From af91e2f7c1b7554bb82f0d399aceec83b953e531 Mon Sep 17 00:00:00 2001
From: Kyle Beauchamp <kyleabeauchamp@gmail.com>
Date: Mon, 8 Dec 2014 15:08:28 -0500
Subject: [PATCH 01/11] Initial checkin of travis cahnges

---
 .travis.yml                     | 13 ++++++-------
 devtools/ci/install.sh          | 20 ++++++++++++++++++++
 devtools/conda-recipe/meta.yaml | 32 ++++++++++++++++++++++++--------
 3 files changed, 50 insertions(+), 15 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index a24948c..ee58b9c 100644
--- a/.travis.yml
+++ b/.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:
@@ -28,3 +26,4 @@ after_success:
   - source devtools/ci/after_sucess.sh
 
 
+zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
diff --git a/devtools/ci/install.sh b/devtools/ci/install.sh
index 449e24f..83242cc 100755
--- a/devtools/ci/install.sh
+++ b/devtools/ci/install.sh
@@ -1,3 +1,23 @@
+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
+
+conda update --yes conda
+conda config --add channels http://conda.binstar.org/omnia
+source activate $python
+conda install --yes conda-build
+
+
+
+
 sudo apt-get update
 sudo apt-get install -qq -y g++ gfortran csh
 sudo apt-get install -qq -y g++-multilib gcc-multilib openbabel
diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
index f85a8ff..6612f6c 100644
--- a/devtools/conda-recipe/meta.yaml
+++ b/devtools/conda-recipe/meta.yaml
@@ -1,27 +1,43 @@
 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    
-
+    - ambermini
   run:
     - python
+    - setuptools
     - pandas
+    - six
+    - mdtraj
+    - numpydoc
     - scipy
-    - mdtraj-dev
     - openmm    
     - ambermini    
 
+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+)

From 9536d09b69bcaf48990de1aed4cee8ff64c3ec35 Mon Sep 17 00:00:00 2001
From: kyleabeauchamp <kyleabeauchamp@gmail.com>
Date: Mon, 8 Dec 2014 15:34:36 -0500
Subject: [PATCH 02/11] Updates

---
 .travis.yml                        |  3 ---
 devtools/ci/install.sh             | 17 ++---------------
 devtools/ci/requirements-conda.txt |  4 ++--
 3 files changed, 4 insertions(+), 20 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index ee58b9c..94ef08b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -24,6 +24,3 @@ env:
 after_success:
   - echo "after_success"
   - source devtools/ci/after_sucess.sh
-
-
-zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
diff --git a/devtools/ci/install.sh b/devtools/ci/install.sh
index 83242cc..2b19f79 100755
--- a/devtools/ci/install.sh
+++ b/devtools/ci/install.sh
@@ -10,25 +10,12 @@ PIP_ARGS="-U"
 
 export PATH=$HOME/miniconda/bin:$PATH
 
-conda update --yes conda
-conda config --add channels http://conda.binstar.org/omnia
-source activate $python
-conda install --yes conda-build
-
-
-
-
 sudo apt-get update
-sudo apt-get install -qq -y g++ gfortran csh
-sudo apt-get install -qq -y g++-multilib gcc-multilib openbabel
-wget http://repo.continuum.io/miniconda/Miniconda-3.6.0-Linux-x86_64.sh
-bash Miniconda-3.6.0-Linux-x86_64.sh -b
-PIP_ARGS="-U"
-
-export PATH=$HOME/miniconda/bin:$PATH
+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
 source activate $python
+conda install --yes conda-build
diff --git a/devtools/ci/requirements-conda.txt b/devtools/ci/requirements-conda.txt
index fae9ac3..c742b70 100644
--- a/devtools/ci/requirements-conda.txt
+++ b/devtools/ci/requirements-conda.txt
@@ -6,8 +6,8 @@ pandas
 pyyaml
 pip
 nose
-mdtraj-dev
-openmm
+mdtraj>=1.2
+openmm>=6.1
 ambermini
 jinja2
 #rdkit # rdkit conda packages are only available on python 2.7, so this will cause travis to screw up.  

