From c60631e3492e12b02710195afc037713056386de Mon Sep 17 00:00:00 2001 From: Tom White Date: Mon, 4 Nov 2024 10:18:35 +0000 Subject: [PATCH] Drop Python 3.9 Try removing Windows cbgen restriction Fix quotes --- .github/workflows/benchmark.yml | 2 +- .github/workflows/build-gpu.yml | 2 +- .github/workflows/build.yml | 2 +- .github/workflows/docs.yml | 2 +- .github/workflows/wheels.yml | 6 +++--- .github/workflows/windows.yml | 2 +- .mergify.yml | 6 ++---- docs/getting_started.rst | 2 +- requirements-dev.txt | 3 +-- requirements-numpy2-dev.txt | 3 +-- setup.cfg | 6 ++---- 11 files changed, 15 insertions(+), 21 deletions(-) diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index 0c6068303..88cee817d 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -23,7 +23,7 @@ jobs: - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: - python-version: '3.9' + python-version: ["3.10"] - name: Install dependencies run: | sudo apt update -y diff --git a/.github/workflows/build-gpu.yml b/.github/workflows/build-gpu.yml index 8c0df28d0..2a8e4ce9f 100644 --- a/.github/workflows/build-gpu.yml +++ b/.github/workflows/build-gpu.yml @@ -17,7 +17,7 @@ jobs: shell: bash -l {0} strategy: matrix: - python-version: ["3.9", "3.10"] + python-version: ["3.10"] steps: - uses: actions/checkout@v2 diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index fac8f7718..f2bab52e5 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.9", "3.10", "3.11"] + python-version: ["3.10", "3.11"] steps: - uses: actions/checkout@v2 diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 33abd3b5e..858eb84cf 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -15,7 +15,7 @@ jobs: - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: - python-version: '3.10' + python-version: ["3.10"] - name: Install dependencies run: | sudo apt update -y diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml index 51ab96c5e..23d512471 100644 --- a/.github/workflows/wheels.yml +++ b/.github/workflows/wheels.yml @@ -17,7 +17,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [3.9] + python-version: ["3.10"] steps: - uses: actions/checkout@v2 @@ -46,7 +46,7 @@ jobs: matrix: # don't use macos-latest as it uses M1 which doesn't work os: [ubuntu-latest, macos-12] - python-version: ["3.9", "3.10", "3.11"] + python-version: ["3.10", "3.11"] runs-on: ${{ matrix.os }} steps: # checkout repo to subdirectory to get access to scripts @@ -76,7 +76,7 @@ jobs: needs: ['build'] strategy: matrix: - python-version: ["3.9"] + python-version: ["3.10"] steps: # checkout repo to subdirectory to get access to scripts - uses: actions/checkout@v2 diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml index 2df069474..5b2ca3313 100644 --- a/.github/workflows/windows.yml +++ b/.github/workflows/windows.yml @@ -14,7 +14,7 @@ jobs: runs-on: windows-latest strategy: matrix: - python-version: ["3.9"] + python-version: ["3.10"] steps: - uses: actions/checkout@v2 diff --git a/.mergify.yml b/.mergify.yml index b47535faf..30abd30fc 100644 --- a/.mergify.yml +++ b/.mergify.yml @@ -2,10 +2,9 @@ queue_rules: - name: default conditions: - base=main - - status-success=build (3.9) - status-success=build (3.10) - status-success=build (3.11) - - status-success=win_build (3.9) + - status-success=win_build (3.10) - approved-reviews-by=@sgkit-dev/committers - "#approved-reviews-by>=1" - label=auto-merge @@ -14,10 +13,9 @@ pull_request_rules: - name: automatic merge conditions: - base=main - - status-success=build (3.9) - status-success=build (3.10) - status-success=build (3.11) - - status-success=win_build (3.9) + - status-success=win_build (3.10) - approved-reviews-by=@sgkit-dev/committers - "#approved-reviews-by>=1" - label=auto-merge diff --git a/docs/getting_started.rst b/docs/getting_started.rst index d549af2df..7656264b6 100644 --- a/docs/getting_started.rst +++ b/docs/getting_started.rst @@ -10,7 +10,7 @@ Getting Started Installation ------------ -You can install sgkit with pip. Python 3.9, 3.10, or 3.11 is required:: +You can install sgkit with pip. Python 3.10, 3.11, or 3.12 is required:: $ pip install sgkit diff --git a/requirements-dev.txt b/requirements-dev.txt index 127bc9bed..d1df99192 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -12,8 +12,7 @@ scikit-learn partd bed-reader rechunker -cbgen < 1.0.5; platform_system != "Windows" -cbgen == 1.0.1; platform_system == "Windows" +cbgen < 1.0.5 bio2zarr; platform_system != "Windows" yarl matplotlib diff --git a/requirements-numpy2-dev.txt b/requirements-numpy2-dev.txt index 275c7d538..a408087b3 100644 --- a/requirements-numpy2-dev.txt +++ b/requirements-numpy2-dev.txt @@ -12,8 +12,7 @@ scikit-learn partd bed-reader rechunker -cbgen > 1.0.5; platform_system != "Windows" -cbgen == 1.0.1; platform_system == "Windows" +cbgen > 1.0.5 yarl matplotlib asv diff --git a/setup.cfg b/setup.cfg index 8bacbf5f7..9ae850220 100644 --- a/setup.cfg +++ b/setup.cfg @@ -16,7 +16,6 @@ classifiers = Intended Audience :: Science/Research 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 @@ -26,7 +25,7 @@ classifiers = packages = sgkit zip_safe = False # https://mypy.readthedocs.io/en/latest/installed_packages.html include_package_data = True -python_requires = >=3.9 +python_requires = >=3.10 install_requires = numpy < 2 xarray @@ -62,8 +61,7 @@ plink = bed-reader bgen = rechunker - cbgen < 1.0.5; platform_system != "Windows" - cbgen == 1.0.1; platform_system == "Windows" + cbgen < 1.0.5 [coverage:report] fail_under = 100