Use pyproject.toml (#631)

* Use pyproject.toml. Remove unnecesary files. Improve CI workflows * name change * stringify python version * Take version from a file. Install optional deps from local as well * Changelog.md -> CHANGELOG.md * add pydata-sphinx-theme to dependencies * try to fix test workflow * lint * Add 'bash -l {0}' to tests * [no ci] update contributing.md * Update CHANGELOG.md Co-authored-by: Ravin Kumar <[email protected]> --------- Co-authored-by: Ravin Kumar <[email protected]>
bambinos · Feb 2, 2023 · c610691 · c610691
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diff --git a/.gitattributes b/.gitattributes
diff --git a/.github/workflows/publish-docs-release.yml b/.github/workflows/publish-docs-release.yml
@@ -12,26 +12,26 @@ jobs:
     strategy:
       fail-fast: false
     steps:
-      - uses: r-lib/actions/setup-pandoc@v1
-      - name: Checkout Source
+      - name: Set up Pandoc
+        uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Checkout source
         uses: actions/checkout@v2
         with:
-          # require all of history to see all tagged versions' docs
           fetch-depth: 0
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - name: Set up Python
+        uses: actions/setup-python@v3
         with:
-          python-version: 3.9
-      # statsmodels is needed to build docs for old releases
-      - name: Install Dependencies
+          python-version: "3.10"
+
+      - name: Install Bambi and all its dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install -r requirements-dev.txt
-          pip install statsmodels 
-          python setup.py build
-          python setup.py install
+          conda install -c conda-forge python-graphviz
+          conda install pip
+          pip install .
+          pip install .[dev]
+          pip install .[jax]
 
       - name: Checkout gh-pages
         uses: actions/checkout@v2
@@ -45,7 +45,7 @@ jobs:
           sphinx-build docs docs/_build/html
           touch docs/_build/html/.nojekyll
 
-      - name: Publish Docs to gh-pages
+      - name: Publish docs to gh-pages
         # We pin to the SHA, not the tag, for security reasons.
         # https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/security-hardening-for-github-actions#using-third-party-actions
         uses: peaceiris/actions-gh-pages@bbdfb200618d235585ad98e965f4aafc39b4c501 # v3.7.3

diff --git a/.github/workflows/publish-docs.yml b/.github/workflows/publish-docs.yml
@@ -12,46 +12,42 @@ jobs:
     strategy:
       fail-fast: false
     steps:
-      - uses: r-lib/actions/setup-pandoc@v1
-      - name: Checkout Source
+      - name: Set up Pandoc
+        uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Checkout source
         uses: actions/checkout@v2
-        with:
-          # require all of history to see all tagged versions' docs
-          fetch-depth: 0
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - name: Set up Python
+        uses: actions/setup-python@v3
         with:
-          python-version: 3.8
+          python-version: "3.10"
 
-      - name: Install Dependencies
+      - name: Install Bambi and all its dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install -r requirements-dev.txt
-          python setup.py build
-          python setup.py install
+          conda install -c conda-forge python-graphviz
+          conda install pip
+          pip install .
+          pip install .[dev]
+          pip install .[jax]
 
       - name: Checkout gh-pages
-        # As we already did a deploy of gh-pages above, it is guaranteed to be there
-        # so check it out so we can selectively build docs below
         uses: actions/checkout@v2
         with:
           ref: gh-pages
           path: docs/_build/html
 
-      - name: Test Build Docs
+      - name: Test build docs
         if: github.ref != 'refs/heads/main' && ! startsWith(github.ref, 'refs/tags')
-        run: |
-          BUILDDIR=_build/html/main make -C docs/ local
+        run: BUILDDIR=_build/html/main make -C docs/ local
 
-      - name: Build Docs
+      - name: Build docs
         if: github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags')
         run: |
           sphinx-build docs docs/_build/html
           touch docs/_build/html/.nojekyll
 
-      - name: Publish Docs to gh-pages
+      - name: Publish docs to gh-pages
         # Only once from main or a tag
         if: github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags')
         # We pin to the SHA, not the tag, for security reasons.

diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml
@@ -6,24 +6,82 @@ on:
       - created
 
 jobs:
-  deploy:
+  build:
+    name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - name: Checkout repository
+        uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v3
         with:
-          python-version: "3.8"
+          python-version: "3.10"
 
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install setuptools wheel twine
-      - name: Build and publish
+        run: python3 -m pip install --upgrade build
+
+      - name: Build
+        run: python3 -m build
+
+      - name: Upload source distribution artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: artifact
+          path: dist/*
+
+  test:
+    name: Upload release to test PyPI 
+    needs: [build]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download source distribution artifact
+        uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+
+      - name: Install twine
+        run: python3 -m pip install --upgrade twine
+
+      - name: Publish library
         env:
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}
+        run: python3 -m twine upload --skip-existing --repository testpypi dist/*
+
+      - name: Test pip install from test.pypi
         run: |
-          python setup.py sdist bdist_wheel
-          twine upload dist/*
+          python -m venv venv-test-pypi
+          venv-test-pypi/bin/python -m pip install --index-url https://test.pypi.org/simple/ bambi
+          venv-test-pypi/bin/python -c "import bambi; assert bambi.__version__ == '${{  github.ref_name }}'"
+
+  publish:
+    name: Upload release to PyPI
+    needs: [build, test]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download source distribution artifact
+        uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+
+      - name: Install twine
+        run: python3 -m pip install --upgrade twine
+
+      - name: Publish library
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: python3 -m twine upload dist/*
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -15,7 +15,8 @@ jobs:
 
     name: Set up Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v2
+      - name: Checkout source
+        uses: actions/checkout@v2
         with:
           fetch-depth: 0
 
