From a4dfc191153dbbe31d88a05121962ebca2e203dd Mon Sep 17 00:00:00 2001 From: rlanglois Date: Wed, 22 Nov 2023 06:16:00 -0800 Subject: [PATCH 1/4] Issue-330: Add Python 3.11 Support Resolves #330 --- .github/workflows/python.yml | 8 ++++---- docs/src/changes.md | 6 ++++++ docs/src/index.md | 2 +- docs/src/install.md | 2 +- 4 files changed, 12 insertions(+), 6 deletions(-) diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml index a4bf063e5..344892f2d 100644 --- a/.github/workflows/python.yml +++ b/.github/workflows/python.yml @@ -15,8 +15,8 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - os: [ubuntu-latest, windows-2019, macOS-latest] # '3.5', - pyver: ['2.7', '3.6', '3.7', '3.8', '3.9', '3.10'] #, '3.11-dev' + os: [ubuntu-latest, windows-2019, macOS-latest] + pyver: ['2.7', '3.6', '3.7', '3.8', '3.9', '3.10', '3.11'] steps: - uses: actions/checkout@v3 @@ -36,7 +36,7 @@ jobs: git --version - name: Package Python 3.9 and earlier - if: matrix.os == 'ubuntu-latest' && matrix.pyver != '3.10' && matrix.pyver != '3.11-dev' + if: matrix.os == 'ubuntu-latest' && matrix.pyver != '3.10' && matrix.pyver != '3.11' run: docker run --rm -v ${{github.workspace}}/:/io ezralanglois/interop sh /io/tools/package.sh /io /io/dist travis OFF - name: Package Python 3.10 @@ -44,7 +44,7 @@ jobs: run: docker run --rm -v ${{github.workspace}}/:/io ezralanglois/interop_centos7 sh /io/tools/package.sh /io /io/dist travis OFF Release cp310-cp310 - name: Package Python 3.11 - if: matrix.os == 'ubuntu-latest' && matrix.pyver == '3.11-dev' + if: matrix.os == 'ubuntu-latest' && matrix.pyver == '3.11' run: docker run --rm -v ${{github.workspace}}/:/io ezralanglois/interop_centos7 sh /io/tools/package.sh /io /io/dist travis OFF Release cp311-cp311 - name: Windows Package Python diff --git a/docs/src/changes.md b/docs/src/changes.md index 66db08a34..2d315b719 100644 --- a/docs/src/changes.md +++ b/docs/src/changes.md @@ -1,5 +1,11 @@ # Changes {#changes} +## v1.3.0 + +| Date | Description | +|------------|------------------------------------| +| 2023-11-22 | Issue-330: Add Python 3.11 Support | + ## v1.2.4 | Date | Description | diff --git a/docs/src/index.md b/docs/src/index.md index de5a92303..4ea4736b5 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -10,7 +10,7 @@ metric files are produced after a run during secondary analysis (index metrics) the original data (collapsed quality scores). *** -> We now support an interface to Python 2.7 (UCS-4), 3.6, 3.7, 3.8, 3.9 and 3.10 (see contents below) +> We now support an interface to Python 3.6 to 3.11 (see contents below) *** Compatibility diff --git a/docs/src/install.md b/docs/src/install.md index 3f4eb9387..15fd680bf 100644 --- a/docs/src/install.md +++ b/docs/src/install.md @@ -35,7 +35,7 @@ For Pythons users, a Wheel package is available on Github Releases or PyPI: $ pip install interop ~~~~~~~~~~~~~ -Supported versions for binary distribution: 2.7 (UCS-4), 3.6, 3.7, 3.8, 3.9 and 3.10. +Supported versions for binary distribution: 3.6 to 3.11. Test the installation From b6bedb5b44bd72e99215e8cc1ad1b6525f63adeb Mon Sep 17 00:00:00 2001 From: rlanglois Date: Wed, 22 Nov 2023 06:23:36 -0800 Subject: [PATCH 2/4] Update docs --- README.md | 4 ++-- docs/src/install.md | 2 +- docs/src/python_binding.md | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 8d0e7469c..bb8dff218 100644 --- a/README.md +++ b/README.md @@ -10,8 +10,8 @@ Illumina sequencers including **NextSeq 1k/2k** and NovaSeqX. These libraries ar with one exception: GA systems have been excluded. *** -> We now support an interface to Python 2.7 (UCS-4) and 3.6-3.10 -> Note that 3.10 is CentOS 7 or later while earlier versions support Centos 5 or later +> We now support an interface to Python 2.7 (UCS-4) and 3.6-3.11 +> Note that 3.10 and 3.11 are CentOS 7 or later while earlier versions support Centos 5 or later > Note: dumptext has been deprecated in favor of imaging_table and will be removed in the next version *** diff --git a/docs/src/install.md b/docs/src/install.md index 15fd680bf..f8597ec0d 100644 --- a/docs/src/install.md +++ b/docs/src/install.md @@ -19,7 +19,7 @@ In addition to the binary archive below, there are language specific packages in Note, we only distribute from GitHub currently, and not PyPi or NuGet.org. These should be compatible with most Linux Versions, Mac OSX and Windows. We support Python 2.7, -Python 3.6, 3.7, 3.8, 3.9 and 3.10. +Python 3.6 to 3.11. ### Binary Archive (C++, C#, Python, Java) diff --git a/docs/src/python_binding.md b/docs/src/python_binding.md index f1b65d91f..34c14d412 100644 --- a/docs/src/python_binding.md +++ b/docs/src/python_binding.md @@ -16,7 +16,7 @@ Older versions (prior to 1.1.3) can be installed using: $ pip install -f https://github.com/Illumina/interop/releases/tag/v1.1.2 interop $ pip install -f https://github.com/Illumina/interop/releases/latest interop -Note, only Python versions 2.7, 3.6, 3.7, 3.8, 3.9 and 3.10 are currently +Note, only Python versions 2.7, 3.6 to 3.11 are currently supported as binary builds. Other Python versions must be built from source. From b1bf60e566980d0589039a1614d0a0716d259f31 Mon Sep 17 00:00:00 2001 From: rlanglois Date: Wed, 22 Nov 2023 06:44:39 -0800 Subject: [PATCH 3/4] Remove Python 2.7 and upgrade to netcore 6 --- .github/workflows/dotnet.yml | 4 ++-- .github/workflows/python.yml | 2 +- README.md | 4 +++- docs/src/install.md | 2 +- docs/src/python_binding.md | 2 +- 5 files changed, 8 insertions(+), 6 deletions(-) diff --git a/.github/workflows/dotnet.yml b/.github/workflows/dotnet.yml index 0b774b37e..19de56a07 100644 --- a/.github/workflows/dotnet.yml +++ b/.github/workflows/dotnet.yml @@ -29,11 +29,11 @@ jobs: - name: Configure Windows if: matrix.os == 'windows-latest' - run: cmake ${{github.workspace}} -Ax64 -B${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{matrix.buildtype}} -DPACKAGE_OUTPUT_FILE_PREFIX=${{github.workspace}}/dist -DENABLE_SWIG=ON -DENABLE_PORTABLE=ON -DENABLE_EXAMPLES=OFF -DENABLE_CSHARP=ON -DENABLE_PYTHON=OFF -DCSHARP_TEST_FRAMEWORK=netcoreapp3 + run: cmake ${{github.workspace}} -Ax64 -B${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{matrix.buildtype}} -DPACKAGE_OUTPUT_FILE_PREFIX=${{github.workspace}}/dist -DENABLE_SWIG=ON -DENABLE_PORTABLE=ON -DENABLE_EXAMPLES=OFF -DENABLE_CSHARP=ON -DENABLE_PYTHON=OFF -DCSHARP_TEST_FRAMEWORK=netcoreapp6 - name: Configure OSX if: matrix.os == 'macOS-latest' - run: cmake ${{github.workspace}} -B${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{matrix.buildtype}} -DPACKAGE_OUTPUT_FILE_PREFIX=${{github.workspace}}/dist -DENABLE_SWIG=ON -DENABLE_PORTABLE=ON -DENABLE_EXAMPLES=OFF -DENABLE_CSHARP=ON -DENABLE_PYTHON=OFF -DCSHARP_TEST_FRAMEWORK=netcoreapp3 + run: cmake ${{github.workspace}} -B${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{matrix.buildtype}} -DPACKAGE_OUTPUT_FILE_PREFIX=${{github.workspace}}/dist -DENABLE_SWIG=ON -DENABLE_PORTABLE=ON -DENABLE_EXAMPLES=OFF -DENABLE_CSHARP=ON -DENABLE_PYTHON=OFF -DCSHARP_TEST_FRAMEWORK=netcoreapp6 - name: Build OSX and Windows if: matrix.os != 'ubuntu-latest' diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml index 344892f2d..24b007137 100644 --- a/.github/workflows/python.yml +++ b/.github/workflows/python.yml @@ -16,7 +16,7 @@ jobs: strategy: matrix: os: [ubuntu-latest, windows-2019, macOS-latest] - pyver: ['2.7', '3.6', '3.7', '3.8', '3.9', '3.10', '3.11'] + pyver: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11'] steps: - uses: actions/checkout@v3 diff --git a/README.md b/README.md index bb8dff218..893ec96b3 100644 --- a/README.md +++ b/README.md @@ -74,7 +74,9 @@ Install ### Python -Supported versions for binary distribution: Python 2.7 and 3.5-3.10. +Supported versions for binary distribution: 3.5-3.10. + +** Python 2.7 support has been removed ** You should have NumPy already installed. diff --git a/docs/src/install.md b/docs/src/install.md index f8597ec0d..a3e283ce5 100644 --- a/docs/src/install.md +++ b/docs/src/install.md @@ -18,7 +18,7 @@ In addition to the binary archive below, there are language specific packages in - Wheel for Python Note, we only distribute from GitHub currently, and not PyPi or NuGet.org. These should -be compatible with most Linux Versions, Mac OSX and Windows. We support Python 2.7, +be compatible with most Linux Versions, Mac OSX and Windows. We support Python 3.6 to 3.11. ### Binary Archive (C++, C#, Python, Java) diff --git a/docs/src/python_binding.md b/docs/src/python_binding.md index 34c14d412..6f80c150d 100644 --- a/docs/src/python_binding.md +++ b/docs/src/python_binding.md @@ -16,7 +16,7 @@ Older versions (prior to 1.1.3) can be installed using: $ pip install -f https://github.com/Illumina/interop/releases/tag/v1.1.2 interop $ pip install -f https://github.com/Illumina/interop/releases/latest interop -Note, only Python versions 2.7, 3.6 to 3.11 are currently +Note, only Python versions 3.6 to 3.11 are currently supported as binary builds. Other Python versions must be built from source. From 97ebdbaf051afd853b83e855a9eb8b323b16a7ce Mon Sep 17 00:00:00 2001 From: rlanglois Date: Wed, 22 Nov 2023 06:54:17 -0800 Subject: [PATCH 4/4] Fix readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 893ec96b3..1dbc9b192 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ Illumina sequencers including **NextSeq 1k/2k** and NovaSeqX. These libraries ar with one exception: GA systems have been excluded. *** -> We now support an interface to Python 2.7 (UCS-4) and 3.6-3.11 +> We now support an interface to 3.6-3.11 > Note that 3.10 and 3.11 are CentOS 7 or later while earlier versions support Centos 5 or later > Note: dumptext has been deprecated in favor of imaging_table and will be removed in the next version ***