Merge branch 'develop'

CHANGELOG.rst

@@ -34,12 +34,18 @@ Version 1.2.0 (2016-07-26)
 
 - Updated changelog, fix version number in documentation
 
-1.2.4 (2016-07-26)
+1.2.4 (2016-08-04)
 ~~~~~~~~~~~~~~~~~~
 
 - Fixed bug that made it impossible to run GO-PCA from the command line
   (`go-pca.py`)
 
+1.2.5 (2016-08-05)
+~~~~~~~~~~~~~~~~~~
+
+- Fixed a bug that prevented the Gene Ontology file from being loaded when
+  running GO-PCA from the command line (`go-pca.py`)
+
 Version 1.1.3 (2016-02-23)
 --------------------------
 

gopca/main.py

@@ -318,9 +318,9 @@ def main(args=None):
     if args.gene_ontology_file is not None:
         p_logger = logging.getLogger(genometools.__name__)
         p_logger.setLevel(logging.ERROR)
-        gene_ontology = GeneOntology()
-        gene_ontology.read_obo(args.gene_ontology_file,
-                                 part_of_cc_only=config.go_part_of_cc_only)
+        gene_ontology = GeneOntology.read_obo(
+            args.gene_ontology_file,
+            part_of_cc_only=config.go_part_of_cc_only)
         p_logger.setLevel(logging.NOTSET)
 
     M = GOPCA(config, E, gene_sets, gene_ontology)

setup.py

@@ -54,14 +54,14 @@
         'scipy >= 0.14, < 1',
         'scikit-learn >= 0.14, < 1',
         'plotly >= 1.9.6, < 2',
-        'genometools >= 2.0rc6',
+        'genometools == 2.0rc6',
         'xlmhg >= 2.0.6, < 3',
     ])
 
 setup(
     name='gopca',
 
-    version='1.2.4',
+    version='1.2.5',
 
     description=description,
     long_description=long_description,

tests/03_cli/test_go_pca.py

@@ -0,0 +1,42 @@
+# Copyright (c) 2016 Florian Wagner
+#
+# This file is part of GO-PCA.
+#
+# GO-PCA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License, Version 3,
+# as published by the Free Software Foundation.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+from __future__ import (absolute_import, division,
+                        print_function, unicode_literals)
+# from builtins import *
+from builtins import open
+from builtins import str as text
+
+import pytest
+
+import subprocess as subproc
+
+@pytest.fixture(scope='session')
+def my_output_file(my_output_pypath):
+    return text(my_output_pypath.join('command-line_output.pickle'))
+
+def test_script(my_expression_file,
+                my_fly_gene_set_file,
+                my_gene_ontology_file,
+                my_output_file):
+
+    p = subproc.Popen(
+        'go-pca.py -o %s -e %s -s %s -t %s -D 5'
+        % (my_output_file, my_expression_file, my_fly_gene_set_file,
+           my_gene_ontology_file),
+        shell=True, stdout=subproc.PIPE, stderr=subproc.PIPE)
+    stdout, stderr = p.communicate()
+    assert p.returncode == 0  # no errors

tests/conftest.py

@@ -50,6 +50,10 @@ def my_data_pypath(tmpdir_factory):
     pypath = tmpdir_factory.mktemp('gopca_data', numbered=False)
     return pypath
 
+@pytest.fixture(scope='session')
+def my_output_pypath(tmpdir_factory):
+    pypath = tmpdir_factory.mktemp('gopca_output', numbered=False)
+    return pypath
 
 @pytest.fixture(scope='session')
 def my_expression_file(my_data_pypath):