Backports for 5.0.0 and update Changelog

CHANGES.txt

@@ -52,6 +52,11 @@ Documentation changes
 Test suite
 ----------
 * Fix AttributeError on Python 3.9 due to usage of ``base64.decodestring`` in tests (#210)
+* Make optional dependencies optional for tests (#260)
+
+Build System
+------------
+* Add extras_require to setup.py for optional dependencies (#257)
 
 Version 4.5.0
 ~~~~~~~~~~~~~

MANIFEST.in

@@ -3,8 +3,7 @@ include CHANGES.txt
 include LICENSE.txt
 include MANIFEST.in
 include image_LICENSE.txt
-include image_LICENSE_Nuvola.txt
-include image_LICENSE_OOo.txt
+include image_LICENSE_CP.txt
 graft docs
 prune docs/build
 recursive-exclude docs *.pyc

README.rst

@@ -37,14 +37,46 @@ All packages in apptools require:
 
 * `traits <https://github.com/enthought/traits>`_
 
+Certain sub-packages within apptools have their own specific dependencies,
+which are optional for apptools overall.
+
 The `apptools.preferences` package requires:
 
 * `configobj <http://pypi.python.org/pypi/configobj>`_
 
+The `apptools.io.h5` package requires:
+
+* `numpy <https://pypi.org/project/numpy/>`_
+* `pandas <https://pypi.org/project/pandas/>`_
+* `tables <https://pypi.org/project/tables/>`_
+
+The `apptools.persistence` package requires:
+
+* `numpy <https://pypi.org/project/numpy/>`_
+
 Many of the packages provide optional user interfaces using Pyface and
 Traitsui. In additon, many of the packages are designed to work with the
 Envisage plug-in system, althought most can be used independently:
 
 * `envisage <https://github.com/enthought/envisage>`_
 * `pyface <https://github.com/enthought/pyface>`_
 * `traitsui <https://github.com/enthought/traitsui>`_
+
+Installation
+------------
+
+To install with `apptools.preferences` dependencies::
+
+    $ pip install apptools[preferences]
+
+To install with `apptools.io.h5` dependencies::
+
+    $ pip install apptools[h5]
+
+To install with `apptools.persistence` dependencies::
+
+    $ pip install apptools[persistence]
+
+To install with additional test dependencies::
+
+    $ pip install apptools[test]

apptools/io/h5/tests/test_dict_node.py

@@ -9,16 +9,23 @@
 # Thanks for using Enthought open source!
 import unittest
 
-import numpy as np
-from numpy.testing import assert_allclose
+from apptools._testing.optional_dependencies import (
+    numpy as np,
+    tables,
+    requires_numpy,
+    requires_tables,
+)
 
-from ..dict_node import H5DictNode
-from .utils import open_h5file, temp_h5_file, temp_file
+if np is not None and tables is not None:
+    from ..dict_node import H5DictNode
+    from .utils import open_h5file, temp_h5_file, temp_file
 
 
 NODE = "/dict_node"
 
 
+@requires_tables
+@requires_numpy
 class DictNodeTestCase(unittest.TestCase):
     def test_create(self):
         with temp_h5_file() as h5:
@@ -56,8 +63,8 @@ def test_create_with_array_data(self):
 
             h5dict = H5DictNode.add_to_h5file(h5, NODE, data)
             assert h5dict["a"] == 10
-            assert_allclose(h5dict["foo"], foo)
-            assert_allclose(h5dict["bar"], bar)
+            np.testing.assert_allclose(h5dict["foo"], foo)
+            np.testing.assert_allclose(h5dict["bar"], bar)
 
     def test_load_saved_dict_node(self):
         with temp_file() as filename:
@@ -91,16 +98,16 @@ def test_load_saved_dict_node_with_array(self):
             # Read dict node and make sure the data was saved.
             with open_h5file(filename, mode="r+") as h5:
                 h5dict = h5[NODE]
-                assert_allclose(h5dict["arr"], arr)
+                np.testing.assert_allclose(h5dict["arr"], arr)
                 # Change data for next test
                 h5dict["arr"] = arr1
                 h5dict["arr_old"] = arr
 
             # Check that data is modified by the previous write.
             with open_h5file(filename) as h5:
                 h5dict = h5[NODE]
-                assert_allclose(h5dict["arr"], arr1)
-                assert_allclose(h5dict["arr_old"], arr)
+                np.testing.assert_allclose(h5dict["arr"], arr1)
+                np.testing.assert_allclose(h5dict["arr_old"], arr)
                 # Make sure that arrays come back as arrays
                 assert isinstance(h5dict["arr"], np.ndarray)
                 assert isinstance(h5dict["arr_old"], np.ndarray)

apptools/io/h5/tests/test_file.py

@@ -11,19 +11,25 @@
 from contextlib import closing
 import unittest
 
-import numpy as np
-from numpy import testing
-import tables
+from apptools._testing.optional_dependencies import (
+    numpy as np,
+    tables,
+    requires_numpy,
+    requires_tables,
+)
 
-from ..file import H5File
-from ..dict_node import H5DictNode
-from ..table_node import H5TableNode
-from .utils import open_h5file, temp_h5_file
+if np is not None and tables is not None:
+    from ..file import H5File
+    from ..dict_node import H5DictNode
+    from ..table_node import H5TableNode
+    from .utils import open_h5file, temp_h5_file
 
 
 H5_TEST_FILE = "_temp_test_filt.h5"
 
 
+@requires_numpy
+@requires_tables
 class FileTestCase(unittest.TestCase):
     def tearDown(self):
         try:
@@ -58,9 +64,9 @@ def test_create_array_with_H5File(self):
         with open_h5file(H5_TEST_FILE, mode="w") as h5:
             h5array = h5.create_array("/array", array)
             # Test returned array
-            testing.assert_allclose(h5array, array)
+            np.testing.assert_allclose(h5array, array)
             # Test stored array
-            testing.assert_allclose(h5["/array"], array)
+            np.testing.assert_allclose(h5["/array"], array)
 
     def test_create_array_with_H5Group(self):
         array = np.arange(3)
@@ -69,9 +75,9 @@ def test_create_array_with_H5Group(self):
             group = h5.create_group("/tardigrade")
             h5array = group.create_array("array", array)
             # Test returned array
-            testing.assert_allclose(h5array, array)
+            np.testing.assert_allclose(h5array, array)
             # Test stored array
-            testing.assert_allclose(h5[node_path], array)
+            np.testing.assert_allclose(h5[node_path], array)
 
     def test_getitem_failure(self):
         array = np.arange(3)
@@ -117,28 +123,28 @@ def test_create_chunked_array_with_H5File(self):
         array = np.arange(3, dtype=np.uint8)
         with open_h5file(H5_TEST_FILE, mode="w") as h5:
             h5array = h5.create_array("/array", array, chunked=True)
-            testing.assert_allclose(h5array, array)
+            np.testing.assert_allclose(h5array, array)
             assert isinstance(h5array, tables.CArray)
 
     def test_create_chunked_array_with_H5Group(self):
         array = np.arange(3, dtype=np.uint8)
         with open_h5file(H5_TEST_FILE, mode="w") as h5:
             h5array = h5.root.create_array("/array", array, chunked=True)
-            testing.assert_allclose(h5array, array)
+            np.testing.assert_allclose(h5array, array)
             assert isinstance(h5array, tables.CArray)
 
     def test_create_extendable_array_with_H5File(self):
         array = np.arange(3, dtype=np.uint8)
         with open_h5file(H5_TEST_FILE, mode="w") as h5:
             h5array = h5.create_array("/array", array, extendable=True)
-            testing.assert_allclose(h5array, array)
+            np.testing.assert_allclose(h5array, array)
             assert isinstance(h5array, tables.EArray)
 
     def test_create_extendable_array_with_H5Group(self):
         array = np.arange(3, dtype=np.uint8)
         with open_h5file(H5_TEST_FILE, mode="w") as h5:
             h5array = h5.root.create_array("/array", array, extendable=True)
-            testing.assert_allclose(h5array, array)
+            np.testing.assert_allclose(h5array, array)
             assert isinstance(h5array, tables.EArray)
 
     def test_str_and_repr(self):
@@ -179,7 +185,7 @@ def test_delete_existing_array_with_H5File(self):
             h5.create_array("/array", old_array)
             # New array with the same node name should delete old array
             h5.create_array("/array", new_array)
-            testing.assert_allclose(h5["/array"], new_array)
+            np.testing.assert_allclose(h5["/array"], new_array)
 
     def test_delete_existing_array_with_H5Group(self):
         old_array = np.arange(3)
