Merge pull request #78 from kyleabeauchamp/travis

[WIP] Simplify travis logic

.travis.yml

@@ -1,18 +1,16 @@
 language: c
 
+branches:
+  only:
+    - master
+
 install:
   - source devtools/ci/install.sh
   - export PYTHONUNBUFFERED=true
 
 script:
-  - export CC="gcc -std=c89"
-  - source deactivate
-  - conda install --yes conda-build
+  # this builds the binary, unpacks it, and runs the tests
   - conda build devtools/conda-recipe
-  - source activate $python
-  - conda install $HOME/miniconda/conda-bld/linux-64/gaff2xml-dev-*
-  - conda list -e
-  - nosetests
 
 env:
   matrix:
@@ -26,5 +24,3 @@ env:
 after_success:
   - echo "after_success"
   - source devtools/ci/after_sucess.sh
-
-

README.md

@@ -1,10 +1,13 @@
 [![Build Status](https://travis-ci.org/choderalab/gaff2xml.svg)](https://travis-ci.org/choderalab/gaff2xml)
 [![Code Health](https://landscape.io/github/choderalab/gaff2xml/master/landscape.svg)](https://landscape.io/github/choderalab/gaff2xml/master)
 
-## gaff2xml: Converting Antechamber GAFF files to OpenMM XML format
+## gaff2xml: Tools for Small Molecules, Antechamber, OpenMM, and More.
 
-This set of tools allows users to automate the conversion of ligand
-force field parameters from Antechamber formats to OpenMM XML format.
+This set of tools allows users to automate the conversion of GAFF ligand
+force field parameters from Antechamber formats to OpenMM XML format.  
+It also contains several python tools for working with small molecules,
+packing boxes (python wrappers for packmol), and parameterizing small
+molecules.
 
 This tool is in BETA testing: use at your own risk!
 
@@ -13,7 +16,21 @@ Installation:
 
 ```
 python setup.py install
+
+or
+
+conda config --add channels http://conda.binstar.org/omnia
+conda config --add channels https://conda.binstar.org/rdkit
+conda install gaff2xml
+
+```
+
+To test your installation, use the following command:
+
 ```
+nosetests gaff2xml -v
+```
+
 
 Usage:
 

devtools/ci/install.sh

@@ -1,14 +1,20 @@
-sudo apt-get update
-sudo apt-get install -qq -y g++ gfortran csh
-sudo apt-get install -qq -y g++-multilib gcc-multilib openbabel
-wget http://repo.continuum.io/miniconda/Miniconda-3.6.0-Linux-x86_64.sh
-bash Miniconda-3.6.0-Linux-x86_64.sh -b
+MINICONDA=Miniconda-latest-Linux-x86_64.sh
+MINICONDA_MD5=$(curl -s http://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *<td>\(.*\)<\/td> */\1/p')
+wget http://repo.continuum.io/miniconda/$MINICONDA
+if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then
+    echo "Miniconda MD5 mismatch"
+    exit 1
+fi
+bash $MINICONDA -b
 PIP_ARGS="-U"
 
 export PATH=$HOME/miniconda/bin:$PATH
 
+sudo apt-get update
+sudo apt-get install -qq -y g++ gfortran csh g++-multilib gcc-multilib openbabel
+
 conda update --yes conda
 conda config --add channels http://conda.binstar.org/omnia
-conda config --add channels https://conda.binstar.org/ric
-conda create --yes -n ${python} python=${python} --file devtools/ci/requirements-conda.txt
+conda config --add channels https://conda.binstar.org/rdkit
 source activate $python
+conda install --yes conda-build

devtools/conda-recipe/build.sh

@@ -1,10 +1,5 @@
 #!/bin/bash
-
 cp -r $RECIPE_DIR/../.. $SRC_DIR
+$PYTHON setup.py clean
 $PYTHON setup.py install
 
-# Add more build steps here, if they are necessary.
-
-# See
-# http://docs.continuum.io/conda/build.html
-# for a list of environment variables that are set during the build process.

