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:           '^<'

.flake8

@@ -0,0 +1,2 @@
+[flake8]
+extend-ignore = E203, E701, E741, W503

.github/workflows/merge.yaml

@@ -65,4 +65,4 @@ jobs:
         uses: github-actions-x/[email protected]
         with:
           push-branch: generated_data
-          commit-message: Automatically updated reference data using GitHub Actions
+          commit-message: Automatically updated reference data using GitHub Actions

.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"
 
   test_nwx_docs:
     uses: NWChemEx/.github/.github/workflows/test_nwx_docs.yaml@master

.github/workflows/scripts/download_reference_data.sh

@@ -6,7 +6,7 @@
 #   download_reference_data.sh
 #
 # Notes:
-#   - This script assumes the dependencies in reference_data/requirements.txt 
+#   - This script assumes the dependencies in reference_data/requirements.txt
 #     have been installed using PIP into a virtual environment called "venv"
 
 set -e # Exit with error if any command fails

.github/workflows/scripts/generate_reference_data.sh

@@ -45,7 +45,7 @@ python ${SCRIPTS_DIR}/generate_basis.py ${BASIS_SETS} ${BASES} -r
 echo "Calling ${SCRIPTS_DIR}/generate_molecules.py ${MOLECULES} ${MOLES} -r"
 python ${SCRIPTS_DIR}/generate_molecules.py ${MOLECULES} ${MOLES} -r
 
-echo "Calling ${SCRIPTS_DIR}/generate_densities.py ${DENSITIES} ${ATOM_DEN} -r" 
+echo "Calling ${SCRIPTS_DIR}/generate_densities.py ${DENSITIES} ${ATOM_DEN} -r"
 python ${SCRIPTS_DIR}/generate_densities.py ${DENSITIES} ${ATOM_DEN} -r
 
 # echo "Calling ${SCRIPTS_DIR}/generate_elec_configs.py ${ATOMIC_INFO} ${ELEC_CONFIGS}"

.gitignore

@@ -48,4 +48,4 @@ toolchain.cmake
 
 # Recommended directory for downloading basis sets
 reference_data/basis_sets
-!reference_data/basis_set/default
+!reference_data/basis_set/default

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

@@ -19,6 +19,8 @@ header:
 
   paths-ignore:
     - .github/
+    - .flake8
+    - build/
     - docs/Makefile
     - docs/source/nitpick_exceptions
     - reference_data/atomic_densities/default

LICENSE

@@ -174,4 +174,4 @@
       incurred by, or claims asserted against, such Contributor by reason
       of your accepting any such warranty or additional liability.
 
-   END OF TERMS AND CONDITIONS
+   END OF TERMS AND CONDITIONS

README.md

@@ -19,23 +19,23 @@ ChemCache
 
 [Documentation](https://nwchemex.github.io/ChemCache)
 
-This repo contains chemical reference data, *e.g.*, atomic basis sets, physical 
+This repo contains chemical reference data, *e.g.*, atomic basis sets, physical
 constants, molecular geometries, *etc.*.
 
 # Repo structure
 
 ChemCache has two release branches: `master` and `generated_data`. `master` only
-version controls the scripts for obtaining the reference data and the scripts 
-for generating the source files. `generated_data` additionally contains the 
-reference data and generated source files. Users of the repo can use whichever 
-branch of the repo is more convenient for them, as the branches are 
-automatically synchronized (*i.e*, changes to `master` will automatically cause 
+version controls the scripts for obtaining the reference data and the scripts
+for generating the source files. `generated_data` additionally contains the
+reference data and generated source files. Users of the repo can use whichever
+branch of the repo is more convenient for them, as the branches are
+automatically synchronized (*i.e*, changes to `master` will automatically cause
 `generated_data` to be updated).
 
