UC/LBNL permissive license; `LICENSES/BBMap-UC-LBL.txt` | +| pv | 1.6.20 | Artistic License 2.0; `LICENSES/Artistic-2.0.txt` | +| Graphviz | 7.1.0 | Eclipse Public License 1.0; `LICENSES/Graphviz-EPL-1.0.txt` | +| Azul Zulu OpenJDK | 8.0.112 / Zulu 8.19.0.1 | GPLv2 with Classpath Exception and accompanying exceptions/notices; see `LICENSES/OpenJDK-*` | +| Miniconda/Conda | Conda 4.3.21 | BSD-3-Clause plus individual package licenses; `LICENSES/Miniconda.txt` | +| Debian base packages | pinned bookworm-slim image | Mixed licenses; package copyright files remain under `/usr/share/doc` | + +Ghostscript requires special explanation. The official Ghostscript 9.25 +source archive contains the GNU Affero GPL v3 text, while the prebuilt binary +archive embedded by ShapeMapper contains a GNU GPL v3 `COPYING` file. Both are +retained (`AGPL-3.0.txt` and +`Ghostscript-bundled-COPYING-GPL-3.0.txt`), and the redistribution package +conservatively identifies Ghostscript 9.25 as AGPL-covered. + +The Zulu distribution's historical source-offer text identifies build code +`Zulu 8.19.0.1 d0cf8daf3adb`. Its three-year offer is not relied on for NERD's +redistribution. Until complete corresponding source for that exact build is +obtained or the runtime is replaced with a source-traceable OpenJDK build, the +container is not ready for public binary distribution. + +## Source availability + +For a public release, the files fetched and checksum-verified by +`fetch-compliance-sources.sh` should be retained as immutable release +artifacts beside the image. Upstream links alone are discovery locations, not +a promise that NERD will keep required source available. + +No project or institution named by a third-party license endorses NERD or this +container. All components are supplied without additional warranty. diff --git a/containers/shapemapper2/build-metadata.json b/containers/shapemapper2/build-metadata.json new file mode 100644 index 0000000..2557610 --- /dev/null +++ b/containers/shapemapper2/build-metadata.json @@ -0,0 +1,40 @@ +{ + "schema_version": 2, + "image": { + "intended_repository": "ghcr.io/edr-choi/nerd-shapemapper2", + "intended_release_tag": "2.3-r0", + "platform": "linux/amd64", + "publication_approved": false, + "pushed": false + }, + "public_candidate": { + "recipe": "Dockerfile", + "strategy": "compile unchanged upstream source; install Debian runtime packages", + "upstream_source_url": "https://codeload.github.com/Weeks-UNC/shapemapper2/tar.gz/refs/tags/v2.3", + "upstream_source_sha256": "1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f866b6f", + "local_build_2026_08_18": { + "image_tag": "nerd-shapemapper2:2.3-public-candidate", + "image_size_bytes": 508942308, + "local_manifest_list_id": "sha256:68fdce9e7531b06b0749c79fed8399e946438cdfb54fb2b91c9d35a8c3383330", + "compile": "pass", + "runtime_validation": "pending: host disk exhaustion damaged both local container stores before runtime checks; the source compiled in two independent builds and the second installed all runtime packages before final-layer assembly failed", + "sbom": "pending", + "debian_package_inventory": "pending" + } + }, + "private_reference": { + "recipe": "Dockerfile.reference", + "upstream_release_url": "https://github.com/Weeks-UNC/shapemapper2/releases/download/v2.3/shapemapper2-2.3.tar.gz", + "upstream_release_size_bytes": 1028394655, + "upstream_release_sha256": "c3f14fdd782266522b377b1c22986b98cf9949164ec3f4d582fbe65da5e53ec6", + "local_image_tag": "nerd-shapemapper2:2.3-compliance", + "local_image_size_bytes": 2053836415, + "local_manifest_list_id": "sha256:cbf1cbff48b12459db966e1973d2ef8f56677e5d960da8ec63330b98e1903157", + "upstream_tests": "208/208 pass", + "distribution": "keep private" + }, + "base_image": { + "reference": "debian:bookworm-slim", + "linux_amd64_manifest_digest": "sha256:362e64223cc0da95422b3b13c045186fc0a81250e765d31c025fbddf257f6143" + } +} diff --git a/containers/shapemapper2/checksums.txt b/containers/shapemapper2/checksums.txt new file mode 100644 index 0000000..94695da --- /dev/null +++ b/containers/shapemapper2/checksums.txt @@ -0,0 +1,10 @@ +# ShapeMapper2 v2.3 release asset downloaded from: +# https://github.com/Weeks-UNC/shapemapper2/releases/download/v2.3/shapemapper2-2.3.tar.gz +c3f14fdd782266522b377b1c22986b98cf9949164ec3f4d582fbe65da5e53ec6 shapemapper2-2.3.tar.gz + +# linux/amd64 manifest for docker.io/library/debian:bookworm-slim +362e64223cc0da95422b3b13c045186fc0a81250e765d31c025fbddf257f6143 debian-bookworm-slim-linux-amd64.oci-manifest + +# ShapeMapper2 v2.3 source-tag archive used by the public candidate: +# https://codeload.github.com/Weeks-UNC/shapemapper2/tar.gz/refs/tags/v2.3 +1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f866b6f shapemapper2-v2.3-source.tar.gz diff --git a/containers/shapemapper2/conda-packages.tsv b/containers/shapemapper2/conda-packages.tsv new file mode 100644 index 0000000..70d1f4b --- /dev/null +++ b/containers/shapemapper2/conda-packages.tsv @@ -0,0 +1,219 @@ +environment name version build license url sha256 md5 +base asn1crypto 0.22.0 py36_0 MIT https://repo.continuum.io/pkgs/free/linux-64/asn1crypto-0.22.0-py36_0.tar.bz2 e3cbd73d4a89916f4566aca89ac1d0f6 +base cffi 1.10.0 py36_0 MIT https://repo.continuum.io/pkgs/free/linux-64/cffi-1.10.0-py36_0.tar.bz2 ec49a7e8e68d3264bd3ff853c312b149 +base conda 4.3.21 py36_0 BSD https://repo.continuum.io/pkgs/free/linux-64/conda-4.3.21-py36_0.tar.bz2 0940e36a5dba1d8f027e8ff3e72fed47 +base conda-env 2.6.0 0 BSD https://repo.continuum.io/pkgs/free/linux-64/conda-env-2.6.0-0.tar.bz2 2960d60b70d36823df7d9daea41decd0 +base cryptography 1.8.1 py36_0 Apache 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"${target}" | awk '{print $1}')" + if [[ "${actual}" == "${expected}" ]]; then + echo "verified existing ${name}" + return + fi + fi + + curl --fail --location --retry 3 --output "${partial}" "${url}" + actual="$("${checksum_command[@]}" "${partial}" | awk '{print $1}')" + if [[ "${actual}" != "${expected}" ]]; then + echo "checksum mismatch for ${name}: ${actual}" >&2 + exit 1 + fi + mv "${partial}" "${target}" + echo "downloaded and verified ${name}" +} + +fetch bowtie2-v2.3.4.3-source.tar.gz \ + f10fc386277677329f4b9d1cb6951e6b8e6c125f07438476bd3653c79ad00b07 \ + https://codeload.github.com/BenLangmead/bowtie2/tar.gz/refs/tags/v2.3.4.3 +fetch STAR-2.5.2a-source.tar.gz \ + 2a372d9bcab1dac8d35cbbed3f0ab58291e4fbe99d6c1842b094ba7449d55476 \ + https://codeload.github.com/alexdobin/STAR/tar.gz/refs/tags/2.5.2a +fetch ghostscript-9.25-source.tar.gz \ + baafa64740b090bff50b220a6df3be95c46069b7e30f4b4effed28316e5b2389 \ + https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs925/ghostscript-9.25.tar.gz +fetch BBMap_37.78-source.tar.gz \ + f2da19f64d2bfb7db4c0392212668b425c96a27c77bd9d88d8f0aea90a193509 \ + https://downloads.sourceforge.net/project/bbmap/BBMap_37.78.tar.gz +fetch graphviz-7.1.0-source.tar.gz \ + 8b28a283644a8442e6925b15d95055228d25172c7c30681810625616cbb23913 \ + https://gitlab.com/graphviz/graphviz/-/archive/7.1.0/graphviz-7.1.0.tar.gz +fetch openjdk-jdk8u112-b16-upstream-baseline.tar.gz \ + 62447a6609b46055b80ad6c9b22a99f60d240bc63bfb5274d05bc811f5dfeca7 \ + https://codeload.github.com/openjdk/jdk8u/tar.gz/64ad20c00f850c3ed4c796c72ade483460a7897f + +fetch bbmap-37.78-0.tar.bz2 \ + dd8dcf31f2fdffd22a79583d4ba56f7da21beb20282118fb8750402f4d4e23a2 \ + https://conda.anaconda.org/bioconda/linux-64/bbmap-37.78-0.tar.bz2 +fetch star-2.5.2a-0.tar.bz2 \ + 7af6e4aa48ade269e4e9435da02ce01dae45c8072af8a0045fde131d5f6c3da2 \ + https://conda.anaconda.org/bioconda/linux-64/star-2.5.2a-0.tar.bz2 +fetch graphviz-7.1.0-h2e5815a_0.conda \ + cecaa9e6dce7f2df042768d9a794f0126565a30384fcd59879e107d760bed7f1 \ + https://conda.anaconda.org/conda-forge/linux-64/graphviz-7.1.0-h2e5815a_0.conda +fetch openjdk-8.0.112-zulu8.19.0.1_3.tar.bz2 \ + 14e90e90593065802e36147c801ed89c12924b695059aecc179a756eaf5386da \ + https://conda.anaconda.org/conda-forge/linux-64/openjdk-8.0.112-zulu8.19.0.1_3.tar.bz2 +fetch zulu8.19.0.1-jdk8.0.112-linux_x64.tar.gz \ + 9ddcfa6d5a549af216cc4efbde972a6d017e72cf1633313921f6a4106c348bc5 \ + https://cdn.azul.com/zulu/bin/zulu8.19.0.1-ca-jdk8.0.112-linux_x64.tar.gz + +echo "Source collection complete. The OpenJDK archive is an upstream baseline," +echo "not yet confirmed as complete corresponding source for the Azul build." diff --git a/containers/shapemapper2/sbom.spdx.json b/containers/shapemapper2/sbom.spdx.json new file mode 100644 index 0000000..83626ca --- /dev/null +++ b/containers/shapemapper2/sbom.spdx.json @@ -0,0 +1,40331 @@ +{ + "SPDXID": "SPDXRef-DOCUMENT", + "name": "nerd-shapemapper2-2.3-poc", + "spdxVersion": "SPDX-2.2", + "creationInfo": { + "created": "2026-08-18T21:48:37.20655Z", + "creators": [ + "Organization: Anchore, Inc", + "Tool: syft-[not provided]" + ], + "licenseListVersion": "3.16" + }, + "dataLicense": "CC0-1.0", + "documentNamespace": "https://anchore.com/syft/image/nerd-shapemapper2-2.3-poc-da93f508-72fa-4ff5-83d1-b7728d6e2124", + "packages": [ + { + "SPDXID": "SPDXRef-be3ecfdd29585a14", + "name": "Pillow", + "licenseConcluded": "HPND", + "downloadLocation": "NOASSERTION", + "externalRefs": [ + { + "referenceCategory": "SECURITY", + 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b/containers/shapemapper2/source-manifest.tsv @@ -0,0 +1,11 @@ +component version license distributed_artifact distributed_sha256 corresponding_source_url corresponding_source_sha256 status +ShapeMapper2 2.3 (runtime reports 2.3.0) MIT shapemapper2-2.3.tar.gz c3f14fdd782266522b377b1c22986b98cf9949164ec3f4d582fbe65da5e53ec6 https://github.com/Weeks-UNC/shapemapper2/releases/download/v2.3/shapemapper2-2.3.tar.gz c3f14fdd782266522b377b1c22986b98cf9949164ec3f4d582fbe65da5e53ec6 Release contains source and bundled binaries; MIT notice retained +Bowtie2 2.3.4.3 GPL-3.0-only bowtie2-2.3.4.3-linux-x86_64.zip d6c608d882a0fc121ee4b81f900cba05ef5d2b8b49d4dd7588f7c51aa5a6e11b https://codeload.github.com/BenLangmead/bowtie2/tar.gz/refs/tags/v2.3.4.3 f10fc386277677329f4b9d1cb6951e6b8e6c125f07438476bd3653c79ad00b07 