Issue-330: Add Python 3.11 Support (#331)

* Issue-330: Add Python 3.11 Support

Resolves #330

* Update docs

* Remove Python 2.7 and upgrade to netcore 6

* Fix readme

.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'

.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: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11']
 
     steps:
       - uses: actions/checkout@v3
@@ -36,15 +36,15 @@ 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
         if: matrix.os == 'ubuntu-latest' && matrix.pyver == '3.10'
         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

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 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
 ***
 
@@ -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.
 

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                                                                            |

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

docs/src/install.md

@@ -18,8 +18,8 @@ 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,
-Python 3.6, 3.7, 3.8, 3.9 and 3.10.
+be compatible with most Linux Versions, Mac OSX and Windows. We support
+Python 3.6 to 3.11.
 
 ### Binary Archive (C++, C#, Python, Java)
 
@@ -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
 

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 3.6 to 3.11 are currently 
 supported as binary builds. Other Python versions must be built 
 from source.