Pre-commit Update

.clang-format

@@ -34,7 +34,7 @@ AlwaysBreakBeforeMultilineStrings: false
 AlwaysBreakTemplateDeclarations: true
 BinPackArguments: true
 BinPackParameters: true
-BraceWrapping:   
+BraceWrapping:
   AfterClass:      false
   AfterControlStatement: false
   AfterEnum:       false
@@ -65,7 +65,7 @@ DisableFormat:   false
 ExperimentalAutoDetectBinPacking: false
 FixNamespaceComments: true
 ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
-IncludeCategories: 
+IncludeCategories:
   - Regex:           '^"'
     Priority:        1
   - Regex:           '^<'

.github/workflows/pull_request.yaml

@@ -24,7 +24,7 @@ jobs:
   check_formatting:
     uses: NWChemEx/.github/.github/workflows/check_formatting.yaml@master
     with:
-      license_config: ".github/.licenserc.yaml"
+      license_config: ".licenserc.yaml"
       cpp_source_dirs: ""
 
   test_nwx_docs:
@@ -36,4 +36,3 @@ jobs:
     uses: NWChemEx/.github/.github/workflows/test_nwx_library.yaml@master
     with:
       compilers: '["gcc-11", "clang-14"]'
-

.github/.licenserc.yaml → .licenserc.yaml

@@ -26,5 +26,6 @@ header:
     - docs/source/nitpick_exceptions
     - version.txt
     - cmake/friends.py.in
+    - build/
 
   comment: never

README.md

@@ -19,7 +19,7 @@ FriendZone
 
 [Documentation](https://nwchemex.github.io/FriendZone)
 
-Provides SimDE compatible APIs so that NWChemEx can play nicely with its 
+Provides SimDE compatible APIs so that NWChemEx can play nicely with its
 friends, *i.e.*, this repo wraps existing electronic structure packages in
 modules so they can be called as submodules in NWChemEx.
 
@@ -29,20 +29,20 @@ Packages supported through FriendZone include:
 - NWChem
 
 # Warnings
-Existing packages come with a lot of different licenses. At the moment we only 
-consider interfaces to packages that have licenses compatible with 
-[SimDE](https://github.com/NWChemEx/SimDE) (and 
+Existing packages come with a lot of different licenses. At the moment we only
+consider interfaces to packages that have licenses compatible with
+[SimDE](https://github.com/NWChemEx/SimDE) (and
 [NWChemEx](https://github.com/NWChemEx/NWChemEx)).
 
-Many of the other packages are by default configured/called suboptimally and 
-thus the modules in this repo should **NOT** be used for direct timing 
-comparisons unless otherwise noted. Performance contributions are greatly 
+Many of the other packages are by default configured/called suboptimally and
+thus the modules in this repo should **NOT** be used for direct timing
+comparisons unless otherwise noted. Performance contributions are greatly
 appreciated.
 