Versioned source and build scripts verified; preserve as release source artifact +STAR 2.5.2a GPL-3.0 star-2.5.2a-0.tar.bz2 7af6e4aa48ade269e4e9435da02ce01dae45c8072af8a0045fde131d5f6c3da2 https://codeload.github.com/alexdobin/STAR/tar.gz/refs/tags/2.5.2a 2a372d9bcab1dac8d35cbbed3f0ab58291e4fbe99d6c1842b094ba7449d55476 Exact Conda package contains its recipe; recipe copies the static binary from this source release +Ghostscript 9.25 AGPL-3.0-or-later ghostscript-9.25.tar.gz (prebuilt Linux binary archive) bc730e16aa3379744e852a350ec57941059edc92534f46e46868693b1f3ba222 https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs925/ghostscript-9.25.tar.gz baafa64740b090bff50b220a6df3be95c46069b7e30f4b4effed28316e5b2389 Official source is AGPL; ShapeMapper's adjacent COPYING is GPLv3, so retain both and document the mismatch +BBMap/BBMerge 37.78 UC-LBL permissive bbmap-37.78-0.tar.bz2 dd8dcf31f2fdffd22a79583d4ba56f7da21beb20282118fb8750402f4d4e23a2 https://downloads.sourceforge.net/project/bbmap/BBMap_37.78.tar.gz f2da19f64d2bfb7db4c0392212668b425c96a27c77bd9d88d8f0aea90a193509 Exact Conda package, source, recipe, and license verified; installed package also contains Java source +pv 1.6.20 Artistic-2.0 pv-1.6.20.tar.gz b5f1ee79a370c5287e092b6e8f1084f026521fe0aecf25c44b9460b870319a9e embedded in ShapeMapper release: internals/thirdparty/pv-1.6.20.tar.gz b5f1ee79a370c5287e092b6e8f1084f026521fe0aecf25c44b9460b870319a9e Bundled archive is source and contains Artistic 2.0 COPYING +Graphviz 7.1.0 EPL-1.0 graphviz-7.1.0-h2e5815a_0.conda cecaa9e6dce7f2df042768d9a794f0126565a30384fcd59879e107d760bed7f1 https://gitlab.com/graphviz/graphviz/-/archive/7.1.0/graphviz-7.1.0.tar.gz 8b28a283644a8442e6925b15d95055228d25172c7c30681810625616cbb23913 Exact Conda package contains recipe and patches; preserve both package and source +Azul Zulu OpenJDK 8.0.112 / Zulu 8.19.0.1 GPL-2.0 with Classpath Exception and additional notices openjdk-8.0.112-zulu8.19.0.1_3.tar.bz2 14e90e90593065802e36147c801ed89c12924b695059aecc179a756eaf5386da https://codeload.github.com/openjdk/jdk8u/tar.gz/64ad20c00f850c3ed4c796c72ade483460a7897f 62447a6609b46055b80ad6c9b22a99f60d240bc63bfb5274d05bc811f5dfeca7 Upstream 8u112-b16 baseline verified but not confirmed as complete corresponding source for Azul build d0cf8daf3adb; public-release gap +Miniconda/Conda Conda 4.3.21 BSD-3-Clause plus per-package licenses miniconda.sh e9089c735b4ae53cb1035b1a97cec9febe6decf76868383292af589218304a90 see conda-packages.tsv Installer notice retained; all 218 embedded package records require their own license/source treatment +Debian base bookworm-slim linux/amd64 mixed debian:bookworm-slim@sha256:362e64223cc0da95422b3b13c045186fc0a81250e765d31c025fbddf257f6143 sha256:362e64223cc0da95422b3b13c045186fc0a81250e765d31c025fbddf257f6143 https://sources.debian.org/ Retain /usr/share/doc copyright files and map exact binary packages to Debian sources before public release diff --git a/containers/shapemapper2/test-container.sh b/containers/shapemapper2/test-container.sh new file mode 100755 index 0000000..19c8220 --- /dev/null +++ b/containers/shapemapper2/test-container.sh @@ -0,0 +1,35 @@ +#!/usr/bin/env bash +set -euo pipefail + +image="${1:-nerd-shapemapper2:2.3-public-candidate}" +container_engine="${CONTAINER_ENGINE:-docker}" +work_dir="$(mktemp -d "${TMPDIR:-/tmp}/nerd-shapemapper2-test.XXXXXX")" +host_user="$(id -u):$(id -g)" +trap 'rm -rf "${work_dir}"' EXIT + +"${container_engine}" image inspect "${image}" --format '{{.Architecture}}' | grep -qx amd64 +"${container_engine}" run --rm --platform linux/amd64 "${image}" --version | grep -F 'ShapeMapper v2.3' + +"${container_engine}" run --rm --platform linux/amd64 --entrypoint tar "${image}" \ + -C /opt/shapemapper2 -cf - example_data | tar -xf - -C "${work_dir}" + +"${container_engine}" run --rm \ + --platform linux/amd64 \ + --user "${host_user}" \ + --entrypoint /opt/shapemapper2/shapemapper \ + --mount "type=bind,src=${work_dir},dst=/work" \ + --workdir /work \ + "${image}" \ + --name example-results \ + --target example_data/TPP.fa \ + --amplicon \ + --overwrite \ + --min-depth 1000 \ + --modified --folder example_data/TPPplus \ + --untreated --folder example_data/TPPminus \ + --denatured --folder example_data/TPPdenat + +test -s "${work_dir}/shapemapper_out/example-results_TPP_profile.txt" +test -s "${work_dir}/shapemapper_out/example-results_TPP.shape" + +echo "ShapeMapper2 v2.3 container smoke test passed" diff --git a/containers/shapemapper2/test-upstream.sh b/containers/shapemapper2/test-upstream.sh new file mode 100755 index 0000000..1e37efe --- /dev/null +++ b/containers/shapemapper2/test-upstream.sh @@ -0,0 +1,47 @@ +#!/usr/bin/env bash +set -euo pipefail + +image="${1:-nerd-shapemapper2:2.3-public-candidate}" +container_engine="${CONTAINER_ENGINE:-docker}" +log_file="$(mktemp "${TMPDIR:-/tmp}/nerd-shapemapper2-upstream.XXXXXX")" +trap 'rm -f "${log_file}"' EXIT + +set +e +"${container_engine}" run --rm \ + --platform linux/amd64 \ + --entrypoint bash \ + "${image}" \ + /opt/shapemapper2/internals/test/run_all_tests.sh 2>&1 | tee "${log_file}" +test_status="${PIPESTATUS[0]}" +set -e + +if [[ "${test_status}" -eq 0 ]] \ + && grep -Fxq 'All tests passed' "${log_file}" \ + && grep -Fxq 'SUCCESS' "${log_file}"; then + echo "All ShapeMapper2 upstream tests passed" + exit 0 +fi + +# Upstream documents that one environment-dependent module-failure injection +# test may be ignored. Accept only that exact aggregate result; normal pipeline, +# unit, variant-correction, and ROC failures still fail this validation. +expected_summaries=( + $'0 / 98\tc++ unit test(s) failed.' + $'0 / 32\tend-to-end success test(s) failed.' + $'1 / 63\tmodule failure detection test(s) failed.' + $'0 / 13\tsequence variant correction test(s) failed.' + $'0 / 2\tarea under ROC curve test(s) failed.' + $'1 / 208\ttotal test(s) failed.' +) + +if [[ "${test_status}" -eq 1 ]]; then + for summary in "${expected_summaries[@]}"; do + grep -Fxq "${summary}" "${log_file}" || exit 1 + done + grep -Fxq 'FAILURE' "${log_file}" || exit 1 + echo "Accepted the single environment-dependent failure allowed by upstream" + exit 0 +fi + +echo "ShapeMapper2 upstream validation failed with status ${test_status}" >&2 +exit "${test_status}" diff --git a/containers/shapemapper2/validate-sif-on-quest.sh b/containers/shapemapper2/validate-sif-on-quest.sh new file mode 100755 index 0000000..f29b6e3 --- /dev/null +++ b/containers/shapemapper2/validate-sif-on-quest.sh @@ -0,0 +1,57 @@ +#!/usr/bin/env bash +set -euo pipefail + +image_ref="${1:-}" +if [[ -z "${image_ref}" || "${image_ref}" != *@sha256:* ]]; then + echo "usage: $0 ghcr.io/edr-choi/nerd-shapemapper2@sha256: [cache-directory]" >&2 + exit 2 +fi + +if command -v apptainer >/dev/null 2>&1; then + runtime=apptainer +elif command -v singularity >/dev/null 2>&1; then + runtime=singularity +else + echo "Apptainer or Singularity is required" >&2 + exit 2 +fi + +cache_root="${2:-${SCRATCH:-${TMPDIR:-/tmp}}/nerd-shapemapper2-cache}" +mkdir -p "${cache_root}/oci" "${cache_root}/work" +export APPTAINER_CACHEDIR="${cache_root}/oci" +export SINGULARITY_CACHEDIR="${cache_root}/oci" + +digest="${image_ref##*@sha256:}" +sif="${cache_root}/shapemapper2-${digest}.sif" +work_dir="$(mktemp -d "${cache_root}/work/validation.XXXXXX")" +trap 'rm -rf "${work_dir}"' EXIT + +if [[ ! -s "${sif}" ]]; then + "${runtime}" pull "${sif}" "docker://${image_ref}" +fi + +"${runtime}" exec "${sif}" /opt/shapemapper2/shapemapper --version \ + | grep -F 'ShapeMapper v2.3' + +"${runtime}" exec "${sif}" tar -C /opt/shapemapper2 -cf - example_data \ + | tar -xf - -C "${work_dir}" + +"${runtime}" exec \ + --bind "${work_dir}:/work" \ + --pwd /work \ + "${sif}" \ + /opt/shapemapper2/shapemapper \ + --name example-results \ + --target example_data/TPP.fa \ + --amplicon \ + --overwrite \ + --min-depth 1000 \ + --modified --folder example_data/TPPplus \ + --untreated --folder example_data/TPPminus \ + --denatured --folder example_data/TPPdenat + +test -s "${work_dir}/shapemapper_out/example-results_TPP_profile.txt" +test -s "${work_dir}/shapemapper_out/example-results_TPP.shape" + +sha256sum "${sif}" +echo "SIF validation passed with ${runtime}: ${sif}" From a1cf83c26135abe0cb5891eb590015ee6fb2c203 Mon Sep 17 00:00:00 2001 From: Edric Choi Date: Tue, 18 Aug 2026 22:30:03 -0500 Subject: [PATCH 02/11] Use self-contained ShapeMapper CI --- .../workflows/shapemapper2-container-poc.yml | 152 +++++++++++++----- containers/shapemapper2/COMPLIANCE.md | 6 +- containers/shapemapper2/README.md | 23 +-- 3 files changed, 134 insertions(+), 47 deletions(-) diff --git a/.github/workflows/shapemapper2-container-poc.yml b/.github/workflows/shapemapper2-container-poc.yml index 7e99357..1a08131 100644 --- a/.github/workflows/shapemapper2-container-poc.yml +++ b/.github/workflows/shapemapper2-container-poc.yml @@ -1,4 +1,4 @@ -name: ShapeMapper2 public candidate validation +name: ShapeMapper2 candidate build and private publish on: pull_request: @@ -6,57 +6,137 @@ on: - .github/workflows/shapemapper2-container-poc.yml - containers/shapemapper2/** workflow_dispatch: + inputs: + publish_private: + description: Push a uniquely tagged private development image after tests pass + required: true + type: boolean + default: false permissions: contents: read +env: + LOCAL_IMAGE: nerd-shapemapper2:2.3-public-candidate + jobs: build-and-test: runs-on: ubuntu-latest timeout-minutes: 60 steps: - - name: Check out NERD - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 - - - name: Set up Docker Buildx - uses: docker/setup-buildx-action@bb05f3f5519dd87d3ba754cc423b652a5edd6d2c # v4.2.0 + # LucksLab permits only LucksLab-owned actions. Check out the exact event + # ref directly instead of using actions/checkout. + - name: Check out the exact revision + env: + CHECKOUT_REF: ${{ github.ref }} + REPOSITORY: ${{ github.repository }} + run: | + git init . + git remote add origin "https://github.com/${REPOSITORY}.git" + git fetch --no-tags --depth=1 origin "${CHECKOUT_REF}" + git checkout --detach