fix: installation options and test on py36

Author: satra

nipype/external/due.py

@@ -54,11 +54,7 @@ def _donothing_func(*args, **kwargs):
     if 'due' in locals() and not hasattr(due, 'cite'):
         raise RuntimeError(
             "Imported due lacks .cite. DueCredit is now disabled")
-except Exception as e:
-    if type(e).__name__ != 'ImportError':
-        import logging
-        logging.getLogger("duecredit").error(
-            "Failed to import duecredit due to %s" % str(e))
+except ImportError:
     # Initiate due stub
     due = InactiveDueCreditCollector()
     BibTeX = Doi = Url = _donothing_func

nipype/info.py

@@ -55,6 +55,7 @@ def get_nipype_gitversion():
                'Programming Language :: Python :: 2.7',
                'Programming Language :: Python :: 3.4',
                'Programming Language :: Python :: 3.5',
+               'Programming Language :: Python :: 3.6',
                'Topic :: Scientific/Engineering']
 
 description = 'Neuroimaging in Python: Pipelines and Interfaces'
@@ -94,16 +95,16 @@ def get_nipype_gitversion():
 """
 
 # versions
-NIBABEL_MIN_VERSION = '2.0.1'
+NIBABEL_MIN_VERSION = '2.1.0'
 NETWORKX_MIN_VERSION = '1.7'
 NUMPY_MIN_VERSION = '1.6.2'
 SCIPY_MIN_VERSION = '0.11'
 TRAITS_MIN_VERSION = '4.6'
 DATEUTIL_MIN_VERSION = '1.5'
 PYTEST_MIN_VERSION = '3.0'
-FUTURE_MIN_VERSION = '0.15.2'
+FUTURE_MIN_VERSION = '0.16.0'
 SIMPLEJSON_MIN_VERSION = '3.8.0'
-PROV_MIN_VERSION = '1.4.0'
+PROV_MIN_VERSION = '1.5.0'
 CLICK_MIN_VERSION = '6.6.0'
 
 NAME = 'nipype'
@@ -138,23 +139,20 @@ def get_nipype_gitversion():
     'click>=%s' % CLICK_MIN_VERSION,
     'funcsigs',
     'configparser',
-    'pytest>=%s' % PYTEST_MIN_VERSION
+    'pytest>=%s' % PYTEST_MIN_VERSION,
+    'mock',
+    'pydotplus'
 ]
 
 TESTS_REQUIRES = [
-    'pytest>=%s' % PYTEST_MIN_VERSION,
     'pytest-cov',
-    'mock',
-    'codecov',
-    'dipy',
-    'nipy',
-    'matplotlib'
+    'codecov'
 ]
 
 EXTRA_REQUIRES = {
     'doc': ['Sphinx>=1.4', 'matplotlib', 'pydotplus'],
     'tests': TESTS_REQUIRES,
-    'fmri': ['nitime', 'nilearn', 'dipy', 'nipy', 'matplotlib'],
+    'nipy': ['nitime', 'nilearn', 'dipy', 'nipy', 'matplotlib'],
     'profiler': ['psutil'],
     'duecredit': ['duecredit'],
     'xvfbwrapper': ['xvfbwrapper'],

nipype/pipeline/engine/tests/test_engine.py

@@ -677,7 +677,8 @@ def test_write_graph_runs(tmpdir):
             mod2 = pe.Node(interface=EngineTestInterface(), name='mod2')
             pipe.connect([(mod1, mod2, [('output1', 'input1')])])
             try:
-                pipe.write_graph(graph2use=graph, simple_form=simple)
+                pipe.write_graph(graph2use=graph, simple_form=simple,
+                                 format='dot')
             except Exception:
                 assert False, \
                     'Failed to plot {} {} graph'.format(
@@ -708,7 +709,8 @@ def test_deep_nested_write_graph_runs(tmpdir):
             mod1 = pe.Node(interface=EngineTestInterface(), name='mod1')
             parent.add_nodes([mod1])
             try:
-                pipe.write_graph(graph2use=graph, simple_form=simple)
+                pipe.write_graph(graph2use=graph, simple_form=simple,
+                                 format='dot')
             except Exception as e:
                 assert False, \
                     'Failed to plot {} {} deep graph: {!s}'.format(

