Merge pull request #81 from kyleabeauchamp/recipe

Switched from hard-coded jenkins / travis detection in tests to nose attribute 'slow'

.travis.yml

@@ -15,7 +15,7 @@ script:
 env:
   matrix:
     - python=2.7  CONDA_PY=27
-    - python=3.3  CONDA_PY=33
+    - python=3.4  CONDA_PY=34
 
   global:
     # encrypted BINSTAR_TOKEN for push of dev package to binstar

devtools/ci/install.sh

@@ -17,4 +17,4 @@ conda update --yes conda
 conda config --add channels http://conda.binstar.org/omnia
 conda config --add channels https://conda.binstar.org/rdkit
 source activate $python
-conda install --yes conda-build
+conda install --yes conda-build jinja2

devtools/conda-recipe/meta.yaml

@@ -1,6 +1,6 @@
 package:
-  name: gaff2xml-dev
-  version: !!str 3.0.0
+  name: gaff2xml
+  version: !!str dev
 
 #source:
 #  fn: master.zip
@@ -20,7 +20,6 @@ requirements:
     - pandas    
     - openmm
     - ambermini
-    - jinja2
 #    - rdkit    # rdkit is an optional dependency, may want to comment this out for the release version.
   run:
     - python
@@ -32,7 +31,6 @@ requirements:
     - scipy
     - openmm
     - ambermini
-    - jinja2
 #    - rdkit    # rdkit is an optional dependency, may want to comment this out for the release version.
 
 test:
@@ -41,7 +39,7 @@ test:
   imports:
     - gaff2xml
   commands:
-    - nosetests gaff2xml -v
+    - nosetests gaff2xml -v -a '!slow'
 
 about:
   home: https://github.com/choderalab/gaff2xml

gaff2xml/tests/test_drugs.py

@@ -1,3 +1,4 @@
+from nose.plugins.attrib import attr
 from unittest import skipIf
 from gaff2xml import utils
 import os
@@ -17,6 +18,7 @@
 
 
 @skipIf(not HAVE_OE, "Cannot run test_drugs() module without OpenEye tools.")
+@attr('slow')
 def test_drugs():
     import openeye.oechem
     database_filename = utils.get_data_filename("chemicals/drugs/Zdd.mol2.gz")

gaff2xml/tests/test_drugs_no_oechem.py

@@ -1,21 +1,20 @@
+from nose.plugins.attrib import attr
 from unittest import skipIf
 import tempfile
 import os
 from gaff2xml import utils
 
-def test_drugs():
+def _drug_tester(n_molecules=3404, charge_method="bcc"):
+    """Helper function for running various versions of the drug parameterization benchmark."""
+    assert n_molecules <= 3404, "The maximum number of molecules is 3404."
+    assert charge_method in ["bcc", None], "Charge method must be either None or 'bcc'"
+
     path = tempfile.mkdtemp()
     database_filename = utils.get_data_filename("chemicals/drugs/Zdd.mol2.gz")
     cmd = "gunzip -c %s > %s/Zdd.mol2" % (database_filename, path)
     os.system(cmd)
     cmd = """awk '/MOLECULE/{close(x);x="%s/molecule_"i++".mol2"}{print > x}' %s/Zdd.mol2""" % (path, path)
     os.system(cmd)
-
-    n_molecules = 3404
-    CHARGE_METHOD = "bcc"
-    if (os.environ.get("TRAVIS", None) == 'true') or (os.environ.get("JENKINS_URL", None) is not None):
-        n_molecules = 25  # If running on travis, only test the first 25 molecules due to speed.
-        CHARGE_METHOD = None  # Travis is actually too slow to do a single bcc calculation!
 
     for k in range(n_molecules):
         molecule_name = "molecule_%d" % k
@@ -24,3 +23,12 @@ def test_drugs():
         os.system(cmd)  # Have to remove the <0> because it leads to invalid XML in the forcefield files.
         with utils.enter_temp_directory():
             yield utils.tag_description(lambda : utils.test_molecule("LIG", mol2_filename, charge_method=CHARGE_METHOD), "Testing drugs %s with charge method %s" % (molecule_name, CHARGE_METHOD))
+
+# This version is too slow to run during the conda-build post-test, on jenkins, or on travis.
+# In fact, Travis is actually too slow to do even a single AM1-BCC calculation
+@attr('slow')
+def test_drugs_all():
+    _drug_tester()
+
+def test_drugs_fast():
+    _drug_tester(n_molecules=20, charge_method=None)

gaff2xml/tests/test_freesolv.py

@@ -1,3 +1,4 @@
+from nose.plugins.attrib import attr
 from unittest import skipIf
 import tempfile
 import os
@@ -13,19 +14,13 @@
 
 
 @skipIf(find_executable('obabel') is None, 'You need obabel installed to run this test')
-@skipIf(os.environ.get("TRAVIS", None) == 'true', "Skip testing of entire FreeSolv database on Travis.")
-@skipIf(os.environ.get("JENKINS_URL", None) is not None, "Skip testing of entire FreeSolv database on Jenkins.")
-def test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb():
+def _tester_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb(charge_method="bcc"):
     with utils.enter_temp_directory():        
 
         tar_filename = utils.get_data_filename("chemicals/freesolv/freesolve_v0.3.tar.bz2")
         tar = tarfile.open(tar_filename, mode="r:bz2")
         tar.extractall()
         tar.close()
-
-        CHARGE_METHOD = "bcc"
-        if os.environ.get("TRAVIS", None) == 'true':
-            CHARGE_METHOD = None  # Travis is actually too slow to do a single bcc calculation!        
 
         database = pickle.load(open("./v0.3/database.pickle"))
         for key in database:
@@ -38,4 +33,12 @@ def test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb():
                 t_gaff = md.load(gaff_filename)
 
                 with utils.enter_temp_directory():        
-                     yield utils.tag_description(lambda : utils.test_molecule("LIG", gaff_filename, charge_method=CHARGE_METHOD), "Testing freesolv %s %s with charge model %s" % (directory, key, CHARGE_METHOD))
+                     yield utils.tag_description(lambda : utils.test_molecule("LIG", gaff_filename, charge_method=charge_method), "Testing freesolv %s %s with charge model %s" % (directory, key, charge_method))
+
+@attr("slow")
+def test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb():
+    _tester_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb()
+
+# Faster version because it skips AM1-BCC
+def test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb_nobcc():
+    _tester_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb(charge_method=None)