Add support for GitHub Actions CI

.github/workflows/ci.yaml

@@ -0,0 +1,81 @@
+name: CI
+
+on: [push, pull_request]
+
+jobs:
+  test:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macOS-latest, ubuntu-latest]
+    env:
+      CI_OS: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Additional info about the build
+      shell: bash
+      run: |
+        uname -a
+        df -h
+        ulimit -a
+    # - name: Lint with flake8
+    #   shell: bash
+    #   run: |
+    #     . resources/initialize_conda.sh
+    #     conda activate
+    #     sudo ${CONDA}/bin/conda install flake8
+    #     # stop the build if there are Python syntax errors or undefined names
+    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+    #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Install UCSF Chimera
+      shell: bash
+      run: |
+        if [[ ${CI_OS} == ubuntu-* ]]; then
+          if [[ ! -e $GITHUB_WORKSPACE/chimera/bin/chimera ]]; then
+            bash resources/install_chimera.sh
+          fi
+          echo "::set-env name=CHIMERADIR::$GITHUB_WORKSPACE/chimera"
+        else
+          if [[ ! -e $GITHUB_WORKSPACE/chimera/Chimera.app/Contents/Resources/bin/chimera ]]; then
+            bash resources/install_chimera.sh
+            rm -rf $GITHUB_WORKSPACE/chimera/Chimera.app/Contents/Resources/lib/python2.7/site-packages/{AutoDockTools,MolKit,PyBabel,mglutil,mmLib,mslib}
+            rm -rf $GITHUB_WORKSPACE/chimera/Chimera.app/Contents/Resources/lib/python2.7/site-packages/setuptools*
+          fi
+          echo "::set-env name=CHIMERADIR::$GITHUB_WORKSPACE/chimera/Chimera.app/Contents/Resources"
+        fi
+    - name: Configure conda
+      shell: bash
+      run: |
+        . resources/initialize_conda.sh
+        conda activate
+        conda info
+        conda config --set always_yes yes
+        conda config --remove-key channels || true
+        conda config --add channels conda-forge
+        conda config --add channels bioconda
+        conda config --add channels salilab
+        conda config --add channels omnia
+        conda config --add channels insilichem
+        conda config --add channels defaults
+        sudo ${CONDA}/bin/conda install -q conda conda-build
+    - name: Build package
+      shell: bash
+      run: |
+        . resources/initialize_conda.sh
+        env | sort
+        ls -lh $CHIMERADIR/*
+        test -f $CHIMERADIR/bin/chimera
+        sudo ${CONDA}/bin/conda build -c local --python=2.7 conda-recipe
+    # - name: Deploy
+    #   shell: bash
+    #   run: |
+    #     . resources/initialize_conda.sh
+    #     sudo ${CONDA}/bin/conda install -q anaconda-client
+    #     anaconda -t {{ $secrets.ANACONDA_TOKEN }} upload -u insilichem ${CONDA}/conda-bld/**/gaudi-*.tar.bz2
+    #   on:
+    #     push:
+    #       tags:
+    #       - 'v*'

conda-recipe/meta.yaml

@@ -57,6 +57,6 @@ test:
   source_files:
     - tests
   requires:
-    - pytest 4.0.*
+    - pytest
     - pytest-benchmark
 

resources/initialize_conda.sh

@@ -0,0 +1,8 @@
+case ${CI_OS} in
+    windows*)
+        eval "$(${CONDA}/condabin/conda.bat shell.bash hook)";;
+    macOS*)
+        eval "$(${CONDA}/condabin/conda shell.bash hook)";;
+    *)
+        eval "$(conda shell.bash hook)";;
+esac

