From 806658e5f8e44715e6bf3fe41f00477eda80f925 Mon Sep 17 00:00:00 2001
From: Jaime RGP <jaime.rogue@gmail.com>
Date: Mon, 9 Dec 2019 16:31:27 +0100
Subject: [PATCH 01/12] Add support for GitHub Actions CI

---
 .github/workflows/ci.yaml     | 79 +++++++++++++++++++++++++++++++++++
 resources/initialize_conda.sh |  8 ++++
 2 files changed, 87 insertions(+)
 create mode 100644 .github/workflows/ci.yaml
 create mode 100644 resources/initialize_conda.sh

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
new file mode 100644
index 0000000..ecd75e0
--- /dev/null
+++ b/.github/workflows/ci.yaml
@@ -0,0 +1,79 @@
+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
+        pip 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: |
+        wget https://raw.githubusercontent.com/insilichem/pychimera/master/scripts/install_chimera.sh
+
+        if [[ ${CI_OS} == linux-* ]]; then
+          if [[ ! -e $HOME/chimera/bin/chimera ]]; then
+            bash install_chimera.sh
+          fi
+          echo "::set-env name=CHIMERADIR::$HOME/chimera"
+        else
+          if [[ ! -e $HOME/chimera/Chimera.app/Contents/Resources/bin/chimera ]]; then
+            bash install_chimera.sh
+            rm -rf $HOME/chimera/Chimera.app/Contents/Resources/lib/python2.7/site-packages/{AutoDockTools,MolKit,PyBabel,mglutil,mmLib,mslib}
+            rm -rf $HOME/chimera/Chimera.app/Contents/Resources/lib/python2.7/site-packages/setuptools*
+          fi
+          echo "::set-env name=CHIMERADIR::$HOME/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
+        conda install -q conda conda-build
+    - name: Build package
+      shell: bash
+      run: |
+        . resources/initialize_conda.sh
+        conda build -c local --python=2.7 conda-recipe
+    # - name: Deploy
+    #   shell: bash
+    #   run: |
+    #     conda install -q anaconda-client
+    #     anaconda -t {{ $secrets.ANACONDA_TOKEN }} upload -u insilichem $HOME/miniconda/conda-bld/**/gaudi-*.tar.bz2
+    #   on:
+    #     push:
+    #       tags:
+    #       - 'v*'
\ No newline at end of file
diff --git a/resources/initialize_conda.sh b/resources/initialize_conda.sh
new file mode 100644
index 0000000..64c4749
--- /dev/null
+++ b/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

From 9bc16df080a4b157dcdc709c0b494589af2c9cf4 Mon Sep 17 00:00:00 2001
From: Jaime RGP <jaime.rogue@gmail.com>
Date: Mon, 9 Dec 2019 16:36:11 +0100
Subject: [PATCH 02/12] Disable linting for now

---
 .github/workflows/ci.yaml | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index ecd75e0..81ba3f8 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -20,16 +20,16 @@ jobs:
         uname -a
         df -h
         ulimit -a
-    - name: Lint with flake8
-      shell: bash
-      run: |
-        . resources/initialize_conda.sh
-        conda activate
-        pip 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: Lint with flake8
+    #   shell: bash
+    #   run: |
+    #     . resources/initialize_conda.sh
+    #     conda activate
+    #     pip 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: |

From 11802b657a42c240eec4f5078418bb386eca70d2 Mon Sep 17 00:00:00 2001
From: Jaime RGP <jaime.rogue@gmail.com>
Date: Mon, 9 Dec 2019 16:40:22 +0100
Subject: [PATCH 03/12] Disable OSX for now - will re-enable later

---
 .github/workflows/ci.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 81ba3f8..494d9ca 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -8,7 +8,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macOS-latest, ubuntu-latest]
+        # os: [macOS-latest, ubuntu-latest]
+        os: [ubuntu-latest]
     env:
       CI_OS: ${{ matrix.os }}
 

From 200b12c1f48457c0638f5fa625e0fe5d1c4c6450 Mon Sep 17 00:00:00 2001
From: Jaime RGP <jaime.rogue@gmail.com>
Date: Mon, 9 Dec 2019 16:44:08 +0100
Subject: [PATCH 04/12] Fix CI_OS checks