FETCH_HEAD - name: Build amd64 image without publishing - uses: docker/build-push-action@53b7df96c91f9c12dcc8a07bcb9ccacbed38856a # v7.3.0 - with: - context: containers/shapemapper2 - platforms: linux/amd64 - load: true - push: false - tags: nerd-shapemapper2:2.3-public-candidate + run: | + docker build \ + --platform linux/amd64 \ + --tag "${LOCAL_IMAGE}" \ + containers/shapemapper2 + + - name: Confirm required runtime commands + run: | + docker run --rm \ + --platform linux/amd64 \ + --entrypoint bash \ + "${LOCAL_IMAGE}" \ + -lc ' + set -e + for tool in bbmerge.sh bowtie2 bowtie2-build STAR dot gs pv; do + command -v "${tool}" + done + python3 -c "import matplotlib, numpy, scipy, sklearn" + ' - name: Run upstream example smoke test - run: containers/shapemapper2/test-container.sh nerd-shapemapper2:2.3-public-candidate + run: containers/shapemapper2/test-container.sh "${LOCAL_IMAGE}" - name: Run complete upstream test suite - run: containers/shapemapper2/test-upstream.sh nerd-shapemapper2:2.3-public-candidate + run: containers/shapemapper2/test-upstream.sh "${LOCAL_IMAGE}" - - name: Capture exact Debian binary and source package inventory + - name: Record image size and Debian package inventory run: | docker run --rm --entrypoint dpkg-query \ - nerd-shapemapper2:2.3-public-candidate \ + "${LOCAL_IMAGE}" \ -W '-f=${binary:Package}\t${Version}\t${source:Package}\t${source:Version}\n' \ - | LC_ALL=C sort > shapemapper2-2.3-r0.debian-packages.tsv - - - name: Upload Debian package inventory - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2 - with: - name: shapemapper2-2.3-r0-debian-packages - path: shapemapper2-2.3-r0.debian-packages.tsv - retention-days: 30 - if-no-files-found: error - - - name: Generate SPDX SBOM - uses: anchore/sbom-action@e22c389904149dbc22b58101806040fa8d37a610 # v0.24.0 - with: - image: nerd-shapemapper2:2.3-public-candidate - format: spdx-json - output-file: shapemapper2-2.3-r0.spdx.json - artifact-name: shapemapper2-2.3-r0.spdx.json - upload-artifact-retention: 30 - upload-release-assets: false + | LC_ALL=C sort \ + | tee shapemapper2-2.3-r0.debian-packages.tsv + + image_size_bytes="$(docker image inspect "${LOCAL_IMAGE}" --format '{{.Size}}')" + package_count="$(wc -l < shapemapper2-2.3-r0.debian-packages.tsv | tr -d ' ')" + { + echo '### ShapeMapper2 candidate' + echo "- Image size: ${image_size_bytes} bytes" + echo "- Installed Debian packages: ${package_count}" + echo "- Source revision: ${GITHUB_SHA}" + } >> "${GITHUB_STEP_SUMMARY}" + + - name: Push uniquely tagged private development image + if: ${{ github.event_name == 'workflow_dispatch' && inputs.publish_private }} + env: + GHCR_TOKEN: ${{ secrets.EDR_CHOI_GHCR_TOKEN }} + run: | + set -euo pipefail + test -n "${GHCR_TOKEN}" + + package_api_url='https://api.github.com/users/edr-choi/packages/container/nerd-shapemapper2' + status_code="$(curl --silent --show-error \ + --output package-before.json \ + --write-out '%{http_code}' \ + --header "Authorization: Bearer ${GHCR_TOKEN}" \ + --header 'Accept: application/vnd.github+json' \ + --header 'X-GitHub-Api-Version: 2022-11-28' \ + "${package_api_url}")" + + if [[ "${status_code}" == '200' ]]; then + test "$(jq -r '.visibility' package-before.json)" == 'private' + elif [[ "${status_code}" != '404' ]]; then + echo "Unable to confirm the existing package visibility (HTTP ${status_code})" >&2 + exit 1 + fi + + printf '%s' "${GHCR_TOKEN}" \ + | docker login ghcr.io --username edr-choi --password-stdin + trap 'docker logout ghcr.io >/dev/null 2>&1 || true' EXIT + + short_sha="${GITHUB_SHA:0:12}" + image_ref="ghcr.io/edr-choi/nerd-shapemapper2:2.3-dev-${short_sha}-run${GITHUB_RUN_ID}" + docker tag "${LOCAL_IMAGE}" "${image_ref}" + docker push "${image_ref}" 2>&1 | tee docker-push.log + + digest="$(sed -n 's/^.*digest: \(sha256:[0-9a-f]\{64\}\).*$/\1/p' docker-push.log | tail -1)" + test -n "${digest}" + + for attempt in 1 2 3 4 5; do + status_code="$(curl --silent --show-error \ + --output package-after.json \ + --write-out '%{http_code}' \ + --header "Authorization: Bearer ${GHCR_TOKEN}" \ + --header 'Accept: application/vnd.github+json' \ + --header 'X-GitHub-Api-Version: 2022-11-28' \ + "${package_api_url}")" + [[ "${status_code}" == '200' ]] && break + sleep 3 + done + test "${status_code}" == '200' + test "$(jq -r '.visibility' package-after.json)" == 'private' + + digest_ref="ghcr.io/edr-choi/nerd-shapemapper2@${digest}" + { + echo '### Private development image' + echo "- Tag: \`${image_ref}\`" + echo "- Digest-pinned reference: \`${digest_ref}\`" + echo '- Visibility confirmed: `private`' + } >> "${GITHUB_STEP_SUMMARY}" + + echo "Private image: ${image_ref}" + echo "Digest-pinned reference: ${digest_ref}" diff --git a/containers/shapemapper2/COMPLIANCE.md b/containers/shapemapper2/COMPLIANCE.md index 7ce0bb6..38ebe14 100644 --- a/containers/shapemapper2/COMPLIANCE.md +++ b/containers/shapemapper2/COMPLIANCE.md @@ -32,8 +32,10 @@ Azul Zulu and historical Conda source gaps described later in this document. command name, especially Debian's BBMerge launcher. - [ ] Record the final image digest, CI run, package inventory, SBOM, and source bundle checksums together. -- [ ] Obtain explicit owner approval before the first GHCR push or public - visibility change. +- [x] Obtain explicit owner approval before pushing a uniquely tagged private + development image for NERD integration testing. +- [ ] Obtain explicit owner approval before creating a release tag or changing + GHCR visibility to public. The first local source build produced a 508,942,308-byte amd64 image. Runtime inspection was interrupted by host disk exhaustion immediately after the diff --git a/containers/shapemapper2/README.md b/containers/shapemapper2/README.md index 1486da7..5f20615 100644 --- a/containers/shapemapper2/README.md +++ b/containers/shapemapper2/README.md @@ -100,15 +100,20 @@ This is an infrastructure failure, not a ShapeMapper compile or test failure. ## Publication gate -Do not push either image or change GHCR visibility until the public candidate's -built-in tests, image-size report, Debian package inventory, SBOM, and source -availability record have been presented to and approved by the project owner. -Release tags must never be overwritten; NERD should consume a published image -by OCI digest. - -The manual GitHub Actions workflow builds, runs both test levels, and retains -an SPDX SBOM. It has no package-write permission, registry login, or push step. -All third-party actions are pinned to immutable commits. +Do not create a release tag or change GHCR visibility until the public +candidate's built-in tests, image-size report, Debian package inventory, SBOM, +and source-availability record have been presented to and approved by the +project owner. Release tags must never be overwritten; NERD should consume an +image by OCI digest. + +The GitHub Actions workflow uses only built-in Git and Docker commands because +LucksLab's organization policy disallows third-party actions. Pull requests +build and test without registry access. A manual run can, after all tests pass, +push a uniquely tagged private development image using the repository secret +`EDR_CHOI_GHCR_TOKEN`. It verifies that the GHCR package remains private and +prints the immutable digest for NERD testing. This private development image is +not a public release; generating and retaining a fresh SPDX SBOM remains part +of the public-release gate. ## Licensing status From 381b3fd2098fec8221df0e4e254e496c0c100a54 Mon Sep 17 00:00:00 2001 From: Edric Choi Date: Tue, 18 Aug 2026 22:32:36 -0500 Subject: [PATCH 03/11] Preserve container PATH in CI check --- .github/workflows/shapemapper2-container-poc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/shapemapper2-container-poc.yml b/.github/workflows/shapemapper2-container-poc.yml index 1a08131..789dd98 100644 --- a/.github/workflows/shapemapper2-container-poc.yml +++ b/.github/workflows/shapemapper2-container-poc.yml @@ -49,7 +49,7 @@ jobs: --platform linux/amd64 \ --entrypoint bash \ "${LOCAL_IMAGE}" \ - -lc ' + -c ' set -e for tool in bbmerge.sh bowtie2 bowtie2-build STAR dot gs pv; do command -v "${tool}" From 6247231488f7b8ff60b63b1548ad7f8db5c2cf74 Mon Sep 17 00:00:00 2001 From: Edric Choi Date: Tue, 18 Aug 2026 22:45:15 -0500 Subject: [PATCH 04/11] Add Python 3.11 compatibility patch --- containers/shapemapper2/COMPLIANCE.md | 9 +- containers/shapemapper2/Dockerfile | 10 +- .../PUBLIC_THIRD_PARTY_NOTICES.md | 11 +- containers/shapemapper2/README.md | 24 +- containers/shapemapper2/build-metadata.json | 10 +- containers/shapemapper2/checksums.txt | 3 + .../patches/python311-open-mode.patch | 316 ++++++++++++++++++ 7 files changed, 364 insertions(+), 19 deletions(-) create mode 100644 containers/shapemapper2/patches/python311-open-mode.patch diff --git a/containers/shapemapper2/COMPLIANCE.md b/containers/shapemapper2/COMPLIANCE.md index 38ebe14..50c8291 100644 --- a/containers/shapemapper2/COMPLIANCE.md +++ b/containers/shapemapper2/COMPLIANCE.md @@ -6,14 +6,17 @@ and the project owner gives explicit approval. ## Public candidate (`Dockerfile`) -The public candidate compiles the unchanged upstream v2.3 source tag and uses -Debian 12 packages. It excludes the official release archive's Miniconda +The public candidate compiles the checksum-pinned upstream v2.3 source tag, +after applying one documented Python 3.11 file-mode compatibility patch, and +uses Debian 12 packages. It excludes the official release archive's Miniconda environment and old prebuilt third-party executables. That removes the exact Azul Zulu and historical Conda source gaps described later in this document. - [x] Pin the upstream ShapeMapper v2.3 source archive by SHA-256. - [x] Preserve the ShapeMapper MIT notice in the source tree and image. -- [x] Compile without patching or vendoring the upstream repository. +- [x] Apply only the documented `python311-open-mode.patch` (`rU` to `r` in + 30 file-open calls across 18 files); do not change scientific logic or + vendor/fork the upstream repository. - [x] Use distribution packages for