Merge pull request #132 from rigdenlab/changes

Fixed issues with CCP4 tests

CHANGELOG.rst

@@ -2,6 +2,14 @@
 Changelog
 =========
 
+0.2.1
+-----
+
+Changed
+~~~~~~~
+- Fixed issues with simbad-database code
+- Changed how the tests are called to allow automatic testing in ccp4 
+
 0.2.0
 -----
 

simbad/db/tests/test_db.py

@@ -8,15 +8,22 @@
 import simbad
 import simbad.db
 
-SIMBAD_ROOT = os.environ['SIMBAD_ROOT']
+try:
+    ROOT_DIR = SHARE_DIR = os.environ['SIMBAD_ROOT']
+    EXAMPLE_DIR = os.path.join(ROOT_DIR, "test_data")
+except KeyError:
+    from simbad.command_line import CCP4RootDirectory
+    ROOT_DIR = str(CCP4RootDirectory())
+    SHARE_DIR = os.path.join(ROOT_DIR, "share", "simbad")
+    EXAMPLE_DIR = os.path.join(ROOT_DIR, "examples")
 
 
 class Test(unittest.TestCase):
     """Unit test"""
 
     def test_from_dat(self):
         """Test case for simbad.db._from_dat"""
-        input_dat = os.path.join(SIMBAD_ROOT, "static", "contaminants", "CHICK", "LYSC_CHICK", "P6122", "2fbb.dat")
+        input_dat = os.path.join(SHARE_DIR, "static", "contaminants", "CHICK", "LYSC_CHICK", "P6122", "2fbb.dat")
         with open(input_dat, "r") as f_in:
             output_str = simbad.db._from_dat(f_in)
 
@@ -27,7 +34,8 @@ def test_from_dat(self):
 
     def test_to_dat(self):
         """Test case for simbad.db._to_dat"""
-        input_pdb = os.path.join(SIMBAD_ROOT, "test_data", "toxd.pdb")
+        input_pdb = os.path.join(EXAMPLE_DIR, "toxd", "toxd.pdb")
+
         output_dat = os.path.join(os.getcwd(), "test.dat")
         with open(input_pdb, "r") as f_in, open(output_dat, "wb") as f_out:
             f_out.write(simbad.db._to_dat(f_in))
@@ -60,15 +68,15 @@ def test_str_to_dat(self):
 
     def test_find_simbad_dat_files(self):
         """Test case for simbad.db.find_simbad_dat_files"""
-        test_dat_db = os.path.join(SIMBAD_ROOT, "static", "contaminants", "CHICK", "LYSC_CHICK", "P6122")
+        test_dat_db = os.path.join(SHARE_DIR, "static", "contaminants", "CHICK", "LYSC_CHICK", "P6122")
         data = os.path.basename(simbad.db.find_simbad_dat_files(test_dat_db)[0])
         reference_data = "2fbb.dat"
 
         self.assertEqual(data, reference_data)
 
     def test_convert_pdb_to_dat(self):
         """Test case for simbad.db.convert_pdb_to_dat"""
-        input_pdb = os.path.join(SIMBAD_ROOT, "test_data", "toxd.pdb")
+        input_pdb = os.path.join(EXAMPLE_DIR, "toxd", "toxd.pdb")
         output_dat = os.path.join(os.getcwd(), "test.dat")
         simbad.db.convert_pdb_to_dat(input_pdb, output_dat)
 
@@ -79,7 +87,7 @@ def test_convert_pdb_to_dat(self):
 
     def test_convert_dat_to_pdb(self):
         """Test case for simbad.db.convert_dat_to_pdb"""
-        input_dat = os.path.join(SIMBAD_ROOT, "static", "contaminants", "CHICK", "LYSC_CHICK", "P6122", "2fbb.dat")
+        input_dat = os.path.join(SHARE_DIR, "static", "contaminants", "CHICK", "LYSC_CHICK", "P6122", "2fbb.dat")
         output_pdb = os.path.join(os.getcwd(), "test.pdb")
         simbad.db.convert_dat_to_pdb(input_dat, output_pdb)
 
