Python box model (#147)

* setting up a cmake structure for c++ * python box model iniital classes * added method for generating species config * added relative tolerance to spec config * added method to generate reaction config * added generateConfig documentation and todo solve function * added todo readfromjson function * added params to reaction * updated Reaction and getReactionConfig to handle A B D E and Ea paramaters * can mostly parse json file from UI * implemented skeleton logic for solver * extracted concentrations and reaction rates from evolving conditions * added initial reaction rates, need to verify * made conversion functions to shorten code * tested parsing with example that had every option * added other reaction types and refactored some code * fixed bug in species list * fixed bug in reaction list * generateReactionConfig accounts for the different types of reactions * added funciton to create micm solver based on config * added funciton to create micm solver based on config * working towards box model test * adds function to read config json and tests basic reaction * fixed solve to inc by seconds * convert time steps to seconds * updated solve with new time units * Changed readFromJson to readFromUIJosn * convert_pressure converts to Pa now * outputs results to file and creates file for initial test * reads species name from config * sets up test config and get analytical concentrations * aserts concentrations * fixed comment typo * fixed output outputted based on output time step * changed time in output to output step time * added hr to time conversion: * removed print stat * removed print statement * config files generatable * initial reaction rates added to generate config * reads species from json from camp_data * box model pr * handle cases without pressure and temperature in evolving conditions for UI parsing * able to recreate test config in UI, parse it, and use in python_test_1 * reads reaction list from config json * restructured functions * fixed missing reaction list param in from_config_JSON * can generate evolving_conditions.csv for config * implemented species and rate ordering in solve * moved where ordered arrays are computed * updated headers to match ordered array * fixed evolving conditions not setting attributes correctly * fixed unit issue with pressure for setting up evolving conditions * added reaction type prefixes in order_reaction_ratesz * changed evolving conditions to update in a while loop in case chem time step is greater than time between evolving conditions * updated python test 3 * creates test for chapman in python_test_3.py * renamed tests to be more descriptive * added test file for wall-loss * include base values for reactions, change C back to Ea * add species not present in initial conditions for order_species_concentration * removed unused files * removed unused files * created .whl for music_box package * make sure time in evolving conditions is float * check reaction names correctly for evolving conditions config, ensure floats for rate constants * added function to read from UI json string * removing fortran things, using musica python module, creating installation suitable for pypi * converting tests to pytest * correcting setup python? * adding a space * strategy * installing music_box in CI * newer checkout * pypi publish --------- Co-authored-by: Kyle Shores <[email protected]> Co-authored-by: Evan De la Garza <[email protected]> Co-authored-by: Evan De la Garza <[email protected]>
NCAR · Apr 9, 2024 · d77109b · d77109b
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diff --git a/.dockerignore b/.dockerignore
diff --git a/.github/workflows/publish-package.yml b/.github/workflows/publish-package.yml
@@ -1,52 +1,35 @@
-name: Create and publish a Docker image
+name: Publish a pypi package
 
 on:
-  push:
-    branches: ['release']
-    tags:
-      - '*'
-
-env:
-  REGISTRY: ghcr.io
-  IMAGE_NAME: ${{ github.repository }}
+  release:
+    types: [created]
 
 jobs:
-  build-and-push-image:
+  publish_to_pypi:
     runs-on: ubuntu-latest
     permissions:
       contents: read
       packages: write
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
-        with:
-          submodules: recursive
-
-      - name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
-
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-
-      - name: Log in to the Container repository
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
-        with:
-          registry: ${{ env.REGISTRY }}
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Extract metadata (tags, labels) for Docker
-        id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
-        with:
-          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+        uses: actions/checkout@v4
 
-      - name: Build and push Docker image
-        uses: docker/build-push-action@v5
+      - name: Set up Python
+        uses: actions/setup-python@v2
         with:
-          context: .
-          platforms: linux/amd64,linux/arm64
-          push: true
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
+          python-version: '3.9'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      - name: Build and publish package
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: |
+          pipx run build
+          pipx run twine check dist/*
+          python -m twine upload --repository pypi dist/*
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -1,17 +1,36 @@
 name: build
 
-on: [push, pull_request]
+on: [push, workflow_dispatch]
 
 jobs:
   build:
+    strategy:
+        matrix:
+          os: [ubuntu-latest, macos-latest, windows-latest]
 
-    runs-on: ubuntu-latest
-
+    runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v2
+
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
-    - name: build Docker image
-      run: docker build -t music-box-test . --build-arg TAG_ID=chapman
-    - name: run tests in container
-      run: docker run --name test-container -t music-box-test bash -c 'cd /music-box/build; make test'
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.9'
+        cache: 'pip' 
+
+    - run: pip install -r requirements.txt
+
+    - name: Install this package
+      run: pip install -e .
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+    
+    - name: Run tests
+      run: |
+        cd tests
+        pytest
diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,6 @@ CMakeFiles/
 doc/html/
 doc/latex/
 data/
+__pycache__/
+*.pyc
+dist
diff --git a/.gitmodules b/.gitmodules
diff --git a/.travis.yml b/.travis.yml
diff --git a/CMakeLists.txt b/CMakeLists.txt
diff --git a/Dockerfile b/Dockerfile