Merge pull request #182 from Autodesk/testsize

Reduce the size of the test data files
Autodesk · Oct 12, 2017 · 085a87a · 085a87a
2 parents 6900a9c + eef42de
commit 085a87a
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Showing 16 changed files with 11 additions and 13,428 deletions.
diff --git a/moldesign/_tests/data/1pyn.pdb b/moldesign/_tests/data/1pyn.pdb
diff --git a/moldesign/_tests/data/1pyn.pdb.gz b/moldesign/_tests/data/1pyn.pdb.gz
diff --git a/moldesign/_tests/data/3ac2.pdb b/moldesign/_tests/data/3ac2.pdb
diff --git a/moldesign/_tests/data/3ac2.pdb.bz2 b/moldesign/_tests/data/3ac2.pdb.bz2
diff --git a/moldesign/_tests/data/3aid.cif b/moldesign/_tests/data/3aid.cif
diff --git a/moldesign/_tests/data/3aid.cif.bz2 b/moldesign/_tests/data/3aid.cif.bz2
diff --git a/moldesign/_tests/data/3aid.pdb b/moldesign/_tests/data/3aid.pdb
diff --git a/moldesign/_tests/data/3aid.pdb.gz b/moldesign/_tests/data/3aid.pdb.gz
diff --git a/moldesign/_tests/data/3p3k.pdb b/moldesign/_tests/data/3p3k.pdb
diff --git a/moldesign/_tests/data/3p3k.pdb.gz b/moldesign/_tests/data/3p3k.pdb.gz
diff --git a/moldesign/_tests/molecule_fixtures.py b/moldesign/_tests/molecule_fixtures.py
@@ -29,7 +29,7 @@ def fixture_wrapper(func):
 # Tests around PDB ID 3AID
 @typedfixture('molecule')
 def pdb3aid():
-    mol = mdt.read(get_data_path('3aid.pdb'))
+    mol = mdt.read(get_data_path('3aid.pdb.gz'))
     return mol
 
 

diff --git a/moldesign/_tests/test_atom_containers.py b/moldesign/_tests/test_atom_containers.py
@@ -30,7 +30,7 @@ def fixture_wrapper(func):
 
 @typedfixture('container')
 def protein():
-    return mdt.read(helpers.get_data_path('3aid.pdb'))
+    return mdt.read(helpers.get_data_path('3aid.pdb.gz'))
 
 
 @pytest.fixture

diff --git a/moldesign/_tests/test_biopython_xface.py b/moldesign/_tests/test_biopython_xface.py
@@ -1,4 +1,4 @@
-
+import io
 import pytest
 import Bio.PDB
 import moldesign as mdt
@@ -9,8 +9,10 @@
 
 @pytest.fixture
 def biopy_3aid():
+    import gzip
     parser = Bio.PDB.PDBParser()
-    structure = parser.get_structure('3aid', get_data_path('3aid.pdb'))
+    s = gzip.open(get_data_path('3aid.pdb.gz'), 'r').read().decode('utf-8')
+    structure = parser.get_structure('3aid', io.StringIO(s))
     return structure
 
 

diff --git a/moldesign/_tests/test_pdb_processing.py b/moldesign/_tests/test_pdb_processing.py
@@ -15,7 +15,7 @@
 
 @pytest.fixture
 def pdb_3ac2():
-    return mdt.read(get_data_path('3ac2.pdb'))
+    return mdt.read(get_data_path('3ac2.pdb.bz2'))
 
 
 @pytest.fixture
@@ -97,7 +97,7 @@ def test_missing_residues_nmr_5b7a():
 
 @pytest.fixture
 def pdb_1pyn():
-    return mdt.read(get_data_path('1pyn.pdb'))
+    return mdt.read(get_data_path('1pyn.pdb.gz'))
 
 
 @pytest.fixture

diff --git a/moldesign/_tests/test_protein_primary_structure.py b/moldesign/_tests/test_protein_primary_structure.py
@@ -25,12 +25,12 @@ def fixture_wrapper(func):
 
 @typedfixture('3AID', 'protein')
 def protease_pdb():
-    return mdt.read(get_data_path('3aid.pdb'))
+    return mdt.read(get_data_path('3aid.pdb.gz'))
 
 
 @typedfixture('3AID', 'protein')
 def protease_cif():
-    return mdt.read(get_data_path('3aid.cif'))
+    return mdt.read(get_data_path('3aid.cif.bz2'))
 
 
 def test_chain_types(protease_pdb):

diff --git a/moldesign/_tests/test_tools.py b/moldesign/_tests/test_tools.py
@@ -108,7 +108,7 @@ def test_add_hydrogen_to_c2(c2_no_hydrogen_from_smiles):
 
 
 def test_split_chains_3p3k():
-    mol = mdt.read(get_data_path('3p3k.pdb'))
+    mol = mdt.read(get_data_path('3p3k.pdb.gz'))
     assert mol.num_chains == 1  # not really testing this, just for sanity's sake
 
     newmol = mdt.split_chains(mol)