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/enable_sigma.cmake

@@ -1 +1 @@
-set(ENABLE_SIGMA ON)
+set(ENABLE_SIGMA ON)

.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/.licenserc.yaml → .licenserc.yaml

@@ -22,6 +22,7 @@ header:
     - docs/Makefile
     - LICENSE
     - docs/requirements.txt
-    - version.txt 
+    - version.txt
+    - build/
 
   comment: never

CMakeLists.txt

@@ -92,7 +92,7 @@ if("${BUILD_TESTING}")
         INCLUDE_DIRS "${INTEGRALS_SOURCE_DIR}/${PROJECT_NAME}"
         DEPENDS Catch2 ${PROJECT_NAME}
     )
-    
+
     nwx_pybind11_tests(
         py_integrals "${PYTHON_TEST_DIR}/unit_tests/test_integrals.py"
         SUBMODULES pluginplay chemist parallelzone simde

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

@@ -26,32 +26,32 @@ Repository for the generic integral API and implementations for specific integra
 Building Integrals
 ------------------
 
-Integrals is built using 
+Integrals is built using
 [CPP](https://github.com/CMakePackagingProject/CMakePackagingProject.git).
-Assuming you have already installed CPP, that you are on a sane Unix-like 
-computer, and you are willing to let Integrals build all dependencies, then 
+Assuming you have already installed CPP, that you are on a sane Unix-like
+computer, and you are willing to let Integrals build all dependencies, then
 the following will suffice to build Integrals:
 
 ```
 git clone https://github.com/NWChemEx/Integrals.git
 cd SDE
 cmake -H. -Bbuild -DCPP_GITHUB_TOKEN=<your super-secret token> \
                   -DMPI_ROOT=<path/to/your/mpi/installation> \
-                  -DCMAKE_PREFIX_PATH=<where/you/installed/CPP> \                  
+                  -DCMAKE_PREFIX_PATH=<where/you/installed/CPP> \
                   -DCMAKE_INSTALL_PREFIX=<where/you/want/to/install/Integrals>
 cd build
 cmake --build .
 #May need to run as an admin depending on where you are installing
-cmake --build . --target install  
+cmake --build . --target install
 ```
 The build process is not capable of building MPI so you will have to provide a
 path to a known installation via the `MPI_ROOT` variable. The GitHub token is
-necessary because, at the moment, Chemist, TAMM, SDE, and Utilities are 
-private repositories (instructions for generating a token are 
+necessary because, at the moment, Chemist, TAMM, SDE, and Utilities are
+private repositories (instructions for generating a token are
 [here](https://help.github.com/articles/creating-a-personal-access-token-for-the-command-line/)).
 
-For finer-grained control over the build we direct the reader to the more 
-thorough CPP build instructions located 
+For finer-grained control over the build we direct the reader to the more
+thorough CPP build instructions located
 [here](https://cmakepackagingproject.readthedocs.io/en/latest/end_user/quick_start.html)
 
 and note that Integrals depends on several other projects:
@@ -62,17 +62,17 @@ and note that Integrals depends on several other projects:
   - [pybind11](https://github.com/pybind/pybind11)
     - Requires a development version of Python
   - [cereal](https://github.com/USCiLab/cereal)
-- [Chemist](https://github.com/NWChemEx/Chemist)  
+- [Chemist](https://github.com/NWChemEx/Chemist)
 - [TAMM](https://github.com/NWChemEx/TAMM)
   - [HPTT](https://github.com/ajaypanyala/hptt)
   - [MSGSL](https://github.com/Microsoft/GSL)
   - [LAPACKE](http://www.netlib.org/lapack/)
   - [Eigen3](https://github.com/eigenteam/eigen-git-mirror)
   - [GlobalArrays](https://github.com/GlobalArrays/ga)
   - MPI
-- [LibInt](https://github.com/evaleev/libint)     
+- [LibInt](https://github.com/evaleev/libint)
 - (For testing only)[Catch2](https://github.com/catchorg/Catch2)
 
-We recommend building Libint separately for the moment because a proper 
-autotools build (the only autotools variant supported by CPP) builds the 
+We recommend building Libint separately for the moment because a proper
+autotools build (the only autotools variant supported by CPP) builds the
 generator and many more integrals than are necessary.

docs/source/conf.py

@@ -21,13 +21,14 @@
 # http://www.sphinx-doc.org/en/master/config
 
 import os
+
 import git
 
 # -- Project information -----------------------------------------------------
 
-project = u'Integrals'
-copyright = u'2020, NWChemEx Team'
-author = u'NWChemEx Team'
+project = "Integrals"
+copyright = "2020, NWChemEx Team"
+author = "NWChemEx Team"
 
 ##############################################################################
 #           Shouldn't need to change anything below this point               #
@@ -61,42 +62,46 @@
 
 # If your documentation needs a minimal Sphinx version, state it here.
 #
-needs_sphinx = '7.2.6'
+needs_sphinx = "7.2.6"
 
 # 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.autodoc', 'sphinx.ext.mathjax', 'sphinx.ext.githubpages',
-    'sphinx.ext.autosummary', 'sphinx_rtd_theme', 'sphinx.ext.intersphinx'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.autosummary",
+    "sphinx_rtd_theme",
+    "sphinx.ext.intersphinx",
 ]
 
