PI-5 NGWPC-3694 Delivery

.github/ISSUE_TEMPLATE/capability.md

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+---
+name: JIRA Story/Capability
+about: The structure for outlining work being done on a JIRA story
+labels: JIRA Story
+---
+
+# Capability
+
+<!-- Please link below the JIRA Story for coupling this issue to the scheduled work -->
+
+## Task
+
+<!-- Provide a clear and concise description of the task / work to be done to the repo
+
+* This ticket is meant to do XYZ and to accomplish the following:
+- ...
+- ...
+ -->
+
+## Plan/Outline
+
+<!-- Provide a few sentences about how this issue / story will be completed
+
+* This work will be done by creating a BMI module in the XYZ dir
+ -->
+
+
+### TODOS
+
+<!-- Create a checklist of what needs to be accomplished in this work -->
+- [ ]
+
+### Additional components / Context
+
+<!-- Add any other context or screenshots about the story here. You can also include links to examples of other programs that have something similar to your request. For example:
+
+* Another project [...] solved this by [...]
+-->

.gitignore

@@ -1,77 +1,216 @@
-# Compiled source #
-###################
-*.com
-*.class
-*.dll
-*.exe
-*.o
-*.so
-_site/
-
-# Packages #
-############
-# it's better to unpack these files and commit the raw source
-# git has its own built in compression methods
-*.7z
-*.dmg
-*.gz
-*.iso
-*.jar
-*.rar
-*.tar
-*.zip
-
-# Logs and databases #
-######################
-*.log
-*.sql
-*.sqlite
-
-# OS generated files #
-######################
-.DS_Store
-.DS_Store?
-.Spotlight-V100
-.Trashes
-Icon?
-ehthumbs.db
-Thumbs.db
-
-# Vim swap files #
-##################
-*.swp
-
-# Python #
-#################
-*.pyc
-*.egg-info/
+# Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
-.env
-.python-version
+*$py.class
 
-# pyenv #
-#########
-.python-version
+# C extensions
+*.so
 
-# Django #
-#################
-*.egg-info
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
 .installed.cfg
+*.egg
+MANIFEST
+.DS_Store
+
+# 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
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
 
 # Unit test / coverage reports
-#################
 htmlcov/
 .tox/
+.nox/
 .coverage
+.coverage.*
 .cache
 nosetests.xml
 coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
 
-# Front-End #
-#############
-node_modules/
-bower_components/
-.grunt/
-src/vendor/
-dist/
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# 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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+uv.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/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+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/
+.vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+Pipfile
+
+.qodo
+src/icefabric/_version.py
+*.db
+*.zarr
+.zarr
+*.tiff
+*.tif
+examples/iceberg_catalog/metadata/
+
+# Local Terraform state
+*.tfstate
+*.tfstate.backup
+
+# Crash log files
+crash.log
+
+# CLI configuration
+.terraform/
+
+# Terraform plan output (optional unless you want to inspect later)
+*.tfplan
+
+# tiles
+*.pmtiles
+examples/icechunk_data_viewer/martin/tiles/quantiles/*
+examples/icechunk_data_viewer/martin/tiles/legends/*
+examples/icechunk_data_viewer/martin/tiles/legend.png
+tests/data/topo_tifs
+
+# all data files
+data
+
+# R code
+.Rproj.user
+.Rdata
+.Rhistory
+icefabric.Rproj

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: LICENSE|\.csv$
+      - id: end-of-file-fixer
+        exclude: LICENSE|\.csv$
+      - id: check-yaml
+        exclude: mkdocs.yml$
+      - id: debug-statements
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.12.3
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
+
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.7.20
+    hooks:
+      - id: uv-lock
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.8.1
+    hooks:
+      - id: nbstripout

.pyiceberg.yaml

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+catalog:
+  glue:
+    type: glue
+    s3.endpoint: s3.us-east-1.amazonaws.com
+    warehouse: s3://52fcde3e7-5582-477d-7686ou4ij1ptxj8equ83a5xc51fsuse1b--table-s3
+    region: us-east-1
+    glue_region: us-east-1
+  sql:
+    type: sql
+    uri: sqlite:////tmp/warehouse/pyiceberg_catalog.db
+    warehouse: file:///tmp/warehouse

LICENSE

@@ -1,3 +1,14 @@
+Copyright 2025 Raytheon Company
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+Licensed under: https://opensource.org/license/bsd-2-clause
+
+- - - - - - - - - - - - - -
+
 
                                  Apache License
                            Version 2.0, January 2004

NOTICE.txt

@@ -0,0 +1,14 @@
+--
+
+The Hydrofabric data used in this repo is credited to Lynker and its contributors
+
+Johnson, J. M. (2022). National Hydrologic Geospatial Fabric (hydrofabric) for the Next Generation (NextGen) Hydrologic Modeling Framework,
+HydroShare http://www.hydroshare.org/resource/129787b468aa4d55ace7b124ed27dbde
+
+--
+
+Inspiration and assistance in the creation, and storage of network graphs comes from the following repos. Credit to the authors:
+- https://github.com/DeepGroundwater/ddr/blob/master/engine/adjacency.py
+- https://github.com/CIROH-UA/NGIAB_data_preprocess/blob/main/modules/data_processing/graph_utils.py
+
+--