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/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
+  comment: never

CMakeLists.txt

@@ -39,7 +39,7 @@ cmaize_option_list(
     BUILD_PYBIND11_PYBINDINGS ON "Should we build pybind11 python bindings?"
     BUILD_CPP_JOULES OFF "Enable energy usage tracking with CPP Joules library?"
     BUILD_CUDA_BINDINGS OFF "Enable CUDA Bindings"
-    BUILD_HIP_BINDINGS  OFF "Enable HIP Bindings" 
+    BUILD_HIP_BINDINGS  OFF "Enable HIP Bindings"
     BUILD_SYCL_BINDINGS OFF "Enable SYCL Bindings"
     BUILD_PAPI_BINDINGS OFF "Enable PAPI Bindings"
 )

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/build_device.cmake

@@ -38,7 +38,7 @@ function(build_device)
       set(CMAKE_CXX_STANDARD 17)
     endif()
 
-endfunction()       
+endfunction()
 
 # Call the function we just wrote to get CMakePP
 build_device()

docs/source/conf.py

@@ -21,13 +21,14 @@
 # http://www.sphinx-doc.org/en/master/config
 
 import os
-import subprocess
+
+# import subprocess
 
 # -- Project information -----------------------------------------------------
 
-project = u'parallelzone'
-copyright = u'2021, NWChemEx Team'
-author = u'NWChemEx Team'
+project = "parallelzone"
+copyright = "2021, NWChemEx Team"
+author = "NWChemEx Team"
 
 # Get the version from the git tag
 # git_cmd = ['git', 'describe', '--tags', '--abbrev=0']
@@ -50,40 +51,45 @@
 # 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',
-    'sphinx.ext.githubpages', 'sphinx_tabs.tabs'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.githubpages",
+    "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
 numfig_secnum_depth = 0
@@ -93,7 +99,7 @@
 # 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
@@ -104,7 +110,7 @@
 # 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.
@@ -119,23 +125,20 @@
 # -- 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',
@@ -145,33 +148,46 @@
 # (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)}
 
 # -- Options for todo extension ----------------------------------------------
 

docs/source/developer/design/compp.rst

@@ -26,10 +26,10 @@ discuss the design of the ``CommPP`` class.
 Why Do We Need CommPP?
 **********************
 
-ParallelZone needs access to MPI. ParallelZone is object-oriented and needs 
-something to bridge the gap between objects and types recognized by MPI. At a 
-high-level this leads to serialization, but naive application of serializaiton 
-in an MPI context can lead to inefficiencies. CommPP should automate the 
+ParallelZone needs access to MPI. ParallelZone is object-oriented and needs
+something to bridge the gap between objects and types recognized by MPI. At a
+high-level this leads to serialization, but naive application of serializaiton
+in an MPI context can lead to inefficiencies. CommPP should automate the
 conversion from objects to MPI data types in the most efficient manner possible.
 
 *********************

docs/source/developer/design/logger.rst

@@ -28,15 +28,15 @@ What is the Logger Class?
 
 The ``Logger`` class is the user-facing API of ParallelZone's logging
 component. The ``Logger`` class is used by users of ParallelZone to log
-events, *i.e.*, errors, warnings, progress, etc. 
+events, *i.e.*, errors, warnings, progress, etc.
 
 ********************************
 Why do we need the Logger Class?
 ********************************
 
 As summarized in :ref:`logging_design`, we are not aware of any existing logging
 solutions that do everything we need. We have thus chosen to implement the
-missing features, to our liking, within the ``Logger`` class. The 
+missing features, to our liking, within the ``Logger`` class. The
 ``Logger`` class also provides a stable API for ParallelZone users in the event
 we should need to add additional logging capabilities or switch out the backend.
 The ``Logger`` class also separates the concern of "what to log" from "how to
@@ -74,8 +74,8 @@ Existing Logger Solutions
 *************************
 
 :ref:`existing_logging_solutions` covered the existing logging solutions in
-detail and will not be replicated here. Instead we point out that of the 
-available choices, Spdlog has most of the features we want and is heavily 
+detail and will not be replicated here. Instead we point out that of the
+available choices, Spdlog has most of the features we want and is heavily
 supported. As seen in the next section we have opted to build our ``Logger``
 infrastructure around Spdlog.
 
@@ -92,22 +92,22 @@ Logger Design
 
 For the first implementation of the logging component we adopted the simple
 architecture shown in Figure :numref:`logger_arch`. Users of ParallelZone see
-one class, ``Logger``. As a first pass, ``Logger`` simply provides APIs 
+one class, ``Logger``. As a first pass, ``Logger`` simply provides APIs
 for printing arbitrary data, already in a ``std::string`` (or implicitly
-convertible to a ``std::string``) at various severity levels. Eventually, this 
+convertible to a ``std::string``) at various severity levels. Eventually, this
 may be expanded to support more fine-grained control over the log formatting.
 
