Pyproject reqs

Author: benjeffery

.github/workflows/docs.yml

@@ -8,8 +8,7 @@ on:
   merge_group:
 jobs:
   Docs:
-    uses: tskit-dev/.github/.github/workflows/docs-build-template.yml@main
+    uses: tskit-dev/.github/.github/workflows/docs-build-template.yml@v1
     with:
-      requirements-path: requirements/CI-docs/requirements.txt
       additional-setup: sudo apt-get install -y tabix
-      make-command: make all
+      make-command: make all

.github/workflows/tests.yml

@@ -20,7 +20,6 @@ jobs:
         with:
           python-version: '3.10'
       - name: install clang-format
-        if: steps.clang_format.outputs.cache-hit != 'true'
         run: |
           sudo pip install clang-format==6.0.1
           sudo ln -s /usr/local/bin/clang-format /usr/local/bin/clang-format-6.0
@@ -48,70 +47,68 @@ jobs:
         with:
           submodules: true
 
-      - name: Cache conda and dependancies
-        id: cache
-        uses: actions/cache@v4.2.2
-        with:
-          path: ${{ env.CONDA }}/envs
-          key: ${{ runner.os }}-${{ runner.arch }}-${{ matrix.python}}-conda-v5-${{ hashFiles('requirements/CI-tests-conda/requirements.txt')}}
-
-      - name: Install Miniconda with Mamba
+      - name: Install conda (needed for msprime on Windows)
         uses: conda-incubator/setup-miniconda@v3.1.1
-        if: steps.cache.outputs.cache-hit != 'true'
         with:
           activate-environment: anaconda-client-env
           python-version: ${{ matrix.python }}
           channels: conda-forge
-#          channel-priority: strict
           auto-update-conda: true
-#          mamba-version: "*"
-#          use-mamba: true
 
       - name: Fix windows .profile
-        if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
+        if: matrix.os == 'windows-latest'
         run: |
           cp ~/.bash_profile ~/.profile
 
       # Work around weird issues on OSX possibly caused by mixed compilers
       # https://github.com/tskit-dev/tsinfer/issues/376
       - name: Install compiler from conda
-        if: steps.cache.outputs.cache-hit != 'true'
         shell: bash -l {0} #We need a login shell to get conda
         run: conda install --yes c-compiler
 
       - name: Install conda deps
-        if: steps.cache.outputs.cache-hit != 'true'
         shell: bash -l {0} #We need a login shell to get conda
-        run: conda install --yes --file=requirements/CI-tests-conda/requirements.txt
+        run: conda install msprime
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          version: "0.8.15"
 
       - name: Install cyvcf2 #Fails if done via conda due to no windows support.
-        if: steps.cache.outputs.cache-hit != 'true' && matrix.os != 'windows-latest'
+        if: matrix.os != 'windows-latest'
         run: |
           source ~/.profile
           conda activate anaconda-client-env
           #Install these by pip so we don't pull in cbgen with conda as it isn't available on 3.12
-          pip install sgkit==0.9.0 cyvcf2==0.31.1 yarl==1.9.4 aiohttp==3.9.5 requests==2.32.3 
+          uv pip install sgkit==0.9.0 cyvcf2==0.31.1 yarl==1.9.4 aiohttp==3.9.5 requests==2.32.3 
 
       - name: Install sgkit only on windows
-        if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
+        if: matrix.os == 'windows-latest'
         run: |
           source ~/.profile
           conda activate anaconda-client-env
           #Install these by pip so we don't pull in cbgen with conda as it isn't available on 3.12
-          pip install sgkit==0.9.0 
+          uv pip install sgkit==0.9.0 
+
+      - name: Install pip deps
+        run: |
+          source ~/.profile
+          conda activate anaconda-client-env
+          uv pip install -r pyproject.toml --extra test
 
       - name: Build module
         run: |
           source ~/.profile
           conda activate anaconda-client-env
           # Use numpy2 to build the module
-          pip install "numpy>=2"
+          uv pip install "numpy>=2"
           python setup.py build_ext --inplace
 
       - name: Run tests
         run: |
           source ~/.profile
           conda activate anaconda-client-env
           # Test with numpy<2 for numba
-          pip install "numpy<2"
+          uv pip install "numpy<2"
           python -m pytest -xv

pyproject.toml

@@ -54,7 +54,7 @@ dependencies = [
     "humanize",
     "daiquiri",
     "tskit>=0.5.3",
-    "numcodecs>=0.6",
+    "numcodecs>=0.6,<0.15.1", #Pinned due to https://github.com/zarr-developers/numcodecs/issues/733
     "zarr>=2.2,!=2.11.0,!=2.11.1,!=2.11.2,<3",
     "lmdb",
     "sortedcontainers",
@@ -73,6 +73,77 @@ Changelog = "https://tskit.dev/tsinfer/docs/stable/CHANGELOG.html"
 [project.scripts]
 tsinfer = "tsinfer.__main__:main"
 
+[project.optional-dependencies]
+test = [
+    "build==1.2.2.post1",
+    "colorama==0.4.6",
+    "daiquiri==3.2.5.1",
+    "humanize==4.12.1",
+    "lmdb==1.6.2",
+    "matplotlib==3.9.4",
+    "meson==1.7.0",
+    "msprime==1.3.3",
+    "pytest==8.3.5",
+    "pytest-cov==6.0.0",
+    "seaborn==0.13.2",
+    "sgkit[vcf]==0.9.0; sys_platform != 'win32'",
+    "tskit==0.6.0",
+    "tqdm==4.67.1",
+    "twine==6.1.0"
+]
+
+docs = [
+    "jupyter-book==1.0.4.post1",
+    "sphinx-issues==5.0.0",
+    "sphinx-argparse==0.5.2",
+    "humanize==4.12.1",
+    "lmdb==1.6.2",
+    "tqdm==4.67.1",
+    "daiquiri==3.3.0",
+    "msprime==1.3.3",
+    "sgkit[vcf]==0.9.0",
+    "ipywidgets==8.1.5",
+    "Bio==1.7.1",
+    "bio2zarr==0.1.4",
+    "sphinx-book-theme",
+    "pyfaidx==0.8.1.3"
+]
+
+dev = [
+    "attrs",
+    "codecov",
+    "coverage",
+    "flake8",
+    "six",
+    "tqdm",
+    "humanize",
+    "daiquiri",
+    "msprime>=1.0.0",
+    "tskit>=0.5.3",
+    "lmdb",
+    "pre-commit",
+    "pytest",
+    "pytest-coverage",
+    "h5py",
+    "sortedcontainers",
+    "python-prctl; sys_platform == 'linux'",
+    "numa; sys_platform == 'linux'",
+    "sphinx",
+    "sphinx-argparse",
+    "sphinx_rtd_theme",
+    "setuptools>=45",
+    "setuptools_scm",
+    "matplotlib",
+    "seaborn",
+    "colorama",
+    "sgkit[vcf]",
+    "sphinx-book-theme",
+    "jupyter-book",
+    "sphinx-issues",
+    "ipywidgets",
+    "pyfaidx"
+]
+
 [tool.setuptools]
 packages = ["tsinfer"]
 include-package-data = true