From 14f462caf2c03e1beb829565d3f79ca4a02542a7 Mon Sep 17 00:00:00 2001
From: kyleabeauchamp <kyleabeauchamp@gmail.com>
Date: Mon, 8 Dec 2014 15:58:16 -0500
Subject: [PATCH 03/11] Updates

---
 devtools/ci/install.sh         | 2 ++
 devtools/conda-recipe/build.sh | 7 +------
 2 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/devtools/ci/install.sh b/devtools/ci/install.sh
index 2b19f79..1cd6b64 100755
--- a/devtools/ci/install.sh
+++ b/devtools/ci/install.sh
@@ -14,8 +14,10 @@ sudo apt-get update
 sudo apt-get install -qq -y g++ gfortran csh g++-multilib gcc-multilib openbabel
 
 conda update --yes conda
+echo "Update 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
 source activate $python
 conda install --yes conda-build
+echo "install conda build"
diff --git a/devtools/conda-recipe/build.sh b/devtools/conda-recipe/build.sh
index fff95df..d3e1d70 100755
--- a/devtools/conda-recipe/build.sh
+++ b/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.

From dcea0206d06e124d38028c1bbf54ba94979b37ae Mon Sep 17 00:00:00 2001
From: kyleabeauchamp <kyleabeauchamp@gmail.com>
Date: Mon, 8 Dec 2014 16:20:22 -0500
Subject: [PATCH 04/11] Some updates

---
 devtools/ci/install.sh          |  2 +-
 devtools/conda-recipe/meta.yaml | 14 ++++++++------
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/devtools/ci/install.sh b/devtools/ci/install.sh
index 1cd6b64..a7e334b 100755
--- a/devtools/ci/install.sh
+++ b/devtools/ci/install.sh
@@ -17,7 +17,7 @@ conda update --yes conda
 echo "Update 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 create --yes -n ${python} python=${python} --file devtools/ci/requirements-conda.txt  # Now using conda to automatically handle environment creation / testing
 source activate $python
 conda install --yes conda-build
 echo "install conda build"
diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
index 6612f6c..a83e4b4 100644
--- a/devtools/conda-recipe/meta.yaml
+++ b/devtools/conda-recipe/meta.yaml
@@ -14,21 +14,24 @@ requirements:
   build:
     - python
     - setuptools
-    - mdtraj
+    - mdtraj>=1.2
     - numpy
     - scipy
-    - openmm    
+    - pandas    
+    - openmm>=6.1
     - ambermini
+    - jinja2
   run:
     - python
     - setuptools
     - pandas
     - six
-    - mdtraj
+    - mdtraj>=1.2
     - numpydoc
     - scipy
-    - openmm    
-    - ambermini    
+    - openmm>=6.1
+    - ambermini
+
 
 test:
   requires:
@@ -41,4 +44,3 @@ test:
 about:
   home: https://github.com/choderalab/gaff2xml
   license: GNU Lesser General Public License v2 or later (LGPLv2+)
-

From bd03376947cd3977b9cb17c7ba4935d3f4dda8f9 Mon Sep 17 00:00:00 2001
From: kyleabeauchamp <kyleabeauchamp@gmail.com>
Date: Mon, 8 Dec 2014 16:43:50 -0500
Subject: [PATCH 05/11] Updates

---
 devtools/conda-recipe/meta.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
index a83e4b4..5b1fdc7 100644
--- a/devtools/conda-recipe/meta.yaml
+++ b/devtools/conda-recipe/meta.yaml
@@ -14,11 +14,11 @@ requirements:
   build:
     - python
     - setuptools
-    - mdtraj>=1.2
+    - mdtraj
     - numpy
     - scipy
     - pandas    
-    - openmm>=6.1
+    - openmm
     - ambermini
     - jinja2
   run:
@@ -26,12 +26,12 @@ requirements:
     - setuptools
     - pandas
     - six
-    - mdtraj>=1.2
+    - mdtraj
     - numpydoc
     - scipy
-    - openmm>=6.1
+    - openmm
     - ambermini
-
+    - jinja2    
 
 test:
   requires:

From f108f18b38e290954da7095c37f4a89d7a1883ea Mon Sep 17 00:00:00 2001
From: kyleabeauchamp <kyleabeauchamp@gmail.com>
Date: Mon, 8 Dec 2014 17:07:58 -0500
Subject: [PATCH 06/11] Include tests in package