@@ -188,7 +194,7 @@ def test_delete_existing_array_with_H5Group(self):
             h5.create_array("/array", old_array)
             # New array with the same node name should delete old array
             h5.root.create_array("/array", new_array, delete_existing=True)
-            testing.assert_allclose(h5["/array"], new_array)
+            np.testing.assert_allclose(h5["/array"], new_array)
 
     def test_delete_existing_dict_with_H5File(self):
         old_dict = {"a": "Goose"}
@@ -371,8 +377,8 @@ def test_groups(self):
             group_b = group_a["b"]
             # Check that __contains__ works for arrays
             assert "array" in group_b
-            testing.assert_allclose(group_b["array"], array)
-            testing.assert_allclose(group_a["b/array"], array)
+            np.testing.assert_allclose(group_b["array"], array)
+            np.testing.assert_allclose(group_a["b/array"], array)
 
     def test_group_attributes(self):
         value_1 = "foo"
@@ -419,7 +425,7 @@ def test_mapping_interface_for_file(self):
             assert len(h5) == 2
             assert "/group" in h5
             assert "/array" in h5
-            testing.assert_allclose(h5["/array"], array)
+            np.testing.assert_allclose(h5["/array"], array)
             assert set(n.name for n in h5) == set(["array", "group"])
 
     def test_mapping_interface_for_group(self):
@@ -431,7 +437,7 @@ def test_mapping_interface_for_group(self):
             assert len(group) == 2
             assert "subgroup" in group
             assert "array" in group
-            testing.assert_allclose(group["array"], array)
+            np.testing.assert_allclose(group["array"], array)
             assert set(n.name for n in group) == set(["array", "subgroup"])
 
     def test_group_str_and_repr(self):
@@ -447,7 +453,7 @@ def test_attribute_translation(self):
         with open_h5file(H5_TEST_FILE, mode="w") as h5:
             h5["/"].attrs["name"] = value_1
             assert isinstance(h5["/"].attrs["name"], np.ndarray)
-            testing.assert_allclose(h5["/"].attrs["name"], value_1_array)
+            np.testing.assert_allclose(h5["/"].attrs["name"], value_1_array)
 
     def test_get_attribute(self):
         with open_h5file(H5_TEST_FILE, mode="w") as h5:

apptools/logger/log_point.py

@@ -15,8 +15,6 @@
 
 # Standard library imports.
 import inspect
-
-# Third-party library imports.
 from io import StringIO
 
 

apptools/logger/plugin/logger_service.py

@@ -8,13 +8,11 @@
 #
 # Thanks for using Enthought open source!
 # Standard library imports
+from io import BytesIO
 import logging
 import os
 import zipfile
 
-# Third-party library imports
-from io import BytesIO
-
 # Enthought library imports
 from pyface.workbench.api import View as WorkbenchView
 from traits.api import (

apptools/persistence/tests/test_file_path.py

@@ -21,16 +21,24 @@
 # 3rd party imports.
 from importlib_resources import files
 
+from apptools._testing.optional_dependencies import (
+    numpy as np,
+    requires_numpy,
+)
+
 # Enthought library imports.
-from apptools.persistence import state_pickler
-from apptools.persistence import file_path
+if np is not None:
+    from apptools.persistence import state_pickler
+    from apptools.persistence import file_path
 
 
+@requires_numpy
 class Test:
     def __init__(self):
         self.f = file_path.FilePath()
 
 
+@requires_numpy
 class TestFilePath(unittest.TestCase):
     def setUp(self):
         # If the cwd is somewhere under /tmp, that confuses the tests below.

apptools/persistence/tests/test_state_pickler.py

@@ -19,7 +19,10 @@
 import os
 import tempfile
 
-import numpy
+try:
+    import numpy
+except ImportError:
+    raise unittest.SkipTest("Can't import NumPy: skipping")
 
 from traits.api import (
     Bool,
@@ -48,6 +51,7 @@
 
 # A simple class to test instances.
 class A(object):
+
     def __init__(self):
         self.a = "a"
 

apptools/persistence/tests/test_version_registry.py

@@ -19,7 +19,12 @@
 # Enthought library imports.
 from traits.api import HasTraits
 
-from apptools.persistence import version_registry, state_pickler
+from apptools._testing.optional_dependencies import (
+    numpy as np,
+    requires_numpy,
+)
+if np is not None:
+    from apptools.persistence import version_registry, state_pickler
 
 
 class Classic:
@@ -52,6 +57,7 @@ def upgrade1(self, state, version):
         self.calls.append(("upgrade1", state, version))
 
 
+@requires_numpy
 class TestVersionRegistry(unittest.TestCase):
     def test_get_version(self):
         """Test the get_version function."""