Modernize PyRCN for scikit-learn 1.6+ (Python 3.10+)

.github/workflows/python-publish-pypi.yml

@@ -13,9 +13,9 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: '3.x'
       - name: Install dependencies

.github/workflows/python-test-push.yml

@@ -8,26 +8,23 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9, 3.11, 3.12]  # 3
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
+      - name: Install package with test dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pytest flake8 pytest-flake8-v2 mypy pytest-mypy pytest-cov \
-          types-setuptools
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+          pip install -e .[test]
       - name: Lint with flake8
-        run: |
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --exit-zero --show-source --statistics  # --max-complexity=10
+        run: flake8 src/pyrcn tests
+      - name: Type-check with mypy
+        run: mypy src/pyrcn
       - name: Test with pytest
-        run: |
-          pytest
+        run: pytest --cov=src/pyrcn --cov-branch --cov-report=xml --cov-report=term-missing
       - name: Test installed PyRCN
         run: |
           pip install .

.readthedocs.yml

@@ -7,9 +7,9 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.12"
     # You can also specify other tool versions:
     # nodejs: "16"
     # rust: "1.55"

README.md

@@ -63,7 +63,7 @@ If you plan to contribute to ``PyRCN``, you can also install the package from so
 Clone the Git repository:
 
 ```
-git clone https://github.com/TUD-STKS/PyRCN.git
+git clone https://github.com/PlasmaControl/PyRCN.git
 ```
 