Bowtie2, STAR, BBMap/BBMerge, Graphviz, Ghostscript, pv, OpenJDK, Python, Boost, zlib, and transitive dependencies. - [x] Preserve Debian package copyright records under diff --git a/containers/shapemapper2/Dockerfile b/containers/shapemapper2/Dockerfile index cc2a4da..be3cc58 100644 --- a/containers/shapemapper2/Dockerfile +++ b/containers/shapemapper2/Dockerfile @@ -1,6 +1,7 @@ # syntax=docker/dockerfile:1.7 -# Public candidate: compile the unchanged upstream v2.3 source tag and use +# Public candidate: compile the checksum-pinned upstream v2.3 source tag with +# one documented Python 3.11 file-mode compatibility patch, and use # source-traceable Debian packages for runtime dependencies. FROM --platform=linux/amd64 debian:bookworm-slim@sha256:362e64223cc0da95422b3b13c045186fc0a81250e765d31c025fbddf257f6143 AS build @@ -18,6 +19,7 @@ RUN apt-get update \ libboost-program-options-dev \ libboost-system-dev \ make \ + patch \ zlib1g-dev \ && rm -rf /var/lib/apt/lists/* @@ -25,12 +27,16 @@ ADD --checksum=sha256:1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f https://codeload.github.com/Weeks-UNC/shapemapper2/tar.gz/refs/tags/v2.3 \ /tmp/shapemapper2-v2.3.tar.gz +COPY patches/python311-open-mode.patch /tmp/python311-open-mode.patch + RUN test "${SHAPEMAPPER_VERSION}" = "2.3" \ && test "${SHAPEMAPPER_SOURCE_SHA256}" = "1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f866b6f" \ && test "${SHAPEMAPPER_SOURCE_URL}" = "https://codeload.github.com/Weeks-UNC/shapemapper2/tar.gz/refs/tags/v2.3" \ && tar -xzf /tmp/shapemapper2-v2.3.tar.gz -C /opt \ && mv /opt/shapemapper2-2.3 /opt/shapemapper2 \ && rm /tmp/shapemapper2-v2.3.tar.gz \ + && patch --batch --forward --strip=2 --directory=/opt/shapemapper2 < /tmp/python311-open-mode.patch \ + && rm /tmp/python311-open-mode.patch \ && cmake -S /opt/shapemapper2 -B /tmp/shapemapper-build -DCMAKE_BUILD_TYPE=Release \ && cmake --build /tmp/shapemapper-build --parallel 2 @@ -40,7 +46,7 @@ ARG SHAPEMAPPER_VERSION=2.3 ARG SHAPEMAPPER_SOURCE_SHA256=1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f866b6f LABEL org.opencontainers.image.title="NERD ShapeMapper2" \ - org.opencontainers.image.description="ShapeMapper2 v2.3 built from the unchanged upstream source tag with Debian runtime packages" \ + org.opencontainers.image.description="ShapeMapper2 v2.3 built from its checksum-pinned upstream source tag with a documented Python 3.11 compatibility patch" \ org.opencontainers.image.source="https://github.com/LucksLab/nerd" \ org.opencontainers.image.url="https://github.com/LucksLab/nerd" \ org.opencontainers.image.version="2.3-r0-candidate" \ diff --git a/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md b/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md index c84eb16..7300a67 100644 --- a/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md +++ b/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md @@ -1,9 +1,12 @@ # Third-party notices for the source-built public candidate -This image compiles the unchanged ShapeMapper2 v2.3 source tag and installs -runtime dependencies as Debian 12 (bookworm) packages. It does not contain the -official ShapeMapper release archive's bundled Miniconda environment or its -historical prebuilt executables. +This image compiles the checksum-pinned ShapeMapper2 v2.3 source tag after +applying `patches/python311-open-mode.patch`. That patch replaces Python's +removed `rU` file mode with equivalent `r` mode in 30 file-open calls and +changes no scientific logic. The image installs runtime dependencies as +Debian 12 (bookworm) packages. It does not contain the official ShapeMapper +release archive's bundled Miniconda environment or historical prebuilt +executables. ShapeMapper2 is Copyright (c) 2018 Steven Busan and is distributed under the MIT License. The complete notice is installed beside this file and remains in diff --git a/containers/shapemapper2/README.md b/containers/shapemapper2/README.md index 5f20615..bde7684 100644 --- a/containers/shapemapper2/README.md +++ b/containers/shapemapper2/README.md @@ -1,12 +1,14 @@ # ShapeMapper2 v2.3 container -This directory contains two Linux-amd64 container recipes for the unmodified -upstream ShapeMapper2 v2.3 code. Neither recipe forks ShapeMapper, and neither -image is currently published to GHCR. +This directory contains two Linux-amd64 container recipes based on upstream +ShapeMapper2 v2.3. Neither recipe forks ShapeMapper, and neither image is +currently published to GHCR. - `Dockerfile` is the smaller public candidate. It downloads the upstream v2.3 - source tag directly, verifies its SHA-256, compiles ShapeMapper, and uses - Debian packages for runtime dependencies. + source tag directly, verifies its SHA-256, applies the documented + `patches/python311-open-mode.patch`, compiles ShapeMapper, and uses Debian + packages for runtime dependencies. The patch replaces Python's removed + `rU` file mode with equivalent `r` mode; it changes no scientific logic. - `Dockerfile.reference` is the private reference recipe. It wraps the official upstream release archive, including its historical Miniconda environment. This image remains useful as a behavioral comparison but is not the public @@ -42,9 +44,9 @@ docker build --platform linux/amd64 \ ``` Both recipes pin the amd64 Debian base manifest. The public candidate pins the -upstream source-tag archive; the private reference recipe pins the official -release asset. No ShapeMapper source files are copied into this repository or -patched during either build. +upstream source-tag archive and carries one small, auditable compatibility +patch rather than a ShapeMapper fork; the private reference recipe pins the +official release asset and does not patch it. ## Test levels @@ -90,13 +92,17 @@ failure-injection miss while rejecting any normal execution failure. ### Smaller public candidate result On 2026-08-18, the source-based candidate compiled successfully from the -unchanged upstream v2.3 source archive. Its local amd64 image size was +checksum-pinned upstream v2.3 source archive. Its local amd64 image size was 508,942,308 bytes (about 485 MiB), approximately 75% smaller than the private reference image. A second low-memory build also compiled successfully with the recipe's two-job compiler limit and installed the full Debian runtime. Runtime and built-in test validation is pending because the host ran out of disk space during final layer assembly, leaving both local container stores unavailable. This is an infrastructure failure, not a ShapeMapper compile or test failure. +A subsequent GitHub Actions smoke test exposed Python 3.11's removal of the +legacy `rU` open mode. The documented compatibility patch fixes all 30 such +uses across 18 upstream Python files; final runtime validation is pending the +CI rerun. ## Publication gate diff --git a/containers/shapemapper2/build-metadata.json b/containers/shapemapper2/build-metadata.json index 2557610..adf3be0 100644 --- a/containers/shapemapper2/build-metadata.json +++ b/containers/shapemapper2/build-metadata.json @@ -9,9 +9,17 @@ }, "public_candidate": { "recipe": "Dockerfile", - "strategy": "compile unchanged upstream source; install Debian runtime packages", + "strategy": "compile checksum-pinned upstream source with a documented Python 3.11 file-mode compatibility patch; install Debian runtime packages", "upstream_source_url": "https://codeload.github.com/Weeks-UNC/shapemapper2/tar.gz/refs/tags/v2.3", "upstream_source_sha256": "1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f866b6f", + "compatibility_patch": { + "path": "patches/python311-open-mode.patch", + "sha256": "30746f44ed4756b208f010784c09be813481f83353231bc18aee4a7532d3663f", + "change": "replace removed Python rU file mode with equivalent r mode", + "occurrences": 30, + "files": 18, + "scientific_logic_changed": false + }, "local_build_2026_08_18": { "image_tag": "nerd-shapemapper2:2.3-public-candidate", "image_size_bytes": 508942308, diff --git a/containers/shapemapper2/checksums.txt b/containers/shapemapper2/checksums.txt index 94695da..5a01006 100644 --- a/containers/shapemapper2/checksums.txt +++ b/containers/shapemapper2/checksums.txt @@ -8,3 +8,6 @@ c3f14fdd782266522b377b1c22986b98cf9949164ec3f4d582fbe65da5e53ec6 shapemapper2-2 # ShapeMapper2 v2.3 source-tag archive used by the public candidate: # https://codeload.github.com/Weeks-UNC/shapemapper2/tar.gz/refs/tags/v2.3 1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f866b6f shapemapper2-v2.3-source.tar.gz + +# Auditable Python 3.11 file-mode compatibility patch applied by Dockerfile +30746f44ed4756b208f010784c09be813481f83353231bc18aee4a7532d3663f patches/python311-open-mode.patch diff --git a/containers/shapemapper2/patches/python311-open-mode.patch b/containers/shapemapper2/patches/python311-open-mode.patch new file mode 100644 index 0000000..9bb471f --- /dev/null +++ b/containers/shapemapper2/patches/python311-open-mode.patch @@ -0,0 +1,316 @@ +diff --git a/shapemapper2-2.3/internals/bin/area_under_ROC_curve.py b/shapemapper2-2.3/internals/bin/area_under_ROC_curve.py +--- a/shapemapper2-2.3/internals/bin/area_under_ROC_curve.py ++++ b/shapemapper2-2.3/internals/bin/area_under_ROC_curve.py +@@ -6,7 +6,7 @@ import numpy as np + from sklearn.metrics import roc_curve, auc + + def load_ct(filename): +- f = open(filename, "rU") ++ f = open(filename, "r") + f.readline() + paired = [] + for line in f: +@@ -21,7 +21,7 @@ def load_ct(filename): + + + def load_map(filename): +- f = open(filename, "rU") ++ f = open(filename, "r") + profile = [] + for line in f: + s = line.strip().split() +diff --git a/shapemapper2-2.3/internals/bin/compare_fasta.py b/shapemapper2-2.3/internals/bin/compare_fasta.py +--- a/shapemapper2-2.3/internals/bin/compare_fasta.py ++++ b/shapemapper2-2.3/internals/bin/compare_fasta.py +@@ -15,7 +15,7 @@ import traceback + + + def load_fasta(fastaname, rna=None, convert_to_rna=True): +- f = open(fastaname, "rU") ++ f = open(fastaname, "r") + seq = "" + rna_count = 0 + in_selected_rna = False +diff --git a/shapemapper2-2.3/internals/bin/deinterleave_fastq.py