@@ -27,15 +28,19 @@ jobs:
           python-version: ${{ matrix.python-version }}
           auto-update-conda: true
 
-      - name: Install dev environment & bambi
+      - shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+
+      - name: Install Bambi and all its dependencies
         shell: bash -l {0}
         run: |
           conda install -c conda-forge python-graphviz
           conda install pip
-          pip install -r requirements.txt
-          pip install -r requirements-dev.txt
-          pip install -r requirements-optional.txt
           pip install .
+          pip install .[dev]
+          pip install .[jax]
 
           python --version
           conda list
@@ -44,16 +49,15 @@ jobs:
       - name: Run linters
         shell: bash -l {0}
         run: |
-          python -m black bambi --check
-          echo "Success!"
+          echo "Running black..."
+          black bambi --check
 
           echo "Checking code style with pylint..."
-          python -m pylint bambi/
+          pylint bambi
 
       - name: Run tests
         shell: bash -l {0}
-        run: |
-          python -m pytest -vv --cov=bambi --cov-report=term --cov-report=xml tests
+        run: python -m pytest -vv --cov=bambi --cov-report=term --cov-report=xml tests
         env:
           PYTHON_VERSION: ${{ matrix.python-version }}
 

diff --git a/Changelog.md → CHANGELOG.md b/Changelog.md → CHANGELOG.md
@@ -12,6 +12,7 @@
 
 * Moved the `tests` directory to the root of the repository (#607)
 * Don't pass `dims` to the response of the likelihood distribution anymore (#629)
+* Remove requirements.txt and replace with `pyproject.toml` config file to distribute the package (#631)
 
 ### Documentation
 

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -46,30 +46,36 @@ Please reasonably document any additions or changes to the codebase, when in dou
 
 1. Fork the [project repository](https://github.com/bambinos/bambi/) by clicking on the 'Fork' button near the top right of the main repository page. This creates a copy of the code under your GitHub user account.
 
-2. Clone your fork of the Bambi repo from your GitHub account to your local disk, and add the base repository as a remote:
+1. Clone your fork of the Bambi repo from your GitHub account to your local disk, and add the base repository as a remote:
 
    ```bash
    git clone [email protected]:<your GitHub handle>/bambi.git
    cd bambi
    git remote add upstream [email protected]:bambinos/bambi.git
    ```
 
-3. Create a feature branch (e.g. `my-feature`) to hold your development changes:
+1. Create a feature branch (e.g. `my-feature`) to hold your development changes:
 
    ```bash
    git checkout -b my-feature
    ```
 
    Always use a feature branch. It's good practice to never routinely work on the `main` branch of any repository.
 
-4. Project requirements are in `requirements.txt`, and libraries used for development are in `requirements-dev.txt`. To set up a development environment, you may run:
+1. Install the package in editable mode and its development dependencies.
 
    ```bash
-   pip install -r requirements.txt
-   pip install -r requirements-dev.txt
+   pip install -e .
+   pip install .[dev]
    ```
 
-5. Develop the feature on your feature branch. Add changed files using `git add` and then `git commit` files:
+   If you're going to develop futures related to JAX, install jax-related dependencies.
+
+   ```bash
+   pip install .[jax]
+   ```
+
+1. Develop the feature on your feature branch. Add changed files using `git add` and then `git commit` files:
 
    ```bash
    git add modified_files
@@ -117,19 +123,19 @@ We recommend that your contribution complies with the following guidelines befor
 - Code coverage **cannot** decrease. Coverage can be checked with **pytest-cov** package:
 
   ```bash
-  pytest --cov=bambi --cov-report=html tests/
+  pytest --cov=bambi --cov-report=html tests
   ```
 
 - Your code passes black
 
   ```bash
-  black bambi/
+  black bambi
   ```
 
 - Your code passes pylint
 
   ```bash
-  pylint bambi/
+  pylint bambi
   ```
 
 **This guide was derived from the [ArviZ guide to contributing](https://github.com/arviz-devs/arviz/blob/master/CONTRIBUTING.md)**
diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/README.md b/README.md
@@ -25,7 +25,7 @@ Alternatively, if you want the bleeding edge version of the package you can inst
 
 ### Dependencies
 
-Bambi requires working versions of ArviZ, formulae, NumPy, pandas and PyMC. Dependencies are listed in `requirements.txt`, and should all be installed by the Bambi installer; no further action should be required.
+Bambi requires working versions of ArviZ, formulae, NumPy, pandas and PyMC. Dependencies are listed in `pyproject.toml` and should all be installed by the Bambi installer; no further action should be required.
 
 ## Example
 

diff --git a/bambi/VERSION.txt b/bambi/VERSION.txt
@@ -0,0 +1 @@
+0.9.3
diff --git a/bambi/version.py b/bambi/version.py
@@ -1 +1,12 @@
-__version__ = "0.9.3"
+import os
+
+here = os.path.dirname(os.path.realpath(__file__))
+
+
+def read_version():
+    version_file = os.path.join(here, "VERSION.txt")
+    with open(version_file, encoding="utf-8") as buff:
+        return buff.read()
+
+
+__version__ = read_version()
diff --git a/docs/index.rst b/docs/index.rst
@@ -25,7 +25,7 @@ Bambi is a high-level Bayesian model-building interface written in Python. It wo
 
 Dependencies
 ============
-Bambi is tested on Python 3.8+ and depends on ArviZ, formulae, NumPy, pandas and PyMC (see `requirements.txt <https://github.com/bambinos/bambi/blob/main/requirements.txt>`_ for version information).
+Bambi is tested on Python 3.8+ and depends on ArviZ, formulae, NumPy, pandas and PyMC (see `pyproject.toml <https://github.com/bambinos/bambi/blob/main/pyproject.toml>`_ for version information).
 
 Installation
 ============