Merge pull request #936 from benjeffery/numpy2

Upgrade actions, build with numpy2
tskit-dev · Jul 12, 2024 · 8c636ab · 8c636ab
2 parents e455221 + dc61b6a
commit 8c636ab
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Showing 14 changed files with 167 additions and 90 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -41,6 +41,30 @@ jobs:
             # Write out the status for debugging purposes. Are we checked out at tags?
             git submodule status --recursive
 
+      - run:
+          name: Build the distribution tarball.
+          command: |
+            python -m build --sdist
+            python setup.py check
+            python -m twine check dist/*.tar.gz --strict
+            rm dist/*
+            python -m build
+
+      - run:
+          name: Install from the distribution tarball
+          command: |
+            python -m venv venv
+            source venv/bin/activate
+            pip install dist/*.tar.gz
+            python -c 'import tsinfer; print(tsinfer.__version__)'
+
+            #Also check the wheel
+            pip uninstall --yes tsinfer
+            pip install dist/*.whl
+            python -c 'import tsinfer; print(tsinfer.__version__)'
+            deactivate
+            rm -rf venv
+
       - run:
           name: Compile Python
           command: |
@@ -101,25 +125,4 @@ jobs:
           command: |
             ninja -C build-clang test
 
-      - run:
-          name: Build the distribution tarball.
-          command: |
-            python setup.py sdist
-            python setup.py check
-            python -m twine check dist/*.tar.gz --strict
-            rm dist/*
-            python -m build
-
-      - run:
-          name: Install from the distribution tarball
-          command: |
-            python -m venv venv
-            source venv/bin/activate
-            pip install dist/*.tar.gz
-            python -c 'import tsinfer; print(tsinfer.__version__)'
-
-            #Also check the wheel
-            pip uninstall --yes tsinfer
-            pip install dist/*.whl
-            python -c 'import tsinfer; print(tsinfer.__version__)'
 
diff --git a/.github/workflows/docker/shared.env b/.github/workflows/docker/shared.env
@@ -1,6 +1,6 @@
 PYTHON_VERSIONS=(
+    cp312-cp312
+    cp311-cp311
     cp310-cp310
     cp39-cp39
-    cp38-cp38
-    cp37-cp37m
 )
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -19,23 +19,23 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.11.0
+        uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
             submodules: true
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
 
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         id: venv-cache
         with:
           path: venv
-          key: docs-venv-v5-${{ hashFiles('requirements/CI-docs/requirements.txt') }}
+          key: docs-venv-v6-${{ hashFiles('requirements/CI-docs/requirements.txt') }}
 
       - name: Create venv and install deps (one by one to avoid conflict errors)
         if: steps.venv-cache.outputs.cache-hit != 'true'

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -11,11 +11,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.11.0
+        uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
       - name: install clang-format
@@ -31,28 +31,28 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: [ 3.9, "3.10" ]
+        python: [ 3.9, "3.12" ]
         os:  [ macos-latest, ubuntu-latest, windows-latest ]
     defaults:
       run:
         shell: bash
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.11.0
+        uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
 
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: true
 
       - name: Cache conda and dependancies
         id: cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.CONDA }}/envs
-          key: ${{ runner.os }}-${{ runner.arch }}-${{ matrix.python}}-conda-v1-${{ hashFiles('requirements/CI-tests-conda/requirements.txt')}}
+          key: ${{ runner.os }}-${{ runner.arch }}-${{ matrix.python}}-conda-v5-${{ hashFiles('requirements/CI-tests-conda/requirements.txt')}}
 
       - name: Install Miniconda with Mamba
         uses: conda-incubator/setup-miniconda@v3
@@ -61,10 +61,10 @@ jobs:
           activate-environment: anaconda-client-env
           python-version: ${{ matrix.python }}
           channels: conda-forge
-          channel-priority: strict
+#          channel-priority: strict
           auto-update-conda: true
-          mamba-version: "*"
-          use-mamba: true
+#          mamba-version: "*"
+#          use-mamba: true
 
       - name: Fix windows .profile
         if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
@@ -76,29 +76,41 @@ jobs:
       - 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: mamba install --yes c-compiler
+        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: mamba install --yes --file=requirements/CI-tests-conda/requirements.txt
+        run: conda install --yes --file=requirements/CI-tests-conda/requirements.txt
 
       - name: Install cyvcf2 #Fails if done via conda due to no windows support.
         if: steps.cache.outputs.cache-hit != 'true' && matrix.os != 'windows-latest'
         run: |
           source ~/.profile
           conda activate anaconda-client-env
-          pip install cyvcf2==0.30.18
+          #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 
 
+      - name: Install sgkit only on windows
+        if: steps.cache.outputs.cache-hit != 'true' && 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 
 
       - name: Build module
         run: |
           source ~/.profile
           conda activate anaconda-client-env
+          # Use numpy2 to build the module
+          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"
           python -m pytest -xv
diff --git a/.mergify.yml b/.mergify.yml
@@ -5,11 +5,11 @@ queue_rules:
       - "#changes-requested-reviews-by=0"
       - status-success=Lint
       - status-success=Python (3.9, macos-latest)
-      - status-success=Python (3.10, macos-latest)
+      - status-success=Python (3.12, macos-latest)
       - status-success=Python (3.9, ubuntu-latest)
-      - status-success=Python (3.10, ubuntu-latest)
+      - status-success=Python (3.12, ubuntu-latest)
       - status-success=Python (3.9, windows-latest)
-      - status-success=Python (3.10, windows-latest)
+      - status-success=Python (3.12, windows-latest)
       - "status-success=ci/circleci: build"
 