resources/install_chimera.sh

@@ -0,0 +1,104 @@
+#!/bin/bash
+
+PKG_VERSION="1.13.1"
+
+[[ $ARCH = 32 ]] && echo "32-bit builds are not supported anymore" && exit 1;
+
+# Linux
+uname_out="$(uname -s)"
+case "$uname_out" in
+  Linux* )
+    _file="chimera-${PKG_VERSION}-linux_x86_64.bin"
+    _filepath="linux_x86_64/${_file}"
+    _installdir="UCSF-Chimera64-${PKG_VERSION}"
+    _hash="80d2c95f78c603da3acda42f4bbceca0" # v1.13.1
+    _agent="Mozilla/5.0 (X11; Linux x86_64; rv:64.0) Gecko/20100101 Firefox/64.0"
+  ;;
+# MacOS X
+  Darwin* )
+    _file="chimera-${PKG_VERSION}-mac64.dmg"
+    _filepath="mac64/${_file}"
+    _installdir="UCSF-Chimera64-${PKG_VERSION}"
+    _hash="62251f8677846e367de3cab4b5b1e8af" # v1.13.1
+    _agent="Mozilla/5.0 (Macintosh; Intel Mac OS X 10_12_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/60.0.3112.90 Safari/537.36"
+  ;;
+# Emulated Windows
+  CYGWIN*|MINGW*|MSYS*|*windows*)
+    _file="chimera-${PKG_VERSION}-win64.exe"
+    _filepath="win64/${_file}"
+    _installdir="Chimera_${PKG_VERSION}"
+    _hash="1cb7f1f4138fc4ff34a5c3383623b4a4" # v1.13.1
+    _agent="Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML like Gecko) Chrome/51.0.2704.79 Safari/537.36 Edge/14.14931"
+  ;;
+  *)
+    echo "Platform ${uname_out} not supported"
+    exit 1
+  ;;
+esac
+
+_downloader="https://www.rbvi.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py"
+
+download(){
+  _download=$(command curl -A "${_agent}" -F file=${_filepath} -F choice=Accept "${_downloader}" | grep href | sed -E 's/.*href="(.*)">/\1/');
+  sleep 3;
+  command curl -A "${_agent}" "https://www.cgl.ucsf.edu${_download}" -o "${_file}";
+}
+
+download_retry(){
+  n=0;
+  until [ $n -ge 10 ]; do
+    download;
+    echo "${_hash}  ${_file}" | md5sum -c --strict --quiet && break;
+    n=$[$n+1];
+    sleep 3;
+  done;
+  echo "${_hash}  ${_file}" | md5sum -c --strict --quiet || exit 1;
+}
+
+installation_linux() {
+  chmod +x "${_file}";
+  echo "$GITHUB_WORKSPACE/chimera" | "./${_file}";
+}
+
+installation_mac() {
+  cd "${SRC_DIR}"
+  hdiutil convert "${_file}" -format UDRW -o chimerarw
+  _mountdir=$(echo `hdiutil attach -mountpoint "$GITHUB_WORKSPACE/chimera" chimerarw.dmg | tail -1 | awk '{$1=$2=""; print $0}'` | xargs -0 echo)
+  echo "Installed at ${_mountdir}"
+}
+
+installation_win() {
+  cd "${SRC_DIR}"
+  cmd.exe /C "START /WAIT ${_file} /VERYSILENT /DIR=$CHIMERADIR"
+}
+
+
+set +x
+echo 'IMPORTANT: By downloading you accept the UCSF Chimera Non-Commercial Software License Agreement!'
+echo 'IMPORTANT: The license agreement can be found here: http://www.cgl.ucsf.edu/chimera/license.html'
+echo 'IMPORTANT: If you do not agree, please press Ctrl-C now.'
+echo 'IMPORTANT: Downloading in 10 seconds...'
+sleep 10
+set -x
+
+# Linux
+case "$uname_out" in
+  Linux* )
+    download_retry
+    installation_linux
+  ;;
+# MacOS X
+  Darwin* )
+    download
+    installation_mac
+  ;;
+# Emulated Windows
+  CYGWIN*|MINGW*|MSYS*|*windows*)
+    download
+    installation_win
+  ;;
+  *)
+    echo "Platform ${uname_out} not supported"
+    exit 1
+  ;;
+esac