Move dependency management to uv

.github/workflows/docs.yaml

@@ -22,17 +22,25 @@ 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
+
+      # uv sync will handle this
+      # - name: Build package
+      #   run: |
+      #     # Generate the version string which appears in the docs.
+      #     python -m build --sdist
 
       - 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

@@ -41,17 +41,19 @@ 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: |

.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/

_setup.cfg

@@ -0,0 +1,88 @@
+[metadata]
+name = demes
+author = PopSim Consortium
+license = ISC
+# description = tools for describing demographic models"
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/popsim-consortium/demes-python
+classifiers =
+    Development Status :: 4 - Beta
+    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
+project_urls =
+    Documentation = https://popsim-consortium.github.io/demes-docs/
+    Source Code = https://github.com/popsim-consortium/demes-python/
+    Bug Tracker = https://github.com/popsim-consortium/demes-python/issues
+
+[options]
+packages = demes
+zip_safe = False  # https://mypy.readthedocs.io/en/latest/installed_packages.html
+include_package_data = True
+python_requires = >=3.7
+install_requires =
+    attrs >= 20.3.0  # for attr.asdict(value_serializer=...)
+    ruamel.yaml >= 0.15.78  # attempts to install earlier versions failed
+setup_requires =
+    setuptools
+    setuptools_scm
+
+[options.entry_points]
+console_scripts =
+    demes = demes.__main__:cli
+
+[flake8]
+extend-exclude = docs/_build
+# black-compatible settings
+max-line-length = 88
+extend-ignore = E203, W503
+# There's no way to ignore specific warnings in the files themselves.
+# "flake8: noqa: F401" on its own line will just ignore all warnings.
+per-file-ignores =
+    tests/test_import_visibility.py:F403,F405
+
+[mypy]
+files = demes, tests
+warn_unused_ignores = True
+show_error_codes = True
+# We support python 3.7, so should really be using 3.7 here,
+# but we're forced to set this higher because of positional-only
+# type annotations in numpy (which are only supported in >=3.8).
+python_version = 3.8
+
+[mypy-numpy.*]
+ignore_missing_imports = True
+
+[mypy-ruamel.*]
+ignore_missing_imports = True
+
+[tool.black]
+target_version = py37
+
+[tool:pytest]
+addopts = -n auto
+testpaths = tests
+
+[pylint.messages_control]
+disable =
+    chained-comparison,
+    fixme,
+    invalid-name,
+    missing-docstring,
+    missing-module-docstring,
+    superfluous-parens,
+    protected-access,
+    too-few-public-methods,
+    too-many-arguments,
+    too-many-branches,
+    too-many-instance-attributes,
+    too-many-lines,
+    too-many-locals,
+    too-many-nested-blocks,
+    too-many-statements,
+    unspecified-encoding,
+    unused-argument,

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)

pyproject.toml

@@ -1,3 +1,87 @@
 [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 :: 4 - Beta",
+    "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"
+
+# [tool.flake8]
+# extend-exclude = docs/_build
+# # black-compatible settings
+# max-line-length = 88
+# extend-ignore = E203, W503
+# # There's no way to ignore specific warnings in the files themselves.
+# # "flake8: noqa: F401" on its own line will just ignore all warnings.
+# per-file-ignores =
+#     tests/test_import_visibility.py:F403,F405
+
+# [tool.mypy]
+# files = ["demes", "tests"]
+# warn_unused_ignores = true
+# show_error_codes = true
+# # We support python 3.7, so should really be using 3.7 here,
+# # but we're forced to set this higher because of positional-only
+# # type annotations in numpy (which are only supported in >=3.8).
+# python_version = 3.8