CI: skip nwchem tests in OSX & rework chimera install

.travis.yml

@@ -25,9 +25,10 @@ cache:
   directories:
   - $HOME/download
   - $HOME/miniconda
+  - $HOME/chimera
 
 before_cache:
-- if ! [[ $TRAVIS_TAG ]]; then rm -rf $HOME/miniconda/conda-bld; fi
+- if [[ ! $TRAVIS_TAG ]]; then rm -rf $HOME/miniconda/conda-bld; fi
 - rm -rf $HOME/pychimera $HOME/miniconda/locks $HOME/miniconda/pkgs $HOME/miniconda/var $HOME/miniconda/conda-meta/history
 - conda remove --force gaudi
 - rm $HOME/.nwchemrc || true
@@ -54,8 +55,8 @@ before_install:
     bash $HOME/download/miniconda.sh -b -p $HOME/miniconda;
   fi
 # Configure conda and get a few essentials
-- source $HOME/miniconda/bin/activate
-- hash -r
+- source $HOME/miniconda/etc/profile.d/conda.sh
+- conda activate
 - conda config --set always_yes yes
 - conda config --remove-key channels || true
 - conda config --add channels conda-forge
@@ -69,13 +70,22 @@ before_install:
 # Show conda info for debugging
 - conda info -a
 # Get Chimera
-- git clone https://github.com/insilichem/pychimera.git $HOME/pychimera;
 - if [ "${TRAVIS_OS_NAME}" = "linux" ]; then
-    if [[ ! -e $HOME/miniconda/bin/chimera ]]; then
-      conda build -q $HOME/pychimera/conda-recipes/ucsf-chimera-headless;
-      conda install -y -c $HOME/miniconda/conda-bld ucsf-chimera-headless;
-      ln -s $HOME/miniconda/bin/chimera-headless $HOME/miniconda/bin/chimera || true;
+    if [[ ! -e $HOME/chimera/bin/chimera ]]; then
+      _file="chimera-1.12-linux_x86_64.bin";
+      _filepath="linux_x86_64/${_file}";
+      _downloader="https://www.rbvi.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py";
+      _download=`curl -s -F file="${_filepath}" -F choice=Accept "${_downloader}" | grep href | sed -E 's/.*href="(.*)">/\1/'`;
+      curl "https://www.rbvi.ucsf.edu""${_download}" -o "${_file}";
+      chmod +x "${_file}";
+      mkdir -p "$HOME/chimera";
+      echo "$HOME/chimera" | "./${_file}";
+      ln -s $HOME/chimera/bin/chimera $HOME/miniconda/bin/chimera || true;
+      rm -rf $HOME/chimera/lib/python2.7/site-packages/{AutoDockTools,MolKit,PyBabel,mglutil,mmLib,mslib};
+      rm -rf $HOME/chimera/lib/python2.7/site-packages/setuptools*;
+      pip install -U setuptools numpy=1.11 -t $HOME/chimera/lib/python2.7/site-packages;
     fi;
+    export CHIMERADIR="$HOME/chimera";
   else
     if [[ ! -e $HOME/chimera/Chimera.app/Contents/Resources/bin/chimera ]]; then
         set +x;
@@ -92,8 +102,9 @@ before_install:
         curl "https://www.rbvi.ucsf.edu""${_download}" -o "${_file}";
         hdiutil convert "${_file}" -format UDRW -o chimerarw;
         hdiutil attach -mountpoint "$HOME/chimera" chimerarw.dmg;
+        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*;
-        pip install -U setuptools -t $HOME/chimera/Chimera.app/Contents/Resources/lib/python2.7/site-packages;
+        pip install -U setuptools numpy=1.11 -t $HOME/chimera/Chimera.app/Contents/Resources/lib/python2.7/site-packages;
     fi;
     export CHIMERADIR="$HOME/chimera/Chimera.app/Contents/Resources";
   fi

conda-recipe/meta.yaml

@@ -8,7 +8,11 @@ about:
   summary: Genetic Algorithms with Unrestricted Descriptors for Intuitive Molecular Modeling
 
 source:
+{% if environ.get('TRAVIS') %}
+  git_url: ../
+{% else %}
   git_url: https://github.com/insilichem/gaudi.git
+{% endif %}
   git_tag: {{ environ.get('GIT_DESCRIBE_TAG', '') }}
 
 requirements:
@@ -31,7 +35,8 @@ requirements:
     - imp
     - autodock-vina
     - autodocktools-prepare
-    - nwchem
+    - nwchem  # [linux]
+
 test:
   imports:
     - gaudi

tests/test_objectives_nwchem.py

@@ -25,10 +25,12 @@
 import sys
 import pytest
 from conftest import datapath, expressed
-from gaudi.objectives.nwchem import NWChem
 from gaudi.genes.molecule import Molecule
+from gaudi.objectives.nwchem import NWChem
 
 
+@pytest.mark.skipif(sys.platform != 'linux2',
+                    reason='NWChem conda package only available in Linux')
 @pytest.mark.parametrize("ligand, energy", [
     ('butane.pdb', -156.87859414774),
 ])