 # 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"
 
 numfig = True
 numfig_secnum_depth = 0
@@ -106,7 +111,7 @@
 # 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
@@ -117,7 +122,7 @@
 # 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.
@@ -132,23 +137,20 @@
 # -- 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',
@@ -158,30 +160,43 @@
 # (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 -------------------------------------------------
 
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'python': ('https://docs.python.org/3', None)}
+intersphinx_mapping = {"python": ("https://docs.python.org/3", None)}

docs/source/index.rst

@@ -21,5 +21,3 @@ Welcome to Integral's documentation!
 
    module_api/index
    C++ API <https://nwchemex.github.io/Integrals/integrals_cxx_api/index.html>
-
-

docs/source/module_api/index.rst

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

src/integrals/ao_integrals/ao_integrals.hpp

@@ -53,4 +53,4 @@ inline void load_modules(pluginplay::ModuleManager& mm) {
     mm.add_module<UQDriver>("UQ Driver");
 }
 
-} // namespace integrals::ao_integrals
+} // namespace integrals::ao_integrals

src/integrals/ao_integrals/ao_integrals_driver.cpp

@@ -103,4 +103,4 @@ MODULE_RUN(AOIntegralsDriver) {
     return pt::wrap_results(rv, std::move(t));
 }
 
-} // namespace integrals::ao_integrals
+} // namespace integrals::ao_integrals

src/integrals/ao_integrals/coulomb_metric.cpp

@@ -89,4 +89,4 @@ MODULE_RUN(CoulombMetric) {
     return pt::wrap_results(rv, M);
 }
 
-} // namespace integrals::ao_integrals
+} // namespace integrals::ao_integrals

src/integrals/ao_integrals/df_integral.cpp

@@ -56,4 +56,4 @@ MODULE_RUN(DFIntegral) {
     return pt::wrap_results(rv, std::move(L));
 }
 
-} // namespace integrals::ao_integrals
+} // namespace integrals::ao_integrals

src/integrals/ao_integrals/j_density_fitted.cpp

@@ -65,4 +65,4 @@ MODULE_RUN(JDensityFitted) {
     return pt::wrap_results(rv, std::move(j));
 }
 
-} // namespace integrals::ao_integrals
+} // namespace integrals::ao_integrals

src/integrals/ao_integrals/j_four_center.cpp

@@ -58,4 +58,4 @@ MODULE_RUN(JFourCenter) {
     return pt::wrap_results(rv, std::move(j));
 }
 
-} // namespace integrals::ao_integrals
+} // namespace integrals::ao_integrals

src/integrals/ao_integrals/k_density_fitted.cpp

@@ -66,4 +66,4 @@ MODULE_RUN(KDensityFitted) {
     return pt::wrap_results(rv, std::move(k));
 }
 
-} // namespace integrals::ao_integrals
+} // namespace integrals::ao_integrals

src/integrals/ao_integrals/k_four_center.cpp

@@ -59,4 +59,4 @@ MODULE_RUN(KFourCenter) {
     return pt::wrap_results(rv, std::move(k));
 }
 
-} // namespace integrals::ao_integrals
+} // namespace integrals::ao_integrals

src/integrals/ao_integrals/uq_driver.cpp

@@ -93,4 +93,4 @@ MODULE_RUN(UQDriver) {
     auto rv = results();
     return eri_pt::wrap_results(rv, t_w_error);
 }
-} // namespace integrals::ao_integrals
+} // namespace integrals::ao_integrals

src/integrals/libint/libint.cpp

@@ -182,4 +182,4 @@ void load_modules(pluginplay::ModuleManager& mm) {
 #undef LOAD_LIBINT
 #undef LIBINT
 
-} // namespace integrals::libint
+} // namespace integrals::libint

src/integrals/libint/libint_visitor.hpp

@@ -27,7 +27,7 @@ class LibintVisitor : public chemist::qm_operator::OperatorVisitor {
 
     LibintVisitor(const std::vector<libint2::BasisSet>& bases, double thresh,
                   std::size_t deriv = 0) :
-      m_bases(bases), m_thresh(thresh), m_deriv(deriv){};
+      m_bases(bases), m_thresh(thresh), m_deriv(deriv) {};
 
     void run(const s_e_type& S_e) {
         m_engine = detail_::make_engine(m_bases, S_e, m_thresh, m_deriv);
@@ -54,4 +54,4 @@ class LibintVisitor : public chemist::qm_operator::OperatorVisitor {
     libint2::Engine m_engine;
 };
 
-} // namespace integrals::libint
+} // namespace integrals::libint

src/integrals/uncertain_types.hpp

@@ -35,4 +35,4 @@ using uncertain_float  = float;
 using uncertain_double = double;
 #endif
 
-} // namespace integrals::type
+} // namespace integrals::type

tests/cxx/unit/integrals/ao_integrals/ao_integrals_driver.cpp

@@ -100,4 +100,4 @@ TEST_CASE("AOIntegralsDriver") {
         const auto& K_corr = kmod.run_as<simde::aos_k_e_aos>(braket);
         compare_matrices(K, K_corr);
     }
-}
+}