---
 .github/workflows/ci.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 494d9ca..11ebc02 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -36,7 +36,7 @@ jobs:
       run: |
         wget https://raw.githubusercontent.com/insilichem/pychimera/master/scripts/install_chimera.sh
 
-        if [[ ${CI_OS} == linux-* ]]; then
+        if [[ ${CI_OS} == ubuntu-* ]]; then
           if [[ ! -e $HOME/chimera/bin/chimera ]]; then
             bash install_chimera.sh
           fi

From 9746aa39a7dba49365d663400204c39e42992b88 Mon Sep 17 00:00:00 2001
From: Jaime RGP <jaime.rogue@gmail.com>
Date: Mon, 9 Dec 2019 16:55:40 +0100
Subject: [PATCH 05/12] Do not pin pytest

---
 conda-recipe/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 0c9cf54..94019a7 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -57,6 +57,6 @@ test:
   source_files:
     - tests
   requires:
-    - pytest 4.0.*
+    - pytest
     - pytest-benchmark
 

From b90dea5bd394c8f28f7caf96190d8b6743db1bea Mon Sep 17 00:00:00 2001
From: Jaime RGP <jaime.rogue@gmail.com>
Date: Tue, 10 Dec 2019 16:11:57 +0100
Subject: [PATCH 06/12] GHA: Re-enable MacOS

---
 .github/workflows/ci.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 11ebc02..04a2eed 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -8,8 +8,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # os: [macOS-latest, ubuntu-latest]
-        os: [ubuntu-latest]
+        os: [macOS-latest, ubuntu-latest]
     env:
       CI_OS: ${{ matrix.os }}
 

From aa9c0368247d66b256e6f59cd060c516b57149c5 Mon Sep 17 00:00:00 2001
From: Jaime RGP <jaime.rogue@gmail.com>
Date: Tue, 10 Dec 2019 16:16:01 +0100
Subject: [PATCH 07/12] GHA: MacOS require sudo permissions for conda root
 installs

---
 .github/workflows/ci.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 04a2eed..2171998 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -62,7 +62,7 @@ jobs:
         conda config --add channels omnia
         conda config --add channels insilichem
         conda config --add channels defaults
-        conda install -q conda conda-build
+        sudo ${CONDA}/bin/conda install -q conda conda-build
     - name: Build package
       shell: bash
       run: |

From 39592b3358cd23a13dc14d60efbc5e0f6a5d904c Mon Sep 17 00:00:00 2001
From: Jaime RGP <jaime.rogue@gmail.com>
Date: Tue, 10 Dec 2019 16:19:39 +0100
Subject: [PATCH 08/12] GHA: More sudo conda

---
 .github/workflows/ci.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 2171998..c1f1a3e 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -25,7 +25,7 @@ jobs:
     #   run: |
     #     . resources/initialize_conda.sh
     #     conda activate
-    #     pip install flake8
+    #     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
@@ -67,7 +67,7 @@ jobs:
       shell: bash
       run: |
         . resources/initialize_conda.sh
-        conda build -c local --python=2.7 conda-recipe
+        sudo ${CONDA}/bin/conda build -c local --python=2.7 conda-recipe
     # - name: Deploy
     #   shell: bash
     #   run: |

From a83f03496c58a3c46dcf79bf15b41251fb16fe54 Mon Sep 17 00:00:00 2001
From: Jaime RGP <jaime.rogue@gmail.com>
Date: Tue, 10 Dec 2019 16:26:48 +0100
Subject: [PATCH 09/12] GHA: Debug env vars

---
 .github/workflows/ci.yaml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index c1f1a3e..be81b1e 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -67,12 +67,14 @@ jobs:
       shell: bash
       run: |
         . resources/initialize_conda.sh
+        env | sort
         sudo ${CONDA}/bin/conda build -c local --python=2.7 conda-recipe
     # - name: Deploy
     #   shell: bash
     #   run: |
-    #     conda install -q anaconda-client
-    #     anaconda -t {{ $secrets.ANACONDA_TOKEN }} upload -u insilichem $HOME/miniconda/conda-bld/**/gaudi-*.tar.bz2
+    #     . 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:

From df18d859bfe2cc70387629910406a584c452ef20 Mon Sep 17 00:00:00 2001
From: Jaime RGP <jaime.rogue@gmail.com>
Date: Tue, 10 Dec 2019 16:39:14 +0100
Subject: [PATCH 10/12] GHA: Install chimera in GITHUB_WORKSPACE

---
 .github/workflows/ci.yaml    |  12 ++--
 resources/install_chimera.sh | 104 +++++++++++++++++++++++++++++++++++
 2 files changed, 110 insertions(+), 6 deletions(-)
 create mode 100644 resources/install_chimera.sh

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index be81b1e..dd4afb2 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -36,17 +36,17 @@ jobs:
         wget https://raw.githubusercontent.com/insilichem/pychimera/master/scripts/install_chimera.sh
 
         if [[ ${CI_OS} == ubuntu-* ]]; then
-          if [[ ! -e $HOME/chimera/bin/chimera ]]; then
+          if [[ ! -e $GITHUB_WORKSPACE/chimera/bin/chimera ]]; then
             bash install_chimera.sh
           fi
-          echo "::set-env name=CHIMERADIR::$HOME/chimera"
+          echo "::set-env name=CHIMERADIR::$GITHUB_WORKSPACE/chimera"
         else
-          if [[ ! -e $HOME/chimera/Chimera.app/Contents/Resources/bin/chimera ]]; then
+          if [[ ! -e $GITHUB_WORKSPACE/chimera/Chimera.app/Contents/Resources/bin/chimera ]]; then
             bash install_chimera.sh
-            rm -rf $HOME/chimera/Chimera.app/Contents/Resources/lib/python2.7/site-packages/{AutoDockTools,MolKit,PyBabel,mglutil,mmLib,mslib}
-            rm -rf $HOME/chimera/Chimera.app/Contents/Resources/lib/python2.7/site-packages/setuptools*
+            rm -rf $GITHUB_WORKSPACE/chimera/Chimera.app/Contents/Resources/lib/python2.7/site-packages/{AutoDockTools,MolKit,PyBabel,mglutil,mmLib,mslib}
+            rm -rf $GITHUB_WORKSPACE/chimera/Chimera.app/Contents/Resources/lib/python2.7/site-packages/setuptools*
           fi
-          echo "::set-env name=CHIMERADIR::$HOME/chimera/Chimera.app/Contents/Resources"
+          echo "::set-env name=CHIMERADIR::$GITHUB_WORKSPACE/chimera/Chimera.app/Contents/Resources"
         fi
     - name: Configure conda
       shell: bash
diff --git a/resources/install_chimera.sh b/resources/install_chimera.sh
new file mode 100644
index 0000000..acca8f5
--- /dev/null
+++ b/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
\ No newline at end of file

From 1b6f489334caae167a7e9724cd97a7b0c2da8535 Mon Sep 17 00:00:00 2001
From: Jaime RGP <jaime.rogue@gmail.com>
Date: Tue, 10 Dec 2019 16:44:55 +0100
Subject: [PATCH 11/12] GHA: Use the new chimera installation script...

---
 .github/workflows/ci.yaml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index dd4afb2..5db03e1 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -33,16 +33,14 @@ jobs:
     - name: Install UCSF Chimera
       shell: bash
       run: |
-        wget https://raw.githubusercontent.com/insilichem/pychimera/master/scripts/install_chimera.sh
-
         if [[ ${CI_OS} == ubuntu-* ]]; then
           if [[ ! -e $GITHUB_WORKSPACE/chimera/bin/chimera ]]; then
-            bash install_chimera.sh
+            bash resources/install_chimera.sh
           fi
           echo "::set-env name=CHIMERADIR::$GITHUB_WORKSPACE/chimera"
         else
           if [[ ! -e $GITHUB_WORKSPACE/chimera/Chimera.app/Contents/Resources/bin/chimera ]]; then
-            bash install_chimera.sh
+            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

From beccb68fa91d586cc413bfa3723bbe3c2b95040f Mon Sep 17 00:00:00 2001
From: Jaime RGP <jaime.rogue@gmail.com>
Date: Tue, 10 Dec 2019 16:53:46 +0100
Subject: [PATCH 12/12] GHA: Is chimera really there?

---
 .github/workflows/ci.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 5db03e1..2230e01 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -66,6 +66,8 @@ jobs:
       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