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

@@ -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

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> --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)

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.
 

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

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

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
 

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.
 

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