Update project configuration

* move dependency management to uv
* move (most) config info to pyproject.toml
* bump minimum supported Python version
* bump development status metadata
* update github workflows
* remove requirements files
* update dev docs re: uv

Author: molpopgen

.github/workflows/dev.yaml

@@ -29,5 +29,7 @@ jobs:
 
       - name: install developer dependencies
         run: |
+          # NOTE: production use of this command
+          # would be python -m pip ...
           pip install --upgrade pip
-          pip install -r requirements.txt
+          pip install -e . --group test --group lint --group docs

.github/workflows/docs.yaml

@@ -22,17 +22,19 @@ jobs:
         with:
           python-version: "3.12"
 
-      - name: Install dependencies
-        run: |
-          pip install --upgrade pip
-          pip install -r requirements_minimal_CI.txt
-          pip install -r requirements_docs_CI.txt
-          python -m pip install build packaging
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          activate-environment: true
+          version: "latest"
+          python-version: ${{ matrix.python }}
 
-      - name: Build package
+      - name: Install python dependencies
         run: |
-          # Generate the version string which appears in the docs.
-          python -m build --sdist
+          # uv sync install the project into the venv
+          # NOTE: we do not specify -p here, so
+          # we rely on python-version above
+          uv sync --frozen --group docs
 
       - name: Build Docs
         run: |

.github/workflows/lint.yaml

@@ -15,14 +15,17 @@ jobs:
         with:
           python-version: "3.12"
 
-      - name: Install dependencies
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          activate-environment: true
+          version: "latest"
+          python-version: ${{ matrix.python }}
+
+      - name: Install python dependencies
         run: |
-          pip install -r requirements_minimal_CI.txt
-          pip install -r requirements_lint_CI.txt
-          # Mypy also checks types in the tests/ folder
-          pip install -r requirements_tests_CI.txt
-          pip install build
-          python -m build .
+          # uv sync install the project into the venv
+          uv sync --frozen --group lint
 
       - name: black
         run: black --check .

.github/workflows/tests.yaml

@@ -41,21 +41,23 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: install dependencies
-        run: |
-          pip install -r requirements_minimal_CI.txt
-          pip install -r requirements_tests_CI.txt
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          activate-environment: true
+          version: "latest"
+          python-version: ${{ matrix.python }}
 
-      # Check that demes installs as expected.
-      # Also check the "demes" CLI entry point.
-      - name: install demes
+      - name: Install python dependencies
         run: |
-          pip install .
-          demes -h
+          # uv sync install the project into the venv
+          # and the -p installs the correct Python
+          # version if it is not the version in $PATH
+          uv sync -p ${{ matrix.python-version }} --frozen --group test
 
       - name: run pytest
         run: |
-          python -m pytest -n auto \
+          uv run -m pytest -n auto \
             --cov=demes --cov-report=term-missing --cov-report=xml -v tests
 
       - name: upload coverage report to codecov

.github/workflows/wheel.yaml

@@ -4,6 +4,8 @@ on:
   push:
     tags:
       - '*'
+  pull_request:
+    branches: [ main ]
   release:
     types: [published]
 
@@ -16,16 +18,18 @@ jobs:
         with:
           python-version: "3.12"
 
-      - name: install dependencies
-        run: |
-          pip install -r requirements_minimal_CI.txt
-          pip install build
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          activate-environment: true
+          version: "latest"
+          python-version: ${{ matrix.python }}
 
       - name: build wheel
-        run: python -m build
+        run: uv build
 
       - name: upload wheel
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v5
         with:
           name: wheel-and-sdist
           path: dist/
@@ -40,11 +44,11 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
 
     steps:
       - name: download wheel
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v6.0.0
         with:
           name: wheel-and-sdist
           path: dist/
@@ -71,7 +75,7 @@ jobs:
     needs: ['wheel_test']
     steps:
       - name: download wheel
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v6.0.0
         with:
           name: wheel-and-sdist
           path: dist/

demes/demes.py

@@ -1349,9 +1349,7 @@ class Graph:
     )
     metadata: collections.abc.Mapping = attr.ib(
         factory=dict,
-        validator=attr.validators.instance_of(
-            collections.abc.Mapping  # type: ignore[type-abstract]
-        ),
+        validator=attr.validators.instance_of(collections.abc.Mapping),
     )
     demes: List[Deme] = attr.ib(factory=list, init=False)
     migrations: List[AsymmetricMigration] = attr.ib(factory=list, init=False)

docs/development.md

@@ -11,37 +11,71 @@ of "pull requests" against our
 `Demes` aims to have minimal dependencies when used as a library by other
 projects. However, additional dependencies are required during development, as
 developers regularly run the test suite, build the documentation, and assess
-whether their code changes conform to style guidelines. The `requirements.txt`
+whether their code changes conform to style guidelines. The `pyproject.toml`
 file in the top-level folder lists all development dependencies, which can
-be installed using `pip`. In the following documentation, we assume the reader
+be installed using `uv`.
+In the following documentation, we assume the reader
 has cloned the source repository and installed the developer requirements as
 follows.
 
