Merge pull request #12 from openkim/devel

Include script generated source file

.github/workflows/pythonpackage.yml → .github/workflows/testing.yml

@@ -1,4 +1,4 @@
-name: Python package
+name: test
 
 on: [push]
 
@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: [3.7, 3.8, 3.9]
     steps:
     - uses: actions/checkout@v2
     - name: Install gcc
@@ -59,7 +59,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: [3.7, 3.8, 3.9]
         compiler: [clang, gcc]
     steps:
     - uses: actions/checkout@v2

.gitignore

@@ -11,33 +11,7 @@ build/
 dist/
 ase_kim_calculator.egg-info/
 
-kimpy/SpeciesName_attributes.cpp
-kimpy/*Unit_bind.cpp
-kimpy/KIM_DataType_bind.cpp
-kimpy/KIM_Numbering_bind.cpp
-kimpy/KIM_SpeciesName_bind.cpp
-kimpy/KIM_LanguageName_bind.cpp
-kimpy/KIM_ModelRoutineName_bind.cpp
-kimpy/KIM_ComputeCallbackName_bind.cpp
-kimpy/KIM_SupportStatus_bind.cpp
-kimpy/KIM_LogVerbosity_bind.cpp
-kimpy/KIM_Collection_bind.cpp
-kimpy/KIM_CollectionItemType_bind.cpp
-
-tests/species_name_attributes.py
-tests/*_unit.py
-tests/test_data_type.py
-tests/test_numbering.py
-tests/test_species_name.py
-tests/test_language_name.py
-tests/test_model_routine_name.py
-tests/test_compute_callback_name.py
-tests/test_support_status.py
-tests/test_log_verbosity.py
-tests/test_collection.py
-tests/test_collection_item_type.py
-
-# Precompiled Headers
+# Pre-compiled Headers
 *.gch
 *.pch
 
@@ -70,3 +44,4 @@ kimpy.egg-info
 kim.log
 .cache
 .pytest_cache/
+.DS_Store

Makefile

@@ -10,13 +10,3 @@ clean:
 	python setup.py clean
 clean_all:
 	rm -rf build/ dist/ kimpy.egg-info/ */*.so */*.pyc */__pycache__  \
-  kimpy/*Unit_bind.cpp \
-  kimpy/KIM_DataType_bind.cpp kimpy/KIM_Numbering_bind.cpp \
-  kimpy/KIM_SpeciesName_bind.cpp kimpy/KIM_LanguageName_bind.cpp \
-  kimpy/KIM_ComputeCallbackName_bind.cpp  kimpy/KIM_LogVerbosity_bind.cpp \
-  kimpy/KIM_Collection_bind.cpp  kimpy/KIM_CollectionItemType_bind.cpp \
-  tests/*_unit.py \
-  tests/test_data_type.py tests/test_numbering.py tests/test_species_name.py \
-  tests/test_language_name.py tests/test_compute_callback_name.py \
-  tests/test_log_verbosity.py tests/test_support_status.py \
-  tests/test_collection.py tests/test_collection_item_type.py \

README.md

@@ -194,6 +194,3 @@ Contributors:\
       Mingjian Wen\
       Yaser Afshar
 
-## Contact
-
-      Mingjian Wen (wenxx151@umn.edu)

api_compatibility.py

@@ -4,7 +4,7 @@
 from collections import OrderedDict
 import sys
 
-sys.path.insert(0, abspath('kimpy'))
+sys.path.insert(0, abspath("kimpy"))
 
 from err import KimPyError
 
@@ -21,24 +21,28 @@ def read_compatible_table():
                     compatible with
     """
     this_dir = dirname(abspath(__file__))
-    file_path = join(this_dir, 'api_compatibility.txt')
+    file_path = join(this_dir, "api_compatibility.txt")
 
     if not isfile(file_path):
         msg = "{} is not an existing regular file.".format(file_path)
         raise KimPyError(msg)
 
     compatible_table = OrderedDict()
-    with open(file_path, 'r') as fin:
+    with open(file_path, "r") as fin:
         for line in fin:
             line = line.strip()
-            if not line or line[0] == '#':
+            if not line or line[0] == "#":
                 continue
 
-            kimpy_version, kim_api_target_version, kim_api_backward_version = line.split()
+            (
+                kimpy_version,
+                kim_api_target_version,
+                kim_api_backward_version,
+            ) = line.split()
 
             compatible_table[kimpy_version] = {
-                'target': kim_api_target_version,
-                'backward': kim_api_backward_version,
+                "target": kim_api_target_version,
+                "backward": kim_api_backward_version,
             }
 
     return compatible_table
@@ -53,28 +57,28 @@ def compare_version(x, y):
             '=' if x equal y
             '>' is x larger than y
     """
-    x_major, x_minor, x_patch = [int(i) for i in x.split('.')]
-    y_major, y_minor, y_patch = [int(i) for i in y.split('.')]
+    x_major, x_minor, x_patch = [int(i) for i in x.split(".")]
+    y_major, y_minor, y_patch = [int(i) for i in y.split(".")]
 
