formatted git ignore, added generated sphinx docs

Author: SamoraHunter

.gitignore

@@ -1,73 +1,64 @@
-# Ignore compiled files
-*.o
-*.out
+# =============================================================================
+# PROJECT-SPECIFIC IGNORES
+# =============================================================================
 
+# Project keys and sensitive data
 anonymization_key.pkl
 
-# Ignore log files
-*.log
-requirements.in
-notebooks/requirements.in
-
-# Ignore temporary files
-*.tmp
-notebooks/treatment_doc_extract/
-treatment_doc_extract/
-# Ignore files generated by your IDE or editor
-.idea/
-.vscode/
-
-t1.ipynb
-
-# Ignore node_modules directory
-node_modules/
-
-# Ignore compiled Python bytecode
-__pycache__/
-
-# Ignore macOS system files
-.DS_Store
-
-# Ignore backup files
-*~
+# Project directories and outputs
+output_directory/
+output_directory/*
+notebooks/output_directory/
+notebooks/output_directory
+backups/
+logs/
 
+# Development and testing
 dev_test/
 test_dev.ipynb
+live_test.ipynb
 paths.py
+temp_annot_file.csv
+notebooks/temp_annot_file.csv
 
-backups/
-
-util/cohort_searcher_dummy.ipynb
-
-notebooks/new_project/*
-notebooks/new_project_ipw/*
-
-output_directory/*
-
-notebooks/pat2vec_projects/*
+# Project-specific notebooks and files
+t1.ipynb
+example_usage_DEV.ipynb
+notebooks/treatment_doc_extract/
+treatment_doc_extract/
+notebooks/treatment_docs.csv
 
+# Pat2vec specific
+notebooks/pat2vec_projects/
 notebooks/pat2vec_projects/notebooks/example_usage_dev.ipynb
+notebooks/pat2vec_projects/new_project/
 notebooks/pat2vec_projects/new_project/*
+notebooks/pat2vec_projects/new_project_ipw/
 notebooks/pat2vec_projects/new_project_ipw/*
+pat2vec/notebooks/
+pat2vec/notebooks/*
 
+# Project directories
+new_project/
+new_project_ipw/
+notebooks/new_project/
+notebooks/new_project/*
+notebooks/new_project_ipw/
+notebooks/new_project_ipw/*
 
+# Utility and cohort files
+util/cohort_searcher_dummy.ipynb
+util/medcat_models/
 util/medcat_models/*
 
-notebooks/output_directory/*
-
-notebooks/output_directory
-example_usage_DEV.ipynb
-
-myenv/*
-
-pat2vec/notebooks/*
-logs/
-myenv
-pat2vec_env
-
-notebooks/treatment_docs.csv
+# Project-specific data files
+notebooks/anonymization_log.json
+notebooks/my_project_outputfile_name_missing_dict.pickle
+notebooks/ipw_dataframe.csv
 
-####### git template for python projects: ########
+# =============================================================================
+# PYTHON STANDARD IGNORES
+# =============================================================================
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -77,6 +68,10 @@ __pycache__/
 # C extensions
 *.so
 
+# Compiled files
+*.o
+*.out
+
 # Distribution / packaging
 .Python
 build/
@@ -98,8 +93,6 @@ share/python-wheels/
 MANIFEST
 
 # PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
 *.manifest
 *.spec
 
@@ -126,21 +119,21 @@ cover/
 *.mo
 *.pot
 
-# Django stuff:
-*.log
+# Django stuff
 local_settings.py
 db.sqlite3
 db.sqlite3-journal
 
-# Flask stuff:
+# Flask stuff
 instance/
 .webassets-cache
 
-# Scrapy stuff:
+# Scrapy stuff
 .scrapy
 
 # Sphinx documentation
 docs/_build/
+docs/source/generated/
 
 # PyBuilder
 .pybuilder/
@@ -153,45 +146,6 @@ target/
 profile_default/
 ipython_config.py
 
-#test file
-live_test.ipynb
-
-new_project
-new_project_ipw
-
-temp_annot_file.csv
-/notebooks/temp_annot_file.csv
-
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/#use-with-ide
-.pdm.toml
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
-__pypackages__/
-
 # Celery stuff
 celerybeat-schedule
 celerybeat.pid
@@ -207,6 +161,9 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+myenv/
+myenv
+pat2vec_env
 
 # Spyder project settings
 .spyderproject
@@ -233,11 +190,44 @@ dmypy.json
 cython_debug/
 
 # PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
-notebooks/anonymization_log.json
-notebooks/my_project_outputfile_name_missing_dict.pickle
-notebooks/ipw_dataframe.csv
+
+# PEP 582
+__pypackages__/
+
+# pdm
+.pdm.toml
+
+# =============================================================================
+# DEVELOPMENT TOOLS AND EDITORS
+# =============================================================================
+
+# IDE and editor files
+.idea/
+.vscode/
+
+# =============================================================================
+# SYSTEM AND TEMPORARY FILES
+# =============================================================================
+
+# Log files
+*.log
+
+# Temporary files
+*.tmp
+
+# macOS system files
+.DS_Store
+
+# Backup files
+*~
+
+# Node.js
+node_modules/
+
+# =============================================================================
+# REQUIREMENTS AND DEPENDENCIES
+# =============================================================================
+
+requirements.in
+notebooks/requirements.in