b/shapemapper2-2.3/internals/bin/deinterleave_fastq.py +--- a/shapemapper2-2.3/internals/bin/deinterleave_fastq.py ++++ b/shapemapper2-2.3/internals/bin/deinterleave_fastq.py +@@ -16,7 +16,7 @@ ap.add_argument('--R2-out', type=str) + # FIXME: combine with deinterleave_fastq_columns.py as a more general utility + + def iterate_fastq(filename): +- f = open(filename, "rU") ++ f = open(filename, "r") + lines = [] + for line in f: + # suppress jdb socket message +diff --git a/shapemapper2-2.3/internals/bin/deinterleave_fastq_columns.py b/shapemapper2-2.3/internals/bin/deinterleave_fastq_columns.py +--- a/shapemapper2-2.3/internals/bin/deinterleave_fastq_columns.py ++++ b/shapemapper2-2.3/internals/bin/deinterleave_fastq_columns.py +@@ -4,7 +4,7 @@ import sys, os + # FIXME: rewrite in c++ + + def iterate_fastq(filename): +- f = open(filename, "rU") ++ f = open(filename, "r") + lines = [] + for line in f: + # suppress jdb socket message +@@ -16,7 +16,7 @@ def iterate_fastq(filename): + yield l + lines = [] + +-input = open(sys.argv[1], 'rU') ++input = open(sys.argv[1], 'r') + r1_out = open(sys.argv[2], 'w') + r2_out = open(sys.argv[3], 'w') + unpaired_out = open(sys.argv[4], 'w') +diff --git a/shapemapper2-2.3/internals/bin/get_sequence_lengths.py b/shapemapper2-2.3/internals/bin/get_sequence_lengths.py +--- a/shapemapper2-2.3/internals/bin/get_sequence_lengths.py ++++ b/shapemapper2-2.3/internals/bin/get_sequence_lengths.py +@@ -15,7 +15,7 @@ import argparse, sys, os + + + def get_lengths(filename): +- f = open(filename, "rU") ++ f = open(filename, "r") + lengths = [] + for line in f: + if line[0] == ">": +diff --git a/shapemapper2-2.3/internals/bin/interleave_fastq.py b/shapemapper2-2.3/internals/bin/interleave_fastq.py +--- a/shapemapper2-2.3/internals/bin/interleave_fastq.py ++++ b/shapemapper2-2.3/internals/bin/interleave_fastq.py +@@ -4,7 +4,7 @@ import sys, os + # FIXME: rewrite in c++ + + def iterate_fastq(filename): +- f = open(filename, "rU") ++ f = open(filename, "r") + lines = [] + for line in f: + lines.append(line.strip()) +diff --git a/shapemapper2-2.3/internals/bin/make_reactivity_profiles.py b/shapemapper2-2.3/internals/bin/make_reactivity_profiles.py +--- a/shapemapper2-2.3/internals/bin/make_reactivity_profiles.py ++++ b/shapemapper2-2.3/internals/bin/make_reactivity_profiles.py +@@ -207,7 +207,7 @@ def write_tab_file(seq, + f.write("\n") + + def load_fasta(fastaname, rna, convert_to_rna=True): +- f = open(fastaname, "rU") ++ f = open(fastaname, "r") + seq = "" + rna_count = 0 + in_selected_rna = False +@@ -239,7 +239,7 @@ def load_counts(filename): + if filename is None: + return None + +- f = open(filename, "rU") ++ f = open(filename, "r") + + # do one pass to determine array length + # TODO: might actually be faster to just resize array in memory and read in one pass +diff --git a/shapemapper2-2.3/internals/bin/make_variant.py b/shapemapper2-2.3/internals/bin/make_variant.py +--- a/shapemapper2-2.3/internals/bin/make_variant.py ++++ b/shapemapper2-2.3/internals/bin/make_variant.py +@@ -40,7 +40,7 @@ len_err = RuntimeError(len_msg) + # TODO: move load_fasta(), load_depth() to their own file utility module, since + # they are used by both make_reactivity_profiles.py and make_variant.py + def load_fasta(fastaname, rna, convert_to_rna=True): +- f = open(fastaname, "rU") ++ f = open(fastaname, "r") + seq = "" + rna_count = 0 + in_selected_rna = False +@@ -205,7 +205,7 @@ def load_variants(variant_filepath, + assert isinstance(warningfreq, float) + + # load depths in first pass +- f = open(variant_filepath, "rU") ++ f = open(variant_filepath, "r") + depths = [] + for line in f: + try: +diff --git a/shapemapper2-2.3/internals/bin/mix_sam.py b/shapemapper2-2.3/internals/bin/mix_sam.py +--- a/shapemapper2-2.3/internals/bin/mix_sam.py ++++ b/shapemapper2-2.3/internals/bin/mix_sam.py +@@ -32,8 +32,8 @@ def iterate_sam(f): + yield lines + + o = open(sys.argv[3], "w") +-f1 = open(sys.argv[1], "rU") +-f2 = open(sys.argv[2], "rU") ++f1 = open(sys.argv[1], "r") ++f2 = open(sys.argv[2], "r") + + for lines1, lines2 in zip_longest(iterate_sam(f1), + iterate_sam(f2)): +diff --git a/shapemapper2-2.3/internals/bin/render_mapped_depths.py b/shapemapper2-2.3/internals/bin/render_mapped_depths.py +--- a/shapemapper2-2.3/internals/bin/render_mapped_depths.py ++++ b/shapemapper2-2.3/internals/bin/render_mapped_depths.py +@@ -128,7 +128,7 @@ def load_primers(filename): + if filename is None or filename == "": + return [] + +- f = open(filename, "rU") ++ f = open(filename, "r") + primers = [] + i = 0 + for line in f: +@@ -159,7 +159,7 @@ class DataColumn: + + + def load_table(filename): +- f = open(filename, 'rU') ++ f = open(filename, 'r') + headers = f.readline().rstrip().split('\t') + seq = [] + seq_index = headers.index("Sequence") +diff --git a/shapemapper2-2.3/internals/bin/render_mutations_ps.py b/shapemapper2-2.3/internals/bin/render_mutations_ps.py +--- a/shapemapper2-2.3/internals/bin/render_mutations_ps.py ++++ b/shapemapper2-2.3/internals/bin/render_mutations_ps.py +@@ -162,7 +162,7 @@ def load_primers(filename): + if filename is None or filename == "": + return [] + +- f = open(filename, "rU") ++ f = open(filename, "r") + primers = [] + for line in f: + if line[0] == '>' or len(line) < 1: +@@ -956,7 +956,7 @@ def main(): + mustspan=p.must_span) + max_pages = p.max_pages + primers = load_primers(p.primers) +- input_file = open(p.input, 'rU') ++ input_file = open(p.input, 'r') + o = open(p.output, "w") + + o.write(header()) +diff --git a/shapemapper2-2.3/internals/bin/split_by_target.py b/shapemapper2-2.3/internals/bin/split_by_target.py +--- a/shapemapper2-2.3/internals/bin/split_by_target.py ++++ b/shapemapper2-2.3/internals/bin/split_by_target.py +@@ -20,7 +20,7 @@ def split_sam(sam=None, + outs=None): + if len(outs) != len(names): + raise RuntimeError("Error: number of output files must match number of sequence target names.") +- f = open(sam, "rU") ++ f = open(sam, "r") + o = [open(x, "w") for x in outs] + for line in f: + # copy any headers/comment lines to all outputs +diff --git a/shapemapper2-2.3/internals/bin/tab6_interleave.py b/shapemapper2-2.3/internals/bin/tab6_interleave.py +--- a/shapemapper2-2.3/internals/bin/tab6_interleave.py ++++ b/shapemapper2-2.3/internals/bin/tab6_interleave.py +@@ -11,7 +11,7 @@ ap.add_argument('--output', type=str) + # FIXME: rewrite in c++ + + def iterate_fastq(filename): +- f = open(filename, "rU") ++ f = open(filename, "r") + lines = [] + for line in f: + # suppress jdb socket message +diff --git a/shapemapper2-2.3/internals/python/pyshapemap/component.py b/shapemapper2-2.3/internals/python/pyshapemap/component.py +--- a/shapemapper2-2.3/internals/python/pyshapemap/component.py ++++ b/shapemapper2-2.3/internals/python/pyshapemap/component.py +@@ -324,7 +324,7 @@ class Component(): + # FIXME: all these isinstances are hacky, should use a unified interface to access file/folder path, move logic to subclass defs + if isinstance(node, ParameterNode): + # load parameter value from intermediate file +- values[node.get_name()] = open(node.input_node.filename,"rU").read().strip() ++ values[node.get_name()] = open(node.input_node.filename,"r").read().strip() + else: + if isinstance(node.input_node, FileNode): + values[node.get_name()] = '"'+node.input_node.filename+'"' +@@ -483,14 +483,14 @@ class Component(): + + def read_stdout(self): + try: +- f = open(self.stdout.output_nodes[0].filename, 'rU') ++ f = open(self.stdout.output_nodes[0].filename, 'r') + return f.read() + except AttributeError: + return "" + + def read_stderr(self): + try: +- f = open(self.stderr.output_nodes[0].filename, 'rU') ++ f = open(self.stderr.output_nodes[0].filename, 'r') + return f.read() + except AttributeError: + return "" +diff --git a/shapemapper2-2.3/internals/python/pyshapemap/components.py b/shapemapper2-2.3/internals/python/pyshapemap/components.py +--- a/shapemapper2-2.3/internals/python/pyshapemap/components.py ++++ b/shapemapper2-2.3/internals/python/pyshapemap/components.py +@@ -625,7 +625,7 @@ class StarAligner(Component): + return cmd + + def after_run_message(self): +- return open(os.path.join(self.logs.output_nodes[0].foldername, "Log.final.out"), "rU").read() ++ return open(os.path.join(self.logs.output_nodes[0].foldername, "Log.final.out"), "r").read() + + + class StarAlignerMixedInput(Component): +diff --git a/shapemapper2-2.3/internals/python/pyshapemap/locate_primers.py b/shapemapper2-2.3/internals/python/pyshapemap/locate_primers.py +--- a/shapemapper2-2.3/internals/python/pyshapemap/locate_primers.py ++++ b/shapemapper2-2.3/internals/python/pyshapemap/locate_primers.py +@@ -58,7 +58,7 @@ def locate_primer_pairs(fastas, + current_RNA = "__ALL_TARGETS__" + if primer_filenames is not None: + for filename in primer_filenames: +- for line in open(filename, "rU"): ++ for line in open(filename, "r"): + if line[0] == '>': + current_RNA = sanitize(line[1:].rstrip()) + else: +@@ -84,7 +84,7 @@ def locate_primer_pairs(fastas, + + def iterate_fasta(filenames): + for filename in filenames: +- f = open(filename, "rU") ++ f = open(filename, "r") + name = None + seq = "" + for line in f: +diff --git a/shapemapper2-2.3/internals/python/pyshapemap/util.py b/shapemapper2-2.3/internals/python/pyshapemap/util.py +--- a/shapemapper2-2.3/internals/python/pyshapemap/util.py ++++ b/shapemapper2-2.3/internals/python/pyshapemap/util.py +@@ -45,7 +45,7 @@ def timestamp(): + def version(): + this_dir = os.path.dirname(os.path.realpath(__file__)) + release_dir = os.path.join(this_dir, "../../release") +- f = open(os.path.join(release_dir, "version.txt"), "rU") ++ f = open(os.path.join(release_dir, "version.txt"), "r") + return f.readline().strip() + + +@@ -191,7 +191,7 @@ def read_fasta_names_lengths(fastas): + lowercase_error += "Please provide at least some unmasked sequence (uppercase characters) for each sequence." + + for filename in fastas: +- f = open(filename, "rU") ++ f = open(filename, "r") + is_all_lower = False + for line in f: + if line[0] == '>': +diff --git a/shapemapper2-2.3/util/scale_nuc.py