 Install the package using ``setup.py``:
@@ -124,19 +124,19 @@ reg.fit(X=X[:8000], y=y[:8000])
 y_pred = reg.predict(X[8000:])  # output is the prediction for each input example
 ```
 
-An extensive introduction to getting started with PyRCN is included in the [examples](https://github.com/TUD-STKS/PyRCN/blob/main/examples) directory. 
-The notebook [digits](https://github.com/TUD-STKS/PyRCN/blob/main/examples/digits.ipynb) or its corresponding [Python script](https://github.com/TUD-STKS/PyRCN/blob/main/examples/digits.py) show how to set up an ESN for a small hand-written digit recognition experiment. 
+An extensive introduction to getting started with PyRCN is included in the [examples](https://github.com/PlasmaControl/PyRCN/blob/main/examples) directory. 
+The notebook [digits](https://github.com/PlasmaControl/PyRCN/blob/main/examples/digits.ipynb) or its corresponding [Python script](https://github.com/PlasmaControl/PyRCN/blob/main/examples/digits.py) show how to set up an ESN for a small hand-written digit recognition experiment. 
 Launch the digits notebook on Binder: 
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TUD-STKS/PyRCN/main?filepath=examples%2Fdigits.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/PlasmaControl/PyRCN/main?filepath=examples%2Fdigits.ipynb)
 
-The notebook [PyRCN_Intro](https://github.com/TUD-STKS/PyRCN/blob/main/examples/PyRCN_Intro.ipynb) or its corresponding [Python script](https://github.com/TUD-STKS/PyRCN/blob/main/examples/PyRCN_Intro.py) show how to construct different RCNs with building blocks. 
+The notebook [PyRCN_Intro](https://github.com/PlasmaControl/PyRCN/blob/main/examples/PyRCN_Intro.ipynb) or its corresponding [Python script](https://github.com/PlasmaControl/PyRCN/blob/main/examples/PyRCN_Intro.py) show how to construct different RCNs with building blocks. 
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TUD-STKS/PyRCN/main?filepath=examples%2FPyRCN_Intro.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/PlasmaControl/PyRCN/main?filepath=examples%2FPyRCN_Intro.ipynb)
 
-The notebook [Impulse responses](https://github.com/TUD-STKS/PyRCN/blob/main/examples/esn_impulse_responses.ipynb) is an interactive tool to demonstrate the impact of different hyper-parameters on the impulse responses of an ESN. 
+The notebook [Impulse responses](https://github.com/PlasmaControl/PyRCN/blob/main/examples/esn_impulse_responses.ipynb) is an interactive tool to demonstrate the impact of different hyper-parameters on the impulse responses of an ESN. 
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TUD-STKS/PyRCN/main?filepath=examples%2Fesn_impulse_responses.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/PlasmaControl/PyRCN/main?filepath=examples%2Fesn_impulse_responses.ipynb)
 
 Fore more advanced examples, please have a look at our [Automatic Music Transcription Repository](https://github.com/TUD-STKS/Automatic-Music-Transcription), in which we provide an entire feature extraction, training and test pipeline for multipitch tracking and for note onset detection using PyRCN. This is currently transferred to this repository.
 

docs/source/development.rst

@@ -29,5 +29,5 @@ Whenever you find something not explained well, please inform Peter Steiner
 `peter.steiner@pyrcn.net <mailto:peter.steiner@pyrcn.net>`_.
 
 
-.. _GitHub: https://github.com/TUD-STKS/PyRCN
-.. _issue tracker on GitHub: https://github.com/TUD-STKS/PyRCN/issues
+.. _GitHub: https://github.com/PlasmaControl/PyRCN
+.. _issue tracker on GitHub: https://github.com/PlasmaControl/PyRCN/issues

docs/source/installation.rst

@@ -14,7 +14,7 @@ command in a PowerShell or CommandLine in Windows, or in a shell in Linux/MacOS:
     python --version
 
 As any package, **PyRCN** has several dependencies as listed in the `requirements.txt
- <https://github.com/TUD-STKS/PyRCN/blob/main/requirements.txt>`_. To avoid any
+ <https://github.com/PlasmaControl/PyRCN/blob/main/requirements.txt>`_. To avoid any
 unexpected interaction with the basic system as installed on your computer, we highly
 recommend  using a virtual environment
 
@@ -55,7 +55,7 @@ Installation from source
 
 We only recommend you the installation of PyRCN from source if you would like to
 contribute to PyRCN. Therefore, please find the source code of **PyRCN** on `GitHub
-<https://github.com/TUD-STKS/PyRCN>`_.
+<https://github.com/PlasmaControl/PyRCN>`_.
 
 You can download the latest stable version from the ``main`` branch. To work with older
 or unstable versions of **PyRCN**,. you can checkout the ``dev`` branch or any other
@@ -68,4 +68,4 @@ The installation then work similar as before using `pip` in your command line:
 
     pip install -e /path/to/pyrcn
 
-.. _issue tracker on GitHub: https://github.com/TUD-STKS/PyRCN/issues
+.. _issue tracker on GitHub: https://github.com/PlasmaControl/PyRCN/issues

docs/source/introduction.rst

@@ -14,7 +14,7 @@ similar, and PyRCN aims to unify the development of ESNs and ELMs.
 
 
 Many examples can be found in the PyRCN repository. Some useful examples can also be
-found in the `PyRCN repository <https://github.com/TUD-STKS/PyRCN/tree/main/examples>`_
+found in the `PyRCN repository <https://github.com/PlasmaControl/PyRCN/tree/main/examples>`_
 with many Jupyter notebooks.
 
 PyRCN is inspired by `ReservoirPy <https://github.com/reservoirpy>`_, another RC toolbox

docs/source/tutorial.rst

@@ -6,35 +6,35 @@ package.
 
 You can view them online or download Python scripts:
 
-https://github.com/TUD-STKS/PyRCN/tree/main/examples
+https://github.com/PlasmaControl/PyRCN/tree/main/examples
 
 The notebook
-`PyRCN_Intro <https://github.com/TUD-STKS/PyRCN/blob/main/examples/PyRCN_Intro.ipynb>`_
+`PyRCN_Intro <https://github.com/PlasmaControl/PyRCN/blob/main/examples/PyRCN_Intro.ipynb>`_
 or its corresponding
