build: use PEP517/518 conventions

.circleci/config.yml

@@ -23,7 +23,7 @@ jobs:
       # Download and cache dependencies
       - restore_cache:
           keys:
-          - v1-dependencies-{{ checksum "requirements-dev.txt" }}
+          - v1-dependencies-{{ checksum "pyproject.toml" }}-{{ checksum "setup.cfg" }}-{{ checksum "setup.py" }}
           # fallback to using the latest cache if no exact match is found
           - v1-dependencies-
 
@@ -33,29 +33,21 @@ jobs:
             python3 -m venv venv
             . venv/bin/activate
             python -m pip install --upgrade pip
-            pip install -r requirements-dev.txt
-            python setup.py install
-
 
       - save_cache:
           paths:
             - ./venv
-          key: v1-dependencies-{{ checksum "requirements-dev.txt" }}
+          key: v1-dependencies-{{ checksum "pyproject.toml" }}-{{ checksum "setup.cfg" }}-{{ checksum "setup.py" }}
 
-      # run tests!
-      # this example uses Django's built-in test-runner
-      # other common Python testing frameworks include pytest and nose
-      # https://pytest.org
-      # https://nose.readthedocs.io
       - run:
           name: run tests
           command: |
             . venv/bin/activate
-            mkdir test-reports
-            py.test --junitxml=test-reports/junit.xml tests/
+            python -m pip install .[dev]
+            python -m pytest
 
       - store_test_results:
-          path: test-reports
+          path: coverage.xml
 
       - store_artifacts:
-          path: test-reports
+          path: coverage.xml

.github/workflows/check-docs.yml

@@ -1,4 +1,4 @@
-name: "Pull Request Docs Check"
+name: "Check docs"
 on:
 - pull_request
 
@@ -7,19 +7,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.x
+    - name: Set up Python 3.8
       uses: actions/setup-python@v2
       with:
-        # Semantic version range syntax or exact version of a Python version
         python-version: '3.8'
-    # You can test your matrix by printing the current Python version
-    - name: Display Python version
-      run: python -c "import sys; print(sys.version)"
     - name: Install ruptures and dependencies
       run: |
         python -m pip install --upgrade pip
-        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
-        python setup.py install
+        python -m pip install .[dev]
     - name: Run notebooks
       run: |
         jupyter nbconvert --inplace --to notebook --ExecutePreprocessor.kernel_name=python --execute $(find ./docs -name '*.ipynb')

.github/workflows/check-linting.yml

@@ -1,4 +1,4 @@
-name: check-linting
+name: Check linting
 
 on:
   push:
@@ -18,7 +18,7 @@ jobs:
     - name: Install pre-commit hooks
       run: |
         python -m pip install --upgrade pip
-        pip install pre-commit
+        python -m pip install pre-commit
     - name: Run pre-commit hooks
       run: |
         pre-commit run --all-files

.github/workflows/publish-doc-to-remote.yml

@@ -1,5 +1,5 @@
-# Publish doc to website on new release (or manual trigger)
-name: "docs"
+# Publish docs to website on new release (or manual trigger)
+name: "Publish docs online"
 
 on:
   release:
@@ -14,23 +14,18 @@ jobs:
     - name: Set up Python 3.x
       uses: actions/setup-python@v2
       with:
-        # Semantic version range syntax or exact version of a Python version
         python-version: '3.8'
-    # You can test your matrix by printing the current Python version
-    - name: Display Python version
-      run: python -c "import sys; print(sys.version)"
     - name: Install ruptures and dependecies
       run: |
         python -m pip install --upgrade pip
-        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
-        python setup.py install
+        python -m pip install .[dev]
     - name: Run notebooks
       run: |
         jupyter nbconvert --inplace --to notebook --ExecutePreprocessor.kernel_name=python --execute $(find ./docs -name '*.ipynb')
     - name: Build documentation
       run: |
         mkdocs build
-    - name: Publish documentation to remote
+    - name: Publish documentation to remote repo
       uses: selenehyun/gh-push@master
       env:
         GITHUB_TOKEN: ${{ secrets.DOC_PUSHER_ACCESS_TOKEN }}

.github/workflows/run-test-coverage.yml

@@ -1,7 +1,9 @@
-# This workflow will install Python dependencies, run tests, generate coverage report and upload it to codecov
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+# This workflow will install Python dependencies, run tests, generate coverage
+# report and upload it to codecov.
+# For more information, see:
+# https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: coverage
+name: Run tests with coverage
 
 on:
   push:
@@ -14,26 +16,20 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.x
+    - name: Set up Python 3.8
       uses: actions/setup-python@v2
       with:
         python-version: '3.8'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements-dev.txt
-        pip install pytest-cov
     - name: Install ruptures
       run: |
-        python setup.py install
+        python -m pip install --upgrade pip
+        python -m pip install .[test]
     - name: Test with pytest
       run: |
-        pytest --cov-report=xml --cov=ruptures tests/
-
+        python -m pytest
     - name: Upload to Codecov
       run: |
         bash <(curl -s https://codecov.io/bash)
-
     - uses: actions/upload-artifact@v2
       with:
         path: coverage.xml

.github/workflows/run-test.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: build
+name: Run tests
 
 on:
   push:
@@ -18,22 +18,17 @@ jobs:
         exclude:
           - os: windows-latest
             python-version: 3.9
-
     runs-on: ${{ matrix.os }}
-
     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 -r requirements-dev.txt
     - name: Install ruptures
       run: |
-        python setup.py install
+        python -m pip install --upgrade pip
+        python -m pip install .[test]
     - name: Test with pytest
       run: |
-        pytest
+        python -m pytest

