Modernize package structure

.github/workflows/docs.yml

@@ -1,31 +1,24 @@
-name: Check documentation
+name: Documentation
 
 on:
   push:
     branches: [main]
+    tags: ["*"]
   pull_request:
     # Check all PR
 
 jobs:
   build:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.10"]
-
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - name: setup Python
+        uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
+          python-version: "3.10"
+      - name: install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install -r docs/requirements.txt
-          pip install .
+          python -m pip install tox
           sudo apt install pandoc
-      - name: Build the documentation
-        run: |
-          cd docs
-          make html
+      - name: build documentation
+        run: tox -e docs

.github/workflows/documentation-links.yml

@@ -0,0 +1,17 @@
+name: readthedocs/actions
+
+on:
+  pull_request_target:
+    types:
+      - opened
+
+permissions:
+  pull-requests: write
+
+jobs:
+  documentation-links:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: readthedocs/actions/preview@v1
+        with:
+          project-slug: scikit-matter

.github/workflows/lint.yml

@@ -1,36 +1,20 @@
 name: Lint
 
 on:
-  push:
-    branches: [main]
   pull_request:
-    # Check all PR
+    branches: [main]
 
 jobs:
-  build:
+  lint:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.10"]
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install flake8 black isort
-      - name: Lint with flake8
-        run: |
-          # ignore formatting, it will be checked by black
-          export FORMATTING_RULES="E101,E111,E114,E115,E116,E117,E12,E13,E2,E3,E401,E5,E70,W1,W2,W3,W5"
-          flake8 --ignore=$FORMATTING_RULES .
-      - name: Lint with black
-        run: |
-          black --check .
-      - name: Check imports
-        run: |
-          isort skmatter/*/*py -m 3 --tc --fgw --up -e -l 88 --check
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - run: pip install tox
+
+    - name: Test Lint
+      run: tox -e lint

.github/workflows/tests.yml

@@ -1,31 +1,35 @@
-name: Test
+name: Tests
 
 on:
   push:
     branches: [main]
   pull_request:
-    # Check all PR
+    branches: [main]
 
 jobs:
-  build:
-    runs-on: ubuntu-latest
+  tests:
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        os: ['ubuntu-latest']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+        include:
+          - os: macos-latest
+            python-version: '3.10'
+          - os: windows-latest
+            python-version: '3.10'
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install tox
-      - name: Run tests
-        run: |
-          tox -e tests,examples
-      - uses: codecov/codecov-action@v1
-        with:
-          file: ./tests/coverage.xml
+    - uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - run: pip install tox
+
+    - name: run Python tests
+      run: tox -e tests,examples
+    - uses: codecov/codecov-action@v3
+      with:
+        files: ./tests/coverage.xml

.gitignore

@@ -8,4 +8,4 @@ __pycache__
 .tox/
 build/
 dist/
-docs/source/read-only-examples
+docs/src/read-only-examples

.readthedocs.yaml

@@ -5,17 +5,22 @@
 # Required
 version: 2
 
+# Set the version of Python and other tools we need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: docs/source/conf.py
+  configuration: docs/src/conf.py
 
 # Optionally build your docs in additional formats such as PDF
 formats:
   - pdf
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.8
   install:
     - requirements: docs/requirements.txt
     - method: pip

MANIFEST.in

@@ -1,2 +1,4 @@
-recursive-include skmatter/datasets/data/ *
-recursive-include skmatter/datasets/descr/ *
+recursive-include src/skmatter/datasets/data/ *
+recursive-include src/skmatter/datasets/descr/ *
+
+prune tests

contributors.txt

@@ -3,4 +3,5 @@ Guillaume Fraux
 Sergei Kliavinek
 Alexander Goscinski
 Benjamin A. Helfrecht
+Victor P. Principe
 Michele Ceriotti

docs/requirements.txt

@@ -1,12 +1,12 @@
 ipykernel
+jinja2 < 3.1
 matplotlib
-nbsphinx==0.8.12
 nbconvert
+nbsphinx==0.8.12
 numpy
+pandas
 scikit-learn >=0.24.0
 sphinx >=3.3
 sphinx_rtd_theme
 tqdm
 traitlets>=5.0
-jinja2 < 3.1
-pandas

docs/source/conf.py → docs/src/conf.py

@@ -15,13 +15,14 @@
 import sphinx_rtd_theme
 from nbconvert import NotebookExporter
 from traitlets.config import Config
+from datetime import datetime
 