devtools/conda-recipe/meta.yaml

@@ -1,28 +1,48 @@
 package:
-  name: gaff2xml
-  version: !!str dev
+  name: gaff2xml-dev
+  version: !!str 3.0.0
 
+#source:
+#  fn: master.zip
+#  url: https://github.com/choderalab/gaff2xml/archive/master.zip
+
+build:
+  preserve_egg_dir: True
+  number: 0
 
 requirements:
   build:
     - python
-    - cython
+    - setuptools
+    - mdtraj
     - numpy
     - scipy
-    - setuptools
-    - mdtraj-dev
-    - openmm    
-    - ambermini    
-
+    - pandas    
+    - openmm
+    - ambermini
+    - jinja2
+#    - rdkit    # rdkit is an optional dependency, may want to comment this out for the release version.
   run:
     - python
+    - setuptools
     - pandas
+    - six
+    - mdtraj
+    - numpydoc
     - scipy
-    - mdtraj-dev
-    - openmm    
-    - ambermini    
+    - openmm
+    - ambermini
+    - jinja2
+#    - rdkit    # rdkit is an optional dependency, may want to comment this out for the release version.
+
+test:
+  requires:
+    - nose
+  imports:
+    - gaff2xml
+  commands:
+    - nosetests gaff2xml -v
 
 about:
   home: https://github.com/choderalab/gaff2xml
   license: GNU Lesser General Public License v2 or later (LGPLv2+)
-

tests/test_drugs.py → gaff2xml/tests/test_drugs.py

@@ -2,7 +2,21 @@
 from gaff2xml import utils
 import os
 
-@skipIf(os.environ.get("TRAVIS", None) == 'true', "Skip testing of entire drug database on Travis.")
+try:
+    oechem = utils.import_("openeye.oechem")
+    if not oechem.OEChemIsLicensed(): raise(ImportError("Need License for OEChem!"))
+    oequacpac = utils.import_("openeye.oequacpac")
+    if not oequacpac.OEQuacPacIsLicensed(): raise(ImportError("Need License for oequacpac!"))
+    oeiupac = utils.import_("openeye.oeiupac")
+    if not oeiupac.OEIUPACIsLicensed(): raise(ImportError("Need License for OEOmega!"))        
+    oeomega = utils.import_("openeye.oeomega")
+    if not oeomega.OEOmegaIsLicensed(): raise(ImportError("Need License for OEOmega!"))    
+    HAVE_OE = True
+except:
+    HAVE_OE = False
+
+
+@skipIf(not HAVE_OE, "Cannot run test_drugs() module without OpenEye tools.")
 def test_drugs():
     import openeye.oechem
     database_filename = utils.get_data_filename("chemicals/drugs/Zdd.mol2.gz")
@@ -12,7 +26,7 @@ def test_drugs():
             molecule_name, tripos_mol2_filename = utils.molecule_to_mol2(molecule)
             yield utils.tag_description(lambda : utils.test_molecule(molecule_name, tripos_mol2_filename), "Testing drugs %s" % molecule_name)
 
-@skipIf(os.environ.get("TRAVIS", None) == 'true', "Skip testing of entire drug database on Travis.")
+@skipIf(not HAVE_OE, "Cannot test test_drug() without OpenEye tools.")
 def test_drug():
     import openeye.oechem
     database_filename = utils.get_data_filename("chemicals/drugs/Zdd.mol2.gz")

setup.py

@@ -62,7 +62,7 @@
       url='http://github.com/choderalab/gaff2xml',
       platforms=['Linux', 'Mac OS-X', 'Unix'],
       classifiers=CLASSIFIERS.splitlines(),
-      packages=["gaff2xml"],
+      packages=["gaff2xml", "gaff2xml.tests"],
       zip_safe=False,
       scripts=['scripts/generate_example_data.py', 'scripts/processAmberForceField.py'],
       ext_modules=extensions,