pre-commit

.github/workflows/build_nwx_buildenv_image.yaml

@@ -39,4 +39,3 @@ jobs:
           docker tag nwx_buildenv:latest ghcr.io/nwchemex/nwx_buildenv:latest
           docker push ghcr.io/nwchemex/nwx_buildenv:latest
         shell: bash
-

.github/workflows/check_formatting.yaml

@@ -80,9 +80,9 @@ jobs:
       - uses: actions/setup-python@v2
         with:
           python-version: "3.x"
-      - name: Install yapf
-        run: pip install yapf
+      - name: Install black
+        run: pip install black
         shell: bash
       - name: Check Python Formatting
-        run: yapf -r -q .
+        run: black --check .
         shell: bash

.github/workflows/deploy_nwx_docs.yaml

@@ -30,7 +30,7 @@ on:
 jobs:
   deploy_docs:
     runs-on: ubuntu-latest
-    container: 
+    container:
       image: ghcr.io/nwchemex/nwx_buildenv:latest
     steps:
       - name: Fail if Target is Blank
@@ -44,7 +44,7 @@ jobs:
       # These next two steps will configure CMake if required
       - name: Configure Only Docs
         if: |
-          inputs.generate_module_docs == false && 
+          inputs.generate_module_docs == false &&
           inputs.doc_target != 'Sphinx'
         run: |
           cmake -Bbuild -H. -GNinja -DBUILD_DOCS=ON -DONLY_BUILD_DOCS=ON
@@ -90,4 +90,4 @@ jobs:
         uses: peaceiris/actions-gh-pages@v3
         with:
           GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
-          publish_dir: ./docs/build/html  
+          publish_dir: ./docs/build/html

.github/workflows/test_nwx_docs.yaml

@@ -28,13 +28,13 @@ on:
         type: boolean
         required: false
         default: true
-      
-      
+
+
 
 jobs:
   test_build_docs:
     runs-on: ubuntu-latest
-    container: 
+    container:
       image: ghcr.io/nwchemex/nwx_buildenv:latest
     steps:
       - name: Fail if Target is Blank
@@ -73,4 +73,3 @@ jobs:
           fi
           make html SPHINXOPTS="${SPHINX_OPTS}"
         shell: bash
-

docs/requirements.txt

@@ -1,5 +1,5 @@
 docutils<=0.16
 sphinx
 sphinx_rtd_theme
-sphinxcontrib.bibtex
 sphinx_tabs
+sphinxcontrib.bibtex

docs/source/conf.py

@@ -24,12 +24,12 @@
 
 # -- Project information -----------------------------------------------------
 
-project = u'Developer Documentation'
-copyright = u'2020, NWChemEx Team'
-author = u'NWChemEx Team'
+project = "Developer Documentation"
+copyright = "2020, NWChemEx Team"
+author = "NWChemEx Team"
 
 # TODO: get version from git
-version = '1.0.0'
+version = "1.0.0"
 
 # The full version, including alpha/beta/rc tags
 release = version
@@ -48,40 +48,45 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx',
-    'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.mathjax',
-    'sphinxcontrib.bibtex', 'sphinx_tabs.tabs'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinxcontrib.bibtex",
+    "sphinx_tabs.tabs",
 ]
 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"
 
 numfig = True
 
@@ -90,18 +95,18 @@
 # 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
 # documentation.
 #
-html_theme_options = {'vcs_pageview_mode': 'edit'}
+html_theme_options = {"vcs_pageview_mode": "edit"}
 
 # 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.
@@ -115,32 +120,29 @@
 
 # Allows the edit on GitHub button to make editing the docs easier.
 html_context = {
-    'display_github': True,
-    'github_user': 'NWChemEx',
-    'github_repo': '.github',
-    'github_version': 'master/docs/source/',
+    "display_github": True,
+    "github_user": "NWChemEx",
+    "github_repo": ".github",
+    "github_version": "master/docs/source/",
 }
 
 # -- 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',
@@ -160,8 +162,8 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = True
 
-# -- Options for bibtex --------------------------------------------------------
+# -- Options for bibtex ------------------------------------------------------
 
-bibtex_bibfiles = ['bibliography/software.bib']
-bibtex_reference_style = 'super'
-bibtex_default_style = 'plain'
+bibtex_bibfiles = ["bibliography/software.bib"]
+bibtex_reference_style = "super"
+bibtex_default_style = "plain"

docs/source/conventions/file_structure.rst

@@ -51,7 +51,7 @@ File Naming Conventions
   files should be "lower_snake_case", i.e., all lowercase letters, underscores
   for separating words.
 - It is strongly recommended you stick to letters, numbers, and underscores
-  only. Notably avoid symbols like ``*``, ``?``, ``(``, ``)``, ``'``, 
+  only. Notably avoid symbols like ``*``, ``?``, ``(``, ``)``, ``'``,
   and ``"``.
 
