Merge branch 'main' into 130-create-musicbox-configuration-for-ts1cap…

…ram-24-reduced-mechanism

.devcontainer/Dockerfile.codespace

@@ -0,0 +1,20 @@
+FROM fedora:37
+
+RUN dnf -y update \
+    && dnf -y install \
+        git \
+        gcc \
+        gcc-c++ \
+        gnuplot \
+        netcdf-devel \
+        python3 \
+        python3-pip \
+        python-devel \
+        tree \
+    && dnf clean all
+
+COPY . /workspaces/music-box
+
+WORKDIR /workspaces/music-box
+
+RUN pip3 install -e '.[dev]'

.devcontainer/devcontainer.json

@@ -0,0 +1,10 @@
+{
+  "name": "MusicBox",
+  "image": "ghcr.io/ncar/music-box:latest",
+  "extensions": [
+    "ms-python.python",
+  ],
+  "settings": {
+  },
+  "postCreateCommand": ""
+}

.github/workflows/CI_Tests.yml

@@ -26,18 +26,36 @@ jobs:
         python-version: '3.9'
         cache: 'pip' 
 
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
-
     - name: Install this package
-      run: pip install -e .
+      run: pip install -e '.[dev]'
 
     - name: Run pytest
-      run: cd tests && pytest
+      run: pytest
 
     - name: Run the smoke tests
       run: |
-        music_box configFile=tests/configs/analytical_config/my_config.json outputDir=tests/configs/analytical_config
+        music_box -c src/acom_music_box/examples/configs/analytical/my_config.json -o output.csv
+        music_box -e Analytical -o output.csv
+        music_box -e Analytical -o output.csv -vv --color-output
+        waccmToMusicBox waccmDir="./sample_waccm_data" date="20240904" time="07:00" latitude=3.1 longitude=101.7
 
+    - name: Check for config.zip
+      if: runner.os != 'Windows'
+      run: |
+        if [ -f "./config.zip" ]; then
+          echo "config.zip created successfully"
+        else
+          echo "config.zip not found"
+          exit 1
+        fi
+
+    - name: Check for config.zip (Windows)
+      if: runner.os == 'Windows'
+      run: |
+        if (Test-Path -Path "./config.zip") {
+          Write-Output "config.zip created successfully"
+        } else {
+          Write-Output "config.zip not found"
+          exit 1
+        }
+      shell: pwsh

.github/workflows/deploy_codespaces_image.yml

@@ -0,0 +1,53 @@
+name: Build and Deploy Docker Image
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - 'v*.*.*'
+  workflow_dispatch:
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v2
+
+    - name: Log in to GitHub Container Registry
+      uses: docker/login-action@v2
+      with:
+        registry: ghcr.io
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Build Docker image
+      uses: docker/build-push-action@v4
+      with:
+        context: .
+        file: .devcontainer/Dockerfile.codespace
+        push: false
+        tags: ghcr.io/ncar/music-box:build-temp
+
+    - name: Build and push Docker image (latest)
+      if: github.ref == 'refs/heads/main'
+      uses: docker/build-push-action@v4
+      with:
+        context: .
+        file: .devcontainer/Dockerfile.codespace
+        push: true
+        tags: ghcr.io/ncar/music-box:latest
+
+    - name: Build and push Docker image (tagged)
+      if: startsWith(github.ref, 'refs/tags/')
+      uses: docker/build-push-action@v4
+      with:
+        context: .
+        file: .devcontainer/Dockerfile.codespace
+        push: true
+        tags: ghcr.io/ncar/music-box:${{ github.ref_name }}

.github/workflows/pep8_autoformat.yml

@@ -15,7 +15,7 @@ jobs:
       - name: autopep8
         uses: peter-evans/autopep8@v2
         with:
-          args: --recursive --in-place --aggressive --aggressive .
+          args: --recursive --in-place --aggressive --aggressive --max-line-length 120 .
 
       - name: Check for changes
         id: check-changes

README.md

@@ -6,56 +6,58 @@ MusicBox: A MUSICA model for boxes and columns.
 
 [![License](https://img.shields.io/github/license/NCAR/music-box.svg)](https://github.com/NCAR/music-box/blob/main/LICENSE)
 [![CI Status](https://github.com/NCAR/music-box/actions/workflows/CI_Tests.yml/badge.svg)](https://github.com/NCAR/music-box/actions/workflows/CI_Tests.yml)
-[![PyPI version](https://badge.fury.io/py/acom_music_box.svg)](https://pypi.org/p/acom_music_box)
+[![PyPI version](https://badge.fury.io/py/acom-music-box.svg)](https://badge.fury.io/py/acom-music-box)
 
 Copyright (C) 2020 National Center for Atmospheric Research
 
 # Installation
+```
+pip install acom_music_box
+```
 
-The project is configured to be installed using `pip` by the `pyproject.toml` file. 
+# Command line tool
+MusicBox provides a command line tool that can run configurations as well as some pre-configured examples. Basic plotting can be done if gnuplot is installed.
 
-To install the `music-box` package into a Python environment, run the following command from the root directory:
+Checkout the command line options
 
 ```
-pip install .
+music_box -h                                        
 ```
 
-The package is also available on PyPi and can be installed in any Python environment through:
+Run an example. Notice that the output, in csv format, is printed to the terminal.
 
 ```
-pip install acom_music_box
+music_box -e Chapman
 ```
 
-# Tests
-
-The tests directory contains 4 different tests that can be ran with [PyTest](https://docs.pytest.org/en/8.2.x/). PyTest can be installed by running:
+You can also run your own configuration
 
 ```
-pip install pytest
+music_box -c my_config.json
 ```
 
-After PyTest is intalled, the tests can be ran through the following commands from the root directory:
+Output can be saved to a file
 
 ```
-cd tests
-pytest
+music_box -e Chapman -o output.csv
 ```
 
-# Documentation
-
-MusicBox documentation can be built using [Sphinx](https://www.sphinx-doc.org/en/master/). Sphinx can be installed by running:
+And, if you have gnuplot installed, some basic plots can be made to show some resulting concentrations
 
 ```
-pip install sphinx
+music_box -e Chapman -o output.csv --color-output --plot CONC.O1D
 ```
 
-After installing Sphinx, the documentation can be generated by running the following commands in the root directory:
+# Development and Contributing
+
+For local development, install `music-box` as an editable installation:
 
 ```
-cd doc/sphinx_files
-make html
+pip install -e '.[dev]'
 ```
 
-Then, open `music-box/doc/sphinx_files/build/html/index.html` in a browser.
+## Tests
 
-The documentation includes more detailed instructions for configuring the model, along with developer resources.
+```
+pytest
+```