Merge pull request #388 from mpsonntag/smallFixes

Minor issue fixes and test reorganisation

LGTM

Author: achilleas-k

README.md

@@ -36,7 +36,7 @@ pip install odml
 ## Tutorial and examples
 
 - We have assembled a set of
- [tutorials](http://github.com/G-Node/python-odml/blob/master/doc/tutorial.rst "Python Tutorial").
+ [tutorials](https://python-odml.readthedocs.io/en/latest/tutorial.html "Python Tutorial").
 
 ## Python convenience scripts
 

odml/__init__.py

@@ -12,9 +12,29 @@
 from .info import VERSION
 from .tools.parser_utils import SUPPORTED_PARSERS as PARSERS
 
-if _python_version.major < 3 or _python_version.major == 3 and _python_version.minor < 6:
+
+def _format_warning(warn_msg, *args, **kwargs):
+    """
+    Used to provide users with deprecation warnings via the warnings module
+    but without spamming them with full stack traces.
+    """
+    final_msg = "%s\n" % str(warn_msg)
+    # If available add category name to the message
+    if args and hasattr(args[0], "__name__"):
+        final_msg = "%s: %s" % (args[0].__name__, final_msg)
+
+    return final_msg
+
+
+# Monkey patch formatting 'warnings' messages for the whole module.
+warnings.formatwarning = _format_warning
+
+if _python_version.major < 3:
+    msg = "Python 2 has been deprecated.\n\todML support for Python 2 will be dropped August 2020."
+    warnings.warn(msg, category=DeprecationWarning, stacklevel=2)
+elif _python_version.major == 3 and _python_version.minor < 6:
     msg = "The '%s' package is not tested with your Python version. " % __name__
-    msg += "Please consider upgrading to the latest Python distribution."
+    msg += "\n\tPlease consider upgrading to the latest Python distribution."
     warnings.warn(msg)
 
 __version__ = VERSION

odml/property.py

@@ -3,6 +3,7 @@
 This module provides the Base Property class.
 """
 import uuid
+import warnings
 
 from . import base
 from . import dtypes
@@ -12,6 +13,10 @@
 from .util import format_cardinality
 
 
+MSG_VALUE_DEPRECATION = "The attribute 'value' is deprecated and will be removed, " \
+                        "use 'values' instead."
+
+
 def odml_tuple_import(t_count, new_value):
     """
     Checks via a heuristic if the values in a string fit the general
@@ -131,6 +136,8 @@ def __init__(self, name=None, values=None, parent=None, unit=None,
         self._values = []
         self.values = values
         if not values and (value or isinstance(value, (bool, int))):
+            # Using stacklevel=2 to avoid file name and code line in the message output.
+            warnings.warn(MSG_VALUE_DEPRECATION, category=DeprecationWarning, stacklevel=2)
             self.values = value
 
         self.parent = parent
@@ -285,7 +292,9 @@ def value(self):
         """
         Deprecated alias of 'values'. Will be removed with the next minor release.
         """
-        print("The attribute 'value' is deprecated. Please use 'values' instead.")
+        # Using stacklevel=2 to avoid file name and code line in the message output.
+        warnings.warn(MSG_VALUE_DEPRECATION, category=DeprecationWarning, stacklevel=2)
+
         return self.values
 
     @value.setter
@@ -295,7 +304,8 @@ def value(self, new_value):
 
         :param new_value: a single value or list of values.
         """
-        print("The attribute 'value' is deprecated. Please use 'values' instead.")
+        # Using stacklevel=2 to avoid file name and code line in the message output.
+        warnings.warn(MSG_VALUE_DEPRECATION, category=DeprecationWarning, stacklevel=2)
         self.values = new_value
 
     def value_str(self, index=0):

odml/section.py

@@ -3,6 +3,7 @@
 This module provides the Base Section class.
 """
 import uuid
+import warnings
 
 try:
     from collections.abc import Iterable
@@ -774,21 +775,32 @@ def reorder(self, new_index):
 
         return self._reorder(self.parent.sections, new_index)
 
-    def create_property(self, name, value=None, dtype=None, oid=None):
+    def create_property(self, name, values=None, dtype=None, oid=None, value=None):
         """
         Create a new property that is a child of this section.
 