 Internally ``Logger`` is implemented by a ``LoggerPIMPL`` object. The literal
-``LoggerPIMPL`` object is an abstract base class which defines the API for 
-actual implementations. Our Spdlog-based implementation derives the 
+``LoggerPIMPL`` object is an abstract base class which defines the API for
+actual implementations. Our Spdlog-based implementation derives the
 ``SpdlogPIMPL`` class from ``LoggerPIMPL`` to implement the parts of the PIMPL
 API common to all Spdlog-based implementations.
 
 For now we have two sinks, and they are implemented by further specializing the
 ``SpdlogPIMPL``. The sinks, ``StdoutSpdlog`` and ``FileSpdlog`` respectively
-output logs to standard out and a specified file. 
+output logs to standard out and a specified file.
 
-This design addresses the considerations remaining from  
+This design addresses the considerations remaining from
 :ref:`logging_design` by:
 
 1. Multiple logging levels.
@@ -143,4 +143,4 @@ particular we note:
   we ultimately need to print strings so supporting of other types is simply
   a convenience mechanism for channeling them into the string paths.
 - Can add wide-character support. Spdlog already supports it so it's just a
-  matter of exposing it.  
+  matter of exposing it.

docs/source/developer/design/logging.rst

@@ -18,7 +18,7 @@
 Designing the Logging Component
 ###############################
 
-ParallelZone provides a ``Logger`` class to facilitate recording of events, 
+ParallelZone provides a ``Logger`` class to facilitate recording of events,
 i.e., print statements. The high-level design is summarized on this page.
 
 *****************
@@ -261,7 +261,7 @@ Logging Design
    Software architecture of ParallelZone's Logging component.
 
 Ultimately none of the widely available logging solutions do everything we want
-and we have chosen to have the user-facing logger be written by us. This 
+and we have chosen to have the user-facing logger be written by us. This
 provides a stable API to users of ParallelZone, while allowing ParallelZone
 developers to graft the missing features onto existing logging libraries.
 
@@ -312,7 +312,7 @@ This architecture addresses the considerations raised above by:
 
 1. Multiple loggers.
 
-   - We can have multiple logger instances. Each instance is configured 
+   - We can have multiple logger instances. Each instance is configured
      for a specific scope (global vs. process-local).
    - Thread-safety should avoid the need for a "thread-local" logger.
 
@@ -324,7 +324,7 @@ This architecture addresses the considerations raised above by:
 
 The remaining issues, including the thread-safety requirement of consideration
 3, are punted to the ``Logger`` class, which is the class actually
-implementing the global and process-local loggers. The design of ``Logger`` 
+implementing the global and process-local loggers. The design of ``Logger``
 is provided here: :ref:`logger_design`.
 
 *********************
@@ -338,7 +338,6 @@ if/when users want to customize logging more. In particular:
   for specific instances. Turning on/off such loggers makes it easier to track
   what's going on with the class and instances.
 - Realistically we probably want a factory, or similar mechanism, for
-  setting up the initial loggers. Since our initialization choices are 
+  setting up the initial loggers. Since our initialization choices are
   presently very limited we punt on the factory until more choices become
   available.
-

include/parallelzone/archive_wrapper.hpp

@@ -64,4 +64,4 @@ class ArchiveWrapper {
 
 using Serializer   = ArchiveWrapper<variant_output>;
 using Deserializer = ArchiveWrapper<variant_input>;
-} // namespace parallelzone
+} // namespace parallelzone

include/parallelzone/hardware/cpu/cpu.hpp

@@ -92,4 +92,4 @@ class CPU {
     profile_return_type profile_it_(task_type&& task) const;
 };
 
-} // namespace parallelzone::hardware
+} // namespace parallelzone::hardware

include/parallelzone/logging/logging.hpp

@@ -16,4 +16,4 @@
 
 #pragma once
 #include <parallelzone/logging/logger.hpp>
-#include <parallelzone/logging/logger_factory.hpp>
+#include <parallelzone/logging/logger_factory.hpp>

include/parallelzone/serialization.hpp

@@ -58,4 +58,4 @@ template<typename T, typename Archive>
 using is_deserializable = cereal::traits::is_input_serializable<T, Archive>;
 using cereal::traits::detail::get_input_from_output;
 using cereal::traits::detail::get_output_from_input;
-} // namespace parallelzone
+} // namespace parallelzone

include/parallelzone/task/argument_traits.hpp

@@ -66,4 +66,4 @@ struct ArgumentTraits {
       std::is_same_v<rvalue_reference, T>;
 };
 
-} // namespace parallelzone::task
+} // namespace parallelzone::task

include/parallelzone/task/argument_wrapper.hpp

@@ -124,4 +124,4 @@ class ArgumentWrapper {
     holder_type m_value_;
 };
 
-} // namespace parallelzone::task
+} // namespace parallelzone::task