     if x_major > y_major:
-        return '>'
+        return ">"
 
     if x_major < y_major:
-        return '<'
+        return "<"
 
     if x_minor > y_minor:
-        return '>'
+        return ">"
 
     if x_minor < y_minor:
-        return '<'
+        return "<"
 
     if x_patch > y_patch:
-        return '>'
+        return ">"
 
     if x_patch < y_patch:
-        return '<'
+        return "<"
 
-    return '='
+    return "="
 
 
 def suggest_kimpy(kim_api_version, compatible_table):
@@ -99,10 +103,10 @@ def suggest_kimpy(kim_api_version, compatible_table):
 
     # search backward
     for key, value in compatible_table.items():
-        if value['target'] == kim_api_version:
+        if value["target"] == kim_api_version:
             target = key
 
-        if value['backward'] == kim_api_version:
+        if value["backward"] == kim_api_version:
             backward = key
 
     if backward:
@@ -129,53 +133,53 @@ def check_kim_api_compatibility(kimpy_version, kim_api_version):
 
     # last key in OrderedDict
     latest_kimpy = next(reversed(compatible_table))
-    latest_target = compatible_table[latest_kimpy]['target']
+    latest_target = compatible_table[latest_kimpy]["target"]
 
     cmp = compare_version(latest_target, kim_api_version)
     cmp_1 = True
-    if cmp == '<':
+    if cmp == "<":
         cmp_1 = False
     else:
-        oldest_target = '2.0.0'
+        oldest_target = "2.0.0"
         cmp = compare_version(oldest_target, kim_api_version)
-        if cmp == '>':
+        if cmp == ">":
             cmp_1 = False
 
     # check whether the current kimpy is compatible with the api
-    target = compatible_table[kimpy_version]['target']
-    backward = compatible_table[kimpy_version]['backward']
+    target = compatible_table[kimpy_version]["target"]
+    backward = compatible_table[kimpy_version]["backward"]
 
     cmp = compare_version(target, kim_api_version)
     cmp_2 = True
-    if cmp == '<':
+    if cmp == "<":
         cmp_2 = False
     else:
         cmp = compare_version(backward, kim_api_version)
-        if cmp == '>':
+        if cmp == ">":
             cmp_2 = False
 
     if not cmp_1 or not cmp_2:
         msg0 = "\n\n\n{}\n".format("=" * 80)
 
         msg1 = 'KIM-API version = "{}" is detected, '.format(kim_api_version)
-        msg1 += 'which is incompatible with the current\n  kimpy version = '
+        msg1 += "which is incompatible with the current\n  kimpy version = "
         msg1 += '"{}".\n\nTry one of these options:\n\n'.format(kimpy_version)
 
-        msg2 = '  (1) Update KIM-API.\n      The current kimpy is '
-        msg2 += 'compatible with KIM-API versions:\n '
+        msg2 = "  (1) Update KIM-API.\n      The current kimpy is "
+        msg2 += "compatible with KIM-API versions:\n "
         msg2 += '     ["{}" - "{}"] (inclusive).\n'.format(backward, target)
 
         if not cmp_1:
-            msg3 = '  (2) Use the latest kimpy.\n      If you are using the '
-            msg3 += 'latest kimpy, which is not compatible '
-            msg3 += 'with this\n      KIM-API version '
+            msg3 = "  (2) Use the latest kimpy.\n      If you are using the "
+            msg3 += "latest kimpy, which is not compatible "
+            msg3 += "with this\n      KIM-API version "
             msg3 += '"{}" yet. Please contact\n      '.format(kim_api_version)
-            msg3 += 'Mingjian Wen (wenxx151@umn.edu)  or\n      '
-            msg3 += 'raise an issue on github so we update the kimpy.\n'
+            msg3 += "Mingjian Wen (wenxx151@umn.edu)  or\n      "
+            msg3 += "raise an issue on github so we update the kimpy.\n"
         else:
             compatible_kimpy = suggest_kimpy(kim_api_version, compatible_table)
-            msg3 = '  (2) Switch kimpy version.\n      The detected KIM-API '
-            msg3 += 'is compatible with kimpy version '
+            msg3 = "  (2) Switch kimpy version.\n      The detected KIM-API "
+            msg3 += "is compatible with kimpy version "
             msg3 += '"{}".\n'.format(compatible_kimpy)
 
         msg = msg0 + msg1 + msg2 + msg3
@@ -185,6 +189,6 @@ def check_kim_api_compatibility(kimpy_version, kim_api_version):
     return msg
 
