Merge pull request #234 from NCAR/main

Version 2.4.0

.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

@@ -26,21 +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 -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 }}

README.md

@@ -11,59 +11,53 @@ MusicBox: A MUSICA model for boxes and columns.
 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
+You can also run your own configuration
+
+```
+music_box -c my_config.json
+```
 
-After installing music box for local development `pip install -e .`
+Output can be saved to a file
 
 ```
-cd tests
-pytest
+music_box -e Chapman -o output.csv
 ```
 
-# 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.
+And, if you have gnuplot installed, some basic plots can be made to show some resulting concentrations
 
 ```
-music_box -h                                        
-usage: music_box [-h] [-c CONFIG] [-e {CB5,Chapman,FlowTube,Analytical}] [-o OUTPUT] [-v] [--color-output] [--plot PLOT]
+music_box -e Chapman -o output.csv --color-output --plot CONC.O1D
+```
+
+# Development and Contributing
 
-MusicBox simulation runner.
+For local development, install `music-box` as an editable installation:
 
-optional arguments:
-  -h, --help            show this help message and exit
-  -c CONFIG, --config CONFIG
-                        Path to the configuration file. If --example is provided, this argument is ignored.
-  -e {CB5,Chapman,FlowTube,Analytical}, --example {CB5,Chapman,FlowTube,Analytical}
-                        Name of the example to use. Overrides --config.
-                        Available examples:
-                        CB5: Carbon bond 5
-                        Chapman: The Chapman cycle with conditions over Boulder, Colorado
-                        FlowTube: A fictitious flow tube experiment
-                        Analytical: An example of an analytical solution to a simple chemical system
-  -o OUTPUT, --output OUTPUT
-                        Path to save the output file, including the file name. If not provided, result will be printed to the console.
-  -v, --verbose         Increase logging verbosity. Use -v for info, -vv for debug.
-  --color-output        Enable color output for logs.
-  --plot PLOT           Plot a comma-separated list of species if gnuplot is available (e.g., CONC.A,CONC.B).
+```
+pip install -e '.[dev]'
 ```
 
-To run one of the examples and plot something you would run
+## Tests
 
 ```
-music_box -e Chapman -o output.csv -vv --color-output --plot CONC.O1D
+pytest
 ```

pyproject.toml

@@ -24,7 +24,9 @@ dependencies = [
   "musica==0.7.3",
   "xarray",
   "colorlog",
-  "pandas"
+  "pandas",
+  "tqdm",
+  "netcdf4"
 ]
 
 [project.urls]
@@ -33,3 +35,9 @@ Home = "https://github.com/NCAR/music-box"
 [project.scripts]
 music_box = "acom_music_box.main:main"
 waccmToMusicBox = "acom_music_box.tools.waccmToMusicBox:main"
+
+[project.optional-dependencies]
+dev = [
+  "pytest",
+  "pytest-mock"
+]

sample_waccm_data/README.md

@@ -0,0 +1,29 @@
+# WACCM
+
+This is data downloaded from [ACOM's data repository](https://www.acom.ucar.edu/waccm/DATA/). Each file has been reduced to have only ground level data and only chemical species needed for the IGAC demo. 
+This brings the file size from 8GB per file to 93MB per file, small enough that it can fit in github and be easily used for the demo. This data is temporary and will be removed after the demo. 
+
+
+The script to reduce the data is this:
+
+
+```
+import xarray as xr
+import os
+
+keep = ['ALKNIT', 'AODVISdn', 'BCARY', 'BENZENE', 'BIGALD', 'BIGALD1', 'BIGALD2', 'BIGALD3', 'BIGALD4', 'BIGALK', 'BIGENE', 'C2H2', 'C2H4', 'C2H5OH', 'C2H6', 'C3H6', 'C3H8', 'CH2O', 'CH3CHO', 'CH3CN', 'CH3COCH3', 'CH3COCHO', 'CH3COOH', 'CH3OH', 'CH3OOH', 'CH4', 'CHBR3', 'CO', 'CO01', 'CO02', 'CO03', 'CO04', 'CO05', 'CO06', 'CO07', 'CO08', 'CO09', 'CRESOL', 'DMS', 'GLYOXAL', 'H2O', 'H2O2', 'HCN', 'HCOOH', 'HNO3', 'HO2', 'HO2NO2', 'HONITR', 'HYAC', 'ISOP', 'ISOPNITA', 'ISOPNITB', 'MACR', 'MEK', 'MPAN', 'MTERP', 'MVK', 'M_dens', 'N2O', 'N2O5', 'NH3', 'NH4', 'NO', 'NO2', 'NO3', 'NOA', 'O3', 'O3S', 'OH', 'ONITR', 'P0', 'PAN', 'PBZNIT', 'PHENOL', 'PS', 'Q', 'SO2', 'T', 'TERPNIT', 'TOLUENE', 'XYLENES', 'Z3', 'ap', 'bc_a1', 'bc_a4', 'ch4vmr', 'co2vmr', 'date', 'dst_a1', 'dst_a2', 'dst_a3', 'f107', 'f107a', 'f107p', 'f11vmr', 'f12vmr', 'kp', 'mdt', 'n2ovmr', 'ncl_a1', 'ncl_a2', 'ncl_a3', 'num_a1', 'num_a2', 'num_a3', 'pom_a1', 'pom_a4', 'so4_a1', 'so4_a2', 'so4_a3', 'soa1_a1', 'soa1_a2', 'soa2_a1', 'soa2_a2', 'soa3_a1', 'soa3_a2', 'soa4_a1', 'soa4_a2', 'soa5_a1', 'soa5_a2', 'soa_a1', 'soa_a2', 'sol_tsi',]
+
+for root, _, files in os.walk('data'):
+    for file in files:
+        file_path = os.path.join(root, file)
+        ds = xr.open_dataset(file_path)
+        # Select the second time index and nearest lev, expand both dimensions
+        ds_sel = ds[keep].isel(time=1).sel(lev=1000.0, method="nearest").expand_dims(['lev', 'time'])
+        ds_sel.to_netcdf(f'sample_waccm_data/{file}')
+```
+
+You can extract a coniguraiton file with 
+
+```
+waccmToMusicBox waccmDir="./sample_waccm_data" date="20240904" time="07:00" latitude=3.1 longitude=101.7
+```

src/acom_music_box/__init__.py

@@ -4,7 +4,7 @@
 This package contains modules for handling various aspects of a music box,
 including species, products, reactants, reactions, and more.
 """
-__version__ = "2.3.2"
+__version__ = "2.4.0"
 
 from .utils import convert_time, convert_pressure, convert_temperature, convert_concentration
 from .species import Species