OSX in conda environments

.travis.yml

@@ -12,44 +12,43 @@ env:
 
 matrix:
   include:
-   #    FIXME: focus on mojave
-   #    - env: DOCKER_IMAGE=quay.io/pypa/manylinux2010_x86_64
-   #      python: 3.6
-   #      os: linux
-   #      dist: trusty
-   #      sudo: required
-   #    - env: CC=gcc PYSAM_VERSION='pysam'
-   #      python: 2.7
-   #      os: linux
-   #      dist: trusty
-   #      sudo: required
-   #    - env: CC=gcc PYSAM_VERSION='pysam'
-   #      python: 3.5
-   #      os: linux
-   #      dist: trusty
-   #      sudo: required
-   #    - env: CC=gcc PYSAM_VERSION='pysam'
-   #      python: 3.6
-   #      os: linux
-   #      dist: trusty
-   #      sudo: required
-   #    - env: CC=gcc PYSAM_VERSION='pysam'
-   #      python: 3.7
-   #      os: linux
-   #      dist: bionic
-   #      sudo: required
-   #    - env: CC=gcc PYSAM_VERSION='pysam'
-   #      python: 3.8
-   #      os: linux
-   #      dist: bionic
-   #      sudo: required
-   #    - env: CC=gcc PYSAM_VERSION='pysam>=0.13.0' PYTHON_VERSION='2.7'
-   #      language: generic
-   #      os: osx
-   #    - env: CC=gcc PYSAM_VERSION='pysam>=0.13.0' PYTHON_VERSION='3.6'
-   #      language: generic
-   #      os: osx
-    - env: CC=gcc PYSAM_VERSION='pysam>=0.13.0' PYTHON_VERSION='3.6'
+   #- env: DOCKER_IMAGE=quay.io/pypa/manylinux2010_x86_64
+   #  python: 3.6
+   #  os: linux
+   #  dist: trusty
+   #  sudo: required
+   #- env: CC=gcc PYSAM_VERSION='pysam'
+   #  python: 2.7
+   #  os: linux
+   #  dist: trusty
+   #  sudo: required
+   #- env: CC=gcc PYSAM_VERSION='pysam'
+   #  python: 3.5
+   #  os: linux
+   #  dist: trusty
+   #  sudo: required
+   #- env: CC=gcc PYSAM_VERSION='pysam'
+   #  python: 3.6
+   #  os: linux
+   #  dist: trusty
+   #  sudo: required
+   #- env: CC=gcc PYSAM_VERSION='pysam'
+   #  python: 3.7
+   #  os: linux
+   #  dist: bionic
+   #  sudo: required
+   #- env: CC=gcc PYSAM_VERSION='pysam'
+   #  python: 3.8
+   #  os: linux
+   #  dist: bionic
+   #  sudo: required
+   #- env: CC=gcc PYSAM_VERSION='pysam>=0.13.0' CONDA_PY='2.7'
+   #  language: generic
+   #  os: osx
+   #- env: CC=gcc PYSAM_VERSION='pysam>=0.13.0' CONDA_PY='3.6'
+   #  language: generic
+   #  os: osx
+    - env: CC=gcc PYSAM_VERSION='pysam>=0.13.0' CONDA_PY='3.8'
       language: generic
       os: osx
       osx_image: xcode11

.travis_before_install.sh

@@ -9,42 +9,19 @@ elif [ $TRAVIS_OS_NAME == 'osx' ]; then
   echo "Find out OSX version"
   osx_version=$(sw_vers -productVersion)
   echo "OSX version: $osx_version"
-  osx_version1=$(echo $osx_version | cut -d. -f1)
-  osx_version2=$(echo $osx_version | cut -d. -f2)
-  if [ $osx_version1 == "10" ] && [ $osx_version2 -ge 14 ]; then
-    #echo "Installing C headers for OSX Mojave and later"
-    #open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
-    #sudo installer -pkg /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_$osx_version1.$osx_version2.pkg -target /
-    echo "Find C++ libraries:"
-    ls /usr/X11R6
-    ls /usr/X11R6/lib
-    echo "Find C headers for OSX Mojave and later"
-    ls /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/
-    echo "Result of scrun --show-sdk-path:"
-    xcrun --show-sdk-path
-    echo "Check the C++ header path:"
-    ls /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/
-  fi
 
