Migrate to better coding practices

.github/workflows/doc.yml

@@ -1,33 +1,30 @@
-name: Python package
-on: [push]
+name: Documentation
+
+on: [push, pull_request]
+
 jobs:
   build:
+    name: Build Documentation
     runs-on: ubuntu-latest
     timeout-minutes: 60
     strategy:
       matrix:
-        python-version: ['3.10']
-        # python-version: ['3.10']
+        python-version: ["3.10"]
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install Pandoc
-      run: |
-        sudo apt-get install pandoc
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install cython
-        pip install ".[dev]"
-
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+      - name: Checkout code
+        uses: actions/checkout@v7
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990
+        with:
+          enable-cache: true
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Pandoc
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y pandoc
 
-    - name: Test doc
-      run: |
-        make doc
+      - name: Build documentation
+        run: |
+          uv run --extra doc make doc

.github/workflows/python.yml

@@ -1,33 +1,42 @@
-name: Python package
-on: [push]
+name: Lint and Test
+
+on: [push, pull_request]
+
 jobs:
-  build:
+  # lint:
+  #   name: Lint with Ruff
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Checkout code
+  #       uses: actions/checkout@v7
+
+  #     - name: Set up uv
+  #       uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990
+  #       with:
+  #         enable-cache: true
+  #         python-version: "3.12"
+
+  #     - name: Lint
+  #       run: |
+  #         uv run --group dev make lint
+
+  test:
+    name: Test on Python ${{ matrix.python-version }}
     runs-on: ubuntu-latest
     timeout-minutes: 60
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
-        # python-version: ['3.10']
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install cython
-        pip install ".[dev]"
-  # pip install cython poetry
-  # poetry config virtualenvs.create false
-  # poetry install --no-interaction --with dev
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        make test
+      - name: Checkout code
+        uses: actions/checkout@v7
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990
+        with:
+          enable-cache: true
+          python-version: ${{ matrix.python-version }}
+
+      - name: Run tests
+        run: |
+          uv run --extra test make test

.gitignore

@@ -229,3 +229,5 @@ generated_datasets/*
 !generated_datasets/71GPa_experimental_data.hspy
 results
 .DS_Store
+espm/_version.py
+

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.15.20
+  hooks:
+    # Run the linter.
+    - id: ruff-check
+      args: [ --fix, --exit-zero ]
+    # Run the formatter.
+    - id: ruff-format

.readthedocs.yaml

@@ -14,4 +14,4 @@ python:
     - method: pip
       path: .
       extra_requirements:
-        - dev
+        - doc

CONTRIBUTING.rst

@@ -17,8 +17,7 @@ development with the following::
     $ pip install -e .[dev]
 
 You can improve or add functionality in the ``espm`` folder, along with
-corresponding unit tests in ``espm/tests/test_*.py`` (with reasonable
-coverage).
+corresponding unit tests in ``tests/test_*.py`` (with reasonable coverage). 
 If you have a nice example to demonstrate the use of the introduced
 functionality, please consider adding a notebook in ``doc/introduction/notebooks``.
 In general, this can be done as a relative symbolic link to a notebook in the
@@ -35,8 +34,8 @@ documentation with the following ::
 To iterate faster, you can partially run the test suite, at various degrees of
 granularity, as follows::
 
-   $ pytest espm.test.test_utils.py
-   $ pytest espm.test.test_estimators.py
+   $ pytest tests/test_utils.py
+   $ pytest tests/test_estimators.py
 
 Making a release
 ----------------
@@ -45,8 +44,7 @@ Making a release
 #. Log to `readthedoc <https://readthedocs.org/projects/espm>`, 
    launch a build on latest and check that it can compile 
    the latest version of the documentation.
-#. Update the version number and release date in ``setup.py``,
-   ``espm/__init__.py`` and ``CHANGELOG.rst``.
+#. Update the release notes and release date in ``CHANGELOG.rst``.
 #. Commit the changes with ``git commit -am "Bump to version 0.2.0"``.
 #. Create a git tag with ``git tag -a v0.2.0 -m "espm v0.2.0"``.
 #. Push the tag to GitHub with ``git push --tag``. The tag should now
@@ -72,22 +70,20 @@ Repository organization
   LICENSE.txt         Project license
   *.rst               Important documentation
   Makefile            Targets for make
-  setup.py            Meta information about package (published on PyPI)
+  pyproject.toml      Meta information about package, dependencies and tools (Ruff, pytest)
   .gitignore          Files ignored by the git revision control system
-  .travis.yml         Defines testing on Travis continuous integration
 