@@ -88,14 +96,14 @@ def test_convert_dat_to_pdb(self):
 
     def test_is_valid_dat(self):
         """Test case for simbad.db.is_valid_dat"""
-        input_dat = os.path.join(SIMBAD_ROOT, "static", "contaminants", "CHICK", "LYSC_CHICK", "P6122", "2fbb.dat")
+        input_dat = os.path.join(SHARE_DIR, "static", "contaminants", "CHICK", "LYSC_CHICK", "P6122", "2fbb.dat")
         data = simbad.db.is_valid_dat(input_dat)
 
         self.assertTrue(data)
 
     def test_read_dat(self):
         """Test case for simbad.db.read_dat"""
-        input_dat = os.path.join(SIMBAD_ROOT, "static", "contaminants", "CHICK", "LYSC_CHICK", "P6122", "2fbb.dat")
+        input_dat = os.path.join(SHARE_DIR, "static", "contaminants", "CHICK", "LYSC_CHICK", "P6122", "2fbb.dat")
         output_str = simbad.db.read_dat(input_dat)
 
         data = output_str.split("\n")[0]

simbad/lattice/tests/test_latticesearch.py

@@ -8,15 +8,19 @@
 import unittest
 from simbad.lattice.lattice_search import LatticeSearch
 
-SIMBAD_ROOT = os.environ['SIMBAD_ROOT']
+try:
+    SHARE_DIR = os.environ['SIMBAD_ROOT']
+except KeyError:
+    from simbad.command_line import CCP4RootDirectory
+    SHARE_DIR = os.path.join(str(CCP4RootDirectory()), "share", "simbad")
 
 
 class Test(unittest.TestCase):
     """Unit test"""
 
     @classmethod
     def setUpClass(cls):
-        lattice_db = os.path.join(SIMBAD_ROOT, "static", "niggli_database.npz")
+        lattice_db = os.path.join(SHARE_DIR, "static", "niggli_database.npz")
         cls.LS = LatticeSearch(lattice_db, os.getcwd())
 
     @unittest.skipIf('THIS_IS_TRAVIS' in os.environ, "not implemented in Travis CI")

simbad/rotsearch/tests/test_rotation_search.py

@@ -8,15 +8,21 @@
 import simbad.rotsearch.amore_search
 import simbad.rotsearch.phaser_search
 
-SIMBAD_ROOT = os.environ['SIMBAD_ROOT']
+try:
+    ROOT_DIR = os.environ['SIMBAD_ROOT']
+    EXAMPLE_DIR = os.path.join(ROOT_DIR, "test_data")
+except KeyError:
+    from simbad.command_line import CCP4RootDirectory
+    ROOT_DIR = str(CCP4RootDirectory())
+    EXAMPLE_DIR = os.path.join(ROOT_DIR, "examples")
 
 
 class Test(unittest.TestCase):
     """Unit test"""
 
     @classmethod
     def setUpClass(cls):
-        mtz = os.path.join(SIMBAD_ROOT, "test_data", "toxd.mtz")
+        mtz = os.path.join(EXAMPLE_DIR, "toxd", "toxd.mtz")
         cls.AS = simbad.rotsearch.amore_search.AmoreRotationSearch(mtz, "molrep", "tmp_dir", "work_dir")
         cls.PS = simbad.rotsearch.phaser_search.PhaserRotationSearch(mtz, "molrep", "tmp_dir", "work_dir")
 

simbad/util/mtz_util.py

@@ -112,7 +112,7 @@ def reindex(hklin, hklout, sg):
     cexec(cmd, stdin=stdin)
 
 
-@deprecate('0.2.1', msg="Use simbad.parsers.mtz_parser.MtzParser instead")
+@deprecate('0.2.2', msg="Use simbad.parsers.mtz_parser.MtzParser instead")
 class GetLabels(object):
     def __init__(self, hklin):
         self.f = None
@@ -154,7 +154,7 @@ def run(self, hklin):
         self.free = mp.free
 
