Python processing

.gitignore

@@ -38,7 +38,10 @@
 /data_processing_rcode/data/
 /data_processing_rcode/output/
 /data_processing_rcode/notforgit/
-
+/ArcGIS-Analysis-Python/
+.vscode
+.github
+.pre-commit-config.yaml
 
 /code/.quarto/
 *.zip

.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+# .pre-commit-config.yaml
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0 # Use the latest version
+    hooks:
+      - id: trailing-whitespace
+#      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: check-json
+      - id: detect-private-key
+#  - repo: https://github.com/psf/black
+#    rev: 24.3.0 # Use the latest version
+#    hooks:
+#      - id: black
+#  - repo: https://github.com/PyCQA/flake8
+#    rev: 7.0.0 # Use the latest version
+#    hooks:
+#      - id: flake8
+#  - repo: https://github.com/PyCQA/isort
+#    rev: 5.13.2 # Use the latest version
+#    hooks:
+#      - id: isort

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "python.defaultInterpreterPath": "C:\\Uses\\john.f.kennedy\\AppData\\Local\\ESRI\\conda\\envs\\arcgispro-py3-clone\\python.exe"
+}

ArcGIS-Analysis-Python/.gitignore

@@ -1,187 +1,42 @@
-#################
-## Visual Studio
-#################
+# Global ignore: everything
+*
 
-## Ignore Visual Studio temporary files, build results, and
-## files generated by popular Visual Studio add-ons.
+# allow directories so we can whitelist specific content
+!*/
 
-# User-specific files
-*.suo
-*.user
-*.sln.docstates
-
-# Build results
-
-[Dd]ebug/
-[Rr]elease/
-x64/
-build/
-[Bb]in/
-[Oo]bj/
-
-# MSTest test Results
-[Tt]est[Rr]esult*/
-[Bb]uild[Ll]og.*
-
-*_i.c
-*_p.c
-*.ilk
-*.meta
-*.obj
-*.pch
-*.pdb
-Initial Data
-Data
-*.pgd
-*.rsp
-*.sbr
-*.tlb
-*.tli
-*.tlh
-*.tmp
-*.tmp_proj
-*.log
-NCEI Archive
-*.pidb
-*.log
-*.scc
-
-# Visual C++ cache files
-ipch/
-*.aps
-*.ncb
-*.opensdf
-*.sdf
-*.cachefile
-
-# Visual Studio profiler
-*.psess
-*.vsp
-*.vspx
-
-#############
-## Windows detritus
-#############
-
-# Windows image file caches
-src/dismap_tools_dev
-ehthumbs.db
-
-# Folder config file
-!src/dismap_tools/*.py
-!src/dismap_tools_dev/*.py
-!src/dismap_tools/dev_*.py
-!src/dismap_tools/__init__.py
-!src/dismap_tools/README.md
-
-# Mac crap
-.DS_Store
-
-#############
-## Python
-#############
-
-*.py[co]
-*.pyc
-# Packages
-*.egg
-*.egg-info
-dist/
-build/
-eggs/
-parts/
-var/
-sdist/
-develop-eggs/
-.installed.cfg
-
-# Installer logs
-pip-log.txt
-
-# Unit test / coverage reports
-.coverage
-.tox
-
-#Translations
-*.mo
-
-#Mr Developer
-.mr.developer.cfg
-
-# Tools, notes, outputs
-___*.*
-___*
-*.log
+# Remove selected directories
+.ipynb_checkpoints
+**/.ipynb_checkpoints
+.backups
+__pycache__
+**/__pycache__
 
-[Ss]ampleData/
-source/[Ss]ampleData/
-source/[Tt]est[Cc]onfigs/
-#src/service_monitor
-error.txt
 
-#############
-## ArcGIS
-#############
-*.gdb
-*.ipynb
-ImportLog
-*.aprx
-*.atbx
-*.mxd
-*.json
+# include python files anywhere
+!*.py
+!*.pyt
+!**/*.py
+!**/*.pyt
 
-#############
-## ArcGIS-Analysis-Python ignores
-#############
-# Ignore Folders
-.backups
-.ipynb_checkpoints
-__pycache__
-April 1 2023
-August 1 2025
-Bathymetry
-Initial Data
-Dataset Shapefiles
-December 1 2024
-February 1 2026
-GpMessages
-ImportLog
-Index
-Initial Data
-July 1 2024
-Layout
-May 16 2022
-NCEI Archive
-Notebooks
-RasterFunctionsHistory
-RasterFunctionTemplates
-Scratch
-# Ignore Files
-*.ags
-*.docx
-.pyHistory
-*.py
+# still ignore py backup variants
 *.~py
-*.pyt 
-*.xml
-*.xsl
-*.zip
+**/*.~py
+# ignore Python init files globally
 __init__.py
-*.txt
-conftest.py
-main.py
-setip.py
-utils.py
-Metadata.md
-src/dismap_tools/esri
-NCEI Archive
-_Dataset Shapefiles
-#src/dismap_tools_dev
-#############
-# Do not ignore these files
+**/__init__.py
+
+# include Scripts folder and its contents
+!/Scripts/dismap_tools
+/Scripts/dismap_tools_dev/*
+
+# include README files in root, Scripts, and dismap_tools
 !README.md
-!src/dismap_tools/*.py
-!src/dismap_tools_dev/*.py
-src/dismap_tools/dev_*.py
-src/dismap_tools/__init__.py
-!src/dismap_tools/README.md
+!Scripts/README.md
+!Scripts/dismap_tools/README.md
+
+# Notebook folder and its notebooks
+/Notebooks/
+# explicitly exclude esri folder under dismap_tools
+/Scripts/dismap_tools/esri/
+/src/
+/Initial Data/*.csv

ArcGIS-Analysis-Python/Scripts/README.md

@@ -0,0 +1,23 @@
+# DisMAP ArcGIS Pro Analysis using Python
+> This code is always in development. Find the code used for various reports in the code [releases](https://github.com/nmfs-fish-tools/DisMAP/releases).
+
+### Explanation of this Folder
+* dismap_tools folder - This folder contains the current version of Python scripts for generating the interpolated biomass and calculating the distribution indicators (latitude, depth, range limits, etc). 
+
+#### Suggestions and Comments
+
+If you see that the data, product, or metadata can be improved, you are invited to create a [pull request](https://github.com/nmfs-fish-tools/DisMAP/pulls) or [submit an issue to the code’s repository](https://github.com/nmfs-fish-tools/DisMAP/issues).
+
+#### NOAA-NMFS GitHub Enterprise Disclaimer
+
+This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. 
+The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.
+
+#### NOAA License
+
+Software code created by U.S. Government employees is not subject to copyright in the United States (17 U.S.C. §105). The United States/Department of Commerce reserve all rights to seek and obtain copyright protection in countries other than the United States for Software authored in its entirety by the Department of Commerce. To this end, the Department of Commerce hereby grants to Recipient a royalty-free, nonexclusive license to use, copy, and create derivative works of the Software outside of the United States.
+
+<img src="https://raw.githubusercontent.com/nmfs-general-modeling-tools/nmfspalette/main/man/figures/noaa-fisheries-rgb-2line-horizontal-small.png" alt="NOAA Fisheries" height="75"/>
+
+[U.S. Department of Commerce](https://www.commerce.gov/) \| [National Oceanographic and Atmospheric Administration](https://www.noaa.gov) \| [NOAA Fisheries](https://www.fisheries.noaa.gov/)
+