---
 {tests => gaff2xml/tests}/test_drugs.py        | 18 ++++++++++++++++--
 .../tests}/test_drugs_no_oechem.py             |  0
 {tests => gaff2xml/tests}/test_freesolv.py     |  0
 {tests => gaff2xml/tests}/test_openeye.py      |  0
 {tests => gaff2xml/tests}/test_packmol.py      |  0
 {tests => gaff2xml/tests}/test_utils.py        |  0
 setup.py                                       |  2 +-
 7 files changed, 17 insertions(+), 3 deletions(-)
 rename {tests => gaff2xml/tests}/test_drugs.py (58%)
 rename {tests => gaff2xml/tests}/test_drugs_no_oechem.py (100%)
 rename {tests => gaff2xml/tests}/test_freesolv.py (100%)
 rename {tests => gaff2xml/tests}/test_openeye.py (100%)
 rename {tests => gaff2xml/tests}/test_packmol.py (100%)
 rename {tests => gaff2xml/tests}/test_utils.py (100%)

diff --git a/tests/test_drugs.py b/gaff2xml/tests/test_drugs.py
similarity index 58%
rename from tests/test_drugs.py
rename to gaff2xml/tests/test_drugs.py
index 45784fb..1b519fe 100644
--- a/tests/test_drugs.py
+++ b/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")
diff --git a/tests/test_drugs_no_oechem.py b/gaff2xml/tests/test_drugs_no_oechem.py
similarity index 100%
rename from tests/test_drugs_no_oechem.py
rename to gaff2xml/tests/test_drugs_no_oechem.py
diff --git a/tests/test_freesolv.py b/gaff2xml/tests/test_freesolv.py
similarity index 100%
rename from tests/test_freesolv.py
rename to gaff2xml/tests/test_freesolv.py
diff --git a/tests/test_openeye.py b/gaff2xml/tests/test_openeye.py
similarity index 100%
rename from tests/test_openeye.py
rename to gaff2xml/tests/test_openeye.py
diff --git a/tests/test_packmol.py b/gaff2xml/tests/test_packmol.py
similarity index 100%
rename from tests/test_packmol.py
rename to gaff2xml/tests/test_packmol.py
diff --git a/tests/test_utils.py b/gaff2xml/tests/test_utils.py
similarity index 100%
rename from tests/test_utils.py
rename to gaff2xml/tests/test_utils.py
diff --git a/setup.py b/setup.py
index 6109eb3..6dced58 100644
--- a/setup.py
+++ b/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,

From a8a4fe2a1a13370e4766b2668cb3c1d2198d1136 Mon Sep 17 00:00:00 2001
From: kyleabeauchamp <kyleabeauchamp@gmail.com>
Date: Mon, 8 Dec 2014 17:18:34 -0500
Subject: [PATCH 07/11] Use updated rdkit repo

---
 devtools/ci/install.sh          | 2 +-
 devtools/conda-recipe/meta.yaml | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/devtools/ci/install.sh b/devtools/ci/install.sh
index a7e334b..15123c5 100755
--- a/devtools/ci/install.sh
+++ b/devtools/ci/install.sh
@@ -16,7 +16,7 @@ sudo apt-get install -qq -y g++ gfortran csh g++-multilib gcc-multilib openbabel
 conda update --yes conda
 echo "Update conda"
 conda config --add channels http://conda.binstar.org/omnia
-conda config --add channels https://conda.binstar.org/ric
+conda config --add channels https://conda.binstar.org/rdkit
 #conda create --yes -n ${python} python=${python} --file devtools/ci/requirements-conda.txt  # Now using conda to automatically handle environment creation / testing
 source activate $python
 conda install --yes conda-build
diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
index 5b1fdc7..2b40bc1 100644
--- a/devtools/conda-recipe/meta.yaml
+++ b/devtools/conda-recipe/meta.yaml
@@ -21,6 +21,7 @@ requirements:
     - openmm
     - ambermini
     - jinja2
+    - rdkit    
   run:
     - python
     - setuptools
@@ -31,7 +32,8 @@ requirements:
     - scipy
     - openmm
     - ambermini
-    - jinja2    
+    - jinja2
+    - rdkit    
 
 test:
   requires:

From 9db3adefd932c363a37208ea95dfaaf664c9c32b Mon Sep 17 00:00:00 2001
From: kyleabeauchamp <kyleabeauchamp@gmail.com>
Date: Mon, 8 Dec 2014 17:28:33 -0500
Subject: [PATCH 08/11] Updates

