Silence pronto warnings when importing ontologies

mzml2isa/imzml.py

@@ -14,6 +14,7 @@
 from __future__ import unicode_literals
 
 import copy
+import warnings
 
 import pronto
 import pkg_resources
@@ -34,10 +35,11 @@ class ImzMLFile(MzMLFile):
         }
     )
 
-    _VOCABULARY = pronto.Ontology(
-        pkg_resources.resource_stream("mzml2isa", "ontologies/imagingMS.obo"),
-        # import_depth=1,
-    )
+    with warnings.catch_warnings(record=True): 
+        warnings.simplefilter('ignore', pronto.warnings.SyntaxWarning)
+        _VOCABULARY = pronto.Ontology(
+            pkg_resources.resource_filename("mzml2isa", "ontologies/imagingMS.obo"),
+        )
 
     @classmethod
     def _assay_parameters(cls):

mzml2isa/mzml.py

@@ -102,11 +102,12 @@ class MzMLFile(object):
         "ref_binary": "{scanList}/s:scan/s:referenceableParamGroupRef",
     }
 
-    # `~pronto.Ontology`: the default MS controlled vocabulary to use.
-    _VOCABULARY = pronto.Ontology(
-        pkg_resources.resource_stream("mzml2isa", "ontologies/psi-ms.obo"),
-        # imports=False,
-    )
+    with warnings.catch_warnings(record=True): 
+        warnings.simplefilter('ignore', pronto.warnings.SyntaxWarning)
+        # `~pronto.Ontology`: the default MS controlled vocabulary to use.
+        _VOCABULARY = pronto.Ontology(
+            pkg_resources.resource_filename("mzml2isa", "ontologies/psi-ms.obo"),
+        )
 
     def __init__(self, filesystem, path, vocabulary=None):
         """Open an ``mzML`` file from the given filesystem and path.

setup.cfg

@@ -30,7 +30,7 @@ project_urls =
 	Changelog = https://github.com/ISA-tools/mzml2isa/blob/master/CHANGELOG.md
 
 [options]
-zip_safe = true
+zip_safe = false
 include_package_data = false
 python_requires = >= 2.7, != 3.0.*, != 3.1.*, != 3.2.*, != 3.3.*
 packages = mzml2isa, mzml2isa.templates, mzml2isa.ontologies