b/shapemapper2-2.3/util/scale_nuc.py +--- a/shapemapper2-2.3/util/scale_nuc.py ++++ b/shapemapper2-2.3/util/scale_nuc.py +@@ -33,7 +33,7 @@ global_scale_factors = { + + + def load_scale_factors(filename): +- f = open(filename, "rU") ++ f = open(filename, "r") + nucs = "AUGC" + scale_factors = {} + for line in f: +@@ -53,7 +53,7 @@ def load_map(filename): + + + def load_map(filename): +- f = open(filename, "rU") ++ f = open(filename, "r") + nums = [] + seq = [] + profile = [] From faed22dc3ae0c77b4e1ffd439696e5c79652b829 Mon Sep 17 00:00:00 2001 From: Edric Choi Date: Tue, 18 Aug 2026 22:47:01 -0500 Subject: [PATCH 05/11] Include compatibility patch in image build --- containers/shapemapper2/.dockerignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/containers/shapemapper2/.dockerignore b/containers/shapemapper2/.dockerignore index 3599c2c..1c9e079 100644 --- a/containers/shapemapper2/.dockerignore +++ b/containers/shapemapper2/.dockerignore @@ -5,6 +5,8 @@ !LICENSES/** !THIRD_PARTY_NOTICES.md !PUBLIC_THIRD_PARTY_NOTICES.md +!patches/ +!patches/python311-open-mode.patch !source-manifest.tsv !conda-packages.tsv !copyleft-conda-packages.tsv From 254f4040fe29bcd7d56298f6930ed2babc023ef6 Mon Sep 17 00:00:00 2001 From: Edric Choi Date: Tue, 18 Aug 2026 22:52:09 -0500 Subject: [PATCH 06/11] Capture ShapeMapper smoke test diagnostics --- containers/shapemapper2/test-container.sh | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/containers/shapemapper2/test-container.sh b/containers/shapemapper2/test-container.sh index 19c8220..4adeb77 100755 --- a/containers/shapemapper2/test-container.sh +++ b/containers/shapemapper2/test-container.sh @@ -5,7 +5,17 @@ image="${1:-nerd-shapemapper2:2.3-public-candidate}" container_engine="${CONTAINER_ENGINE:-docker}" work_dir="$(mktemp -d "${TMPDIR:-/tmp}/nerd-shapemapper2-test.XXXXXX")" host_user="$(id -u):$(id -g)" -trap 'rm -rf "${work_dir}"' EXIT + +cleanup() { + status="$?" + if [[ "${status}" -ne 0 ]]; then + echo "ShapeMapper smoke-test diagnostics from ${work_dir}:" >&2 + find "${work_dir}" -type f \( -name '*.stderr' -o -name '*_log.txt' \) -print -exec tail -n 200 {} \; >&2 || true + fi + rm -rf "${work_dir}" + exit "${status}" +} +trap cleanup EXIT "${container_engine}" image inspect "${image}" --format '{{.Architecture}}' | grep -qx amd64 "${container_engine}" run --rm --platform linux/amd64 "${image}" --version | grep -F 'ShapeMapper v2.3' @@ -24,6 +34,7 @@ trap 'rm -rf "${work_dir}"' EXIT --target example_data/TPP.fa \ --amplicon \ --overwrite \ + --output-temp \ --min-depth 1000 \ --modified --folder example_data/TPPplus \ --untreated --folder example_data/TPPminus \ From bba01d842025799ec03e268742272b9b600de806 Mon Sep 17 00:00:00 2001 From: Edric Choi Date: Tue, 18 Aug 2026 22:55:46 -0500 Subject: [PATCH 07/11] Install BBMap JNI runtime --- .github/workflows/shapemapper2-container-poc.yml | 1 + containers/shapemapper2/COMPLIANCE.md | 5 +++-- containers/shapemapper2/Dockerfile | 1 + .../shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md | 13 +++++++------ 4 files changed, 12 insertions(+), 8 deletions(-) diff --git a/.github/workflows/shapemapper2-container-poc.yml b/.github/workflows/shapemapper2-container-poc.yml index 789dd98..36139a2 100644 --- a/.github/workflows/shapemapper2-container-poc.yml +++ b/.github/workflows/shapemapper2-container-poc.yml @@ -54,6 +54,7 @@ jobs: for tool in bbmerge.sh bowtie2 bowtie2-build STAR dot gs pv; do command -v "${tool}" done + dpkg-query -W bbmap-jni python3 -c "import matplotlib, numpy, scipy, sklearn" ' diff --git a/containers/shapemapper2/COMPLIANCE.md b/containers/shapemapper2/COMPLIANCE.md index 50c8291..12d6f4c 100644 --- a/containers/shapemapper2/COMPLIANCE.md +++ b/containers/shapemapper2/COMPLIANCE.md @@ -17,8 +17,9 @@ Azul Zulu and historical Conda source gaps described later in this document. - [x] Apply only the documented `python311-open-mode.patch` (`rU` to `r` in 30 file-open calls across 18 files); do not change scientific logic or vendor/fork the upstream repository. -- [x] Use distribution packages for Bowtie2, STAR, BBMap/BBMerge, Graphviz, - Ghostscript, pv, OpenJDK, Python, Boost, zlib, and transitive dependencies. +- [x] Use distribution packages for Bowtie2, STAR, BBMap/BBMerge and its + separately packaged JNI library, Graphviz, Ghostscript, pv, OpenJDK, Python, + Boost, zlib, and transitive dependencies. - [x] Preserve Debian package copyright records under `/usr/share/doc//copyright`. - [x] Add `PUBLIC_THIRD_PARTY_NOTICES.md` as an index to those records. diff --git a/containers/shapemapper2/Dockerfile b/containers/shapemapper2/Dockerfile index be3cc58..8a116c0 100644 --- a/containers/shapemapper2/Dockerfile +++ b/containers/shapemapper2/Dockerfile @@ -61,6 +61,7 @@ LABEL org.opencontainers.image.title="NERD ShapeMapper2" \ RUN apt-get update \ && apt-get install -y --no-install-recommends \ bbmap \ + bbmap-jni \ bowtie2 \ ca-certificates \ fonts-dejavu-core \ diff --git a/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md b/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md index 7300a67..f857e3f 100644 --- a/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md +++ b/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md @@ -12,12 +12,13 @@ ShapeMapper2 is Copyright (c) 2018 Steven Busan and is distributed under the MIT License. The complete notice is installed beside this file and remains in the upstream source tree at `/opt/shapemapper2/LICENSE`. -The image includes Debian packages for BBMap/BBMerge, Bowtie2, STAR, Graphviz, -Ghostscript, pv, Python and its scientific libraries, Boost, zlib, and their -runtime dependencies. Their package-specific copyright and license notices -are retained under `/usr/share/doc//copyright`. The corresponding -Debian source packages can be located by the exact binary-package versions -reported by `dpkg-query -W` and retrieved from Debian's source archives. +The image includes Debian packages for BBMap/BBMerge and its separately +packaged JNI library, Bowtie2, STAR, Graphviz, Ghostscript, pv, Python and its +scientific libraries, Boost, zlib, and their runtime dependencies. Their +package-specific copyright and license notices are retained under +`/usr/share/doc//copyright`. The corresponding Debian source packages +can be located by the exact binary-package versions reported by `dpkg-query +-W` and retrieved from Debian's source archives. This notice is an index, not a replacement for the package-specific notices. The CI-generated SPDX SBOM and exact `dpkg-query` inventory are release From 4a43171c3afecec3d2954a7459526a72cfe0157a Mon Sep 17 00:00:00 2001 From: Edric Choi Date: Tue, 18 Aug 2026 22:58:58 -0500 Subject: [PATCH 08/11] Enable verbose smoke test failures --- containers/shapemapper2/test-container.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/containers/shapemapper2/test-container.sh b/containers/shapemapper2/test-container.sh index 4adeb77..57fcd66 100755 --- a/containers/shapemapper2/test-container.sh +++ b/containers/shapemapper2/test-container.sh @@ -35,6 +35,7 @@ trap cleanup EXIT --amplicon \ --overwrite \ --output-temp \ + --verbose \ --min-depth 1000 \ --modified --folder example_data/TPPplus \ --untreated --folder example_data/TPPminus \ From a968da222c8fb610cfef7ef7cbf50290f879fd61 Mon Sep 17 00:00:00 2001 From: Edric Choi Date: Tue, 18 Aug 2026 23:04:32 -0500 Subject: [PATCH 09/11] Declare BBMerge stdin format --- containers/shapemapper2/.dockerignore | 1 + containers/shapemapper2/COMPLIANCE.md | 5 ++++- containers/shapemapper2/Dockerfile | 8 +++++--- .../PUBLIC_THIRD_PARTY_NOTICES.md | 8 +++++--- containers/shapemapper2/README.md | 20 ++++++++++--------- containers/shapemapper2/build-metadata.json | 7 +++++++ containers/shapemapper2/checksums.txt | 3 +++ .../patches/bbmerge-stdin-format.patch | 12 +++++++++++ 8 files changed, 48 insertions(+), 16 deletions(-) create mode 100644 containers/shapemapper2/patches/bbmerge-stdin-format.patch diff --git a/containers/shapemapper2/.dockerignore b/containers/shapemapper2/.dockerignore index 1c9e079..9bf2235 100644 --- a/containers/shapemapper2/.dockerignore +++ b/containers/shapemapper2/.dockerignore @@ -6,6 +6,7 @@ !THIRD_PARTY_NOTICES.md !PUBLIC_THIRD_PARTY_NOTICES.md !patches/ +!patches/bbmerge-stdin-format.patch !patches/python311-open-mode.patch !source-manifest.tsv !conda-packages.tsv diff --git a/containers/shapemapper2/COMPLIANCE.md b/containers/shapemapper2/COMPLIANCE.md index 12d6f4c..419f1e5 100644 --- a/containers/shapemapper2/COMPLIANCE.md +++ b/containers/shapemapper2/COMPLIANCE.md @@ -7,7 +7,7 @@ and the project owner gives explicit approval. ## Public candidate (`Dockerfile`) The public candidate compiles the checksum-pinned upstream v2.3 source tag, -after applying one documented Python 3.11 file-mode compatibility patch, and +after applying two documented runtime compatibility patches, and uses Debian 12 packages. It excludes the official release archive's Miniconda environment and old prebuilt third-party executables. That removes the exact Azul Zulu and historical Conda source gaps described later in this document. @@ -17,6 +17,9 @@ Azul Zulu and historical Conda source gaps described later in this document. - [x] Apply only the documented `python311-open-mode.patch` (`rU` to `r` in 30 file-open calls across 18 files); do not change scientific logic or vendor/fork the upstream repository. +- [x] Apply only the documented `bbmerge-stdin-format.patch` (`in=stdin` to + `in=stdin.fastq`) so Debian BBMap 39.01 pairs the existing FASTQ stream; do + not change BBMerge analysis parameters. - [x] Use distribution packages for Bowtie2, STAR, BBMap/BBMerge and its separately packaged JNI library, Graphviz, Ghostscript, pv, OpenJDK, Python, Boost, zlib, and transitive dependencies. diff --git a/containers/shapemapper2/Dockerfile b/containers/shapemapper2/Dockerfile index 8a116c0..09785c0 100644 --- a/containers/shapemapper2/Dockerfile +++ b/containers/shapemapper2/Dockerfile @@ -1,7 +1,7 @@ # syntax=docker/dockerfile:1.7 # Public candidate: compile the checksum-pinned