 
-@deprecate('0.2.1', msg="Use simbad.parsers.mtz_parser.MtzParser instead")
+@deprecate('0.2.2', msg="Use simbad.parsers.mtz_parser.MtzParser instead")
 def crystal_data(hklin):
     mp = MtzParser(hklin)
     space_group = "".join(mp.spacegroup_symbol.encode("ascii").split())

simbad/util/pdb_util.py

@@ -41,6 +41,7 @@ def assert_structure(self):
     @staticmethod
     def get_pdb_content(pdb_code):
         import iotbx.pdb.fetch
+        import urllib2
         try:
             try:
                 content = iotbx.pdb.fetch.fetch(pdb_code, data_type="pdb", format="pdb", mirror="pdb-redo")

simbad/util/tests/test_matthews_prob.py

@@ -8,7 +8,13 @@
 import unittest
 from simbad.util import matthews_prob
 
-SIMBAD_ROOT = os.environ['SIMBAD_ROOT']
+try:
+    ROOT_DIR = os.environ['SIMBAD_ROOT']
+    EXAMPLE_DIR = os.path.join(ROOT_DIR, "test_data")
+except KeyError:
+    from simbad.command_line import CCP4RootDirectory
+    ROOT_DIR = str(CCP4RootDirectory())
+    EXAMPLE_DIR = os.path.join(ROOT_DIR, "examples")
 
 
 class Test(unittest.TestCase):
@@ -17,7 +23,7 @@ class Test(unittest.TestCase):
     def test_solvent_content(self):
         """Test case for matthews_prob.SolventContent.calculate_from_file"""
 
-        input_model = os.path.join(SIMBAD_ROOT, "test_data", "toxd.pdb")
+        input_model = os.path.join(EXAMPLE_DIR, "toxd", "toxd.pdb")
         volume = 16522.4616729
         SC = matthews_prob.SolventContent(volume)
         data = SC.calculate_from_file(input_model)
@@ -29,7 +35,7 @@ def test_solvent_content(self):
     def test_matthews_prob(self):
         """Test case for matthews_prob.MatthewsProbability.calculate_from_file"""
 
-        input_model = os.path.join(SIMBAD_ROOT, "test_data", "toxd.pdb")
+        input_model = os.path.join(EXAMPLE_DIR, "toxd", "toxd.pdb")
         volume = 16522.4616729
         MC = matthews_prob.MatthewsProbability(volume)
         data = MC.calculate_from_file(input_model)

simbad/util/tests/test_mtz_util.py

@@ -8,7 +8,13 @@
 from simbad.parsers import mtz_parser
 from simbad.util import mtz_util
 
-SIMBAD_ROOT = os.environ['SIMBAD_ROOT']
+try:
+    ROOT_DIR = os.environ['SIMBAD_ROOT']
+    EXAMPLE_DIR = os.path.join(ROOT_DIR, "test_data")
+except KeyError:
+    from simbad.command_line import CCP4RootDirectory
+    ROOT_DIR = str(CCP4RootDirectory())
+    EXAMPLE_DIR = os.path.join(ROOT_DIR, "examples")
 
 
 class Test(unittest.TestCase):
@@ -17,7 +23,7 @@ class Test(unittest.TestCase):
     def test_crystal_data_1(self):
         """Test case for mtz_util.crystal_data"""
 
-        input_mtz = os.path.join(SIMBAD_ROOT, "test_data", "toxd.mtz")
+        input_mtz = os.path.join(EXAMPLE_DIR, "toxd", "toxd.mtz")
         mtz_obj = mtz_parser.MtzParser(input_mtz)
         data = (
             "".join(mtz_obj.spacegroup_symbol.encode("ascii").split()),
@@ -53,7 +59,7 @@ def test_crystal_data_1(self):
     def test_crystal_data_2(self):
         """Test case for mtz_util.crystal_data"""
 
-        input_mtz = os.path.join(SIMBAD_ROOT, "test_data", "rnase25.mtz")
+        input_mtz = os.path.join(EXAMPLE_DIR, "rnase", "rnase25.mtz")
         mtz_obj = mtz_parser.MtzParser(input_mtz)
         data = (
             "".join(mtz_obj.spacegroup_symbol.encode("ascii").split()),
@@ -90,7 +96,7 @@ def test_crystal_data_2(self):
     def test_get_labels_1(self):
         """Test case for mtz_util.get_labels"""
 
-        input_mtz = os.path.join(SIMBAD_ROOT, "test_data", "toxd.mtz")
+        input_mtz = os.path.join(EXAMPLE_DIR, "toxd", "toxd.mtz")
         temp_mtz = os.path.join(os.getcwd(), "input.mtz")
         temp_log = os.path.join(os.getcwd(), "input.log")
         mtz_util.ctruncate(input_mtz, temp_mtz)
@@ -109,7 +115,7 @@ def test_get_labels_1(self):
     def test_get_labels_2(self):
         """Test case for mtz_util.get_labels"""
 