   echo "Installing deps for OSX"
-  if [ $PYTHON_VERSION == "2.7" ]; then
-    CONDA_VER='2'
-    CONDA_URL="https://repo.continuum.io/miniconda/Miniconda${CONDA_VER}-latest-MacOSX-x86_64.sh"
-  elif [ $PYTHON_VERSION == "3.7" ]; then
-    CONDA_VER='3'
-    CONDA_URL="https://repo.continuum.io/miniconda/Miniconda${CONDA_VER}-latest-MacOSX-x86_64.sh"
-  # NOTE: Miniconda stopped supporting 3.6, but pysam is late...
-  elif [ $PYTHON_VERSION == "3.6" ]; then
-    CONDA_VER='3'
-    CONDA_URL='https://repo.continuum.io/miniconda/Miniconda3-4.5.4-MacOSX-x86_64.sh'
-  else
-    echo "OSX install with conda currently supports 2.7, 3.6, and 3.7"
-  fi
+  CONDA_URL="https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh"
   curl "${CONDA_URL}" -o "miniconda.sh"
   bash "miniconda.sh" -b -p $HOME/miniconda
   echo "$PATH"
   export PATH="$HOME/miniconda/bin:$PATH"
   source $HOME/miniconda/bin/activate
+
+  # Make conda environment and activate
+  conda create -n travis python=$CONDA_PY
+  conda activate travis
+
   # Use pip from conda
   conda install -y pip
   pip --version

.travis_deploy.sh

@@ -55,12 +55,18 @@ elif [ $TRAVIS_OS_NAME == 'osx' ]; then
   echo "TWINE_PASSWORD=$TWINE_PASSWORD"
   export PATH="$HOME/miniconda/bin:$PATH"
   source $HOME/miniconda/bin/activate
+  conda activate travis
+
   pip --version
   pip install twine
-  if [ $PYTHON_VERSION == '2.7' ]; then
+  if [ $CONDA_PY == '2.7' ]; then
     PYARCH='cp27-cp27m'
-  elif [ $PYTHON_VERSION == '3.6' ]; then
+  elif [ $CONDA_PY == '3.6' ]; then
     PYARCH='cp36-cp36m'
+  elif [ $CONDA_PY == '3.7' ]; then
+    PYARCH='cp37-cp37m'
+  elif [ $CONDA_PY == '3.8' ]; then
+    PYARCH='cp38-cp38m'
   else
     echo "Python version not recognized"
     exit 1

.travis_install.sh

@@ -15,6 +15,8 @@ else
   if [ $TRAVIS_OS_NAME == 'osx' ]; then
     export PATH="$HOME/miniconda/bin:$PATH"
     source $HOME/miniconda/bin/activate
+    conda activate travis
+
     # Somehow we need this to execute the setup.py at all...
     pip install numpy
     pip install $PYSAM_VERSION

.travis_test.sh

@@ -8,7 +8,9 @@ fi
 if [ "$TRAVIS_OS_NAME" == 'osx' ]; then
   export PATH="$HOME/miniconda/bin:$PATH"
   source $HOME/miniconda/bin/activate
-  PYTHON="$HOME/miniconda/bin/python$PYTHON_VERSION"
+  conda activate travis
+  #PYTHON="$HOME/miniconda/bin/python$CONDA_PY"
+  PYTHON=$(which python)
 else
   PYTHON=${PYTHON:-python}
 fi

setup.py

@@ -106,23 +106,12 @@ def get_include_dirs(cpp=False):
     return include_dirs
 
 
-def get_library_dirs(cpp=False):
+def get_library_dirs_cpp():
     '''OSX 10.14 and later messed up C/C++ library locations'''
-    library_dirs = []
-    paths = {
-        'C': [],
-        'C++': ['/usr/X11R6/lib'],
-        }
-
-    for path in paths['C']:
-        if os.path.isdir(path):
-            library_dirs.append(path)
-    if cpp:
-        for path in paths['C++']:
-            if os.path.isdir(path):
-                library_dirs.append(path)
-
-    return library_dirs
+    if sys.platform == 'darwin':
+        return ['/usr/X11R6/lib']
+    else:
+        return []
 
 
 def get_extra_args_cpp():
@@ -207,7 +196,7 @@ def run(self):
 
 setup(name='HTSeq',
       version=version,
-      author='Simon Anders',
+      author='Simon Anders, Fabio Zanini',
       author_email='sanders@fs.tum.de',
       maintainer='Fabio Zanini',
       maintainer_email='fabio.zanini@stanford.edu',
@@ -236,13 +225,12 @@ def run(self):
              'HTSeq._HTSeq',
              ['src/_HTSeq.c'],
              include_dirs=[numpy_include_dir]+get_include_dirs(),
-             library_dirs=get_library_dirs(),
              extra_compile_args=['-w']),
          Extension(
              'HTSeq._StepVector',
              ['src/StepVector_wrap.cxx'],
              include_dirs=get_include_dirs(cpp=True),
-             library_dirs=get_library_dirs(cpp=True),
+             library_dirs=get_library_dirs_cpp(),
              extra_compile_args=['-w'] + get_extra_args_cpp(),
              extra_link_args=get_extra_args_cpp(),
              ),