feat: Add custom polygon boundary support with automatic clipping

.claude/settings.local.json

@@ -0,0 +1,52 @@
+{
+  "permissions": {
+    "allow": [
+      "WebSearch",
+      "Bash(uv run:*)",
+      "Bash(git checkout:*)",
+      "Bash(uv pip install:*)",
+      "Bash(find:*)",
+      "Bash(awk:*)",
+      "Bash(gh issue create:*)",
+      "Bash(gh issue view:*)",
+      "Bash(git add:*)",
+      "Bash(git push:*)",
+      "Bash(gh pr list:*)",
+      "Bash(gh pr view:*)",
+      "Bash(gh pr diff:*)",
+      "Bash(gh issue close:*)",
+      "Bash(gh issue:*)",
+      "Bash(uv pip:*)",
+      "Bash(echo $SHELL)",
+      "Read(//home/mihiarc/**)",
+      "Bash(export PATH=\"$HOME/.local/bin:$PATH\")",
+      "Bash(echo $PATH)",
+      "Bash(claude --version)",
+      "Bash(source ~/.bashrc)",
+      "Bash(git commit:*)",
+      "Bash(gh auth:*)",
+      "Bash(curl:*)",
+      "Bash(sudo dd:*)",
+      "Bash(sudo chmod:*)",
+      "Bash(sudo tee:*)",
+      "Bash(sudo apt:*)",
+      "Bash(sudo apt install:*)",
+      "Read(//usr/**)",
+      "Bash(python:*)",
+      "Bash(source:*)",
+      "Bash(git reset:*)",
+      "Bash(git fetch:*)",
+      "Bash(git restore:*)",
+      "Bash(/dev/null)",
+      "Bash(echo \"Exit code: $?\")",
+      "Bash(PYTHONPATH=/home/mihiarc/bigmap-zarr python3 -c \"from bigmap.examples import create_sample_zarr; print(''Import successful'')\")",
+      "Bash(pytest:*)",
+      "Bash(git revert:*)",
+      "Bash(python3:*)",
+      "Bash(uv venv:*)",
+      "Bash(chmod:*)"
+    ],
+    "deny": [],
+    "ask": []
+  }
+}

.gitignore

@@ -2,6 +2,7 @@
 __pycache__/
 *.py[cod]
 *$py.class
+*.pyc
 
 # C extensions
 *.so
@@ -27,8 +28,6 @@ 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
 
@@ -76,38 +75,27 @@ docs/_build/
 target/
 
 # Jupyter Notebook
+.ipynb_checkpoints/
 .ipynb_checkpoints
+*.ipynb
 
 # 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
+.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
+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
+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
+.pdm-python
+.pdm-build/
 
 # PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
 __pypackages__/
@@ -137,6 +125,7 @@ venv.bak/
 
 # mkdocs documentation
 /site
+site/
 
 # mypy
 .mypy_cache/
@@ -153,52 +142,186 @@ dmypy.json
 cython_debug/
 
 # PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be added to the global gitignore or merged into this project gitignore.  For a PyCharm
-#  project, it is recommended to include gitignore additions specific to that project.
 .idea/
 
 # VS Code
 .vscode/
 
-# BigMap specific ignores
-# Data files
+# uv
+.python-version
+uv.lock
+
+# ========================================
+# BigMap Project Specific Ignores
+# ========================================
+
+# Large Data Files
+# ----------------
+# Raster files
 *.tif
+*.tiff
+*.img
+*.hdr
+
+# Zarr arrays
 *.zarr/
+*.zarr
+
+# NetCDF files
 *.nc
+*.nc4
+
+# Vector data
 *.geojson
+*.gpkg
 *.shp
 *.shx
 *.dbf
 *.prj
 *.cpg
-
-# Output files
+*.qix
+*.sbn
+*.sbx
+
+# Tabular data
+*.parquet
+*.csv
+*.xlsx
+*.xls
+
+# Compressed files
+*.zip
+*.gz
+*.tar
+*.7z
+*.rar
+
+# Analysis Outputs
+# ----------------
+# All output directories
 output/
+outputs/
+results/
+analysis_*/
+
+# Specific analysis outputs
+analysis_bigmap/
+analysis_heirs/
+analysis_ndvi/
+analysis_comparison/
+
+# Generated reports
+*.html
+*.pdf
+*.docx
+*.md
+!README.md
+!CITATIONS.md
+!docs/**/*.md
+!CLAUDE.md
+
+# Visualization outputs
 *.png
 *.jpg
-*.pdf
-*.html
-
-# Large input data
-input/
+*.jpeg
+*.svg
+*.eps
+!docs/**/*.png
+!docs/**/*.jpg
+
+# Data Directories
+# ----------------
 data/
 raw_data/
+processed_data/
+input/
+inputs/
+downloads/
 
-# Temporary files
+# Temporary and Cache
+# -------------------
 temp/
 tmp/
 *.tmp
+.cache/
+cache/
+scratch/
 
-# Log files
+# Log Files
+# ---------
 *.log
+logs/
 append_errors.log
-
-# OS specific
+processing_*.log
+batch_processing_*.json
+
+# Configuration Files with Secrets
+# ---------------------------------
+config.local.yaml
+config.secret.yaml
+*.secret
+*.key
+*.pem
+
+# OS Specific
+# -----------
+# macOS
 .DS_Store
 .DS_Store?
 ._*
 .Spotlight-V100
 .Trashes
+
+# Windows
 ehthumbs.db
-Thumbs.db 
+Thumbs.db
+desktop.ini
+
+# Linux
+*~
+.directory
+
+# Project-specific large files
+# ----------------------------
+# NC specific data
+nc_biomass*.zarr/
+nc_species*.zarr/
+nc_clipped_rasters/
+nc_*.tif
+
+# Documentation builds
+docs/site/
+docs/_build/
+_build/
+
+# Scripts and notebooks working files
+scripts/*.zarr/
+scripts/*.tif
+scripts/output/
+notebooks/*.zarr/
+notebooks/*.tif
+notebooks/output/
+
+# Batch processing artifacts
+batch_*.json
+batch_processing_*.json
+!batch_processing_template.json
+
+# Analysis JSON outputs
+analysis_*/json/
+analysis_*/*.json
+
+# MkDocs
+site/
+.mkdocs_cache/
+
+# Don't ignore example configurations
+!cfg/*.yaml
+!examples/**/*
+!docs/examples/**/*
+
+# Documentation server scripts
+start_docs.sh
+serve_docs.sh
+build_docs.shoutput/data/montana_species_state_plane/montana_0010_state_plane.tif output/data/montana_species_state_plane/montana_0017_state_plane.tif output/data/montana_species_state_plane/montana_0073_state_plane.tif output/data/montana_species_state_plane/montana_0093_state_plane.tif output/data/montana_species_state_plane/montana_0108_state_plane.tif output/data/montana_species_state_plane/montana_0116_state_plane.tif output/data/montana_species_state_plane/montana_0122_state_plane.tif output/data/montana_species_state_plane/montana_0202_state_plane.tif
+tl_2024_us_county/tl_2024_us_county.shp