-        input_mtz = os.path.join(SIMBAD_ROOT, "test_data", "rnase25F+F-.mtz")
+        input_mtz = os.path.join(EXAMPLE_DIR, "rnase", "rnase25F+F-.mtz")
         temp_mtz = os.path.join(os.getcwd(), "input.mtz")
         temp_log = os.path.join(os.getcwd(), "input.log")
         mtz_util.ctruncate(input_mtz, temp_mtz)
@@ -128,7 +134,7 @@ def test_get_labels_2(self):
     @unittest.skipIf('THIS_IS_TRAVIS' in os.environ, "not implemented in Travis CI")
     def test_change_space_group_1(self):
         """Test case for mtz_util.ExperimentalData.change_space_group"""
-        input_mtz = os.path.join(SIMBAD_ROOT, "test_data", "toxd.mtz")
+        input_mtz = os.path.join(EXAMPLE_DIR, "toxd", "toxd.mtz")
         temp_mtz = os.path.join(os.getcwd(), "input.mtz")
         mtz_util.reindex(input_mtz, temp_mtz, "18")
         mtz_obj = mtz_parser.MtzParser(temp_mtz)

simbad/util/tests/test_pdb_util.py

@@ -17,7 +17,13 @@
     from urllib.request import urlopen
     from urllib.error import URLError
 
-SIMBAD_ROOT = os.environ['SIMBAD_ROOT']
+try:
+    ROOT_DIR = os.environ['SIMBAD_ROOT']
+    EXAMPLE_DIR = os.path.join(ROOT_DIR, "test_data")
+except KeyError:
+    from simbad.command_line import CCP4RootDirectory
+    ROOT_DIR = str(CCP4RootDirectory())
+    EXAMPLE_DIR = os.path.join(ROOT_DIR, "examples")
 
 
 def internet_on():
@@ -35,7 +41,7 @@ class Test(unittest.TestCase):
     def test_calculate_integration_box(self):
         """Test case for PdbStructure.integration_box"""
 
-        input_model = os.path.join(SIMBAD_ROOT, "test_data", "toxd.pdb")
+        input_model = os.path.join(EXAMPLE_DIR, "toxd", "toxd.pdb")
         pdb_struct = PdbStructure.from_file(input_model)
         data = pdb_struct.integration_box
         reference_data = (48.306749999999994, 56.73474999999999, 48.589749999999995, 19.84575)
@@ -45,7 +51,7 @@ def test_calculate_integration_box(self):
     def test_molecular_weight_1(self):
         """Test case for PdbStructure.molecular_weight"""
 
-        input_model = os.path.join(SIMBAD_ROOT, "test_data", "toxd.pdb")
+        input_model = os.path.join(EXAMPLE_DIR, "toxd", "toxd.pdb")
         pdb_struct = PdbStructure.from_file(input_model)
         data = pdb_struct.molecular_weight
         reference_data = 6855.978639999951
@@ -55,7 +61,7 @@ def test_molecular_weight_1(self):
     def test_molecular_weight_2(self):
         """Test case for PdbStructure.molecular_weight"""
 
-        input_model = os.path.join(SIMBAD_ROOT, "test_data", "rnase.pdb")
+        input_model = os.path.join(EXAMPLE_DIR, "rnase", "rnase.pdb")
         pdb_struct = PdbStructure.from_file(input_model)
         data = pdb_struct.molecular_weight
         reference_data = 21163.001080955823
@@ -65,7 +71,7 @@ def test_molecular_weight_2(self):
     def test_molecular_weight_3(self):
         """Test case for PdbStructure.molecular_weight"""
 
-        input_model = os.path.join(SIMBAD_ROOT, "test_data", "3a22.pdb")
+        input_model = os.path.join(EXAMPLE_DIR, "data", "3a22.pdb")
         pdb_struct = PdbStructure.from_file(input_model)
         data = pdb_struct.molecular_weight
         reference_data = 128535.91044924183

simbad/version.py

@@ -2,7 +2,7 @@
 
 # Maintain sematantic versioning. Further information can
 # be found here [http://semver.org/]
-__version_info__ = (0, 2, 0)
+__version_info__ = (0, 2, 1)
 
 # ======================================================
 # Do __NOT__ change anything below here