+To install `uv`, take one of the following paths:
+
+* Follow that project's [documentation](https://docs.astral.sh/uv/).
+* Use the package manager of your choice on your operating system.
+
+Then:
+
 ```sh
 # Clone the repository.
 git clone https://github.com/popsim-consortium/demes-python.git
 cd demes-python
-# Create a virtual environment for development.
-python -m venv venv
-# Activate the environment.
-source venv/bin/activate
-# Install the developer dependencies.
-pip install -r requirements.txt
-# Generate the version string from the most recent git tag/commit.
-python setup.py build
+# update the demes-spec submodule
+git submodule update --init
+# Use uv to install dependencies and build the demes package:
+uv sync --all-groups
 ```
 
-```{warning}
-Due to conflicting version dependencies, it may not be possible to install
-all developer requirements on older versions of Python. If you experience
-problems, please install the latest Python version (3.10 at time of writing).
+You may now do things like run the test suite:
+
+```sh
+uv run python -m pytest tests
 ```
 
+The `--all-groups` flag will install all build dependencies,
+runtime dependencies, and developer dependencies listed in
+`dependency-groups` in `pyproject.toml`.
+If you want to only install specific dependency groups, do
+so following the `uv` [documentation](https://docs.astral.sh/uv/).
+
 ```{note}
-Non-developer requirements are listed in the `install_requires` section
-of the ``setup.cfg`` file in the top-level folder of the sources.
+Non-developer requirements are listed in the `dependency-groups` section
+of the ``pyproject.toml`` file in the top-level folder of the sources.
+```
+
+## Updating `uv.lock` ("dependency management")
+
+If any of the following occur in `pyproject.toml`, then the contents of `uv.lock`
+may no longer by valid:
+
+* Changing a dependency version number pin
+* Adding/removing a dependency
+* Changing the supported range of Python versions
+* Changing the set of supported operating systems / platforms.
+
+To rebuild the lock file:
+
+```sh
+uv lock
 ```
 
+Then, commit the new lock file!
+
+### Updating individual packages in `uv.lock`
+
+One may occastionally need to update the locked version of a specific dependency.
+Currently, this happens via arguments to `uv lock`.
+Counsult the `uv` [documentation](https://docs.astral.sh/uv/) for details.
+
 ## Continuous integration (CI)
 
 After a pull request is submitted, an automated process known as
@@ -107,6 +141,12 @@ manually from the top-level folder of the sources.
 python -m pytest -v tests --cov=demes --cov-report=term-missing
 ```
 
+or
+
+```sh
+uv run python -m pytest -v tests --cov=demes --cov-report=term-missing
+```
+
 This will produce lots of output, indicating which tests passed, and which
 failed (if any). There may also be warnings. Any warnings that are triggered
 by code in `demes` (rather than third-party libraries), should be fixed.

pyproject.toml

@@ -1,3 +1,76 @@
 [build-system]
 # We need setup.cfg support, which setuptools introduced in 30.3.0.
 requires = ["setuptools>=30.3.0", "wheel", "setuptools_scm"]
+
+[project]
+name = "demes"
+authors = [
+    {name = "PopSim Consortium", email =  "krthornt@uci.edu"}
+]
+description = "tools for describing demographic models"
+readme = {file = "README.md", content-type = "text/markdown"}
+license = {text = "ISC"}
+classifiers = [
+    "Development Status :: 5 - Stable",
+    "License :: OSI Approved :: ISC License (ISCL)",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Bio-Informatics"
+]
+
+requires-python = ">=3.10"
+
+dynamic = ["version"]
+
+dependencies = [
+    "attrs>=20.3.0",
+    "ruamel.yaml>=0.15.78"
+]
+
+[project.urls]
+Repository = "https://github.com/popsim-consortium/demes-python"
+Documentation = "https://popsim-consortium.github.io/demes-docs/"
+Issues = "https://github.com/popsim-consortium/demes-python/issues"
+
+[project.scripts]
+demes = "demes.__main__:cli"
+
+[dependency-groups]
+test = [
+    "numpy",
+    "pytest==8.3.3",
+    "pytest-cov",
+    "pytest-xdist"
+]
+
+lint = [
+    "black==24.10.0",
+    "flake8==7.1.1",
+    "mypy==1.13.0",
+    {include-group = "test"},
+]
+
+docs = [
+    "demesdraw",
+    "jupyter-book==0.15.1",
+    "piccolo_theme",
+    "sphinx_issues",
+    "sphinxcontrib-programoutput",
+# Below here are hacks to make the docs
+# build until we can deal w/updating
+# jupyter-book
+    "ipython==8.29.0"
+]
+
+[tool.setuptools_scm]
+write_to = "demes/_version.py"
+
+# NOTE to future developers
+# mypy can be configured here, and perhaps
+# "should" be.
+# For now, we've left its config in setup.cfg
+#
+# flake8 cannot be configured here unless we
+# introduce a dependency on flake8-pyproject.