 pull_request_rules:
@@ -22,11 +22,11 @@ pull_request_rules:
       - label=AUTOMERGE-REQUESTED
       - status-success=Lint
       - status-success=Python (3.9, macos-latest)
-      - status-success=Python (3.10, macos-latest)
+      - status-success=Python (3.12, macos-latest)
       - status-success=Python (3.9, ubuntu-latest)
-      - status-success=Python (3.10, ubuntu-latest)
+      - status-success=Python (3.12, ubuntu-latest)
       - status-success=Python (3.9, windows-latest)
-      - status-success=Python (3.10, windows-latest)
+      - status-success=Python (3.12, windows-latest)
       - "status-success=ci/circleci: build"
     actions:
       queue:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -22,7 +22,7 @@ repos:
     rev: v3.2.2
     hooks:
       - id: pyupgrade
-        args: [ --py3-plus, --py37-plus ]
+        args: [ --py3-plus, --py39-plus ]
   - repo: https://github.com/psf/black
     rev: 22.10.0
     hooks:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,8 @@ In development
 - Remove the `uuid` field from SampleData. SampleData equality is now purely based
   on data. ({pr}`748`, {user}`benjeffery`)
 
+- tsinfer now requires Python 3.9 or later
+
 **Performance improvements**
 
 - Reduce memory usage when running `match_samples` against large cohorts

diff --git a/pyproject.toml b/pyproject.toml
@@ -3,10 +3,79 @@ requires = [
     "setuptools>=42",
     "setuptools_scm",
     "wheel",
-    "oldest-supported-numpy"
+    "numpy>=2"
 ]
-
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
-write_to = "tsinfer/_version.py"
+write_to = "tsinfer/_version.py"
+
+[project]
+name = "tsinfer"
+dynamic = ["version"]
+authors = [
+    {name = "Tskit Developers", email = "[email protected]"},
+]
+description = "Infer tree sequences from genetic variation data."
+readme = "README.md"
+requires-python = ">=3.9"
+license = {text = "GNU GPLv3+"}
+classifiers = [
+    "Programming Language :: C",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3 :: Only",
+    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+    "Development Status :: 3 - Alpha",
+    "Environment :: Other Environment",
+    "Intended Audience :: Science/Research",
+    "Operating System :: POSIX",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+keywords = [
+    "population genetics",
+    "tree sequence",
+    "ancestral recombination graph",
+    "evolutionary tree",
+    "inference",
+    "tsinfer",
+]
+dependencies = [
+    "numpy>=1.23.5",
+    "six",
+    "tqdm",
+    "humanize",
+    "daiquiri",
+    "tskit>=0.5.3",
+    "numcodecs>=0.6",
+    "zarr>=2.2,!=2.11.0,!=2.11.1,!=2.11.2,<3",
+    "lmdb",
+    "sortedcontainers",
+    "attrs>=19.2.0",
+    "dask[array]",
+    "numba",
+]
+
+[project.urls]
+Homepage = "https://tskit.dev/tsinfer"
+Documentation = "https://tskit.dev/tsinfer/docs/stable"
+Changelog = "https://tskit.dev/tsinfer/docs/stable/CHANGELOG.html"
+"Bug Tracker" = "https://github.com/tskit-dev/tsinfer/issues"
+"Source Code" = "https://github.com/tskit-dev/tsinfer/"
+
+[project.scripts]
+tsinfer = "tsinfer.__main__:main"
+
+[tool.setuptools]
+packages = ["tsinfer"]
+include-package-data = true
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
diff --git a/requirements/CI-docs/requirements.txt b/requirements/CI-docs/requirements.txt
@@ -1,11 +1,11 @@
-jupyter-book==0.15.1
-sphinx-issues==3.0.1
+jupyter-book==1.0.2
+sphinx-issues==4.1.0
 sphinx-argparse==0.4.0
-humanize==4.7.0
-lmdb==1.4.1
-tqdm==4.65.0
-daiquiri==3.2.1
-msprime==1.2.0
-sgkit[vcf]==0.7.0
-ipywidgets==8.1.0
+humanize==4.10.0
+lmdb==1.5.1
+tqdm==4.66.4
+daiquiri==3.2.5.1
+msprime==1.3.2
+sgkit[vcf]==0.9.0
+ipywidgets==8.1.3
 sphinx-book-theme #Unpinned to allow easy updating.
diff --git a/requirements/CI-tests-complete/requirements.txt b/requirements/CI-tests-complete/requirements.txt
@@ -1,14 +1,15 @@
 build==1.2.1
 colorama==0.4.6
-daiquiri==3.0.0
-humanize==4.9.0
-lmdb==1.4.1
-matplotlib==3.8.4
-meson==1.4.0
-msprime==1.3.1
-pytest==8.2.0
+daiquiri==3.2.5.1
+humanize==4.10.0
+lmdb==1.5.1
+matplotlib==3.9.1
+meson==1.5.0
+msprime==1.3.2
+pytest==8.2.2
 pytest-cov==5.0.0
 seaborn==0.13.2
-sgkit[vcf]==0.8.0
+sgkit[vcf]==0.9.0
+tskit==0.5.8
 tqdm==4.66.4
-twine==5.0.0
+twine==5.1.1
diff --git a/requirements/CI-tests-conda/requirements.txt b/requirements/CI-tests-conda/requirements.txt
@@ -1,10 +1,10 @@
-pytest==8.2.0
-msprime==1.3.1
-humanize==4.9.0
-python-lmdb==1.3.0 
+pytest==8.2.2
+msprime==1.3.2
+humanize==4.10.0
+python-lmdb==1.4.1
 tqdm==4.66.4
 daiquiri==3.0.0
-sgkit[vcf]==0.8.0
-matplotlib==3.8.4
+matplotlib==3.9.1
 seaborn==0.13.2
 colorama==0.4.6
+tskit==0.5.8