Merge pull request #91 from cropsinsilico/minor

Minor

Author: langmm

.github/workflows/test-install.yml

@@ -2,16 +2,25 @@
 History
 =======
 
-1.8.2 (2021-XX-XX) Migrate tests out of package & into pytest fixtures
+1.8.2 (2021-03-16) Migrate tests out of package into pytest fixtures & various bug fixes
 ------------------
 
 * Move tests out of package to take advantage of pytest conftest.py structure and reduce the size of the package
 * Refactor tests to use pytest fixtures instead of the unittest setup/teardown structure
 * Remove the yggtest CLI and migrate options into pytest CLI options
-* Update the GHA workflow to use the new pytest based CLI
+* Updated the GHA workflow to use the new pytest based CLI and test parameters so that changing the image used won't change the name of the test required to merge pull requests
 * Use lock to prevent parallel compilation for all compiled languages
 * Remove 'initial_state' parameter from Transform and Filter schemas as it is unused
 * Remove unused yggdrasil.communication.cleanup_comms method
+* Updated requirements (pinned libroadrunner to < 2.0.7 and unpinned pytest)
+* Updated tests to allow comparison of class objects imported in different ways
+* Updated the connection and comm schemas to allow for inputs & vars to include datatypes, fixing a bug where turning on debugging caused the validation of connection parameters to fail
+* Updated the connections to allow the input and output patterns to be passed directly
+* Added a method for displaying information about serializers and added that information to comm info displays
+* Fixed a bug in updating the serializer from messages for ForkComms with a scatter communication pattern
+* Added the split_and_merge example of using communication patterns to split and merge messages between multiple inputs/outputs
+* Fixed a bug in pandas serializer where strings are now stored as objects by default
+* Fixed a bug in table serializer where table parameters were not being passed to the header discovery function, resulting in them being ignored in some cases
 
 1.8.1 (2021-10-15) Minor updates to support model submission form development
 ------------------

HISTORY.rst

@@ -2,6 +2,6 @@ astropy       # [astropy]
 pika>=1.0.0   # [rmq]
 pygments      # [pygments]
 trimesh       # [trimesh]
-libroadrunner  # [pip,sbml]
+libroadrunner<2.0.7  # [pip,sbml]
 ccache; platform_system != 'Windows'  # [conda]
 mpi4py        # [mpi]

requirements_optional.txt

@@ -1 +1 @@
-libroadrunner  # [pip,sbml]
+libroadrunner<2.0.7  # [pip,sbml]

requirements_piponly.txt

@@ -3,9 +3,10 @@ coverage
 flake8
 flaky
 nose
-pytest>=4.6  # Required by pytest-cov, but not resolved by pip on linux
+pytest
 pytest-cov
 pytest-timeout
+pytest-mpi
 pytest-drop-dup-tests  # [pip]
 pytest-rerunfailures
 pytest-repeat

requirements_testing.txt

@@ -4,11 +4,24 @@
 import weakref
 
 
-class Dummy(object):  # pragma: debug
+class DummyMeta(type):  # pragma: debug
+    
+    def __eq__(self, solf):
+        import inspect
+        a_str = f"{self.__module__}.{self.__name__}[{inspect.getfile(self)}]"
+        b_str = f"{solf.__module__}.{solf.__name__}[{inspect.getfile(solf)}]"
+        return a_str == b_str
+
+    def __hash__(self):
+        import inspect
+        return hash(f"{self.__module__}.{self.__name__}[{inspect.getfile(self)}]")
+
+
+class Dummy(metaclass=DummyMeta):  # pragma: debug
     pass
 
 
-class ValidArgsClass1(object):
+class ValidArgsClass1(metaclass=DummyMeta):
     test_args = tuple([int(0), Dummy])
     test_kwargs = dict(c=int(1), d=Dummy)
     valid_args = [{'type': 'int'}, {'type': 'class'}]
@@ -25,7 +38,7 @@ def __init__(self, a, b, c=0, d=Dummy):
         self._input_kwargs = {'c': c, 'd': weakref.ref(d)}
 
     def __eq__(self, solf):
-        if not isinstance(solf, self.__class__):  # pragma: debug
+        if solf.__class__ != self.__class__:  # pragma: debug
             return False
         return ((self._input_args == solf._input_args)
                 and (self._input_kwargs == solf._input_kwargs))

tests/metaschema/properties/test_ArgsMetaschemaProperty.py

@@ -1,6 +1,7 @@
 import pytest
 import numpy as np
 from yggdrasil.serialize import AsciiTableSerialize
+from yggdrasil import platform
 from tests.serialize.test_DefaultSerialize import (
     TestDefaultSerialize as base_class)
 
@@ -23,6 +24,32 @@ def test_deserialize_nofmt():
         inst.deserialize(test_msg)
 
 
+def test_discover_header_no_header(tmpdir):
+    r"""Test discover_header with single line, two columns, no header and
+    non-default delimiter."""
+    fd0 = tmpdir.join("temp_table.txt")
+    fd0.write(b"13 berlin", 'wb')
+    fd = fd0.open('rb')
+    inst = AsciiTableSerialize.AsciiTableSerialize(delimiter=b' ')
+    inst.deserialize_file_header(fd)
+    if platform._is_win:  # pragma: windows
+        assert(inst.format_str == b'%d %6s\n')
+    else:
+        assert(inst.format_str == b'%ld %6s\n')
+    assert(inst.field_names == ('f0', 'f1'))
+
+
+def test_discover_header_one_element(tmpdir):
+    r"""Test discover_header with single line, single column, no header."""
+    fd0 = tmpdir.join("temp_table.txt")
+    fd0.write(b"berlin", 'wb')
+    fd = fd0.open('rb')
+    inst = AsciiTableSerialize.AsciiTableSerialize(delimiter=b' ')
+    inst.deserialize_file_header(fd)
+    assert(inst.format_str == b'%6s\n')
+    assert(inst.field_names == ('f0',))
+
+
 _options = [
     {},
     {'explicit_testing_options': {

tests/serialize/test_AsciiTableSerialize.py

@@ -877,7 +877,7 @@ def install_deps(method, return_commands=False, verbose=False,
         pip_flags = '--no-dependencies'
         if verbose:
             pip_flags += ' --verbose'
-        cmds.append('%s -m pip install %s libroadrunner'
+        cmds.append('%s -m pip install %s \"libroadrunner<2.0.7\"'
                     % (python_cmd, pip_flags))
     if install_opts['lpy']:
         if verbose: