Hercules v2.1 release

.github/dependabot.yml

@@ -0,0 +1,12 @@
+version: 2
+updates:
+- package-ecosystem: "pip"
+  directory: "/" # Location of package manifests
+  target-branch: "develop"
+  schedule:
+    interval: "monthly"
+  labels:
+    - "package"
+  ignore:
+    - dependency-name: "*"
+      update-types: ["version-update:semver-minor", "version-update:semver-patch"]

.github/workflows/continuous-integration-workflow.yaml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       fail-fast: False
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: [ "3.11", "3.12", "3.13"]
         os: [ubuntu-latest] #, macos-latest, windows-latest]
 
     steps:
@@ -22,8 +22,6 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -e ".[develop]"
-        pip install git+https://github.com/NREL/electrolyzer.git
-        pip install https://github.com/NREL/SEAS/blob/v1/SEAS.tar.gz?raw=true
 #    - uses: pre-commit/action@v3.0.0
     - name: Run ruff
       run: |
@@ -42,11 +40,10 @@ jobs:
         pip install pytest
         pip install pytest-cov
         pytest --cov=./ --cov-report=xml tests/
-    - name: Upload coverage to Codecov  
+    - name: Upload coverage to Codecov
       if: ${{ env.CODECOV_TOKEN }}  # Don't attempt to upload if the codecov token is not configured
       uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         files: ./coverage.xml
         fail_ci_if_error: true
-

.github/workflows/deploy-pages.yaml

@@ -19,38 +19,11 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: "3.10"
+        python-version: "3.12"
 
     - name: Install dependencies
       run: |
         pip install -e ".[docs]"
-
-    - name: Make copies of example docs
-      run: |
-        mkdir -vp docs/examples
-
-        cp -v examples/00_wind_farm_only/README.md docs/examples/00_wind_farm_only.md
-        cp -v examples/01_wind_farm_dof1_model/README.md docs/examples/01_wind_farm_dof1_model.md
-        cp -v examples/02_wind_farm_realistic_inflow/README.md docs/examples/02_wind_farm_realistic_inflow.md
-        cp -v examples/02b_wind_farm_realistic_inflow_precom_floris/README.md docs/examples/02b_wind_farm_realistic_inflow_precom_floris.md
-        cp -v examples/03_wind_and_solar/README.md docs/examples/03_wind_and_solar.md
-        cp -v examples/04_wind_and_storage/README.md docs/examples/04_wind_and_storage.md
-        ls -l docs/examples
-
-    - name: Debug directory structure
-      run: |
-        echo "Current directory: $(pwd)"
-        echo "GitHub workspace: ${{github.workspace}}"
-        echo "Runner workspace: ${{runner.workspace}}"
-        ls -la
-        ls -la docs/
-        ls -la docs/examples/
-
-    # # Build the book
-    # - name: Build the book
-    #   working-directory: ${{runner.workspace}}/hercules/docs/
-    #   run: |
-    #     jupyter-book build .
 
     # Build the book
     - name: Build the book

.github/workflows/python-publish.yml

@@ -0,0 +1,34 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# Published via GitHub Actions as a PyPI Trusted Publisher.
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+# and: https://docs.pypi.org/trusted-publishers/
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    environment: release-pypi
+    if: github.repository_owner == 'NatLabRockies'
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v6
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.x'
+      - name: Install dependencies and build package
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+          python -m build
+          twine check --strict dist/*
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: True

.gitignore

@@ -1,78 +1,114 @@
-# Gitignore file
+# =============================================================================
+# Python
+# =============================================================================
 *.pyc
-*.log
-*.egg-info
-data.db
+__pycache__/
+*.egg-info/
 *.python-version
-*.DS_Store
-*.conda
-*.sqlite
-slices
 
-# macOS files
+# =============================================================================
+# macOS
+# =============================================================================
 .DS_Store
+__MACOSX/
 
