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/integration_testing.cmake

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

.github/tamm_testing.cmake

@@ -1,3 +1,3 @@
 set(INTEGRATION_TESTING ON)
 set(BUILD_TAMM_SCF ON)
-set(BUILD_PYBIND11_PYBINDINGS OFF)
+set(BUILD_PYBIND11_PYBINDINGS OFF)

.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
@@ -47,4 +47,3 @@ jobs:
   #   with:
   #     compilers: '["gcc-11"]'
   #     repo_toolchain: '.github/tamm_testing.cmake'
-

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

@@ -24,5 +24,6 @@ header:
     - src/scf/common/
     - src/scf/scf/
     - LICENSE
+    - build
 
   comment: never

CMakeLists.txt

@@ -82,7 +82,7 @@ nwx_add_pybind11_module(
     DEPENDS "${PROJECT_NAME}"
 )
 
-if("${BUILD_TESTING}") 
+if("${BUILD_TESTING}")
     include(CTest)
     set(PYTHON_TEST_DIR "${SCF_TESTS_DIR}/python")
     set(CXX_TEST_DIR "${SCF_TESTS_DIR}/cxx")
@@ -113,7 +113,7 @@ if("${BUILD_TESTING}")
         python_mpi_test(
             integration_test_scf
             "${PYTHON_TEST_DIR}/integration_tests/run_integration_tests.py"
-            SUBMODULES nwchemex chemcache integrals simde chemist pluginplay 
+            SUBMODULES nwchemex chemcache integrals simde chemist pluginplay
                        parallelzone friendzone tensorwrapper nux
         )
 

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

cmake/get_nwx_cmake.cmake

@@ -28,4 +28,4 @@ macro(get_nwx_cmake)
     )
 endmacro()
 
-get_nwx_cmake()
+get_nwx_cmake()

cmake/mpi_test.cmake

@@ -28,7 +28,7 @@ macro(python_mpi_test test_name test_script)
         add_test(
             NAME "py_${test_name}"
             COMMAND "${MPIEXEC_EXECUTABLE}" "${MPIEXEC_NUMPROC_FLAG}" "2"
-                    "${Python_EXECUTABLE}" 
+                    "${Python_EXECUTABLE}"
                     "${test_script}"
         )
         nwx_python_path(TEST_PYTHONPATH ${ARGN})
@@ -37,4 +37,4 @@ macro(python_mpi_test test_name test_script)
             PROPERTIES ENVIRONMENT "${TEST_PYTHONPATH}"
         )
     endif()
-endmacro()
+endmacro()

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/source/conf.py

@@ -21,13 +21,14 @@
 # http://www.sphinx-doc.org/en/master/config
 
 import os
+
 import git
 
 # -- Project information -----------------------------------------------------
 
-project = u'SCF'
-copyright = u'2024, NWChemEx Team'
-author = u'NWChemEx Team'
+project = "SCF"
+copyright = "2024, NWChemEx Team"
+author = "NWChemEx Team"
 
 ##############################################################################
 #           Shouldn't need to change anything below this point               #
@@ -61,48 +62,48 @@
 
 # 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.autodoc",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.autosummary",
+    "sphinx_rtd_theme",
     # 'sphinxcontrib.bibtex',
-    'sphinx_tabs.tabs',
-    'sphinx.ext.intersphinx',
+    "sphinx_tabs.tabs",
+    "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
@@ -112,20 +113,20 @@
 # 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"
 
 # html_logo = "assets/logo.png"
 
 # 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
 # documentation.
 #
-html_theme_options = {'logo_only': True}
+html_theme_options = {"logo_only": True}
 
 # 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.
@@ -140,23 +141,20 @@
 # -- 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',
@@ -166,30 +164,43 @@
 # (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/module_api/index.rst

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

examples/driver/scf_driver.cpp

@@ -16,12 +16,11 @@
 
 #include <iostream>
 
-#include <scf/scf.hpp>
 #include <chemcache/chemcache.hpp>
+#include <scf/scf.hpp>
 #include <tamm/tamm.hpp>
 
 int main(int argc, char** argv) {
-
     tamm::initialize(argc, argv);
 
     // Populate modules
@@ -31,24 +30,26 @@ int main(int argc, char** argv) {
 
     // Create ChemicalSystem
     std::string mol_name = "water";
-    auto mol = mm.at("NWX Molecules").run_as<simde::MoleculeFromString>(mol_name);
+    auto mol =
+      mm.at("NWX Molecules").run_as<simde::MoleculeFromString>(mol_name);
     simde::type::chemical_system cs(mol);
 
     // Create BasisSet
-    std::string basis_name = "sto-3g"; // This is the only supported basis in ChemCache
+    std::string basis_name =
+      "sto-3g"; // This is the only supported basis in ChemCache
     auto aos = mm.at(basis_name).run_as<simde::MolecularBasisSet>(mol);
 
     // Run module
     auto E = mm.at("SCF Energy").run_as<simde::AOEnergy>(aos, cs);
     std::cout << "SCF Energy = " << E << " Hartree" << std::endl;
-    
+
     std::vector<std::string> xc_type = {"pbe0"};
     mm.change_input("SCF Energy", "xc_type", xc_type);
     mm.change_input("SCF Energy", "molecule_name", mol_name);
     E = mm.at("SCF Energy").run_as<simde::AOEnergy>(aos, cs);
     std::cout << "SCF Energy = " << E << " Hartree" << std::endl;
-        
+
     tamm::finalize();
-    
+
     return 0;
 }

requirements.txt

@@ -1,6 +1,6 @@
+ase
+networkx
 # This file is a hack to get CI/CD to work. These packages are needed by
 # FriendZone NOT this repo.
 pydantic>=1.10.13
 qcengine
-networkx
-ase