From 2b8b1738bd3b4d223fb33ac6936bc9383715f14c Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 12 Aug 2026 14:49:17 +0000 Subject: [PATCH 1/2] chore(main): release 0.3.3 --- .release-please-manifest.json | 2 +- CHANGELOG.md | 29 +++++++++++++++++++++++++++++ CITATION.cff | 2 +- delaynet/__init__.py | 2 +- docs/conf.py | 2 +- 5 files changed, 33 insertions(+), 4 deletions(-) diff --git a/.release-please-manifest.json b/.release-please-manifest.json index ccdabf8..2e04f95 100644 --- a/.release-please-manifest.json +++ b/.release-please-manifest.json @@ -1 +1 @@ -{ ".": "0.3.2" } +{".":"0.3.3"} diff --git a/CHANGELOG.md b/CHANGELOG.md index c9d548a..f88bd8e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,34 @@ # Changelog +## [0.3.3](https://github.com/cbueth/delaynet/compare/v0.3.2...v0.3.3) (2026-08-12) + + +### Bug Fixes + +* **ci:** align ruff pre-commit with uv.lock and fix commitlint extends ([a90ac2b](https://github.com/cbueth/delaynet/commit/a90ac2bd180e266c3c030abc59498214e023614f)) +* Directed parameter logic in eigenvector centrality for igraph `1.0.0` ([4b479fe](https://github.com/cbueth/delaynet/commit/4b479fe8ebb6a9c261d643abd3238624080f8b39)) +* **docs:** remove header search button so it stops pushing the navbar on scroll ([f72b29d](https://github.com/cbueth/delaynet/commit/f72b29dcd0edb24feab0235bf28ab0735eedbbe1)) +* Handle directed parameter logic in eigenvector centrality and add warning for symmetric matrices in directed mode ([7675b84](https://github.com/cbueth/delaynet/commit/7675b847ecf7d559d6eb7744f483006d7edb2e06)) +* **normalisation:** retry on ValueError when sampling null ensemble ([07e53d3](https://github.com/cbueth/delaynet/commit/07e53d3e6ac7884f9e5643731f4d1ffe2acec50d)) + + +### Performance Improvements + +* **bench:** add benchmarks for detrending, network analysis, and gravity ([e6dfa1a](https://github.com/cbueth/delaynet/commit/e6dfa1a45efa4a3a6d69c559da5ce9f289419472)) +* **codspeed:** Add benchmark suite with CI workflow ([#45](https://github.com/cbueth/delaynet/issues/45)) ([c42071c](https://github.com/cbueth/delaynet/commit/c42071c50a00526458e0f58108799582dba3935c)) +* **delta:** O(n) cumulative sum instead of O(n w) per-element `np.mean` ([8119494](https://github.com/cbueth/delaynet/commit/81194940a7954bf392a7c0b4dd12935bd38d8595)) +* **granger:** merge fast F-test into granger.py, remove dead code ([ea0a647](https://github.com/cbueth/delaynet/commit/ea0a6470b9ed197b5cbd395df2a0edc3ab5e12e9)) +* **metrics:** vectorize global_efficiency inner loop ([7d522e7](https://github.com/cbueth/delaynet/commit/7d522e7f9ab68b7d7348bf2057ca90db479471d2)) +* **ordinal-patterns:** serial path for small data and bypass decorator overhead ([e8f6e0f](https://github.com/cbueth/delaynet/commit/e8f6e0fac738710ace3ee01a1e04537b161f007d)) +* replace statsmodels OLS+f_test with numpy/scipy in Granger F-test ([d5e4952](https://github.com/cbueth/delaynet/commit/d5e4952fe672a1fba3e84d95cd65b7e5b1420471)) +* throttle print_progress to 1 Hz instead of every pair ([37cd00d](https://github.com/cbueth/delaynet/commit/37cd00ddf88ba2c16318197ed6ef50b2d2f9bfbb)) +* vectorize permutation test in gravity with rng.permuted ([5c402c5](https://github.com/cbueth/delaynet/commit/5c402c59b82ff849fd26c2a32c95e6c0f038df9e)) + + +### Documentation + +* Add codspeed badge ([0a01312](https://github.com/cbueth/delaynet/commit/0a01312767568cf962793cdb3b359fef4a1602ea)) + ## 0.3.2 (2025-08-14) - πŸ› Fix: Normalised scalar metrics returned NumPy arrays instead of Python floats; now diff --git a/CITATION.cff b/CITATION.cff index b08c361..3ef80d8 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -19,7 +19,7 @@ keywords: - mutual information - transfer entropy license: BSD-3-Clause -version: 0.3.2 # x-release-please-version +version: 0.3.3 # x-release-please-version # add when code published # doi: 10.5281/zenodo.0000 diff --git a/delaynet/__init__.py b/delaynet/__init__.py index 673beed..fbe5f18 100644 --- a/delaynet/__init__.py +++ b/delaynet/__init__.py @@ -1,6 +1,6 @@ """delaynet init.""" -__version__ = "0.3.2" +__version__ = "0.3.3" from .utils.logging import logging # Expose most common functions diff --git a/docs/conf.py b/docs/conf.py index 46b21a1..7017a29 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -26,7 +26,7 @@ project = "delaynet" copyright = f"2024–{datetime.now().year}, delaynet maintainers" author = "Carlson BΓΌth" -version = "0.3.2" # x-release-please-version +version = "0.3.3" # x-release-please-version # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration From 3f3ab3746dba3912192d47acdb0adabca00e68d5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Carlson=20B=C3=BCth?= Date: Wed, 12 Aug 2026 16:54:52 +0200 Subject: [PATCH 2/2] docs(changelog): restore highlighted 0.3.3 notes with docs search fix --- CHANGELOG.md | 68 ++++++++++++++++++++++++++++++++-------------------- 1 file changed, 42 insertions(+), 26 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f88bd8e..3a45784 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,32 +2,48 @@ ## [0.3.3](https://github.com/cbueth/delaynet/compare/v0.3.2...v0.3.3) (2026-08-12) - -### Bug Fixes - -* **ci:** align ruff pre-commit with uv.lock and fix commitlint extends ([a90ac2b](https://github.com/cbueth/delaynet/commit/a90ac2bd180e266c3c030abc59498214e023614f)) -* Directed parameter logic in eigenvector centrality for igraph `1.0.0` ([4b479fe](https://github.com/cbueth/delaynet/commit/4b479fe8ebb6a9c261d643abd3238624080f8b39)) -* **docs:** remove header search button so it stops pushing the navbar on scroll ([f72b29d](https://github.com/cbueth/delaynet/commit/f72b29dcd0edb24feab0235bf28ab0735eedbbe1)) -* Handle directed parameter logic in eigenvector centrality and add warning for symmetric matrices in directed mode ([7675b84](https://github.com/cbueth/delaynet/commit/7675b847ecf7d559d6eb7744f483006d7edb2e06)) -* **normalisation:** retry on ValueError when sampling null ensemble ([07e53d3](https://github.com/cbueth/delaynet/commit/07e53d3e6ac7884f9e5643731f4d1ffe2acec50d)) - - -### Performance Improvements - -* **bench:** add benchmarks for detrending, network analysis, and gravity ([e6dfa1a](https://github.com/cbueth/delaynet/commit/e6dfa1a45efa4a3a6d69c559da5ce9f289419472)) -* **codspeed:** Add benchmark suite with CI workflow ([#45](https://github.com/cbueth/delaynet/issues/45)) ([c42071c](https://github.com/cbueth/delaynet/commit/c42071c50a00526458e0f58108799582dba3935c)) -* **delta:** O(n) cumulative sum instead of O(n w) per-element `np.mean` ([8119494](https://github.com/cbueth/delaynet/commit/81194940a7954bf392a7c0b4dd12935bd38d8595)) -* **granger:** merge fast F-test into granger.py, remove dead code ([ea0a647](https://github.com/cbueth/delaynet/commit/ea0a6470b9ed197b5cbd395df2a0edc3ab5e12e9)) -* **metrics:** vectorize global_efficiency inner loop ([7d522e7](https://github.com/cbueth/delaynet/commit/7d522e7f9ab68b7d7348bf2057ca90db479471d2)) -* **ordinal-patterns:** serial path for small data and bypass decorator overhead ([e8f6e0f](https://github.com/cbueth/delaynet/commit/e8f6e0fac738710ace3ee01a1e04537b161f007d)) -* replace statsmodels OLS+f_test with numpy/scipy in Granger F-test ([d5e4952](https://github.com/cbueth/delaynet/commit/d5e4952fe672a1fba3e84d95cd65b7e5b1420471)) -* throttle print_progress to 1 Hz instead of every pair ([37cd00d](https://github.com/cbueth/delaynet/commit/37cd00ddf88ba2c16318197ed6ef50b2d2f9bfbb)) -* vectorize permutation test in gravity with rng.permuted ([5c402c5](https://github.com/cbueth/delaynet/commit/5c402c59b82ff849fd26c2a32c95e6c0f038df9e)) - - -### Documentation - -* Add codspeed badge ([0a01312](https://github.com/cbueth/delaynet/commit/0a01312767568cf962793cdb3b359fef4a1602ea)) +- πŸš€ **2-4 times faster network reconstruction!** + The Granger causality hot path was rewritten from `statsmodels.OLS().f_test()` to a + pure numpy/scipy normal-equations F-test with p-values matching to machine precision. + Network reconstruction with the `gc` metric measures **~2.1Γ— faster** on CodSpeed, + and the isolated Granger F-test is **up to ~8Γ— faster** + ([#46](https://github.com/cbueth/delaynet/pull/46), + [`d5e4952`](https://github.com/cbueth/delaynet/commit/d5e4952fe672a1fba3e84d95cd65b7e5b1420471)). + +- ⚑ **More performance improvements** + - Delta detrending is now O(n) via cumulative sums instead of O(n w) + ([`8119494`](https://github.com/cbueth/delaynet/commit/81194940a7954bf392a7c0b4dd12935bd38d8595)) + - `global_efficiency` inner loop vectorised + ([`7d522e7`](https://github.com/cbueth/delaynet/commit/7d522e7f9ab68b7d7348bf2057ca90db479471d2)) + - Continuous ordinal patterns: serial fast path for small data, decorator overhead + bypassed + ([`e8f6e0f`](https://github.com/cbueth/delaynet/commit/e8f6e0fac738710ace3ee01a1e04537b161f007d)) + - Gravity permutation test vectorised with `rng.permuted` + ([`5c402c5`](https://github.com/cbueth/delaynet/commit/5c402c59b82ff849fd26c2a32c95e6c0f038df9e)) + - `print_progress` throttled to 1 Hz instead of printing every pair + ([`37cd00d`](https://github.com/cbueth/delaynet/commit/37cd00ddf88ba2c16318197ed6ef50b2d2f9bfbb)) + +- πŸ“Š **Benchmarks**: new CodSpeed benchmark suite with CI workflow + ([#45](https://github.com/cbueth/delaynet/issues/45), + [`c42071c`](https://github.com/cbueth/delaynet/commit/c42071c50a00526458e0f58108799582dba3935c)) and + benchmarks for detrending, network analysis, and gravity + ([`e6dfa1a`](https://github.com/cbueth/delaynet/commit/e6dfa1a45efa4a3a6d69c559da5ce9f289419472)). + +- πŸ› **Bug fixes** + - Normalisation: retry on `ValueError` when sampling the null ensemble, fixing a flaky + reciprocity test + ([`07e53d3`](https://github.com/cbueth/delaynet/commit/07e53d3e6ac7884f9e5643731f4d1ffe2acec50d)) + - Eigenvector centrality: correct directed handling for igraph `1.0.0` and warn on + symmetric matrices in directed mode + ([`7675b84`](https://github.com/cbueth/delaynet/commit/7675b847ecf7d559d6eb7744f483006d7edb2e06), + [`4b479fe`](https://github.com/cbueth/delaynet/commit/4b479fe8ebb6a9c261d643abd3238624080f8b39)) + - CI: align ruff pre-commit with `uv.lock` and fix commitlint `extends` + ([`a90ac2b`](https://github.com/cbueth/delaynet/commit/a90ac2bd180e266c3c030abc59498214e023614f)) + - Docs: remove the header search button that pushed the sticky navbar down on scroll + ([`f72b29d`](https://github.com/cbueth/delaynet/commit/f72b29dcd0edb24feab0235bf28ab0735eedbbe1)) + +- πŸ“– **Documentation**: CodSpeed badge + ([`0a01312`](https://github.com/cbueth/delaynet/commit/0a01312767568cf962793cdb3b359fef4a1602ea)) ## 0.3.2 (2025-08-14)