-# ide settings and files
-.idea
-.vscode
+# =============================================================================
+# IDE/Editor Settings
+# =============================================================================
+.idea/
+.vscode/
+.cursor/rules/
 
-# Some c++ stuff
-a.out
-*.plist
-test_client.dSYM
+# =============================================================================
+# Jupyter Notebooks
+# =============================================================================
 *checkpoint.ipynb
-hercules/sampling00000.nc
-hercules/front_end.db
-hercules/control_center.db
-hercules/test_client_cpp/test_client
-hercules/df_flow.p
-hercules/flow_data.p
-
-t_*.txt
-hercules/sample_copy.nc
-hercules/t_0*
-hercules/local_amr_wind_demo/sample_copy.nc
+*.nbconvert.ipynb
+.ipynb_checkpoints/
 
-#Ignore csv files
+# =============================================================================
+# Data Files (large/generated)
+# =============================================================================
+# CSV files (except test inputs)
 *.csv
 !tests/test_inputs/*.csv
-!example_case_folders/00_wind_farm_only/inputs/floris_standin_data.csv
-!example_case_folders/00_wind_farm_only/inputs/wind_power_reference_data.csv
 
-# h5 files
+# Binary data formats
 *.h5
 *.hdf5
+*.feather
+*.ftr
+*.parquet
 
-# Larger wind input file
-wind_resource_rex
+# Pickle files (generated input data)
+*.p
+*.pkl
 
-# Wind input pickle files
-wind_input.p
+# Large wind resource data
+wind_resource_rex/
 
-# Solar input pickle files
-solar_input.p
+# =============================================================================
+# Hercules Simulation Outputs
+# =============================================================================
+# Output directories contain generated results
+outputs/
 
-# Intermediate notebook files
-*.nbconvert.ipynb
-*.ipynb_checkpoints
+# Log files (generated during simulation)
+*.log
 
-# Some output files to ignore
+# H_dict echo files (simulation state dumps)
+*.echo
+
+# =============================================================================
+# Documentation Build Artifacts
+# =============================================================================
+docs/_build/
+
+# =============================================================================
+# Testing/CI Artifacts
+# =============================================================================
+.pytest_cache/
+.ruff_cache/
+
+# =============================================================================
+# LEGACY HERCULES - May remove in future cleanup
+# =============================================================================
+# Old example folder path (renamed to examples/)
+!example_case_folders/00_wind_farm_only/inputs/floris_standin_data.csv
+!example_case_folders/00_wind_farm_only/inputs/wind_power_reference_data.csv
+
+# C++ build artifacts (from old AMR-Wind integration)
+a.out
+*.plist
+test_client.dSYM
+hercules/test_client_cpp/test_client
+
+# NetCDF files (from old AMR-Wind demos)
+hercules/sampling00000.nc
+hercules/sample_copy.nc
+hercules/local_amr_wind_demo/sample_copy.nc
+
+# Database files (from old front-end/control center)
+data.db
+*.sqlite
+*.conda
+hercules/front_end.db
+hercules/control_center.db
+
+# Old data/flow pickle files
+hercules/df_flow.p
+hercules/flow_data.p
+
+# AMR-Wind time step outputs
+t_*.txt
+hercules/t_0*
 t_00*
+slices
+
+# Old log file patterns (now covered by *.log)
 logdummy
 loghelics
 loghercules*
 logstandin*
 logfloris*
-*echo
 *out-example.json
-
-.vscode/*
-
-# Doc builds
-docs/_build
-docs/examples
-
-.cursor/rules/
-*.feather
-*.ftr
-*.parquet

CITATION.cff

@@ -5,7 +5,7 @@ authors:
   - family-names: NLR
     given-names:
 title: "HERCULES"
-version: 2
+version: 2.1
 url: https://github.com/NatLabRockies/hercules
 
-date-released: 2025-12-31
+date-released: 2026-03-30