-  espm/              Contains the modules (the actual toolbox implementation)
+  espm/               Contains the modules (the actual toolbox implementation)
    __init.py__        Load modules at package import
    *.py               One file per module
-  espm/tables/       Contains data tables for the EDXS and EDSS models
+  espm/tables/        Contains data tables for the EDXS and EDSS models
    __init.py__        Load modules at package import
    *.json             data_files for the package  
    *.txt              data_files for the package  
 
-  espm/tests/        Contains the test suites (will be distributed to end user)
-   __init.py__        Load modules at package import
+  tests/              Contains the test suites (not distributed to end user)
    test_*.py          One test suite per module
-   test_docstrings.py Test the examples in the docstrings (reference doc)
+   test_docstring.py  Test the examples in the docstrings (reference doc)
 
   doc/                Package documentation
    conf.py            Sphinx configuration

Makefile

@@ -10,19 +10,19 @@ help:
 	@echo "release  package and upload to PyPI"
 
 clean:
-	git clean -Xdf
+	rm -rf build/ dist/ *.egg-info/ .pytest_cache/ .ruff_cache/ doc/_build/
 	jupyter nbconvert --inplace --ClearOutputPreprocessor.enabled=True $(NB)
 
 lint:
-	flake8 --doctests --exclude=doc
+	ruff check
 
 # Matplotlib doesn't print to screen. Also faster.
 export MPLBACKEND = agg
 # Virtual framebuffer nonetheless needed for the pyqtgraph backend.
 export DISPLAY = :99
 
 test:
-	pytest espm
+	pytest
 
 clean-doc:
 	rm -rf doc/_build
@@ -32,8 +32,7 @@ doc:
 	sphinx-build -b linkcheck -d doc/_build/doctrees doc doc/_build/linkcheck
 
 dist: clean
-	python setup.py sdist
-	python setup.py bdist_wheel --universal
+	python -m build
 	ls -lh dist/*
 	twine check dist/*
 

README.rst

@@ -28,8 +28,7 @@ If you want to develop, please use the option::
 
     $ git clone https://github.com/adriente/espm.git
     $ cd espm
-    $ pip install cython
-    $ pip install -e .[dev] 
+    $ pip install -e .[dev]
 
 If you get issues regarding pandoc when using `make doc`, you can install it using::
 
@@ -73,23 +72,23 @@ CITING
 If you use this library, please cite on of the following papers::
 
     @article{teurtrie2023espm,
-    title={espm: A Python library for the simulation of STEM-EDXS datasets},
-    author={Teurtrie, Adrien and Perraudin, Nathana{\"e}l and Holvoet, Thomas and Chen, Hui and Alexander, Duncan TL and Obozinski, Guillaume and H{\'e}bert, C{\'e}cile},
-    journal={Ultramicroscopy},
-    pages={113719},
-    year={2023},
-    publisher={Elsevier}
+        title={espm: A Python library for the simulation of STEM-EDXS datasets},
+        author={Teurtrie, Adrien and Perraudin, Nathana{\"e}l and Holvoet, Thomas and Chen, Hui and Alexander, Duncan TL and Obozinski, Guillaume and H{\'e}bert, C{\'e}cile},
+        journal={Ultramicroscopy},
+        pages={113719},
+        year={2023},
+        publisher={Elsevier}
     }
 
     @article{Teurtrie_2024,
-    doi = {10.1088/2632-2153/ad9192},
-    year = {2024},
-    month = {nov},
-    publisher = {IOP Publishing},
-    volume = {5},
-    number = {4},
-    pages = {045050},
-    author = {Teurtrie, Adrien and Perraudin, Nathanaël and Holvoet, Thomas and Chen, Hui and Alexander, Duncan T L and Obozinski, Guillaume and Hébert, Cécile},
-    title = {From STEM-EDXS data to phase separation and quantification using physics-guided NMF},
-    journal = {Machine Learning: Science and Technology}
+        doi = {10.1088/2632-2153/ad9192},
+        year = {2024},
+        month = {nov},
+        publisher = {IOP Publishing},
+        volume = {5},
+        number = {4},
+        pages = {045050},
+        author = {Teurtrie, Adrien and Perraudin, Nathanaël and Holvoet, Thomas and Chen, Hui and Alexander, Duncan T L and Obozinski, Guillaume and Hébert, Cécile},
+        title = {From STEM-EDXS data to phase separation and quantification using physics-guided NMF},
+        journal = {Machine Learning: Science and Technology}
     }