         :param name: The name of the property.
-        :param value: Some data value, it can be a single value or
-                      a list of homogeneous values.
+        :param values: Some data value, it can be a single value or
+                       a list of homogeneous values.
         :param dtype: The data type of the values stored in the property,
                       if dtype is not given, the type is deduced from the values.
                       Check odml.DType for supported data types.
         :param oid: object id, UUID string as specified in RFC 4122. If no id
                     is provided, an id will be generated and assigned.
+        :param value: Deprecated alias of 'values'. Any content of 'value' is ignored,
+                      if 'values' is set.
+
         :return: The new property.
         """
-        prop = BaseProperty(name=name, value=value, dtype=dtype, oid=oid)
+        if value and values:
+            print("Warning: Both 'values' and 'value' were set; ignoring 'value'.")
+
+        if not values and (value or isinstance(value, (bool, int))):
+            msg = "The attribute 'value' is deprecated and will be removed, use 'values' instead."
+            warnings.warn(msg, category=DeprecationWarning, stacklevel=2)
+            values = value
+
+        prop = BaseProperty(name=name, values=values, dtype=dtype, oid=oid)
         prop.parent = self
 
         return prop

odml/tools/converters/version_converter.py

@@ -13,6 +13,7 @@
 from lxml import etree as ET
 
 from ..parser_utils import ParserException
+from ..xmlparser import XML_HEADER
 
 from ...format import Document, Section, Property
 from ...info import FORMAT_VERSION
@@ -531,5 +532,5 @@ def write_to_file(self, filename, backend="XML"):
 
         if data and "<odML " in data:
             with open(filename, "w") as file:
-                file.write('<?xml version="1.0" encoding="UTF-8"?>\n')
+                file.write("%s\n" % XML_HEADER)
                 file.write(data)

odml/tools/version_converter.py

@@ -2,9 +2,11 @@
 This module provides backwards compatibility for the VersionConverter class.
 It is deprecated and will be removed in future versions.
 """
+import warnings
 
 from .converters import VersionConverter
 
-print("[DEPRECATION WARNING] The VersionConverter file has been moved to "
-      "'odml.tools.converters' and will be removed from 'odml.tools' in future "
-      "odML releases. Please update the imports in your code accordingly.")
+_MSG = "The VersionConverter file has been moved to "\
+       "'odml.tools.converters' and will be removed from 'odml.tools' in future "\
+       "odML releases. Please update the imports in your code accordingly."
+warnings.warn(_MSG, category=DeprecationWarning, stacklevel=2)

test/test_doc.py

@@ -2,6 +2,8 @@
 import os
 import unittest
 
+from glob import glob
+
 try:
     from urllib.request import pathname2url
 except ImportError:
@@ -10,11 +12,23 @@
 from odml import Document, Section, Property
 from odml.doc import BaseDocument
 from odml.dtypes import FORMAT_DATE
+from .util import ODML_CACHE_DIR as CACHE_DIR, TEST_RESOURCES_DIR as RES_DIR
 
 
 class TestSection(unittest.TestCase):
     def setUp(self):
-        pass
+        self.local_repo_file = "local_repository_file_v1.1.xml"
+
+    def tearDown(self):
+        """
+        Remove all files loaded to the terminology cache directory
+        to avoid test cross pollution.
+        """
+        temp_file_glob = "*%s" % self.local_repo_file
+        find_us = os.path.join(CACHE_DIR, temp_file_glob)
+
+        for file_path in glob(find_us):
+            os.remove(file_path)
 
     def test_simple_attributes(self):
         author = "HPL"
@@ -95,8 +109,7 @@ def test_date(self):
             doc.date = "some format"
 