-`Python script <https://github.com/TUD-STKS/PyRCN/blob/main/examples/PyRCN_Intro.py>`_
+`Python script <https://github.com/PlasmaControl/PyRCN/blob/main/examples/PyRCN_Intro.py>`_
 show how to construct different RCNs with building blocks.
 
 .. image:: https://mybinder.org/badge_logo.svg
-    :target: https://mybinder.org/v2/gh/TUD-STKS/PyRCN/main?filepath=examples%2FPyRCN_Intro.ipynb
+    :target: https://mybinder.org/v2/gh/PlasmaControl/PyRCN/main?filepath=examples%2FPyRCN_Intro.ipynb
 
 
 The notebook
 `Impulse responses
-<https://github.com/TUD-STKS/PyRCN/blob/main/examples/esn_impulse_responses.ipynb>`_
+<https://github.com/PlasmaControl/PyRCN/blob/main/examples/esn_impulse_responses.ipynb>`_
 is an interactive tool to demonstrate the impact of different hyper-parameters on the
 impulse responses of an ESN.
 
 .. image:: https://mybinder.org/badge_logo.svg
-    :target: https://mybinder.org/v2/gh/TUD-STKS/PyRCN/main?filepath=examples%2Fesn_impulse_responses.ipynb
+    :target: https://mybinder.org/v2/gh/PlasmaControl/PyRCN/main?filepath=examples%2Fesn_impulse_responses.ipynb
 
 The Jupyter notebook
-`digits <https://github.com/TUD-STKS/PyRCN/blob/main/examples/digits.ipynb>`_
+`digits <https://github.com/PlasmaControl/PyRCN/blob/main/examples/digits.ipynb>`_
 or its corresponding
-`Python script <https://github.com/TUD-STKS/PyRCN/blob/main/examples/digits.py>`_
+`Python script <https://github.com/PlasmaControl/PyRCN/blob/main/examples/digits.py>`_
 show how to set up an ESN for a small hand-written digit recognition experiment.
 
 .. image:: https://mybinder.org/badge_logo.svg
-    :target: https://mybinder.org/v2/gh/TUD-STKS/PyRCN/main?filepath=examples%2Fdigits.ipynb
+    :target: https://mybinder.org/v2/gh/PlasmaControl/PyRCN/main?filepath=examples%2Fdigits.ipynb
 
 Fore more advanced examples, please have a look at our
 `Automatic Music Transcription Repository

examples/PyRCN_Intro.ipynb

@@ -722,7 +722,7 @@
     "\n",
     "This complex use-case requires a serious hyper-parameter tuning. To keep the code example simple, we did not include the optimization in this paper and refer the interested readers to the Jupyter Notebook [^1] that was developed to produce these results.\n",
     "\n",
-    "[^1]: https://github.com/TUD-STKS/PyRCN/blob/main/examples/digits.ipynb"
+    "[^1]: https://github.com/PlasmaControl/PyRCN/blob/main/examples/digits.ipynb"
    ]
   },
   {

mypy.ini

@@ -1,4 +1,6 @@
 [mypy] # global options
+# third-party scientific packages ship no type stubs / py.typed marker
+ignore_missing_imports = True
 # add this to find packages without an __init__.py file
 namespace_packages = True
 strict_optional = True

pyproject.toml

@@ -6,39 +6,63 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "PyRCN"
-version = "0.0.18"
+dynamic = ["version"]
+description = "A scikit-learn-compatible framework for Reservoir Computing in Python"
+readme = "README.md"
+requires-python = ">=3.10"
 authors = [
     { name="Peter Steiner", email="peter.steiner@pyrcn.net" },
 ]
-readme = "README.md"
-requires-python = ">=3.8"
 classifiers = [
     "Development Status :: 2 - Pre-Alpha",
     "Intended Audience :: Science/Research",
     "Programming Language :: Python :: 3",
-    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "License :: OSI Approved :: BSD License",
     "Operating System :: OS Independent",
 ]
 dependencies = [
-    "torch",
-    "torchvision",
-    "torchaudio",
-    "scikit-learn",
-    "pandas",
+    "scikit-learn>=1.6",
+    "numpy>=1.18.1",
+    "scipy>=1.4.0",
+    "joblib>=0.13.2",
+    "pandas>=1.0.0",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest>=6.5.0",
+    "pytest-cov",
+    "pytest-mypy",
+    "mypy",
+    "flake8",
+]
+examples = [
+    "matplotlib",
+    "seaborn",
+    "ipywidgets",
+    "ipympl",
+    "tqdm",
 ]
 
+[project.urls]
+Homepage = "https://pyrcn.net/"
+Documentation = "https://pyrcn.readthedocs.io/"
+Source = "https://github.com/PlasmaControl/PyRCN/"
+Issues = "https://github.com/PlasmaControl/PyRCN/issues"
+
+[tool.setuptools.dynamic]
+version = { attr = "pyrcn._version.__version__" }
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
 [tool.pytest.ini_options]
 minversion = "6.0"
 addopts = "-ra -q"
 testpaths = [
     "tests",
 ]
-
-[tool.setuptools.packages.find]
-where = ["src"]
-
-[project.urls]
-Homepage = "https://pyrcn.net/"
-Documentation = "https://pyrcn.readthedocs.io/"
-Source = "https://github.com/TUD-STKS/PyRCN/"
-Issues = "https://github.com/TUD-STKS/PyRCN/issues"

requirements.txt

@@ -1,12 +1,11 @@
 setuptools>=46.4.0
-scikit-learn>=1.4
+scikit-learn>=1.6
 numpy>=1.18.1
 scipy>=1.4.0
 joblib>=0.13.2
 pandas>=1.0.0
-typing-extensions
-requests[matplotlib]
-requests[seaborn]
-requests[ipywidgets]
-requests[ipympl]
-requests[tqdm]
+matplotlib
+seaborn
+ipywidgets
+ipympl
+tqdm

src/pyrcn/__init__.py

@@ -2,20 +2,19 @@
 
 # Authors: Peter Steiner <peter.steiner@tu-dresden.de>,
 # License: BSD 3 clause
-from ._version import __version__
+from __future__ import annotations
 
 from . import (base, echo_state_network, extreme_learning_machine,
-               linear_model, model_selection, nn, postprocessing,
-               preprocessing, projection, util)
-
+               linear_model, model_selection, postprocessing, preprocessing,
+               projection, util)
+from ._version import __version__
 
 __all__ = ('__version__',
            'base',
            'echo_state_network',
            'extreme_learning_machine',
            'linear_model',
            'model_selection',
-           'nn',
            'postprocessing',
            'preprocessing',
            'projection',

src/pyrcn/_version.py

@@ -1,2 +1,4 @@
 """Version indicator for PyRCN."""
-__version__ = "0.0.17post1"
+from __future__ import annotations
+
+__version__ = "0.0.18"