Pre-commit Update

.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

@@ -22,5 +22,6 @@ header:
     - LICENSE
     - version.txt
     - docs/source/nitpick_exceptions
+    - build/
 
   comment: never

docs/requirements.txt

@@ -1,5 +1,5 @@
 sphinx==v7.2.6
+sphinx-autoapi
 sphinx_rtd_theme==1.3.0
-sphinxcontrib-bibtex
 sphinx_tabs
-sphinx-autoapi
+sphinxcontrib-bibtex

docs/source/conf.py

@@ -21,30 +21,33 @@
 # http://www.sphinx-doc.org/en/master/config
 
 import os
-import sys
 
 # -- Project information -----------------------------------------------------
 
-project = u'StructureFinder'
-copyright = u'2024, NWChemEx Community'
-author = u'NWChemEx Community'
+project = "StructureFinder"
+copyright = "2024, NWChemEx Community"
+author = "NWChemEx Community"
 
 # 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 producable 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)

src/python/structurefinder/__init__.py

@@ -12,8 +12,10 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from .lj_potential.lennard_jones_potential_module import (
+    load_lennard_jones_potential,
+)
 from .pyberny import load_pyberny_modules
-from .lj_potential.lennard_jones_potential_module import load_lennard_jones_potential
 
 
 def load_modules(mm):

src/python/structurefinder/lj_potential/lennard_jones_potential_module.py

@@ -17,8 +17,8 @@
 
 import numpy as np
 import pluginplay as pp
-from simde import TotalEnergy
 import tensorwrapper as tw
+from simde import TotalEnergy
 
 
 class LennardJonesPotential(pp.ModuleBase):
@@ -31,41 +31,41 @@ def __init__(self):
         self.description("Lennard-Jones 1D potential function")
         self.satisfies_property_type(TotalEnergy())
 
-    #--------------------------------------------------------------------------
+    # --------------------------------------------------------------------------
 
     # Module run_ member function ---------------------------------------------
     def run_(self, inputs, submods):
         """
         Parameters
         ----------
-        inputs : Diatomic distance, 
+        inputs : Diatomic distance,
         TYPE ---> Float
-    
+
         Returns
         -------
-        E: Lennard-Jonnes 1D potential Energy, 
-        TYPE ---> Float 
+        E: Lennard-Jonnes 1D potential Energy,
+        TYPE ---> Float
         """
         pt = TotalEnergy()
-        chem_sys, = pt.unwrap_inputs(inputs)
+        (chem_sys,) = pt.unwrap_inputs(inputs)
         mol = chem_sys.molecule
         coor_0 = np.array([mol.at(0).x, mol.at(0).y, mol.at(0).z])
         coor_1 = np.array([mol.at(1).x, mol.at(1).y, mol.at(1).z])
-        #----------------------------------------------------------------------
-        assert (mol.size() == 2)  #<--- To check molcule size contains 2-atoms
-        #----------------------------------------------------------------------
+        # ----------------------------------------------------------------------
+        assert mol.size() == 2  # <--- To check molcule size contains 2-atoms
+        # ----------------------------------------------------------------------
         r = np.linalg.norm(coor_0 - coor_1)
-        #-------------- LENNARD-JONES FUNCTION --------------------------------
+        # -------------- LENNARD-JONES FUNCTION --------------------------------
         E = 4 * ((1 / r**12) - (1 / r**6))
-        #------------- ANALYTIC FORCE -----------------------------------------
-        DE_x = -24 * ((2 / r**13) - (1 / r**7))
-        FC = -DE_x
-        #----------------------------------------------------------------------
+        # ------------- ANALYTIC FORCE -----------------------------------------
+        # DE_x = -24 * ((2 / r**13) - (1 / r**7))
+        # FC = -DE_x
+        # ----------------------------------------------------------------------
         E = tw.Tensor(np.array(E))
         rv = self.results()
         return pt.wrap_results(rv, E)
 
-    #--------------------------------------------------------------------------
+    # --------------------------------------------------------------------------
 
 
 def load_lennard_jones_potential(mm):

src/python/structurefinder/pyberny/__init__.py

@@ -12,20 +12,19 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import chemist
+import numpy as np
 import pluginplay as pp
+from berny import Berny, geomlib
 from simde import (
     EnergyNuclearGradientStdVectorD,
-    TotalEnergyNuclearOptimization,
     MoleculeFromString,
     TotalEnergy,
+    TotalEnergyNuclearOptimization,
 )
-from berny import Berny, geomlib
-import chemist
-import numpy as np
 
 
 class GeomoptViaPyberny(pp.ModuleBase):
-
     def __init__(self):
         pp.ModuleBase.__init__(self)
         self.satisfies_property_type(TotalEnergyNuclearOptimization())
@@ -43,10 +42,18 @@ def run_(self, inputs, submods):
         xyz = ""
         xyz += str(molecule.size()) + "\n\n"
 
-        #TODO ensure points == molecule.nuclei.charges.point_set
+        # TODO ensure points == molecule.nuclei.charges.point_set
         for i in range(points.size()):
-            xyz += (molecule.at(i).name + " " + str(points.at(i).x) + " " +
-                    str(points.at(i).y) + " " + str(points.at(i).z) + "\n")
+            xyz += (
+                molecule.at(i).name
+                + " "
+                + str(points.at(i).x)
+                + " "
+                + str(points.at(i).y)
+                + " "
+                + str(points.at(i).z)
+                + "\n"
+            )
 
         # Loads the geometry string into the Berny optimizer
         # object.
@@ -58,15 +65,17 @@ def run_(self, inputs, submods):
             lines = geom2xyz.split("\n")
             mol_string = "\n".join(lines[2:])
             xyz2chem_mol = submods["StringConv"].run_as(
-                MoleculeFromString(), mol_string)
+                MoleculeFromString(), mol_string
+            )
             geom = chemist.ChemicalSystem(xyz2chem_mol)
             geom_nuclei = geom.molecule.nuclei.as_nuclei()
             geom_points = geom_nuclei.charges.point_set.as_point_set()
 
             # Main optimizer operation
             energy = submods["Energy"].run_as(TotalEnergy(), geom)
             gradients = submods["Gradient"].run_as(
-                EnergyNuclearGradientStdVectorD(), geom, geom_points)
+                EnergyNuclearGradientStdVectorD(), geom, geom_points
+            )
             optimizer.send((np.array(energy).item(), gradients))
 
         opt_geom_nuclei = geom.molecule.nuclei.as_nuclei()