From 3863a7603148f80b566f7e0bc62fbf4fdca3b88c Mon Sep 17 00:00:00 2001 From: Robert Langlois Date: Tue, 5 Jan 2021 15:12:07 -0800 Subject: [PATCH] Fix broken deployment of docs and failing tests on deployment (#247) * Fix broken deployment of docs and failing tests on deployment * Add build for docs * Update docs --- .travis.yml | 7 ++++--- CMakeLists.txt | 4 +++- README.md | 4 ++-- docs/src/changes.md | 8 ++++++++ docs/src/index.md | 2 +- docs/src/install.md | 4 ++-- docs/src/python_binding.md | 2 +- tools/package.sh | 4 +++- 8 files changed, 24 insertions(+), 11 deletions(-) diff --git a/.travis.yml b/.travis.yml index 1fbb6a075..91ba62ef9 100644 --- a/.travis.yml +++ b/.travis.yml @@ -21,8 +21,9 @@ language: cpp env: global: - secure: "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" - HOMEBREW_NO_INSTALL_CLEANUP: 1 + - HOMEBREW_NO_INSTALL_CLEANUP: 1 + - secure: "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" + jobs: fast_finish: true include: @@ -189,7 +190,7 @@ before_deploy: - if [ "$TRAVIS_OS_NAME != "osx ] ; then env "PATH=$PATH" pyenv install 3.5.4 -s || true; fi - if [ "$TRAVIS_OS_NAME != "osx ] ; then env "PATH=$PATH" pyenv global 3.5.4; fi - if [ "$TRAVIS_OS_NAME != "osx ] ; then env "PATH=$PATH" pip install twine; fi - - if [ "$TRAVIS_TAG" != "" ] && [ "$DEPLOY_BUILD" == "true" ] && [ -e $(compgen -G $PWD/dist/*.whl) ] ; then twine upload --skip-existing $PWD/dist/*.whl; fi + - if [ "$TRAVIS_TAG" != "" ] && [ "$DEPLOY_BUILD" == "true" ] && [ ! -z $(compgen -G $PWD/dist/*.whl) ] ; then twine upload --skip-existing $PWD/dist/*.whl; fi deploy: - provider: releases diff --git a/CMakeLists.txt b/CMakeLists.txt index 5e9fc32f0..4b7fea558 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -146,7 +146,9 @@ include(CPack) #https://stackoverflow.com/questions/12302836/renaming-cpack-automatic-target add_custom_target(bundle COMMAND ${CMAKE_CPACK_COMMAND} -C $ --config ${CPACK_OUTPUT_CONFIG_FILE}) - +if(TARGET doc) + add_dependencies(bundle doc) +endif() if(ENABLE_STATIC) set(LIBRARY_TYPE STATIC) set(BUILD_SHARED_LIBS OFF) diff --git a/README.md b/README.md index 7f11a495b..6efad62ec 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ Illumina sequencers including **NextSeq 1k/2k**. These libraries are backwards c with one exception: GA systems have been excluded. *** -> We now support an interface to Python 2.7 (UCS-4) and 3.5-3.8 (see contents below) +> We now support an interface to Python 2.7 (UCS-4) and 3.5-3.9 (see contents below) *** The InterOp files supported by this library include: @@ -72,7 +72,7 @@ Install ### Python -Supported versions for binary distribution: Python 2.7 and 3.5-3.8. +Supported versions for binary distribution: Python 2.7 and 3.5-3.9. You should have NumPy already installed. diff --git a/docs/src/changes.md b/docs/src/changes.md index 83aa6adb0..64aa661b5 100644 --- a/docs/src/changes.md +++ b/docs/src/changes.md @@ -1,5 +1,13 @@ # Changes {#changes} + +## v1.1.19 + +Date | Description +---------- | ----------- +2021-01-05 | Fix broken deployment of docs and failing tests on deployment + + ## v1.1.18 Date | Description diff --git a/docs/src/index.md b/docs/src/index.md index 0f6d7c158..8e82c60fa 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), 3.5, 3.6, 3.7 and 3.8 (see contents below) +> We now support an interface to Python 2.7 (UCS-4), 3.5, 3.6, 3.7, 3.8 and 3.9 (see contents below) *** Compatibility diff --git a/docs/src/install.md b/docs/src/install.md index 2e715ff7e..2dc41ff0e 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 3.5, 3.6, 3.7 and 3.8. +Python 3.5, 3.6, 3.7, 3.8 and 3.9. ### 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), 3.5, 3.6, 3.7 and 3.8. +Supported versions for binary distribution: 2.7 (UCS-4), 3.5, 3.6, 3.7, 3.8 and 3.9. Test the installation diff --git a/docs/src/python_binding.md b/docs/src/python_binding.md index 20558ee4c..38b2def58 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, 3.5, 3.6, 3.7 and 3.8 are currently +Note, only Python versions 2.7, 3.5, 3.6, 3.7, 3.8 and 3.9 are currently supported as binary builds. Other Python versions must be built from source. diff --git a/tools/package.sh b/tools/package.sh index e38261664..be42353d6 100644 --- a/tools/package.sh +++ b/tools/package.sh @@ -171,7 +171,7 @@ fi if [ "$PYTHON_VERSION" != "" ] && [ "$PYTHON_VERSION" != "Disable" ] && [ "$PYTHON_VERSION" != "DotNetStandard" ] ; then if [ "$PYTHON_VERSION" == "ALL" ] ; then - # python_versions="2.7.17 3.5.9 3.6.10 3.7.7 3.8.2" + # python_versions="2.7.17 3.5.9 3.6.10 3.7.7 3.8.2 3.9.x" python_versions="2.7.17 3.5.9" pyenv install --list | grep " 2.7" pyenv install --list | grep " 3\.[45678]" @@ -265,6 +265,8 @@ if [ "$PYTHON_VERSION" == "Disable" ] ; then run "Build" cmake --build $BUILD_PATH -- -j${THREAD_COUNT} run "Test" cmake --build $BUILD_PATH --target check -- -j${THREAD_COUNT} run "Package" cmake --build $BUILD_PATH --target bundle +elif [ "$PYTHON_VERSION" == "None" ] ;then + run "Package" cmake --build $BUILD_PATH --target bundle fi if [ "$PYTHON_VERSION" == "DotNetStandard" ] ; then