diff --git a/.azure-pipelines.yml b/.azure-pipelines.yml index 820005f39..f84d8da51 100644 --- a/.azure-pipelines.yml +++ b/.azure-pipelines.yml @@ -53,10 +53,6 @@ stages: repository: tiledb/tiledbvcf-py context: . test_cmd: -c "import tiledbvcf; print(tiledbvcf.version)" - # dask: - # dockerfile: docker/Dockerfile-dask-py - # repository: tiledb/tiledbvcf-dask - # context: . steps: - template: ci/build-images.yml diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml index 5367f0481..96752bd51 100644 --- a/.github/workflows/macos.yml +++ b/.github/workflows/macos.yml @@ -86,8 +86,6 @@ jobs: with: environment-name: ci create-args: tiledb - - name: Install dependencies - run: python -m pip install --prefer-binary pyarrow==10.0.1 - name: Build tiledbvcf-py env: LIBTILEDBVCF_PATH: "${{ github.workspace }}/dist" @@ -163,8 +161,6 @@ jobs: uses: actions/setup-python@v5 with: python-version: "3.11" - - name: Install dependencies - run: python -m pip install --prefer-binary pyarrow==10.0.1 - name: Build tiledbvcf-py run: cd apis/python && python -m pip install -v .[test] - name: Confirm linking diff --git a/apis/python/conda-env.yml b/apis/python/conda-env.yml deleted file mode 100644 index 9d632ab56..000000000 --- a/apis/python/conda-env.yml +++ /dev/null @@ -1,17 +0,0 @@ -name: tiledbvcf-py -channels: - - conda-forge -dependencies: - - numpy<2 - - python<3.12 # based on available tiledb-py wheels - - pybind11 - - pyarrow>=14.0.2 # for pyarrow security fix - - fsspec - - dask - - pip - - setuptools - - setuptools_scm - - setuptools_scm_git_archive - - pip: - - pytest - - pytest-runner diff --git a/apis/python/pyproject.toml b/apis/python/pyproject.toml index f984f995f..bc179fd86 100644 --- a/apis/python/pyproject.toml +++ b/apis/python/pyproject.toml @@ -29,18 +29,18 @@ dynamic = ["version"] description = "TileDB-VCF Python client" license = { text = "MIT" } authors = [] -requires-python = "~=3.8" +requires-python = "~=3.9" classifiers = [ "Development Status :: 4 - Beta", "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 3 :: Only", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", ] -dependencies = ["pandas", "pyarrow", "pyarrow-hotfix", "numpy<2"] +dependencies = ["pandas", "pyarrow>=14.0.1", "numpy"] [project.optional-dependencies] test = ["dask[distributed]", "pytest", "tiledb"] diff --git a/apis/python/src/tiledbvcf/__init__.py b/apis/python/src/tiledbvcf/__init__.py index 2e833e154..6a629c8ac 100644 --- a/apis/python/src/tiledbvcf/__init__.py +++ b/apis/python/src/tiledbvcf/__init__.py @@ -1,6 +1,5 @@ # Initialize pyarrow first. import pyarrow -import pyarrow_hotfix import ctypes import os diff --git a/ci/gha-win-env.yml b/ci/gha-win-env.yml index 8289dae4b..017ca5ae7 100644 --- a/ci/gha-win-env.yml +++ b/ci/gha-win-env.yml @@ -8,13 +8,12 @@ dependencies: - cmake - git - m2w64-htslib - - tiledb=2.15 + - tiledb=2.25 - vs2019_win-64 # build tiledbvcf-py - - numpy<2 - - pandas<2.0 - - pyarrow=9.0 - - pyarrow-hotfix + - numpy + - pandas + - pyarrow>=14.0.1 - pybind11 - python - rpdb diff --git a/ci/nightly/build-tiledb-py.sh b/ci/nightly/build-tiledb-py.sh index bbc988ace..d9e297458 100644 --- a/ci/nightly/build-tiledb-py.sh +++ b/ci/nightly/build-tiledb-py.sh @@ -19,7 +19,7 @@ fi export TILEDB_PATH=$GITHUB_WORKSPACE/install/ cd TileDB-Py/ -python -m pip install -Cskbuild.cmake.define.TILEDB_REMOVE_DEPRECATIONS=OFF -v . pyarrow==12 +python -m pip install -Cskbuild.cmake.define.TILEDB_REMOVE_DEPRECATIONS=OFF -v . # Can't run the import inside of the Git repo because Python automatically looks # for `./module/__init.py__` diff --git a/ci/nightly/build-tiledbvcf-py.sh b/ci/nightly/build-tiledbvcf-py.sh index ef50f77ce..54fc1af45 100644 --- a/ci/nightly/build-tiledbvcf-py.sh +++ b/ci/nightly/build-tiledbvcf-py.sh @@ -20,7 +20,7 @@ fi export LIBTILEDBVCF_PATH=$GITHUB_WORKSPACE/install/ cd TileDB-VCF/apis/python -python -m pip install .[test] pyarrow==12 +python -m pip install .[test] python -c "import tiledbvcf; print(tiledbvcf.version)" pytest diff --git a/docker/Dockerfile-dask-py b/docker/Dockerfile-dask-py deleted file mode 100644 index 9f61f9fa0..000000000 --- a/docker/Dockerfile-dask-py +++ /dev/null @@ -1,25 +0,0 @@ -FROM daskdev/dask:latest - -RUN conda config --prepend channels conda-forge - -# Install some dependencies -RUN apt-get update \ - && apt-get install --no-install-recommends -y \ - wget cmake git gcc g++ build-essential autoconf automake \ - libssl-dev libbz2-dev liblz4-dev libcurl4-openssl-dev \ - zlib1g-dev liblzma-dev \ - python3 python3-dev python3-venv \ - ninja-build \ - && rm -rf /var/lib/apt/lists/* - -# Copy the TileDB-VCF Python directory and build it. -WORKDIR /tmp/ -COPY . tiledbvcf -RUN cd tiledbvcf \ - && rm -rf libtiledbvcf/build dist \ - && cd apis/python \ - && conda env update -n base -f conda-env.yml \ - && pip install -v . \ - && cd /tmp \ - && rm -rf tiledbvcf \ - && conda clean -a -y