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Merge pull request #82 from benjeffery/numpy2
Update actions infra, pin zarr
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| PYTHON_VERSIONS=( | ||
| cp312-cp312 | ||
| cp311-cp311 | ||
| cp310-cp310 | ||
| cp39-cp39 | ||
| cp38-cp38 | ||
| ) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -11,48 +11,36 @@ jobs: | |
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Cancel Previous Runs | ||
| uses: styfle/[email protected].0 | ||
| uses: styfle/[email protected].1 | ||
| with: | ||
| access_token: ${{ github.token }} | ||
| - uses: actions/checkout@v4 | ||
| - uses: actions/setup-python@v4 | ||
| - uses: actions/setup-python@v5 | ||
| - uses: pre-commit/[email protected] | ||
|
|
||
| test: | ||
| name: Python | ||
| runs-on: ${{ matrix.os }} | ||
| strategy: | ||
| matrix: | ||
| python: [ 3.8, 3.11 ] | ||
| 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@0.6.0 | ||
| uses: styfle/cancel-workflow-action@0.12.1 | ||
| with: | ||
| access_token: ${{ github.token }} | ||
|
|
||
| - name: Checkout | ||
| uses: actions/checkout@v2 | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| submodules: true | ||
|
|
||
| - name: Cache conda and dependancies | ||
| id: cache | ||
| uses: actions/cache@v2 | ||
| with: | ||
| path: | | ||
| c:\Miniconda\envs\anaconda-client-env | ||
| /usr/share/miniconda/envs/anaconda-client-env | ||
| ~/osx-conda | ||
| ~/.profile | ||
| key: ${{ runner.os }}-${{ matrix.python}}-conda-v10-${{ hashFiles('requirements/CI-tests-conda.txt') }} | ||
|
|
||
| - name: Install Conda | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| if: steps.cache.outputs.cache-hit != 'true' | ||
| uses: conda-incubator/setup-miniconda@v3 | ||
| with: | ||
| activate-environment: anaconda-client-env | ||
| python-version: ${{ matrix.python }} | ||
|
|
@@ -66,22 +54,9 @@ jobs: | |
| cp ~/.bash_profile ~/.profile | ||
| - 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 mamba | ||
| mamba install --yes --file=requirements/CI-tests-conda.txt | ||
| - name: Fix OSX Cache Write #OSX Won't let the cache restore due to file perms | ||
| if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'macos-latest' | ||
| run: | | ||
| cp -r /usr/local/miniconda/envs/anaconda-client-env ~/osx-conda | ||
| - name: Fix OSX Cache Restore | ||
| if: steps.cache.outputs.cache-hit == 'true' && matrix.os == 'macos-latest' | ||
| run: | | ||
| mkdir -p /usr/local/miniconda/envs | ||
| sudo cp -r ~/osx-conda /usr/local/miniconda/envs/anaconda-client-env | ||
| conda install --yes --file=requirements/CI-tests-conda.txt | ||
| - name: Run tests | ||
| run: | | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| [build-system] | ||
| requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"] | ||
| build-backend = "setuptools.build_meta" | ||
|
|
||
| [project] | ||
| name = "tszip" | ||
| authors = [ | ||
| {name = "Tskit Developers", email = "[email protected]"}, | ||
| ] | ||
| description = "Compression utilities for tree sequences" | ||
| readme = "README.md" | ||
| requires-python = ">=3.8" | ||
| license = {text = "MIT"} | ||
| classifiers = [ | ||
| "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", | ||
| "Development Status :: 5 - Production/Stable", | ||
| "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", | ||
| "License :: OSI Approved :: MIT License", | ||
| ] | ||
| keywords = ["tree sequence", "tskit"] | ||
| dependencies = [ | ||
| "numpy", | ||
| "humanize", | ||
| "tskit>=0.3.3", | ||
| "numcodecs>=0.6.4", | ||
| "zarr<3", | ||
| ] | ||
| dynamic = ["version"] | ||
|
|
||
| [project.urls] | ||
| Homepage = "http://pypi.python.org/pypi/tszip" | ||
| Documentation = "https://tszip.readthedocs.io/en/latest/" | ||
| Changelog = "https://tszip.readthedocs.io/en/latest/changelog.html" | ||
| "Bug Tracker" = "https://github.com/tskit-dev/tszip/issues" | ||
| GitHub = "https://github.com/tskit-dev/tszip/" | ||
|
|
||
| [project.scripts] | ||
| tszip = "tszip.cli:tszip_main" | ||
| tsunzip = "tszip.cli:tsunzip_main" | ||
|
|
||
| [tool.setuptools] | ||
| packages = ["tszip"] | ||
| include-package-data = true | ||
|
|
||
| [tool.setuptools_scm] | ||
| write_to = "tszip/_version.py" | ||
|
|
||
| [tool.pytest.ini_options] | ||
| addopts = "-n 4" | ||
| testpaths = ["tests"] |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,8 @@ | ||
| humanize==4.8.0 | ||
| jupyter-book==0.15.1 | ||
| humanize==4.10.0 | ||
| jupyter-book==1.0.2 | ||
| numcodecs==0.12.1 | ||
| sphinx-issues==3.0.1 | ||
| sphinx-issues==4.1.0 | ||
| sphinx-argparse==0.4.0 | ||
| setuptools_scm==8.0.4 | ||
| tskit==0.5.6 | ||
| zarr==2.16.1 | ||
| setuptools_scm==8.1.0 | ||
| tskit==0.5.8 | ||
| zarr==2.18.2 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,8 @@ | ||
| humanize==4.8.0 | ||
| h5py==3.7.0 | ||
| msprime==1.2.0 | ||
| pytest==7.4.2 | ||
| pytest-cov==4.1.0 | ||
| pytest-xdist==3.3.1 | ||
| tskit==0.5.6 | ||
| zarr==2.16.1 | ||
| humanize==4.10.0 | ||
| h5py==3.11.0 | ||
| msprime==1.3.2 | ||
| pytest==8.2.2 | ||
| pytest-cov==5.0.0 | ||
| pytest-xdist==3.6.1 | ||
| tskit==0.5.8 | ||
| zarr==2.18.2 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -12,6 +12,6 @@ sphinx_rtd_theme | |
| sphinx-issues | ||
| setuptools_scm | ||
| tskit | ||
| zarr | ||
| zarr<3 | ||
| msprime | ||
| humanize | ||
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