Code and Documentation Cleanup

.flake8

@@ -1,6 +1,6 @@
 [flake8]
 # Global ignores
-ignore = 
+ignore =
     # trailing whitespace
     W291,
     # line break before binary operator
@@ -9,7 +9,7 @@ ignore =
     W504
 
 # Per-file ignores
-per-file-ignores = 
+per-file-ignores =
     # imported but unused
     __init__.py:F401
 

.github/workflows/gh_pages.yml

@@ -0,0 +1,11 @@
+name: GitHub Pages Documentation Generation
+
+on:
+  push:
+    branches:
+      - main
+  pull_request: # Run in every PR
+
+jobs:
+  gh_pages_generation:
+    uses: RxnRover/.github/.github/workflows/gh_pages_sphinx_main.yml@main

.gitignore

@@ -127,3 +127,58 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# Temporary and binary files
+*~
+*.py[cod]
+*.so
+*.cfg
+!.isort.cfg
+!setup.cfg
+*.orig
+*.log
+*.pot
+__pycache__/*
+.cache/*
+.*.swp
+*/.ipynb_checkpoints/*
+.DS_Store
+
+# Project files
+.ropeproject
+.project
+.pydevproject
+.settings
+.idea
+.vscode
+tags
+
+# Package files
+*.egg
+*.eggs/
+.installed.cfg
+*.egg-info
+
+# Unittest and coverage
+htmlcov/*
+.coverage
+.coverage.*
+.tox
+junit*.xml
+coverage.xml
+.pytest_cache/
+
+# Build and docs folder/files
+**/build/*
+**/dist/*
+**/sdist/*
+docs/source/api/*
+docs/source/_rst/*
+docs/build/*
+cover/*
+MANIFEST
+
+# Per-project virtualenvs
+**/venv*/
+**/*conda*/
+.python-version

.pre-commit-config.yaml

@@ -1,8 +1,8 @@
-exclude: '^docs/conf.py'
+exclude: '^docs/source/conf.py'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v6.0.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -17,51 +17,42 @@ repos:
   - id: mixed-line-ending
     args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
 
-## If you want to automatically "modernize" your Python code:
-# - repo: https://github.com/asottile/pyupgrade
-#   rev: v3.3.1
-#   hooks:
-#   - id: pyupgrade
-#     args: ['--py37-plus']
-
-## If you want to avoid flake8 errors due to unused vars or imports:
-# - repo: https://github.com/PyCQA/autoflake
-#   rev: v2.0.2
-#   hooks:
-#   - id: autoflake
-#     args: [
-#       --in-place,
-#       --remove-all-unused-imports,
-#       --remove-unused-variables,
-#     ]
-
-- repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+- repo: https://github.com/pycqa/isort
+  rev: 9.0.0b1
   hooks:
   - id: isort
 
 - repo: https://github.com/psf/black
-  rev: 23.3.0
+  rev: 26.5.1
   hooks:
   - id: black
     language_version: python3
 
-## If like to embrace black styles even in the docs:
-# - repo: https://github.com/asottile/blacken-docs
-#   rev: v1.13.0
-#   hooks:
-#   - id: blacken-docs
-#     additional_dependencies: [black]
+- repo: https://github.com/LilSpazJoekp/docstrfmt
+  rev: v2.2.0
+  hooks:
+    - id: docstrfmt
+      language_version: python3
+      types_or: [rst]  # Options are [python, rst, txt]
 
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.0.0
+  rev: 7.3.0
   hooks:
   - id: flake8
   ## You can add flake8 plugins via `additional_dependencies`:
   #  additional_dependencies: [flake8-bugbear]
 
-## Check for misspells in documentation files:
-# - repo: https://github.com/codespell-project/codespell
-#   rev: v2.2.4
-#   hooks:
-#   - id: codespell
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v2.3.0
+  hooks:
+    - id: mypy
+      args: [--ignore-missing-imports, "--config-file=pyproject.toml"]
+      # NOTE: Any changes to exclude here need to be made in pyproject.toml, too!
+      exclude: |
+        (?x)(
+          ^setup.py$ |
+          ^build |
+          ^venv |
+          ^docs |
+          ^tests
+        )

AUTHORS.rst

@@ -1,5 +1,6 @@
-============
-Contributors
-============
+##############
+ Contributors
+##############
 
-* Zachery Crandall (@zachcran)
+- dulithaprasanna <dulithaprasanna@gmail.com>
+- zachcran <zachcran@iastate.edu>

CHANGELOG.rst

@@ -0,0 +1,54 @@
+###########
+ Changelog
+###########
+
+All notable changes to this project will be documented in this file.
+
+The format is based on `Keep a Changelog
+<https://keepachangelog.com/en/2.0.0/>`_, and this project adheres to `Semantic
+Versioning <https://semver.org/spec/v2.0.0.html>`_.
+
+*************
+ Unreleased_
+*************
+
+- None yet
+
+*********************
+ 0.6.0_ - 2026-07-28
+*********************
+
+Changed
+=======
+
+- Math formatting in docstrings updated
+- Project structure consolidated and modernized
+
+*********************
+ 0.5.0_ - 2023-10-23
+*********************
+
+Added
+=====
+
+- Helper function was added to easily fetch the new function metadata
+
+Changed
+=======
+
+- Refactored the benchmarking functions into classes that make more information
+  about the function available to the user
+
+.. Reference links
+
+.. _0.5.0: https://github.com/RxnRover/cyrxnopt_server/releases/tag/v0.5.0
+
+.. _0.6.0: https://github.com/RxnRover/cyrxnopt_server/releases/tag/v0.5.0...v0.6.0
+
+.. _dulithaprasanna: https://github.com/dulithaprasanna
+
+.. _semver: https://semver.org
+
+.. _unreleased: https://github.com/RxnRover/cyrxnopt_server/compare/v0.6.0...HEAD
+
+.. _zachcran: https://github.com/zachcran