 
-if __name__ == '__main__':
-    kim_api_compatibility = check_kim_api_compatibility('0.2.3', '2.0.1')
+if __name__ == "__main__":
+    kim_api_compatibility = check_kim_api_compatibility("0.2.3", "2.0.1")
     print(kim_api_compatibility)

examples/example_collections.py

@@ -14,17 +14,17 @@ def dirs_for_collection(collection, collections):
             msg = 'Calling "collections.cache_list_of_directory_names" failed.'
             raise kimpy.KimPyError(msg)
 
-        print('{}:{}:'.format(str(collection), str(it)))
+        print("{}:{}:".format(str(collection), str(it)))
 
         for i in range(extent):
             try:
                 name = collections.get_directory_name(i)
             except RuntimeError:
                 msg = 'Calling "collections.get_directory_name" for index = '
-                msg += '{} failed.'.format(i)
+                msg += "{} failed.".format(i)
                 raise kimpy.KimPyError(msg)
 
-            print('    ', name)
+            print("    ", name)
 
 
 def names_for_collection(collection, collections):
@@ -43,18 +43,18 @@ def names_for_collection(collection, collections):
             msg += 'cache_list_of_item_names_by_collection_and_type" failed.'
             raise kimpy.KimPyError(msg)
 
-        print('{}:{}:'.format(str(collection), str(it)))
+        print("{}:{}:".format(str(collection), str(it)))
 
         for i in range(extent):
             try:
                 name = collections.get_item_name_by_collection_and_type(i)
             except RuntimeError:
                 msg = 'Calling "collections.'
                 msg += 'get_item_name_by_collection_and_type" for index = '
-                msg += '{} failed.'.format(i)
+                msg += "{} failed.".format(i)
                 raise kimpy.KimPyError(msg)
 
-            print('    ', name)
+            print("    ", name)
 
 
 def example_main():
@@ -67,8 +67,8 @@ def example_main():
 
     project, semver = collections.get_project_name_and_sem_ver()
 
-    print('Project: {}'.format(project))
-    print('semVer: {}'.format(semver))
+    print("Project: {}".format(project))
+    print("semVer: {}".format(semver))
 
     for it in (
         kimpy.collection_item_type.modelDriver,
@@ -81,16 +81,16 @@ def example_main():
             msg = 'Calling "collections.get_environment_variable_name" failed.'
             raise kimpy.KimPyError(msg)
 
-        print('{} env name:{}'.format(str(it), name))
+        print("{} env name:{}".format(str(it), name))
 
     name, value = collections.get_configuration_file_environment_variable()
 
-    print('config file env name: {}'.format(name))
-    print('config file env value: {}'.format(value))
+    print("config file env name: {}".format(name))
+    print("config file env value: {}".format(value))
 
     filename = collections.get_configuration_file_name()
 
-    print('config file name: {}'.format(filename))
+    print("config file name: {}".format(filename))
 
     for kc in (
         kimpy.collection.system,
@@ -120,29 +120,29 @@ def example_main():
             msg += 'cache_list_of_item_names_by_type" failed.'
             raise kimpy.KimPyError(msg)
 
-        print('{}:'.format(str(it)))
+        print("{}:".format(str(it)))
 
         for i in range(extent):
             try:
                 name = collections.get_item_name_by_type(i)
             except RuntimeError:
                 msg = 'Calling "collections.get_item_name_by_type" '
-                msg += 'for index = {} failed.'.format(i)
+                msg += "for index = {} failed.".format(i)
                 raise kimpy.KimPyError(msg)
 
-            print('    {}'.format(name))
+            print("    {}".format(name))
 
     try:
         filename, collection = collections.get_item_library_file_name_and_collection(
             kimpy.collection_item_type.simulatorModel,
-            'Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu',
+            "Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu",
         )
     except RuntimeError:
         msg = 'Calling "collections.'
         msg += 'get_item_library_file_name_and_collection" failed.'
         raise kimpy.KimPyError(msg)
 
-    msg = 'Simulator Model Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu '
+    msg = "Simulator Model Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu "
     msg += 'has library name "{}" and is part of the '.format(filename)
     msg += '"{}" collection'.format(str(collection))
     print(msg)
@@ -168,15 +168,15 @@ def example_main():
             ) = collections.get_item_metadata_file(i)
         except RuntimeError:
             msg = 'Calling "collections.get_item_metadata_file" '
-            msg += 'for index = {} failed.'.format(i)
+            msg += "for index = {} failed.".format(i)
             raise kimpy.KimPyError(msg)
 
-        msg = 'Metadata file {} ({}) '.format(i, file_name)
-        msg += 'is of length {}'.format(file_length)
+        msg = "Metadata file {} ({}) ".format(i, file_name)
+        msg += "is of length {}".format(file_length)
 
         print(msg)
         print(file_str)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     example_main()