Replace Poetry with uv for dependency management and workflows

.github/setup-env/action.yml

@@ -0,0 +1,32 @@
+name: Setup Python environment
+description: Set up Python environment for the repository
+inputs:
+  python-version:
+    description: "The Python version to set up"
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+      with:
+        # Install a specific version of uv.
+        version: "0.5.9"
+
+    - name: Set up Python ${{ inputs.python-version }}
+      run: uv python install ${{ inputs.python-version }}
+      shell: bash
+
+    - name: Install hssm
+      if: steps.cache.outputs.cache-hit != 'true'
+      run: uv pip install --system ".[dev]"
+      shell: bash

.github/workflows/build_and_publish.yml

@@ -10,13 +10,9 @@ jobs:
     name: Lint and type-check
     uses: ./.github/workflows/linting_and_type_checking.yml
 
-  run_fast_tests:
-    name: Run fast tests
-    uses: ./.github/workflows/run_fast_tests.yml
-
-  run_slow_tests:
-    name: Run slow tests
-    uses: ./.github/workflows/run_slow_tests.yml
+  run_tests:
+    name: Run tests
+    uses: ./.github/workflows/run_tests.yml
 
   publish:
     name: Build wheel and publish to test-PyPI, and then PyPI, and publish docs
@@ -31,26 +27,31 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Setup Poetry environment
-        uses: ./.github/setup-poetry-env
+      - name: Setup environment
+        uses: ./.github/setup-env
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Setup test-PyPI credentials
-        run: |
-          poetry config repositories.testpypi https://test.pypi.org/legacy/
-          poetry config pypi-token.testpypi ${{ secrets.TEST_PYPI_TOKEN }}
-
       - name: Build the wheel
-        run: poetry build
+        run: python -m build
 
       - name: Publish to test-PyPI
-        run: poetry publish -r testpypi
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}
+        run: |
+          python -m twine upload --repository testpypi dist/*
 
       - name: Publish to PyPI
         env:
-          POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
-        run: poetry publish
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: |
+          python -m twine upload dist/*
+
+      - name: Install doc dependencies
+        run: |
+          $HOME/.cargo/bin/uv pip install -e '.[dev]'
 
       - name: Build and publish docs
-        run: poetry run mkdocs gh-deploy --force
+        run: mkdocs gh-deploy --force

.github/workflows/build_docs.yml

@@ -16,10 +16,13 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Setup Poetry environment
-        uses: ./.github/setup-poetry-env
+      - name: Setup environment
+        uses: ./.github/setup-env
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Install dev dependencies
+        run: uv pip install --system -e ".[dev]"
+
       - name: Run mkdocs
-        run: poetry run mkdocs gh-deploy --force
+        run: uv run mkdocs gh-deploy --force

.github/workflows/linting_and_type_checking.yml

@@ -17,16 +17,16 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Setup Poetry environment
-        uses: ./.github/setup-poetry-env
+      - name: Setup environment
+        uses: ./.github/setup-env
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Run mypy
-        run: poetry run mypy src/hssm
+        run: mypy src/hssm
 
       - name: Check formatting
-        run: poetry run ruff format --check .
+        run: ruff format --check .
 
       - name: Linting
-        run: poetry run ruff check src/hssm
+        run: ruff check src/hssm

.github/workflows/run_tests.yml

@@ -20,17 +20,13 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Setup Poetry environment
-        uses: ./.github/setup-poetry-env
+      - name: Setup environment
+        uses: ./.github/setup-env
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install hssm
-        if: steps.cache.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction
-
       - name: Run tests and collect coverage
-        run: poetry run pytest -n=auto --cov=. --cov-report=xml --cov-report=term-missing --exitfirst --capture=no tests/
+        run: uv run pytest -n=auto --cov=. --cov-report=xml --cov-report=term-missing --exitfirst --capture=no tests/
         env:
           PYTENSOR_FLAGS: ${{ env.PYTENSOR_FLAGS }}
 

.gitignore

@@ -37,6 +37,7 @@ htmlcov/
 .mypy_cache/
 .ruff_cache/
 tests/__pycache__
+coverage.xml
 
 # Jupyter Notebook
 .ipynb_checkpoints
@@ -52,8 +53,9 @@ env/
 venv/
 ENV/
 
-# Also ignore poetry.lock
+# Also ignore lock files
 poetry.lock
+uv.lock
 
 # Editor cruft
 .idea/

docs/CONTRIBUTING.md

@@ -61,17 +61,17 @@ The preferred workflow for contributing to HSSM is to fork the GitHub repository
    ```
 
 > [!Note]
-> If your changes require libraries not included in `hssm`, you'll need to use Poetry to update the dependency files. Please visit the [official Poetry documentation](https://python-poetry.org/docs/) and follow the installation instructions to install Poetry on your system.
+> If your changes require libraries not included in `hssm`, you'll need to use `uv` to update the dependency files. Please visit the [official `uv` documentation](https://docs.astral.sh/uv/) and follow the installation instructions.
 >
-> After installing Poetry, you can add the new libraries (dependencies) to [`pyproject.toml`](https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#writing-your-pyproject-toml) by running:
+> After installing `uv`, you can add the new libraries (dependencies) to [`pyproject.toml`](https://docs.astral.sh/uv/guides/projects/#managing-dependencies) by running:
 > ```
-> poetry add <package-name>
+> uv add <package-name>
 > ```
-> Replace `<package-name>` with the name of the library you need to add. This command will update the `pyproject.toml` file and install the new dependency. It will also add changes to the [`poetry.lock`](https://python-poetry.org/docs/basic-usage/#committing-your-poetrylock-file-to-version-control) file.
+> Replace `<package-name>` with the name of the library you need to add. This command will update the `pyproject.toml` file and install the new dependency. It will also add changes to the [`uv.lock`](https://docs.astral.sh/uv/guides/projects/#uvlock) file.
 >
 > Remember to commit the newly changed files.
 > ```
-> git add pyproject.toml poetry.lock
+> git add pyproject.toml uv.lock
 > git commit -m "Add <package-name> dependency"
 > ```
 
@@ -85,4 +85,3 @@ The preferred workflow for contributing to HSSM is to fork the GitHub repository
    - Click the ‘Pull request’ button to send your changes to the project’s maintainers for review.
 
 **This guide is adapted from the [ArviZ contribution guide](https://github.com/arviz-devs/arviz/blob/main/CONTRIBUTING.md)**
-

pyproject.toml

@@ -1,54 +1,54 @@
-[tool.poetry]
+[project]
 name = "HSSM"
 version = "0.2.4"
 description = "Bayesian inference for hierarchical sequential sampling models."
 authors = [
-    "Alexander Fengler <alexander_fengler@brown.edu>",
-    "Paul Xu <yang_xu@brown.edu>",
-    "Aisulu Omar <aisulu_omar@brown.edu>",
-    "Michael Frank <michael_frank@brown.edu>",
+    {name = "Alexander Fengler", email = "alexander_fengler@brown.edu"},
+    {name = "Paul Xu", email = "yang_xu@brown.edu"},
+    {name = "Aisulu Omar", email = "aisulu_omar@brown.edu"},
+    {name = "Michael Frank", email = "michael_frank@brown.edu"}
 ]
 readme = "README.md"
-license = "Copyright 2023, Brown University, Providence, RI."
-packages = [{ include = "hssm", from = "src" }]
+license = "LicenseRef-Proprietary" # TODO: Update license
 repository = "https://github.com/lnccbrown/HSSM"
 keywords = ["HSSM", "sequential sampling models", "bayesian", "bayes", "mcmc"]
 
-[tool.poetry.dependencies]
-python = ">=3.10,<=3.12"
-pymc = ">=5.16.2,<5.17.0"
-arviz = "^0.19.0"
-onnx = "^1.16.0"
-ssm-simulators = "^0.7.5"
-huggingface-hub = "^0.24.6"
-bambi = ">=0.14.0,<0.15.0"
-numpyro = "^0.15.2"
-hddm-wfpt = "^0.1.4"
-seaborn = "^0.13.2"
-tqdm = "^4.66.0"
-jax = { version = "^0.4.25", extras = ["cuda12"], optional = true }
-numpy = ">=1.26.4,<2.0.0"
+requires-python = ">=3.10,<3.13"
 
-[tool.poetry.group.dev.dependencies]
-pytest = "^8.3.1"
-mypy = "^1.11.1"
-pre-commit = "^2.20.0"
-jupyterlab = "^4.2.4"
-ipykernel = "^6.29.5"
-ipywidgets = "^8.1.2"
-ruff = "^0.6.2"
-graphviz = "^0.20.3"
-pytest-xdist = "^3.6.1"
-onnxruntime = "^1.17.1"
-mkdocs = "^1.6.0"
-mkdocs-material = "^9.5.21"
-mkdocstrings-python = "^1.10.0"
-mkdocs-jupyter = "^0.24.8"
-pytest-cov = "^6.0.0"
-coverage = "^7.6.4"
+dependencies = [
+    "pymc>=5.16.2,<5.17.0",
+    "arviz>=0.19.0",
+    "onnx>=1.16.0",
+    "ssm-simulators>=0.7.5",
+    "huggingface-hub>=0.24.6",
+    "bambi>=0.14.0,<0.15.0",
+    "numpyro>=0.15.2",
+    "hddm-wfpt>=0.1.4",
+    "seaborn>=0.13.2",
+    "tqdm>=4.66.0",
+    "numpy>=1.26.4,<2.0.0"
+]
 
-[tool.poetry.extras]
-cuda12 = ["jax"]
+[project.optional-dependencies]
+cuda12 = ["jax[cuda12]"]
+dev = [
+"pytest>=8.3.1",
+"mypy>=1.11.1",
+"pre-commit>=2.20.0",
+"jupyterlab>=4.2.4",
+"ipykernel>=6.29.5",
+"ipywidgets>=8.1.2",
+"ruff>=0.6.2",
+"graphviz>=0.20.3",
+"pytest-xdist>=3.6.1",
+"onnxruntime>=1.17.1",
+"mkdocs>=1.6.0",
+"mkdocs-material>=9.5.21",
+"mkdocstrings-python>=1.10.0",
+"mkdocs-jupyter>=0.24.8",
+"pytest-cov>=6.0.0",
+"coverage>=7.6.4"
+]
 
 [tool.ruff]
 line-length = 88
@@ -168,5 +168,5 @@ ignore_missing_imports = true
 testpaths = ["tests"]
 
 [build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+requires = ["hatchling"]
+build-backend = "hatchling.build"