.github/workflows/publish-to-pypi.yml → .github/workflows/upload-to-pypi.yml

@@ -1,4 +1,4 @@
-name: Publish to Pypi (sdist and wheels)
+name: Upload package to Pypi
 
 on:
   workflow_dispatch:
@@ -48,9 +48,7 @@ jobs:
       - name: Install cibuildwheel and dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install cibuildwheel
-          pip install -r requirements-dev.txt
-          pip install setuptools wheel twine
+          python -m pip install cibuildwheel setuptools wheel twine
 
       - name: Build wheels
         env:
@@ -59,7 +57,7 @@ jobs:
           TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
         run: |
           python -m cibuildwheel --output-dir wheelhouse
-          twine upload wheelhouse/*.whl
+          python -m twine upload wheelhouse/*.whl
 
       - uses: actions/upload-artifact@v2
         with:
@@ -69,26 +67,21 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.x
+      - name: Set up Python 3.8
         uses: actions/setup-python@v2
         with:
-          # Semantic version range syntax or exact version of a Python version
           python-version: '3.8'
-      # You can test your matrix by printing the current Python version
-      - name: Display Python version
-        run: python -c "import sys; print(sys.version)"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements-dev.txt
           pip install setuptools wheel twine
       - name: Build
         env:
           TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
           TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
         run: |
           python setup.py sdist
-          twine upload dist/*.tar.gz
+          python -m twine upload dist/*.tar.gz
       - uses: actions/upload-artifact@v2
         with:
           path: dist/*.tar.gz

.gitignore

@@ -82,7 +82,4 @@ docs/build/*
 .Trashes
 ehthumbs.db
 Thumbs.db
-site/
-ruptures/utils/_utils/convert_path_matrix.c
-ruptures/detection/_detection/continuous_linear_cpd.c
-ruptures/detection/_detection/ekcpd.c
+site/

CONTRIBUTING.md

@@ -5,11 +5,6 @@
 
 In all following steps, it is highly recommended to use a virtual environment.
 
-### Install the requirements
-
-Several packages are needed to compile, format and test the code.
-They are listed in `requirements-dev.txt` and can be installed with the following command.
-
 ### Install the development version
 
 It is important that you contribute to the latest version of the code.
@@ -20,33 +15,30 @@ git clone https://github.com/deepcharles/ruptures
 cd ruptures
 ```
 
-Then install the downloaded package.
+Then install the downloaded package with `pip`.
 
 ```
-python -m pip install --verbose --no-build-isolation --editable .
+python -m pip install --editable .[dev]
 ```
 
-#### With pip
-```
-pip install -r requirements-dev.txt
-```
+Note that `python -m` can be omitted most of the times, but within virtualenvs, it can prevent certain errors.
+Also, in certain terminals (such as zsh), the square brackets must be escaped, e.g. replace `.[dev]` by `.\[dev\]`.
 
-#### With conda
-```
-conda --file requirements-dev.txt
-```
-
-Then run the following command to install the `pre-commit` hooks.
-```
-pre-commit install
-```
+In addition to `numpy`, `scipy` and `ruptures`, this command will install all packages needed to develop `ruptures`.
+The exact list of librairies can be found in the [`setup.cfg` file](https://github.com/deepcharles/ruptures/blob/master/setup.cfg) (section `[options.extras_require]`).
 
 ### Pre-commit hooks
 
 We use `pre-commit` to run Git hooks before submitting the code to review.
 These hook scripts perform simple tasks before each commit (code formatting mostly).
+To activate the hooks, simply run the following command in your terminal.
+
+```
+pre-commit install
+```
+
 
-Note that if you try to commit a non-compliant (i.e. badly formatted) file, `pre-commit` will modify this file and make the commit fail.
+If you try to commit a non-compliant (i.e. badly formatted) file, `pre-commit` will modify this file and make the commit fail.
 However you need to stage the new changes **yourself** as `pre-commit` will not do that for you (this is by design; see [here](https://github.com/pre-commit/pre-commit/issues/806) or [here](https://github.com/pre-commit/pre-commit/issues/747)).
 Fortunately, `pre-commit` outputs useful messages.
 
@@ -61,7 +53,7 @@ If you want to manually run all pre-commit hooks on a repository, run `pre-commi
 The following command executes the test suite.
 
 ```
-pytest
+python -m pytest
 ```
 
 ### Write docstrings

mkdocs.yml

@@ -89,10 +89,6 @@ nav:
           - Binseg: code-reference/detection/binseg-reference.md
           - BottomUp: code-reference/detection/bottomup-reference.md
           - Window: code-reference/detection/window-reference.md
-          # - GreedyAR: code-reference/detection/greedyar-reference.md
-          # - GreedyLinear: code-reference/detection/greedylinear-reference.md
-          # - Omp: code-reference/detection/omp-reference.md
-          # - OmpK: code-reference/detection/ompk-reference.md
       - Cost functions:
           - 'CostL1': code-reference/costs/costl1-reference.md
           - 'CostL2': code-reference/costs/costl2-reference.md

pyproject.toml

@@ -1,7 +1,7 @@
 [build-system]
 # Minimum requirements for the build system to execute.
 requires = [
-    "setuptools",
+    "setuptools>=38.3.0",  # version with most `setup.cfg` bugfixes
     "wheel",
     "Cython>=0.28.5",
 
@@ -28,3 +28,12 @@ requires = [
 
     "scipy>=0.19.1",
 ]
+build-backend = "setuptools.build_meta"
+
+# pytest config
+# For more information, see:
+# https://docs.pytest.org/en/stable/customize.html#pyproject-toml
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = "--cov-report=xml --cov-report=term:skip-covered --cov=ruptures"
+testpaths = ["tests"]