 # Installation
 
-As with the majority of the NWChemEx stack, ChemCache uses CMake and the 
-[CMaize](https://github.com/CMakePP/CMaize) library for configuration and 
+As with the majority of the NWChemEx stack, ChemCache 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
@@ -56,6 +56,6 @@ 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 
+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.

docs/make.bat

@@ -1,17 +1,17 @@
-rem Copyright 2022 NWChemEx-Project
-rem
-rem Licensed under the Apache License, Version 2.0 (the "License");
-rem you may not use this file except in compliance with the License.
-rem You may obtain a copy of the License at
-rem
-rem http://www.apache.org/licenses/LICENSE-2.0
-rem
-rem Unless required by applicable law or agreed to in writing, software
-rem distributed under the License is distributed on an "AS IS" BASIS,
-rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-rem See the License for the specific language governing permissions and
-rem limitations under the License.
-
+rem Copyright 2022 NWChemEx-Project
+rem
+rem Licensed under the Apache License, Version 2.0 (the "License");
+rem you may not use this file except in compliance with the License.
+rem You may obtain a copy of the License at
+rem
+rem http://www.apache.org/licenses/LICENSE-2.0
+rem
+rem Unless required by applicable law or agreed to in writing, software
+rem distributed under the License is distributed on an "AS IS" BASIS,
+rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+rem See the License for the specific language governing permissions and
+rem limitations under the License.
+
 @ECHO OFF
 
 pushd %~dp0

docs/requirements.txt

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

docs/source/conf.py

@@ -29,13 +29,13 @@
 
 # -- Project information -----------------------------------------------------
 
-project = u'ChemCache'
-copyright = u'2020, NWChemEx Team'
-author = u'NWChemEx Team'
+project = "ChemCache"
+copyright = "2020, NWChemEx Team"
+author = "NWChemEx Team"
 
 # Get the version from version.txt
-with open('../../version.txt', 'r') as file:
-    version = file.read().replace('\n', '')
+with open("../../version.txt", "r") as file:
+    version = file.read().replace("\n", "")
 # The full version, including alpha/beta/rc tags
 release = version
 
@@ -53,44 +53,44 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'autoapi.extension',
-    'sphinx.ext.doctest',
-    #'sphinx.ext.intersphinx',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.githubpages'
+    "autoapi.extension",
+    "sphinx.ext.doctest",
+    # "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.githubpages",
 ]
 dir_path = os.path.dirname(os.path.realpath(__file__))
 doc_path = os.path.dirname(dir_path)
 root_path = os.path.dirname(doc_path)
 
 # Add any paths that contain templates here, relative to this directory.
-#templates_path = ['_templates']
+# templates_path = ['_templates']
 
 # The suffix(es) of source filenames.
 # 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
@@ -100,7 +100,7 @@
 # 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
@@ -111,7 +111,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-#html_static_path = ['_static']
+# html_static_path = ['_static']
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -126,23 +126,20 @@
 # -- 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',
@@ -152,47 +149,60 @@
 # (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 = [
-    '../../utils/data_management',
+    "../../utils/data_management",
 ]
 # autoapi_ignore = ['*atomic_densities*']
 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',
 ]
 
 # -- 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 ----------------------------------------------
 
@@ -204,7 +214,7 @@
 # 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

@@ -22,12 +22,12 @@ This page details some of the decisions made in designing ChemCache.
 Generation of Source Files
 **************************
 
-Most of the ChemCache library is autogenerated by the python scripts located in 
+Most of the ChemCache library is autogenerated by the python scripts located in
 ``utils/data_management``, using data either provided in the ``reference_data``
 directory or downloaded from the internet by some of the ``data_management``
 scripts. Of particular note, a limited selection of basis sets is provided in
 the ``master`` branch. The script ``utils/data_management/scrape_bse.py`` can be
-used to download additional basis sets from the 
+used to download additional basis sets from the
 `Basis Set Exchange <https://www.basissetexchange.org/>`__:
 
 .. code-block:: console
@@ -46,8 +46,8 @@ corresponding source files can be generated by the associated script:
     source data_venv/bin/activate
     python utils/data_management/generate_basis.py /reference_data/basis_sets /src/chemcache/bases -r
 
-Consult the ``data_management`` API documentation for more details on the usage 
-of each of these scripts. The ``generated_data`` branch contains a version of 
-ChemCache where a larger selection of basis sets (Dunning, Ahlrichs, and Pople 
-types) have been included and the corresponding source files have been 
+Consult the ``data_management`` API documentation for more details on the usage
+of each of these scripts. The ``generated_data`` branch contains a version of
+ChemCache where a larger selection of basis sets (Dunning, Ahlrichs, and Pople
+types) have been included and the corresponding source files have been
 generated.

docs/source/installation.rst

@@ -80,7 +80,7 @@ ChemCache's build system.
 CMake
 -----
 
-CMake is the basis of CMaize, and minimum version of 3.14 is required to 
+CMake is the basis of CMaize, and minimum version of 3.14 is required to
 properly build ChemCache.