 # Installation
 
-As with the majority of the NWChemEx stack, FriendZone uses CMake and the 
-[CMaize](https://github.com/CMakePP/CMaize) library for configuration and 
+As with the majority of the NWChemEx stack, FriendZone uses CMake and the
+[CMaize](https://github.com/CMakePP/CMaize) library for configuration and
 building. This means that installation is usually achieved via a variation on:
 
 ```.sh
@@ -63,6 +63,6 @@ More detailed install instructions can be found
 
 # Acknowledgments
 
-This research was supported by the Exascale Computing Project (17-SC-20-SC), a 
-collaborative effort of the U.S. Department of Energy Office of Science and the 
-National Nuclear Security Administration.
+This research was supported by the Exascale Computing Project (17-SC-20-SC), a
+collaborative effort of the U.S. Department of Energy Office of Science and the
+National Nuclear Security Administration.

cmake/ase.cmake

@@ -28,4 +28,4 @@ if("${ENABLE_ASE}")
     find_ase()
 endif()
 
-add_library(ase INTERFACE)
+add_library(ase INTERFACE)

docs/requirements.txt

@@ -1,3 +1,3 @@
 sphinx
-sphinx_rtd_theme
 sphinx-autoapi
+sphinx_rtd_theme

docs/source/conf.py

@@ -21,30 +21,33 @@
 # http://www.sphinx-doc.org/en/master/config
 
 import os
-import sys
 
 # -- Project information -----------------------------------------------------
 
-project = u'friendzone'
-copyright = u'2020, NWChemEx Team'
-author = u'NWChemEx Team'
+project = "friendzone"
+copyright = "2020, NWChemEx Team"
+author = "NWChemEx Team"
 
 # Get the version from version.txt
-version = '1.0.0'
+version = "1.0.0"
 # The full version, including alpha/beta/rc tags
 release = version
 
 # -- General configuration ---------------------------------------------------
 
 # We use numref which is introduced in Sphinx 1.3
-needs_sphinx = '1.3'
+needs_sphinx = "1.3"
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.doctest', 'sphinx.ext.todo', 'sphinx.ext.coverage',
-    'sphinx.ext.mathjax', 'sphinx.ext.githubpages', 'autoapi.extension'
+    "sphinx.ext.doctest",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.githubpages",
+    "autoapi.extension",
 ]
 dir_path = os.path.dirname(os.path.realpath(__file__))
 doc_path = os.path.dirname(dir_path)
@@ -57,25 +60,25 @@
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = 'en'
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path .
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # Should figures be numbered?
 numfig = True
@@ -85,7 +88,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -111,23 +114,20 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = project + 'doc'
+htmlhelp_basename = project + "doc"
 
 # -- Options for LaTeX output ------------------------------------------------
 
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -137,49 +137,62 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, project + '.tex', project + ' Documentation', author,
-     'manual'),
+    (
+        master_doc,
+        project + ".tex",
+        project + " Documentation",
+        author,
+        "manual",
+    ),
 ]
 
 # -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, project.lower(), project + ' Documentation',
-              [author], 1)]
+man_pages = [
+    (master_doc, project.lower(), project + " Documentation", [author], 1)
+]
 
 # -- Options for Texinfo output ----------------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, project, project + ' Documentation', author, project,
-     'One line description of project.', 'Miscellaneous'),
+    (
+        master_doc,
+        project,
+        project + " Documentation",
+        author,
+        project,
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 # -- Extension configuration -------------------------------------------------
 autoapi_dirs = [
-    '../../src',
+    "../../src",
     # '../../tests',
 ]
 autoapi_add_toctree_entry = False
 autoapi_options = [
-    'members',
-    'undoc-members',
-    'private-members',
-    'show-inheritance',
-    'show-module-summary',
-    'special-members',
+    "members",
+    "undoc-members",
+    "private-members",
+    "show-inheritance",
+    "show-module-summary",
+    "special-members",
     #    'imported-members',
 ]
 
 
 # This skips classes that derived from ModuleBase, because those classes will
 # have Module API documentation producible by PluginPlay
 def skip_pluginplay_modules(app, what, name, obj, skip, options):
-    bases = obj.obj['bases'] if 'bases' in obj.obj.keys() else []
-    if 'pluginplay.ModuleBase' in bases:
+    bases = obj.obj["bases"] if "bases" in obj.obj.keys() else []
+    if "pluginplay.ModuleBase" in bases:
         skip = True
     return skip
 
@@ -191,7 +204,7 @@ def setup(sphinx):
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {"https://docs.python.org/": None}
 
 # -- Options for todo extension ----------------------------------------------
 
@@ -203,7 +216,7 @@ def setup(sphinx):
 # Nitpick requires all references to be resolved
 # This will ignore those that references that can't be linked
 nitpick_ignore = []
-for line in open('nitpick_exceptions'):
+for line in open("nitpick_exceptions"):
     if line.strip() == "" or line.startswith("#"):
         continue
     dtype, target = line.split(None, 1)

docs/source/design.rst

@@ -52,4 +52,4 @@ Notes on adding ASE:
 
 - ASE requires you to setup a calculator for the backend. The calculator's API
   is backend-specific. We have thus opted to treat each calculator as one
-  module since the setup of the calculator will be the guts of the module.
+  module since the setup of the calculator will be the guts of the module.

docs/source/module_api/index.rst

@@ -18,4 +18,4 @@ Module API
 
 .. toctree::
    :maxdepth: 1
-   :caption: Packages
+   :caption: Packages

docs/source/nitpick_exceptions

@@ -6,4 +6,4 @@ py:class Varies depending on the requested property
 
 py:class qcelemental.models.Molecule
 
-py:obj QCEngineEnergy
+py:obj QCEngineEnergy

requirements.txt

@@ -1,4 +1,4 @@
+ase
+networkx
 pydantic>=1.10.13
 qcengine
-networkx
-ase

src/python/friendzone/__init__.py

@@ -13,8 +13,8 @@
 # limitations under the License.
 
 from .nwx2ase import load_ase_modules
-from .nwx2qcengine import load_qcengine_modules
 from .nwx2qcelemental import load_qcelemental_modules
+from .nwx2qcengine import load_qcengine_modules
 
 
 def load_modules(mm):

src/python/friendzone/nwx2ase/__init__.py

@@ -17,14 +17,14 @@
 
 
 def load_ase_modules(mm):
-    if not is_friend_enabled('ase'):
+    if not is_friend_enabled("ase"):
         return
 
-    if is_friend_enabled('nwchem'):
-        for method in ['SCF', 'MP2', 'CCSD', 'CCSD(T)']:
-            egy_key = 'ASE(NWChem) : ' + method
-            grad_key = egy_key + ' gradient'
+    if is_friend_enabled("nwchem"):
+        for method in ["SCF", "MP2", "CCSD", "CCSD(T)"]:
+            egy_key = "ASE(NWChem) : " + method
+            grad_key = egy_key + " gradient"
             mm.add_module(egy_key, NWChemEnergyViaASE())
             mm.add_module(grad_key, NWChemGradientViaASE())
             for key in [egy_key, grad_key]:
-                mm.change_input(key, 'method', method)
+                mm.change_input(key, "method", method)