upstream v2.3 source tag with -# one documented Python 3.11 file-mode compatibility patch, and use +# two documented runtime compatibility patches, and use # source-traceable Debian packages for runtime dependencies. FROM --platform=linux/amd64 debian:bookworm-slim@sha256:362e64223cc0da95422b3b13c045186fc0a81250e765d31c025fbddf257f6143 AS build @@ -28,6 +28,7 @@ ADD --checksum=sha256:1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f /tmp/shapemapper2-v2.3.tar.gz COPY patches/python311-open-mode.patch /tmp/python311-open-mode.patch +COPY patches/bbmerge-stdin-format.patch /tmp/bbmerge-stdin-format.patch RUN test "${SHAPEMAPPER_VERSION}" = "2.3" \ && test "${SHAPEMAPPER_SOURCE_SHA256}" = "1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f866b6f" \ @@ -36,7 +37,8 @@ RUN test "${SHAPEMAPPER_VERSION}" = "2.3" \ && mv /opt/shapemapper2-2.3 /opt/shapemapper2 \ && rm /tmp/shapemapper2-v2.3.tar.gz \ && patch --batch --forward --strip=2 --directory=/opt/shapemapper2 < /tmp/python311-open-mode.patch \ - && rm /tmp/python311-open-mode.patch \ + && patch --batch --forward --strip=2 --directory=/opt/shapemapper2 < /tmp/bbmerge-stdin-format.patch \ + && rm /tmp/python311-open-mode.patch /tmp/bbmerge-stdin-format.patch \ && cmake -S /opt/shapemapper2 -B /tmp/shapemapper-build -DCMAKE_BUILD_TYPE=Release \ && cmake --build /tmp/shapemapper-build --parallel 2 @@ -46,7 +48,7 @@ ARG SHAPEMAPPER_VERSION=2.3 ARG SHAPEMAPPER_SOURCE_SHA256=1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f866b6f LABEL org.opencontainers.image.title="NERD ShapeMapper2" \ - org.opencontainers.image.description="ShapeMapper2 v2.3 built from its checksum-pinned upstream source tag with a documented Python 3.11 compatibility patch" \ + org.opencontainers.image.description="ShapeMapper2 v2.3 built from its checksum-pinned upstream source tag with documented runtime compatibility patches" \ org.opencontainers.image.source="https://github.com/LucksLab/nerd" \ org.opencontainers.image.url="https://github.com/LucksLab/nerd" \ org.opencontainers.image.version="2.3-r0-candidate" \ diff --git a/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md b/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md index f857e3f..261d852 100644 --- a/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md +++ b/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md @@ -1,9 +1,11 @@ # Third-party notices for the source-built public candidate This image compiles the checksum-pinned ShapeMapper2 v2.3 source tag after -applying `patches/python311-open-mode.patch`. That patch replaces Python's -removed `rU` file mode with equivalent `r` mode in 30 file-open calls and -changes no scientific logic. The image installs runtime dependencies as +applying the two documented files under `patches/`. One replaces Python's +removed `rU` file mode with equivalent `r` mode in 30 file-open calls. The +other identifies BBMerge's standard-input stream as FASTQ for Debian's newer +BBMap. Neither changes scientific logic or analysis parameters. The image +installs runtime dependencies as Debian 12 (bookworm) packages. It does not contain the official ShapeMapper release archive's bundled Miniconda environment or historical prebuilt executables. diff --git a/containers/shapemapper2/README.md b/containers/shapemapper2/README.md index bde7684..ef55b68 100644 --- a/containers/shapemapper2/README.md +++ b/containers/shapemapper2/README.md @@ -5,10 +5,12 @@ ShapeMapper2 v2.3. Neither recipe forks ShapeMapper, and neither image is currently published to GHCR. - `Dockerfile` is the smaller public candidate. It downloads the upstream v2.3 - source tag directly, verifies its SHA-256, applies the documented - `patches/python311-open-mode.patch`, compiles ShapeMapper, and uses Debian - packages for runtime dependencies. The patch replaces Python's removed - `rU` file mode with equivalent `r` mode; it changes no scientific logic. + source tag directly, verifies its SHA-256, applies the two documented files + under `patches/`, compiles ShapeMapper, and uses Debian packages for runtime + dependencies. One patch replaces Python's removed `rU` file mode with + equivalent `r` mode. The other identifies BBMerge's standard-input stream as + FASTQ for Debian's newer BBMap. Neither changes scientific logic or analysis + settings. - `Dockerfile.reference` is the private reference recipe. It wraps the official upstream release archive, including its historical Miniconda environment. This image remains useful as a behavioral comparison but is not the public @@ -45,7 +47,7 @@ docker build --platform linux/amd64 \ Both recipes pin the amd64 Debian base manifest. The public candidate pins the upstream source-tag archive and carries one small, auditable compatibility -patch rather than a ShapeMapper fork; the private reference recipe pins the +patch set rather than a ShapeMapper fork; the private reference recipe pins the official release asset and does not patch it. ## Test levels @@ -99,10 +101,10 @@ recipe's two-job compiler limit and installed the full Debian runtime. Runtime and built-in test validation is pending because the host ran out of disk space during final layer assembly, leaving both local container stores unavailable. This is an infrastructure failure, not a ShapeMapper compile or test failure. -A subsequent GitHub Actions smoke test exposed Python 3.11's removal of the -legacy `rU` open mode. The documented compatibility patch fixes all 30 such -uses across 18 upstream Python files; final runtime validation is pending the -CI rerun. +Subsequent GitHub Actions smoke tests exposed Python 3.11's removal of the +legacy `rU` open mode and BBMap 39.01's need for an explicit FASTQ suffix when +reading interleaved pairs from standard input. The two documented compatibility +patches address those runtime-interface changes; final validation is pending. ## Publication gate diff --git a/containers/shapemapper2/build-metadata.json b/containers/shapemapper2/build-metadata.json index adf3be0..2b52593 100644 --- a/containers/shapemapper2/build-metadata.json +++ b/containers/shapemapper2/build-metadata.json @@ -20,6 +20,13 @@ "files": 18, "scientific_logic_changed": false }, + "bbmerge_stream_patch": { + "path": "patches/bbmerge-stdin-format.patch", + "sha256": "6ed6a5de862df74f1b4b45a219963a1e9ed6cd2b3709a6c81a5fc30f5245345e", + "change": "identify BBMerge standard input as FASTQ for Debian BBMap 39.01", + "analysis_parameters_changed": false, + "scientific_logic_changed": false + }, "local_build_2026_08_18": { "image_tag": "nerd-shapemapper2:2.3-public-candidate", "image_size_bytes": 508942308, diff --git a/containers/shapemapper2/checksums.txt b/containers/shapemapper2/checksums.txt index 5a01006..ee5e57b 100644 --- a/containers/shapemapper2/checksums.txt +++ b/containers/shapemapper2/checksums.txt @@ -11,3 +11,6 @@ c3f14fdd782266522b377b1c22986b98cf9949164ec3f4d582fbe65da5e53ec6 shapemapper2-2 # Auditable Python 3.11 file-mode compatibility patch applied by Dockerfile 30746f44ed4756b208f010784c09be813481f83353231bc18aee4a7532d3663f patches/python311-open-mode.patch + +# Auditable BBMerge standard-input format compatibility patch +6ed6a5de862df74f1b4b45a219963a1e9ed6cd2b3709a6c81a5fc30f5245345e patches/bbmerge-stdin-format.patch diff --git a/containers/shapemapper2/patches/bbmerge-stdin-format.patch b/containers/shapemapper2/patches/bbmerge-stdin-format.patch new file mode 100644 index 0000000..3dd8e0a --- /dev/null +++ b/containers/shapemapper2/patches/bbmerge-stdin-format.patch @@ -0,0 +1,12 @@ +diff --git a/shapemapper2-2.3/internals/python/pyshapemap/components.py b/shapemapper2-2.3/internals/python/pyshapemap/components.py +--- a/shapemapper2-2.3/internals/python/pyshapemap/components.py ++++ b/shapemapper2-2.3/internals/python/pyshapemap/components.py +@@ -274,7 +274,7 @@ class Merger(Component): + def cmd(self): + cmd = ["bbmerge.sh", + "vstrict=t", +- "in=stdin", ++ "in=stdin.fastq", + "out=stdout", + "outu=stdout", + "interleaved=t", From 83aafb316d7d9916f814667a6d864efc95ddccd2 Mon Sep 17 00:00:00 2001 From: Edric Choi Date: Tue, 18 Aug 2026 23:08:19 -0500 Subject: [PATCH 10/11] Replace removed NumPy integer alias --- containers/shapemapper2/.dockerignore | 1 + containers/shapemapper2/COMPLIANCE.md | 5 ++++- containers/shapemapper2/Dockerfile | 6 ++++-- .../PUBLIC_THIRD_PARTY_NOTICES.md | 7 ++++--- containers/shapemapper2/README.md | 14 ++++++++------ containers/shapemapper2/build-metadata.json | 7 +++++++ containers/shapemapper2/checksums.txt | 3 +++ .../patches/numpy-removed-aliases.patch | 19 +++++++++++++++++++ 8 files changed, 50 insertions(+), 12 deletions(-) create mode 100644 containers/shapemapper2/patches/numpy-removed-aliases.patch diff --git a/containers/shapemapper2/.dockerignore b/containers/shapemapper2/.dockerignore index 9bf2235..2da1290 100644 --- a/containers/shapemapper2/.dockerignore +++ b/containers/shapemapper2/.dockerignore @@ -7,6 +7,7 @@ !PUBLIC_THIRD_PARTY_NOTICES.md !patches/ !patches/bbmerge-stdin-format.patch +!patches/numpy-removed-aliases.patch !patches/python311-open-mode.patch !source-manifest.tsv !conda-packages.tsv diff --git a/containers/shapemapper2/COMPLIANCE.md b/containers/shapemapper2/COMPLIANCE.md index 419f1e5..134e5d9 100644 --- a/containers/shapemapper2/COMPLIANCE.md +++ b/containers/shapemapper2/COMPLIANCE.md @@ -7,7 +7,7 @@ and the project owner gives explicit approval. ## Public candidate (`Dockerfile`) The public candidate compiles the checksum-pinned upstream v2.3 source tag, -after applying two documented runtime compatibility patches, and +after applying three documented runtime compatibility patches, and uses Debian 12 packages. It excludes the official release archive's Miniconda environment and old prebuilt third-party executables. That removes the exact Azul Zulu and historical Conda source gaps described later in this document. @@ -20,6 +20,9 @@ Azul Zulu and historical Conda source gaps described later in this document. - [x] Apply only the documented `bbmerge-stdin-format.patch` (`in=stdin` to `in=stdin.fastq`) so Debian BBMap 39.01 pairs the