 Extensions
@@ -61,7 +61,7 @@ Extensions
 - C++ source files end with ``*.cpp``, e.g., ``file_name.cpp``.
 - C++ inline implementation files end with ``*.ipp``, e.g., ``file_name.ipp``.
 - CMake modules end with ``*.cmake``, e.g., ``file_name.cmake``.
-- (GitHub-flavored) Markdown end with ``*.md``, e.g., ``file_name.md``. 
+- (GitHub-flavored) Markdown end with ``*.md``, e.g., ``file_name.md``.
 - Python source files end with ``.py``, e.g., ``file_name.py``.
 - ReStructured Text files end with ``.rst``, e.g., ``file_name.py``.
 

docs/source/testing/integration.rst

@@ -19,13 +19,13 @@ Writing Integration Tests for NWChemEx
 ######################################
 
 NWChemEx is a modular ecosystem designed with separation of concerns as a key
-design point. An example of this separation can be found with the 
-SCF, integrals, ChemCache libraries. These components of NWX are linked by 
-SimDE and are intended to be used together, but are not explicitly required for 
-the development of the other (see :numref:`fig_deps_chart`). The unit tests for 
-these libraries are intended to ensure basic functionality and correctness, 
-which can usually be accomplished with simple test data that allow the unit 
-tests to run quickly. 
+design point. An example of this separation can be found with the
+SCF, integrals, ChemCache libraries. These components of NWX are linked by
+SimDE and are intended to be used together, but are not explicitly required for
+the development of the other (see :numref:`fig_deps_chart`). The unit tests for
+these libraries are intended to ensure basic functionality and correctness,
+which can usually be accomplished with simple test data that allow the unit
+tests to run quickly.
 
 .. _fig_deps_chart:
 
@@ -38,8 +38,8 @@ tests to run quickly.
     within NWChemEx. Arrows point from a dependency to the dependent library.
 
 
-With that said, the initial development and testing of the SCF becomes very 
-awkward when one is unable to easily acquire real integrals for real molecular 
+With that said, the initial development and testing of the SCF becomes very
+awkward when one is unable to easily acquire real integrals for real molecular
 systems. Additionally, changes to the integrals code could have deleterious
 effects on the SCF code, which we would like to detect before merging. For these
 (and other) reasons, it can be useful to implement integration tests to ensure
@@ -56,7 +56,7 @@ don't break interoperability with the others.
     :scale: 50 %
 
     A diagram illustrating the relationship between the integration tests, the
-    library they test, and the top-level NWChemEx library. Arrows point from a 
+    library they test, and the top-level NWChemEx library. Arrows point from a
     dependency to the dependent library.
 
 
@@ -149,4 +149,3 @@ needed by a module in our project.
         def setUp(self):
             self.mm = ModuleManager()
             nwchemex.load_modules(mm) # Also loads out SCF modules
-

docs/source/testing/unit.rst

@@ -18,19 +18,19 @@
 Writing Unit Tests for NWChemEx
 ###############################
 
-Within the first party NWChemEx libraries, we aim for extensive unit testing to 
+Within the first party NWChemEx libraries, we aim for extensive unit testing to
 ensure functionality and correctness. All classes, functions, and modules added
 to any of the first party libraries will be expected to have corresponding unit
-tests. Testing of functions (as well as Plugin modules) should minimally ensure 
-that all return routes and errors are checked. Tests for classes should do the 
-same for all member functions, while additionally testing that the state of all 
+tests. Testing of functions (as well as Plugin modules) should minimally ensure
+that all return routes and errors are checked. Tests for classes should do the
+same for all member functions, while additionally testing that the state of all
 instances is consistent at construction and after modifications. Generally, the
-unit tests should be able to run quickly, and use simplified data with the 
+unit tests should be able to run quickly, and use simplified data with the
 minimum level of complexity need to ensure completeness in the testing.
 
 The C++ unit tests use the `Catch2 framework <https://github.com/catchorg/Catch2>`_,
 while python tests use the `unittest framework <https://docs.python.org/3/library/unittest.html>`_.
-Assume the following class and related comparison function are intended to be 
+Assume the following class and related comparison function are intended to be
 added to one of the first party libraries:
 
 .. tabs::
@@ -51,12 +51,12 @@ added to one of the first party libraries:
                 ToBeTested(value_type a_value = 0) : my_value_(a_value) {}
 
                 value_type check_my_value() { return my_value_; }
-                
+
                 void change_my_value(value_type new_value) {
                     if(new_value == 13) throw std::runtime_error("Unlucky Number");
                     my_value_ = new_value;
                 }
-                
+
                 bool operator==(const ToBeTested& rhs) const noexcept {
                     return my_value_ == rhs.my_value_;
                 }
@@ -74,14 +74,14 @@ added to one of the first party libraries:
 
             class ToBeTested():
 
-            def __init__(self, a_value = 0): 
+            def __init__(self, a_value = 0):
                 self.__my_value = a_value
 
             def check_my_value(self):
                 return self.__my_value
 
             def change_my_value(self, new_value):
-                if new_value == 13: 
+                if new_value == 13:
                     raise RuntimeError("Unlucky Number")
                 self.__my_value = new_value
 
@@ -112,8 +112,8 @@ An example unit test for the above looks like:
                         REQUIRE(with_value == ToBeTested(3));
                         REQUIRE_FALSE(defaulted == with_value);
                     }
-                    SECTION("operator!=") { 
-                        REQUIRE(defaulted != with_value); 
+                    SECTION("operator!=") {
+                        REQUIRE(defaulted != with_value);
                     }
                 }
 

nwx_build_environment/scripts/generate_module_dox.py

@@ -12,10 +12,11 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import os
 import glob
-import sys
 import importlib
+import os
+import sys
+
 """This script will generate the module api documentation for a plugin library.
 
 Usage