     def test_get_terminology_equivalent(self):
-        dir_path = os.path.dirname(os.path.realpath(__file__))
-        repo_file = os.path.join(dir_path, "resources", "local_repository_file_v1.1.xml")
+        repo_file = os.path.join(RES_DIR, self.local_repo_file)
         local_url = "file://%s" % pathname2url(repo_file)
 
         doc = Document(repository=local_url)

test/test_doc_integration.py

@@ -5,17 +5,17 @@
 
 import os
 import shutil
-import tempfile
 import unittest
 
 import odml
+from .util import create_test_dir
 
 
 class TestDocumentIntegration(unittest.TestCase):
 
     def setUp(self):
         # Set up test environment
-        self.tmp_dir = tempfile.mkdtemp(suffix=".odml")
+        self.tmp_dir = create_test_dir(__file__)
 
         self.json_file = os.path.join(self.tmp_dir, "test.json")
         self.xml_file = os.path.join(self.tmp_dir, "test.xml")
@@ -26,7 +26,7 @@ def setUp(self):
         self.doc = doc
 
     def tearDown(self):
-        if os.path.exists(self.tmp_dir):
+        if self.tmp_dir and os.path.exists(self.tmp_dir):
             shutil.rmtree(self.tmp_dir)
 
     def save_load(self):

test/test_dtypes_integration.py

@@ -7,17 +7,17 @@
 import datetime as dt
 import os
 import shutil
-import tempfile
 import unittest
 
 import odml
+from .util import create_test_dir
 
 
 class TestTypesIntegration(unittest.TestCase):
 
     def setUp(self):
         # Set up test environment
-        self.tmp_dir = tempfile.mkdtemp(suffix=".odml")
+        self.tmp_dir = create_test_dir(__file__)
 
         self.json_file = os.path.join(self.tmp_dir, "test.json")
         self.xml_file = os.path.join(self.tmp_dir, "test.xml")
@@ -29,7 +29,7 @@ def setUp(self):
         self.doc = doc
 
     def tearDown(self):
-        if os.path.exists(self.tmp_dir):
+        if self.tmp_dir and os.path.exists(self.tmp_dir):
             shutil.rmtree(self.tmp_dir)
 
     def test_time(self):

test/test_fileio.py

@@ -1,40 +1,44 @@
-import unittest
-import sys
 import os
-import odml
+import sys
+import unittest
 
 try:
     from StringIO import StringIO
 except ImportError:
     from io import StringIO
 
+import odml
+
+from .util import TEST_RESOURCES_DIR as RES_DIR
+
 
 class TestTypes(unittest.TestCase):
 
     def setUp(self):
-        self.dir_path = os.path.dirname(os.path.realpath(__file__))
-        self.file = os.path.join(self.dir_path, 'resources', 'example.odml')
+        self.file = os.path.join(RES_DIR, "example.odml")
         # Do not allow anything to be printed on STDOUT
         self.captured_stdout = StringIO()
         sys.stdout = self.captured_stdout
 
     def test_load_save(self):
         doc = odml.load(self.file)
         self.assertTrue(isinstance(doc, odml.doc.BaseDocument))
-        odml.save(doc, self.file + '_copy')
-        os.remove(self.file + '_copy')
+        file_name = "%s_copy" % self.file
+        odml.save(doc, file_name)
+        os.remove(file_name)
 
     def test_display(self):
         doc = odml.load(self.file)
         odml.display(doc)
 
     def test_invalid_parser(self):
         with self.assertRaises(NotImplementedError):
-            odml.load(self.file, 'html')
+            odml.load(self.file, "html")
 
         doc = odml.load(self.file)
         with self.assertRaises(NotImplementedError):
-            odml.save(doc, self.file + '_copy_html', 'html')
+            file_name = "%s_copy_html" % self.file
+            odml.save(doc, file_name, "html")
 
         with self.assertRaises(NotImplementedError):
-            odml.display(doc, 'html')
+            odml.display(doc, "html")