Add Python 3.13 and switch to uv package management

.github/workflows/test.yml

@@ -26,6 +26,7 @@ jobs:
         - "3.10"
         - "3.11"
         - "3.12"
+        - "3.13"
 
     steps:
     - uses: actions/checkout@v3
@@ -37,17 +38,25 @@ jobs:
       with:
         python-version: ${{matrix.python}}
 
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+
     - name: Set up dev environment
       run: |
-        pip install -e '.[test]'
+        uv sync --only-group test
+        uv pip install .
 
     - name: Run tests
-      run: python -m pytest --cov=seedbank --cov-report=xml tests
+      run: |
+        uv run --no-sync pytest --cov=seedbank --cov-report=xml tests
 
-    - name: Save test results
-      uses: lenskit/lkbuild/actions/save-test-results@main
+    - name: Upload logs
+      uses: actions/upload-artifact@v3
       with:
-        artifact-name: test-${{matrix.platform}}-py${{matrix.python}}
+        name: test-${{matrix.platform}}-py${{matrix.python}}
+        path: |
+          test*.log
+          coverage.xml
 
   test-extra:
     name: Test single extra ${{matrix.extra}}
@@ -71,17 +80,25 @@ jobs:
       with:
         python-version: 3.11
 
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+
     - name: Set up dev environment
       run: |
-        pip install -e '.[test,${{matrix.extra}}]'
+        uv sync --only-group test
+        uv pip install ".[${{matrix.extra}}]"
 
     - name: Run tests
-      run: python -m pytest --cov=seedbank --cov-report=xml tests
+      run: |
+        uv run --no-sync pytest --cov=seedbank --cov-report=xml tests
 
-    - name: Save test results
-      uses: lenskit/lkbuild/actions/save-test-results@main
+    - name: Upload logs
+      uses: actions/upload-artifact@v3
       with:
-        artifact-name: test-extra-${{matrix.extra}}
+        name: test-extra-${{matrix.extra}}
+        path: |
+          test*.log
+          coverage.xml
 
   report:
     name: Process test results
@@ -96,7 +113,6 @@ jobs:
     - name: Report test results
       uses: lenskit/lkbuild/actions/report-test-results@main
 
-
   sdist:
     name: Build and Publish Packages
     runs-on: ubuntu-latest
@@ -113,7 +129,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: "3.10"
+        python-version: "3.13"
 
     - name: Install Python deps
       run: pip install -U build twine

.gitignore

@@ -48,3 +48,5 @@ conda-lock.yml
 *~
 *.tmp
 .vs/
+
+_version.py

.readthedocs.yml

@@ -10,7 +10,6 @@ sphinx:
 
 python:
   install:
-  - method: pip
-    path: .
-    extra_requirements:
-    - doc
+    - requirements: doc-requirements.txt
+    - method: pip
+      path: .

doc-requirements.txt

@@ -0,0 +1,195 @@
+# This file was autogenerated by uv via the following command:
+#    uv export --format requirements-txt --only-group doc
+alabaster==1.0.0 \
+    --hash=sha256:c00dca57bca26fa62a6d7d0a9fcce65f3e026e9bfe33e9c538fd3fbb2144fd9e \
+    --hash=sha256:fc6786402dc3fcb2de3cabd5fe455a2db534b371124f1f21de8731783dec828b
+babel==2.16.0 \
+    --hash=sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316 \
+    --hash=sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b
+beautifulsoup4==4.12.3 \
+    --hash=sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051 \
+    --hash=sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed
+certifi==2024.8.30 \
+    --hash=sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9 \
+    --hash=sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8
+charset-normalizer==3.4.0 \
+    --hash=sha256:223217c3d4f82c3ac5e29032b3f1c2eb0fb591b72161f86d93f5719079dae93e \
+    --hash=sha256:4f9fc98dad6c2eaa32fc3af1417d95b5e3d08aff968df0cd320066def971f9a6 \
+    --hash=sha256:0de7b687289d3c1b3e8660d0741874abe7888100efe14bd0f9fd7141bcbda92b \
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+    --hash=sha256:70761cfe03c773ceb22aa2f671b4757976145175cdfca038c02654d061d6dcc6
+snowballstemmer==2.2.0 \
+    --hash=sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1 \
+    --hash=sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a
+soupsieve==2.6 \
+    --hash=sha256:e2e68417777af359ec65daac1057404a3c8a5455bb8abc36f1a9866ab1a51abb \
+    --hash=sha256:e72c4ff06e4fb6e4b5a9f0f55fe6e81514581fca1515028625d0f299c602ccc9
+sphinx==8.1.3 \
+    --hash=sha256:43c1911eecb0d3e161ad78611bc905d1ad0e523e4ddc202a58a821773dc4c927 \
+    --hash=sha256:09719015511837b76bf6e03e42eb7595ac8c2e41eeb9c29c5b755c6b677992a2
+sphinx-basic-ng==1.0.0b2 \
+    --hash=sha256:9ec55a47c90c8c002b5960c57492ec3021f5193cb26cebc2dc4ea226848651c9 \
+    --hash=sha256:eb09aedbabfb650607e9b4b68c9d240b90b1e1be221d6ad71d61c52e29f7932b
+sphinxcontrib-applehelp==2.0.0 \
+    --hash=sha256:2f29ef331735ce958efa4734873f084941970894c6090408b079c61b2e1c06d1 \
+    --hash=sha256:4cd3f0ec4ac5dd9c17ec65e9ab272c9b867ea77425228e68ecf08d6b28ddbdb5
+sphinxcontrib-devhelp==2.0.0 \
+    --hash=sha256:411f5d96d445d1d73bb5d52133377b4248ec79db5c793ce7dbe59e074b4dd1ad \
+    --hash=sha256:aefb8b83854e4b0998877524d1029fd3e6879210422ee3780459e28a1f03a8a2
+sphinxcontrib-htmlhelp==2.1.0 \
+    --hash=sha256:c9e2916ace8aad64cc13a0d233ee22317f2b9025b9cf3295249fa985cc7082e9 \
+    --hash=sha256:166759820b47002d22914d64a075ce08f4c46818e17cfc9470a9786b759b19f8
+sphinxcontrib-jsmath==1.0.1 \
+    --hash=sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8 \
+    --hash=sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178
+sphinxcontrib-qthelp==2.0.0 \
+    --hash=sha256:4fe7d0ac8fc171045be623aba3e2a8f613f8682731f9153bb2e40ece16b9bbab \
+    --hash=sha256:b18a828cdba941ccd6ee8445dbe72ffa3ef8cbe7505d8cd1fa0d42d3f2d5f3eb
+sphinxcontrib-serializinghtml==2.0.0 \
+    --hash=sha256:e9d912827f872c029017a53f0ef2180b327c3f7fd23c87229f7a8e8b70031d4d \
+    --hash=sha256:6e2cb0eef194e10c27ec0023bfeb25badbbb5868244cf5bc5bdc04e4464bf331
+sphinxext-opengraph==0.9.1 \
+    --hash=sha256:dd2868a1e7c9497977fbbf44cc0844a42af39ca65fe1bb0272518af225d06fc5 \
+    --hash=sha256:b3b230cc6a5b5189139df937f0d9c7b23c7c204493b22646273687969dcb760e
+tomli==2.1.0 ; python_full_version < '3.11' \
+    --hash=sha256:3f646cae2aec94e17d04973e4249548320197cfabdf130015d023de4b74d8ab8 \
+    --hash=sha256:a5c57c3d1c56f5ccdf89f6523458f60ef716e210fc47c4cfb188c5ba473e0391
+urllib3==2.2.3 \
+    --hash=sha256:e7d814a81dad81e6caf2ec9fdedb284ecc9c73076b62654547cc64ccdcae26e9 \
+    --hash=sha256:ca899ca043dcb1bafa3e262d73aa25c465bfb49e0bd9dd5d59f1d0acba2f8fac

pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
-requires = ["setuptools>=64", "setuptools_scm>=8"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling ~=1.0", "hatch-vcs ~=0.4.0"]
+build-backend = "hatchling.build"
 
 [project]
 name = "seedbank"
@@ -26,17 +26,26 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
+numba = ["numba >=0.54"]
+torch = ["torch"]
+cupy = ["cupy"]
+cuda11x = ["cupy-cuda11x"]
+tf = ["tensorflow >=2,<3"]
+jax = ["jax[cpu]>=0.4.16"]
+
+[project.urls]
+Homepage = "https://seedbank.lenksit.org"
+GitHub = "https://github.com/lenskit/seedbank"
+
+[dependency-groups]
 dev = [
-  "setuptools>=64",
-  "setuptools_scm>=8",
   "wheel",
-  "build ==1.*",       # p2c: -s python-build==1
+  "build ~=1.0",
   "ruff >= 0.2",
   "pyright",
   "copier ==9.*",
-  "unbeheader ~= 1.3", # p2c: -p
+  "unbeheader ~= 1.3",
   "ipython",
-  "pyproject2conda ",
   "sphinx-autobuild",
 ]
 test = [
@@ -52,28 +61,20 @@ doc = [
   "sphinxext-opengraph >= 0.5",
   "furo",
 ]
-numba = ["numba"]
-torch = ["torch"]
-cupy = ["cupy"]
-cuda11x = ["cupy-cuda11x"]
-tf = ["tensorflow >=2,<3"]
-jax = ["jax[cpu]>=0.4.16"]
-
-[project.urls]
-Homepage = "https://seedbank.lenksit.org"
-GitHub = "https://github.com/lenskit/seedbank"
 
 # configure build tools
-[tool.setuptools.packages.find]
-include = ["seedbank*"]
+[tool.hatch.build.targets.wheel]
+packages = ["seedbank"]
+
+[tool.hatch.version]
+source = "vcs"
+raw-options = { version_scheme = "guess-next-dev" }
 
-[tool.setuptools_scm]
-version_scheme = "guess-next-dev"
+[tool.hatch.build.hooks.vcs]
+version-file = "seedbank/_version.py"
 
-# settings for generating conda environments for dev & CI, when needed
-[tool.pyproject2conda]
-channels = ["conda-forge"]
-deps = ["just"]
+[tool.uv]
+default-groups = ["dev", "test", "doc"]
 
 [tool.coverage.run]
 relative_files = true

seedbank/__init__.py

@@ -13,7 +13,6 @@
 
 import logging
 from importlib import import_module
-from importlib.metadata import PackageNotFoundError, version
 from types import ModuleType
 
 import numpy as np
@@ -24,8 +23,8 @@
 from seedbank._state import SeedState
 
 try:
-    __version__ = version("seedbank")
-except PackageNotFoundError:
+    from ._version import version as __version__  # noqa: F401
+except ImportError:
     # package is not installed
     pass