nipype/pipeline/engine/utils.py

@@ -1019,20 +1019,22 @@ def export_graph(graph_in, base_dir=None, show=False, use_execgraph=False,
                                use_ext=False,
                                newpath=base_dir)
     _write_detailed_dot(graph, outfname)
-    cmd = 'dot -T%s -O %s' % (format, outfname)
-    res = CommandLine(cmd, terminal_output='allatonce').run()
-    if res.runtime.returncode:
-        logger.warn('dot2png: %s', res.runtime.stderr)
+    if format != 'dot':
+        cmd = 'dot -T%s -O %s' % (format, outfname)
+        res = CommandLine(cmd, terminal_output='allatonce').run()
+        if res.runtime.returncode:
+            logger.warn('dot2png: %s', res.runtime.stderr)
     pklgraph = _create_dot_graph(graph, show_connectinfo, simple_form)
     simplefname = fname_presuffix(dotfilename,
                                   suffix='.dot',
                                   use_ext=False,
                                   newpath=base_dir)
     nx.drawing.nx_pydot.write_dot(pklgraph, simplefname)
-    cmd = 'dot -T%s -O %s' % (format, simplefname)
-    res = CommandLine(cmd, terminal_output='allatonce').run()
-    if res.runtime.returncode:
-        logger.warn('dot2png: %s', res.runtime.stderr)
+    if format != 'dot':
+        cmd = 'dot -T%s -O %s' % (format, simplefname)
+        res = CommandLine(cmd, terminal_output='allatonce').run()
+        if res.runtime.returncode:
+            logger.warn('dot2png: %s', res.runtime.stderr)
     if show:
         pos = nx.graphviz_layout(pklgraph, prog='dot')
         nx.draw(pklgraph, pos)
@@ -1045,18 +1047,17 @@ def export_graph(graph_in, base_dir=None, show=False, use_execgraph=False,
     return simplefname if simple_form else outfname
 
 
-def format_dot(dotfilename, format=None):
+def format_dot(dotfilename, format='png'):
     """Dump a directed graph (Linux only; install via `brew` on OSX)"""
-    cmd = 'dot -T%s -O \'%s\'' % (format, dotfilename)
-    try:
-        CommandLine(cmd).run()
-    except IOError as ioe:
-        if "could not be found" in str(ioe):
-            raise IOError("Cannot draw directed graph; executable 'dot' is unavailable")
-        else:
-            raise ioe
-
     if format != 'dot':
+        cmd = 'dot -T%s -O \'%s\'' % (format, dotfilename)
+        try:
+            CommandLine(cmd).run()
+        except IOError as ioe:
+            if "could not be found" in str(ioe):
+                raise IOError("Cannot draw directed graph; executable 'dot' is unavailable")
+            else:
+                raise ioe
         dotfilename += '.%s' % format
     return dotfilename
 

nipype/sphinxext/plot_workflow.py

@@ -113,22 +113,30 @@
 from errno import EEXIST
 import traceback
 
-from docutils.parsers.rst import directives
-from docutils.parsers.rst.directives.images import Image
-
+missing_imports = []
+try:
+    from docutils.parsers.rst import directives
+    from docutils.parsers.rst.directives.images import Image
+    align = Image.align
+except ImportError as e:
+    missing_imports = [str(e)]
 
 try:
     # Sphinx depends on either Jinja or Jinja2
     import jinja2
     def format_template(template, **kw):
         return jinja2.Template(template).render(**kw)
-except ImportError:
-    import jinja
-    def format_template(template, **kw):
-        return jinja.from_string(template, **kw)
+except ImportError as e:
+    missing_imports.append(str(e))
+    try:
+        import jinja
+        def format_template(template, **kw):
+            return jinja.from_string(template, **kw)
+        missing_imports.pop()
+    except ImportError as e:
+        missing_imports.append(str(e))
 
 from builtins import str, bytes
-align = Image.align
 
 PY2 = sys.version_info[0] == 2
 PY3 = sys.version_info[0] == 3
@@ -152,7 +160,10 @@ def _mkdirp(folder):
 
 def wf_directive(name, arguments, options, content, lineno,
                    content_offset, block_text, state, state_machine):
-    return run(arguments, content, options, state_machine, state, lineno)
+    if len(missing_imports) == 0:
+        return run(arguments, content, options, state_machine, state, lineno)
+    else:
+        raise ImportError('\n'.join(missing_imports))
 wf_directive.__doc__ = __doc__
 
 def _option_boolean(arg):

requirements.txt

@@ -3,13 +3,13 @@ scipy>=0.11
 networkx>=1.7
 traits>=4.6
 python-dateutil>=1.5
-nibabel>=2.0.1
-future>=0.15.2
+nibabel>=2.1.0
+future>=0.16.0
 simplejson>=3.8.0
-prov>=1.4.0
+prov>=1.5.0
 click>=6.6.0
-psutil
 funcsigs
 configparser
 pytest>=3.0
-pytest-cov
+mock
+pytdotplus

rtd_requirements.txt

@@ -3,13 +3,14 @@ scipy>=0.11
 networkx>=1.7
 traits>=4.6
 python-dateutil>=1.5
-nibabel>=2.0.1
-pytest>=3.0
-pytest-cov
-future>=0.15.2
+nibabel>=2.1.0
+future>=0.16.0
 simplejson>=3.8.0
-prov>=1.4.0
-psutil
+prov>=1.5.0
 funcsigs
 configparser
+pytest>=3.0
+mock
+pytdotplus
+psutil
 matplotlib