existing FASTQ stream; do not change BBMerge analysis parameters. +- [x] Apply only the documented `numpy-removed-aliases.patch` (`np.int` to + equivalent built-in `int` in four array allocations); do not change array + values or scientific logic. - [x] Use distribution packages for Bowtie2, STAR, BBMap/BBMerge and its separately packaged JNI library, Graphviz, Ghostscript, pv, OpenJDK, Python, Boost, zlib, and transitive dependencies. diff --git a/containers/shapemapper2/Dockerfile b/containers/shapemapper2/Dockerfile index 09785c0..88ea966 100644 --- a/containers/shapemapper2/Dockerfile +++ b/containers/shapemapper2/Dockerfile @@ -1,7 +1,7 @@ # syntax=docker/dockerfile:1.7 # Public candidate: compile the checksum-pinned upstream v2.3 source tag with -# two documented runtime compatibility patches, and use +# three documented runtime compatibility patches, and use # source-traceable Debian packages for runtime dependencies. FROM --platform=linux/amd64 debian:bookworm-slim@sha256:362e64223cc0da95422b3b13c045186fc0a81250e765d31c025fbddf257f6143 AS build @@ -29,6 +29,7 @@ ADD --checksum=sha256:1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f COPY patches/python311-open-mode.patch /tmp/python311-open-mode.patch COPY patches/bbmerge-stdin-format.patch /tmp/bbmerge-stdin-format.patch +COPY patches/numpy-removed-aliases.patch /tmp/numpy-removed-aliases.patch RUN test "${SHAPEMAPPER_VERSION}" = "2.3" \ && test "${SHAPEMAPPER_SOURCE_SHA256}" = "1c1fb1e6e03249715eedb822217c8c3b5d18a0d60724ca4d403d88f29f866b6f" \ @@ -38,7 +39,8 @@ RUN test "${SHAPEMAPPER_VERSION}" = "2.3" \ && rm /tmp/shapemapper2-v2.3.tar.gz \ && patch --batch --forward --strip=2 --directory=/opt/shapemapper2 < /tmp/python311-open-mode.patch \ && patch --batch --forward --strip=2 --directory=/opt/shapemapper2 < /tmp/bbmerge-stdin-format.patch \ - && rm /tmp/python311-open-mode.patch /tmp/bbmerge-stdin-format.patch \ + && patch --batch --forward --strip=2 --directory=/opt/shapemapper2 < /tmp/numpy-removed-aliases.patch \ + && rm /tmp/python311-open-mode.patch /tmp/bbmerge-stdin-format.patch /tmp/numpy-removed-aliases.patch \ && cmake -S /opt/shapemapper2 -B /tmp/shapemapper-build -DCMAKE_BUILD_TYPE=Release \ && cmake --build /tmp/shapemapper-build --parallel 2 diff --git a/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md b/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md index 261d852..08aa59a 100644 --- a/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md +++ b/containers/shapemapper2/PUBLIC_THIRD_PARTY_NOTICES.md @@ -1,11 +1,12 @@ # Third-party notices for the source-built public candidate This image compiles the checksum-pinned ShapeMapper2 v2.3 source tag after -applying the two documented files under `patches/`. One replaces Python's +applying the three documented files under `patches/`. One replaces Python's removed `rU` file mode with equivalent `r` mode in 30 file-open calls. The other identifies BBMerge's standard-input stream as FASTQ for Debian's newer -BBMap. Neither changes scientific logic or analysis parameters. The image -installs runtime dependencies as +BBMap. The third replaces NumPy's removed `np.int` alias with equivalent +built-in `int`. None changes scientific logic or analysis parameters. The +image installs runtime dependencies as Debian 12 (bookworm) packages. It does not contain the official ShapeMapper release archive's bundled Miniconda environment or historical prebuilt executables. diff --git a/containers/shapemapper2/README.md b/containers/shapemapper2/README.md index ef55b68..c4e4984 100644 --- a/containers/shapemapper2/README.md +++ b/containers/shapemapper2/README.md @@ -5,12 +5,13 @@ ShapeMapper2 v2.3. Neither recipe forks ShapeMapper, and neither image is currently published to GHCR. - `Dockerfile` is the smaller public candidate. It downloads the upstream v2.3 - source tag directly, verifies its SHA-256, applies the two documented files + source tag directly, verifies its SHA-256, applies the three documented files under `patches/`, compiles ShapeMapper, and uses Debian packages for runtime dependencies. One patch replaces Python's removed `rU` file mode with equivalent `r` mode. The other identifies BBMerge's standard-input stream as - FASTQ for Debian's newer BBMap. Neither changes scientific logic or analysis - settings. + FASTQ for Debian's newer BBMap. The third replaces NumPy's removed `np.int` + alias with its equivalent built-in `int`. None changes scientific logic or + analysis settings. - `Dockerfile.reference` is the private reference recipe. It wraps the official upstream release archive, including its historical Miniconda environment. This image remains useful as a behavioral comparison but is not the public @@ -102,9 +103,10 @@ and built-in test validation is pending because the host ran out of disk space during final layer assembly, leaving both local container stores unavailable. This is an infrastructure failure, not a ShapeMapper compile or test failure. Subsequent GitHub Actions smoke tests exposed Python 3.11's removal of the -legacy `rU` open mode and BBMap 39.01's need for an explicit FASTQ suffix when -reading interleaved pairs from standard input. The two documented compatibility -patches address those runtime-interface changes; final validation is pending. +legacy `rU` open mode, BBMap 39.01's need for an explicit FASTQ suffix when +reading interleaved pairs from standard input, and NumPy's removal of `np.int`. +The three documented compatibility patches address those runtime-interface +changes; final validation is pending. ## Publication gate diff --git a/containers/shapemapper2/build-metadata.json b/containers/shapemapper2/build-metadata.json index 2b52593..9ee5139 100644 --- a/containers/shapemapper2/build-metadata.json +++ b/containers/shapemapper2/build-metadata.json @@ -27,6 +27,13 @@ "analysis_parameters_changed": false, "scientific_logic_changed": false }, + "numpy_alias_patch": { + "path": "patches/numpy-removed-aliases.patch", + "sha256": "aa6edb3ba633fff2148db0de185898e29a50fe659cee39ca76ac929e91696bd3", + "change": "replace removed NumPy np.int alias with equivalent built-in int", + "occurrences": 4, + "scientific_logic_changed": false + }, "local_build_2026_08_18": { "image_tag": "nerd-shapemapper2:2.3-public-candidate", "image_size_bytes": 508942308, diff --git a/containers/shapemapper2/checksums.txt b/containers/shapemapper2/checksums.txt index ee5e57b..3362fa9 100644 --- a/containers/shapemapper2/checksums.txt +++ b/containers/shapemapper2/checksums.txt @@ -14,3 +14,6 @@ c3f14fdd782266522b377b1c22986b98cf9949164ec3f4d582fbe65da5e53ec6 shapemapper2-2 # Auditable BBMerge standard-input format compatibility patch 6ed6a5de862df74f1b4b45a219963a1e9ed6cd2b3709a6c81a5fc30f5245345e patches/bbmerge-stdin-format.patch + +# Auditable NumPy removed-alias compatibility patch +aa6edb3ba633fff2148db0de185898e29a50fe659cee39ca76ac929e91696bd3 patches/numpy-removed-aliases.patch diff --git a/containers/shapemapper2/patches/numpy-removed-aliases.patch b/containers/shapemapper2/patches/numpy-removed-aliases.patch new file mode 100644 index 0000000..fcdaf38 --- /dev/null +++ b/containers/shapemapper2/patches/numpy-removed-aliases.patch @@ -0,0 +1,19 @@ +diff --git a/shapemapper2-2.3/internals/bin/make_reactivity_profiles.py b/shapemapper2-2.3/internals/bin/make_reactivity_profiles.py +--- a/shapemapper2-2.3/internals/bin/make_reactivity_profiles.py ++++ b/shapemapper2-2.3/internals/bin/make_reactivity_profiles.py +@@ -329,12 +329,12 @@ def load_counts(filename): + effective_depth_column = headers.index(effective_depth_header) + + # now load counts and depths +- counts = np.zeros(length, dtype=np.int) +- read_depths = np.zeros(length, dtype=np.int) +- effective_depths = np.zeros(length, dtype=np.int) ++ counts = np.zeros(length, dtype=int) ++ read_depths = np.zeros(length, dtype=int) ++ effective_depths = np.zeros(length, dtype=int) + addtl_data = [] + for i in range(len(addtl_column_names)): +- addtl_data.append(np.zeros(length, dtype=np.int)) ++ addtl_data.append(np.zeros(length, dtype=int)) + try: + for i in range(length): From 5121ea613a9913d676f5a142c02438c865eaf402 Mon Sep 17 00:00:00 2001 From: Edric Choi Date: Tue, 18 Aug 2026 23:21:51 -0500 Subject: [PATCH 11/11] Provide Python 3 compatibility command --- .github/workflows/shapemapper2-container-poc.yml | 2 +- containers/shapemapper2/COMPLIANCE.md | 3 ++- containers/shapemapper2/Dockerfile | 1 + 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/shapemapper2-container-poc.yml b/.github/workflows/shapemapper2-container-poc.yml index 36139a2..24298a2 100644 --- a/.github/workflows/shapemapper2-container-poc.yml +++ b/.github/workflows/shapemapper2-container-poc.yml @@ -51,7 +51,7 @@ jobs: "${LOCAL_IMAGE}" \ -c ' set -e - for tool in bbmerge.sh bowtie2 bowtie2-build STAR dot gs pv; do + for tool in bbmerge.sh bowtie2 bowtie2-build STAR dot gs pv python python3; do command -v "${tool}" done dpkg-query -W bbmap-jni diff --git a/containers/shapemapper2/COMPLIANCE.md b/containers/shapemapper2/COMPLIANCE.md index 134e5d9..114fe55 100644 --- a/containers/shapemapper2/COMPLIANCE.md +++ b/containers/shapemapper2/COMPLIANCE.md @@ -25,7 +25,8 @@ Azul Zulu and historical Conda source gaps described later in this document. values or scientific logic. - [x] Use distribution packages for Bowtie2, STAR, BBMap/BBMerge and its separately packaged JNI library, Graphviz, Ghostscript, pv, OpenJDK, Python, - Boost, zlib, and transitive dependencies. + Debian's Python-to-Python-3 command compatibility link, Boost, zlib, and + transitive dependencies. - [x] Preserve Debian package copyright records under `/usr/share/doc//copyright`. - [x] Add `PUBLIC_THIRD_PARTY_NOTICES.md` as an index to those records. diff --git a/containers/shapemapper2/Dockerfile b/containers/shapemapper2/Dockerfile index 88ea966..ec48a85 100644 --- a/containers/shapemapper2/Dockerfile +++ b/containers/shapemapper2/Dockerfile @@ -77,6 +77,7 @@ RUN apt-get update \ libboost-system1.74.0 \ pv \ python3 \ + python-is-python3 \ python3-matplotlib \ python3-numpy \ python3-scipy \