 ROOT = os.path.abspath(os.path.join("..", ".."))
 sys.path.insert(0, ROOT)
 
 # Copying and Compiling of Examples
-if not os.path.exists(os.path.join(ROOT, "docs/source/read-only-examples")):
-    os.mkdir(os.path.join(ROOT, "docs/source/read-only-examples"))
+if not os.path.exists(os.path.join(ROOT, "docs/src/read-only-examples")):
+    os.mkdir(os.path.join(ROOT, "docs/src/read-only-examples"))
 
 # Set up nbconvert configuration to strip empty cells and tables of contents
 c = Config()
@@ -45,15 +46,15 @@
     # Skip any non-notebooks
     if nb.endswith("ipynb") and "no-doc" not in nb:
         nb_in = os.path.join(ROOT, "examples", nb)
-        nb_out = os.path.join(ROOT, "docs/source/read-only-examples", nb)
+        nb_out = os.path.join(ROOT, "docs/src/read-only-examples", nb)
 
         # Skip any notebooks which already exist
         if not os.path.exists(nb_out):
             with open(nb_out, "w") as out_stream:
                 converted = exporter.from_filename(nb_in)[0]
                 out_stream.write(converted)
 
-import skmatter  # noqa
+import skmatter  # NoQa
 
 # -- Project information -----------------------------------------------------
 
@@ -62,7 +63,7 @@
 
 project = "scikit-matter"
 author = ", ".join(open(os.path.join(ROOT, "contributors.txt")))
-copyright = "2020, " + author
+copyright = f"{datetime.now().date().year}, {author}"
 
 # The full version, including alpha/beta/rc tags
 release = skmatter.__version__

docs/source/contributing.rst → docs/src/contributing.rst

@@ -27,12 +27,9 @@ Running the tests
 .. code-block:: bash
 
   cd <scikit-matter PATH>
-  # run unit tests
-  tox
-  # run the code formatter
-  black --check .
-  # run the linter
-  flake8
+  tox -e tests         # unit tests
+  tox -e lint          # code style
+  tox -e format        # format all files
 
 You may want to setup your editor to automatically apply the
 `black <https://black.readthedocs.io/en/stable/>`_ code formatter when saving your
@@ -43,9 +40,11 @@ editors <https://black.readthedocs.io/en/stable/editor_integration.html>`_.
 Issues and Pull Requests
 ########################
 
-Having a problem with scikit-matter? Please let us know by `submitting an issue <https://github.com/lab-cosmo/scikit-matter/issues>`_.
+Having a problem with scikit-matter? Please let us know by
+`submitting an issue <https://github.com/lab-cosmo/scikit-matter/issues>`_.
 
-Submit new features or bug fixes through a `pull request <https://github.com/lab-cosmo/scikit-matter/pulls>`_.
+Submit new features or bug fixes through a `pull request
+<https://github.com/lab-cosmo/scikit-matter/pulls>`_.
 
 
 Contributing Datasets
@@ -54,9 +53,10 @@ Contributing Datasets
 Have an example dataset that would fit into scikit-matter?
 
 Contributing a dataset is easy. First, copy your numpy file into
-``skmatter/datasets/data/`` with an informative name. Here, we'll call it ``my-dataset.npz``.
+``src/skmatter/datasets/data/`` with an informative name. Here, we'll call it
+``my-dataset.npz``.
 
-Next, create a documentation file in ``skmatter/datasets/data/my-dataset.rst``.
+Next, create a documentation file in ``src/skmatter/datasets/data/my-dataset.rst``.
 This file should look like this:
 
 .. code-block::
@@ -132,9 +132,9 @@ Then, show ``scikit-matter`` how to load your data by adding a loader function t
 
       return Bunch(data=data, DESCR=fdescr)
 
-Add this function to ``skmatter/datasets/__init__.py``.
+Add this function to ``src/skmatter/datasets/__init__.py``.
 
-Finally, add a test to ``skmatter/tests/test_datasets.py`` to see that your dataset
+Finally, add a test to ``tests/test_datasets.py`` to see that your dataset
 loads properly. It should look something like this:
 
 .. code-block:: python
@@ -158,5 +158,5 @@ You're good to go! Time to submit a `pull request. <https://github.com/lab-cosmo
 License
 #######
 
-This project is distributed under the BSD-3-Clauses license. By contributing to
-it you agree to distribute your changes under the same license.
+This project is distributed under the BSD-3-Clauses license. By contributing to it you
+agree to distribute your changes under the same license.