Add Hatch (#468)

* Add Hatch

* Update workflows

* Update workflows

* Update workflows

* Add networkx

* Update tests

* Add formatters

* Drop Poetry refs

* Respond to PR comments

Author: thomaspinder

.github/pull_request_template.md

@@ -1,14 +1,6 @@
-## Type of changes
-
-- [ ] Bug fix
-- [ ] New feature
-- [ ] Documentation / docstrings
-- [ ] Tests
-- [ ] Other
-
 ## Checklist
 
-- [ ] I've formatted the new code by running `poetry run pre-commit run --all-files --show-diff-on-failure` before committing.
+- [ ] I've formatted the new code by running `hatch run dev:format` before committing.
 - [ ] I've added tests for new code.
 - [ ] I've added docstrings for the new code.
 

.github/workflows/build_docs.yml

@@ -46,20 +46,15 @@ jobs:
       - name: Install KaTeX
         run: |
           npm install katex
-      # Install Poetry and build the documentation
-      - name: Install and configure Poetry
-        uses: snok/install-poetry@v1
-        with:
-          version: 1.5.1
-          virtualenvs-create: false
-          virtualenvs-in-project: false
-          installer-parallel: true
+
+      # Install Hatch
+      - name: Install Hatch
+        uses: pypa/hatch@install
 
       - name: Build the documentation with MKDocs
         run: |
-          poetry install --all-extras --with docs
           conda install pandoc
-          poetry run python docs/scripts/gen_examples.py --execute && poetry run mkdocs build
+          hatch run docs:build
 
       - name: Deploy Page 🚀
         uses: JamesIves/github-pages-deploy-action@v4.4.1

.github/workflows/integration.yml

@@ -25,22 +25,10 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      # Install Poetry
-      - name: Install Poetry
-        uses: snok/install-poetry@v1.3.3
-        with:
-          version: 1.5.1
-
-      # Configure Poetry to use the virtual environment in the project
-      - name: Setup Poetry
-        run: |
-          poetry config virtualenvs.in-project true
-
-      # Install the dependencies
-      - name: Install Package
-        run: |
-          poetry install --with docs
+      # Install Hatch
+      - name: Install Hatch
+        uses: pypa/hatch@install
 
       # Run the unit tests and build the coverage report
       - name: Run Integration Tests
-        run: poetry run python tests/integration_tests.py
+        run: hatch run docs:integration

.github/workflows/test_docs.yml

@@ -33,17 +33,11 @@ jobs:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
 
-      # Install Poetry and build the documentation
-      - name: Install and configure Poetry
-        uses: snok/install-poetry@v1
-        with:
-          version: 1.5.1
-          virtualenvs-create: false
-          virtualenvs-in-project: false
-          installer-parallel: true
+      # Install Hatch
+      - name: Install Hatch
+        uses: pypa/hatch@install
 
       - name: Build the documentation with MKDocs
         run: |
-          poetry install --all-extras --with docs
           conda install pandoc
-          poetry run python docs/scripts/gen_examples.py --execute && poetry run mkdocs build
+          hatch run docs:build

.github/workflows/tests.yml

@@ -25,32 +25,18 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      # Install Poetry
-      - name: Install and configure Poetry
-        uses: snok/install-poetry@v1
-        with:
-          version: 1.5.1
-          virtualenvs-create: false
-          virtualenvs-in-project: false
-          installer-parallel: true
-
-      # Configure Poetry to use the virtual environment in the project
-      - name: Setup Poetry
-        run: |
-          poetry config virtualenvs.in-project true
+      # Install Hatch
+      - name: Install Hatch
+        uses: pypa/hatch@install
 
       # Install the dependencies
-      - name: Install Package
-        run: |
-          poetry install --with dev
-
       - name: Check docstrings
         run: |
-          poetry run xdoctest ./gpjax
+          hatch run dev:docstrings
 
       # Run the unit tests and build the coverage report
       - name: Run Tests
-        run: poetry run pytest -v --cov=./gpjax --cov-report=xml:./coverage.xml
+        run: hatch run dev:coverage
 
       - name: Upload code coverage
         uses: codecov/codecov-action@v3

.pre-commit-config.yaml

@@ -205,13 +205,14 @@ configuration in development mode.
 ```bash
 git clone https://github.com/JaxGaussianProcesses/GPJax.git
 cd GPJax
-poetry install
+hatch env create
+hatch shell
 ```
 
 > We recommend you check your installation passes the supplied unit tests:
 >
 > ```python
-> poetry run pytest
+> hatch run dev:test
 > ```
 
 # Citing GPJax

README.md

@@ -72,36 +72,19 @@ you through every detail!
   Always use a `feature` branch. It's good practice to avoid
   work on the ``main`` branch of any repository.
 
-4.  We use [Poetry](https://python-poetry.org/) for packaging and dependency management, and project requirements are in       ``pyproject.toml``. We suggest using a [virtual environment](https://docs.python-guide.org/dev/virtualenvs/) for
-development. For those using Apple Silicon chips, we advise using [Conda miniforge](https://github.com/conda-forge/miniforge). Once the virtual environment is activated, run:
+4.  We use [Hatch](https://hatch.pypa.io/latest/) for packaging and dependency management. Project requirements are in ``pyproject.toml``. To install GPJax into a Hatch virtual environment, run:
 
   ```bash
-  $ poetry install
+  $ hatch env create
   ```
 
   At this point we recommend you check your installation passes the supplied unit tests:
 
   ```bash
-  $ poetry run pytest
+  $ hatch run dev:all-tests
   ```
 
-5.  Install the pre-commit hooks.
-
-  ```bash
-  $ pre-commit install
-  ```
-
-  Please ensure you have done this before committing any files. If
-  successful, this will print the following output `pre-commit installed at
-  .git/hooks/pre-commit`.
-
-6.  At this point you can manually run the pre-commit hooks with the following command:
-
-  ```bash
-  poetry run pre-commit run --all-files
-  ```
-
-7.  Add changed files using `git add` and then `git commit` files to record your
+5.  Add changed files using `git add` and then `git commit` files to record your
   changes locally:
 
   ```bash
@@ -122,7 +105,7 @@ development. For those using Apple Silicon chips, we advise using [Conda minifor
   $ git push -u origin my-feature
   ```
 
-8.  Go to the GitHub web page of your fork of the GPJax repo. Click the 'Pull
+6.  Go to the GitHub web page of your fork of the GPJax repo. Click the 'Pull
   request' button to send your changes to the project's maintainers for
   review.
 
@@ -159,7 +142,7 @@ request, we recommend you check the following:
   accepted. Test coverage can be checked with:
 
     ```bash
-    $ poetry run pytest tests --cov=./ --cov-report=html
+    $ hatch run dev:coverage
     ```
 
   Navigate to the newly created folder `htmlcov` and open `index.html` to view

docs/contributing.md

@@ -31,7 +31,7 @@ hardware acceleration support as detailed in the
     ```bash
     git clone https://github.com/thomaspinder/GPJax.git
     cd GPJax
-    poetry install
+    hatch shell create
     ```
 
 !!! tip
@@ -45,5 +45,5 @@ hardware acceleration support as detailed in the
     and recommend you check your installation passes the supplied unit tests:
 
     ```bash
-    poetry run pytest tests/
+    hatch run dev:all-tests
     ```