---
 README.md                       | 23 ++++++++++++++++++++---
 devtools/conda-recipe/meta.yaml |  4 ++--
 2 files changed, 22 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 18957eb..dc68c9c 100644
--- a/README.md
+++ b/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:
 
diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
index 2b40bc1..d4ccb00 100644
--- a/devtools/conda-recipe/meta.yaml
+++ b/devtools/conda-recipe/meta.yaml
@@ -21,7 +21,7 @@ requirements:
     - openmm
     - ambermini
     - jinja2
-    - rdkit    
+    - rdkit    # rdkit is an optional dependency, may want to comment this out for the release version.
   run:
     - python
     - setuptools
@@ -33,7 +33,7 @@ requirements:
     - openmm
     - ambermini
     - jinja2
-    - rdkit    
+    - rdkit    # rdkit is an optional dependency, may want to comment this out for the release version.
 
 test:
   requires:

From 3099981c349830618c1ee8206d42760a3c237fa2 Mon Sep 17 00:00:00 2001
From: kyleabeauchamp <kyleabeauchamp@gmail.com>
Date: Mon, 8 Dec 2014 18:13:41 -0500
Subject: [PATCH 09/11] Don't include rdkit in conda recipe.

---
 devtools/conda-recipe/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
index d4ccb00..4bae78b 100644
--- a/devtools/conda-recipe/meta.yaml
+++ b/devtools/conda-recipe/meta.yaml
@@ -21,7 +21,7 @@ requirements:
     - openmm
     - ambermini
     - jinja2
-    - rdkit    # rdkit is an optional dependency, may want to comment this out for the release version.
+#    - rdkit    # rdkit is an optional dependency, may want to comment this out for the release version.
   run:
     - python
     - setuptools
@@ -33,7 +33,7 @@ requirements:
     - openmm
     - ambermini
     - jinja2
-    - rdkit    # rdkit is an optional dependency, may want to comment this out for the release version.
+#    - rdkit    # rdkit is an optional dependency, may want to comment this out for the release version.
 
 test:
   requires:

From dc6224aa9d20e96f47527fd931d3484f3498d857 Mon Sep 17 00:00:00 2001
From: kyleabeauchamp <kyleabeauchamp@gmail.com>
Date: Mon, 8 Dec 2014 18:43:51 -0500
Subject: [PATCH 10/11] More cleanup

---
 devtools/ci/install.sh | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/devtools/ci/install.sh b/devtools/ci/install.sh
index 15123c5..31c7734 100755
--- a/devtools/ci/install.sh
+++ b/devtools/ci/install.sh
@@ -14,10 +14,7 @@ sudo apt-get update
 sudo apt-get install -qq -y g++ gfortran csh g++-multilib gcc-multilib openbabel
 
 conda update --yes conda
-echo "Update conda"
 conda config --add channels http://conda.binstar.org/omnia
 conda config --add channels https://conda.binstar.org/rdkit
-#conda create --yes -n ${python} python=${python} --file devtools/ci/requirements-conda.txt  # Now using conda to automatically handle environment creation / testing
 source activate $python
 conda install --yes conda-build
-echo "install conda build"

From 3ab253c9014bc550dde02ab83b2ae4f73719ca3e Mon Sep 17 00:00:00 2001
From: kyleabeauchamp <kyleabeauchamp@gmail.com>
Date: Mon, 8 Dec 2014 18:44:31 -0500
Subject: [PATCH 11/11] Don't need requirements-conda anymore

---
 devtools/ci/requirements-conda.txt | 13 -------------
 1 file changed, 13 deletions(-)
 delete mode 100644 devtools/ci/requirements-conda.txt

diff --git a/devtools/ci/requirements-conda.txt b/devtools/ci/requirements-conda.txt
deleted file mode 100644
index c742b70..0000000
--- a/devtools/ci/requirements-conda.txt
+++ /dev/null
@@ -1,13 +0,0 @@
-numpy
-scipy
-pytables
-cython
-pandas
-pyyaml
-pip
-nose
-mdtraj>=1.2
-openmm>=6.1
-ambermini
-jinja2
-#rdkit # rdkit conda packages are only available on python 2.7, so this will cause travis to screw up.