Merge pull request #300 from NCAR/main

v2.6.0

.github/workflows/CI_Tests.yml

@@ -29,9 +29,28 @@ jobs:
     - name: Install this package
       run: pip install -e '.[dev]'
 
-    - name: Run pytest
-      run: pytest
+    - name: Install gnuplot
+      if: runner.os == 'Linux'
+      run: sudo apt-get install gnuplot
+
+    - name: Install gnuplot
+      if: runner.os == 'macOS'
+      run: brew install gnuplot
+
+    - name: Install gnuplot
+      if: runner.os == 'Windows'
+      run: choco install gnuplot
+
+    - name: Run tests and generate coverage reports
+      run: pytest --cov src/
 
+    - name: Upload coverage reports to codecov
+      if: runner.os == 'Linux'
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        files: coverage.info
+
     - name: Run the smoke tests
       run: |
         music_box -c src/acom_music_box/examples/configs/analytical/my_config.json -o output.csv

.github/workflows/pep8_autoformat.yml

@@ -15,7 +15,7 @@ jobs:
       - name: autopep8
         uses: peter-evans/autopep8@v2
         with:
-          args: --recursive --in-place --aggressive --aggressive --max-line-length 180 .
+          args: --recursive --in-place --aggressive --max-line-length 180 --indent-size=4 .
 
       - name: Check for changes
         id: check-changes
@@ -28,7 +28,7 @@ jobs:
         run: |
           git config --global user.name "GitHub Actions"
           git config --global user.email "[email protected]"
-          git commit -am "Auto-format code using Clang-Format" || echo "No changes to commit"
+          git commit -am "Auto-format code using pep8" || echo "No changes to commit"
 
       - name: Push changes to main-autopep8 branch
         if: steps.check-changes.outcome != 'success'
@@ -42,4 +42,4 @@ jobs:
           commit-message: "Auto-format code using autopep8"
           title: "Auto-format code by autopep8"
           body: "This is an auto-generated PR with fixes by autopep8."
-          branch: main-autopep8
+          branch: main-autopep8

.gitignore

@@ -9,4 +9,6 @@ __pycache__/
 *.pyc
 dist
 
-.vscode/
+.vscode/
+.coverage
+src/acom_music_box/examples/configs/ts1/initial_config.json

CITATION.cff

@@ -1,7 +1,7 @@
 cff-version: 1.2.0
 message: If you use this software, please cite it as below.
 title: MusicBox
-version: v2.5.5
+version: v2.6.0
 authors:
   - family-names: Dawson
     given-names: Matthew
@@ -19,5 +19,7 @@ authors:
     given-names: Brendan
   - family-names: Drews
     given-names: Carl
+  - family-names: Kiran
+    given-names: Aditya
 license: Apache-2.0
 url: "https://github.com/NCAR/music-box"

README.md

@@ -6,9 +6,12 @@ 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)
+[![codecov](https://codecov.io/github/NCAR/music-box/graph/badge.svg?token=OR7JEQJSRQ)](https://codecov.io/github/NCAR/music-box)
 [![PyPI version](https://badge.fury.io/py/acom-music-box.svg)](https://badge.fury.io/py/acom-music-box)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14008358.svg)](https://doi.org/10.5281/zenodo.14008358)
 
-Copyright (C) 2020 National Center for Atmospheric Research
+
+Copyright (C) 2020 National Science Foundation - National Center for Atmospheric Research
 
 # Installation
 ```
@@ -30,22 +33,77 @@ Run an example. Notice that the output, in csv format, is printed to the termina
 music_box -e Chapman
 ```
 
+Output can be saved to a csv file and printed to the terminal.
+
+```
+music_box -e Chapman -o output.csv
+```
+
+Output can be saved to a csv file and the terminal output can be suppressed by specifying the `--output-format`
+
+```
+music_box --output-format csv -e Chapman -o output.csv
+```
+
+Output can be saved to a file as netcdf file when `--output-format` netcdf is passed
+
+```
+music_box --output-format netcdf -e Chapman -o output.nc
+```
+
+Output can be saved to a file in csv format when a filename is not specified. In this case a timestamped csv file is made
+
+```
+music_box --output-format csv -e Chapman
+```
+
+Output can be saved to a file in netcdf format when a filename is not specified. In this case a timestamped netcdf file is made
+
+```
+music_box --output-format netcdf -e Chapman
+```
+
 You can also run your own configuration
 
 ```
 music_box -c my_config.json
 ```
 
-Output can be saved to a file
+## Plotting
+Some basic plots can be made to show concentrations throughout the simulation
+
+### matplotlib
 
 ```
-music_box -e Chapman -o output.csv
+music_box -e Chapman -o output.csv --plot O1D
+```
+
+You can also make multiple plots by specifying groupings of species
+
+```
+music_box -e TS1 --plot O3 --plot PAN,HF 
+```
+
+Note that the windows may overlap each other
+
+By default all plot units are in `mol m-3`. You can see a list of unit options to specify with `--plot-output-unit`
+
+```
+music_box -h
+```
+
+It is used like this
+
+```
+ music_box -e TS1 --output-format csv --plot O3 --plot-output-unit "ppb"
 ```
 
-And, if you have gnuplot installed, some basic plots can be made to show some resulting concentrations
+### gnuplot
+If you want ascii plots (maybe you're running over ssh and can't view a graphical window), you can set
+the plot tool to gnuplo (`--plot-tool gnuplot`) to view some output
 
 ```
-music_box -e Chapman -o output.csv --color-output --plot CONC.O1D
+music_box -e Chapman -o output.csv --plot O1D --plot-tool gnuplot
 ```
 
 # Development and Contributing

docs/source/conf.py

@@ -14,8 +14,8 @@
 
 version = acom_music_box.__version__
 project = f'Music Box ({version})'
-copyright = f'2024-{datetime.datetime.now().year}, NCAR/UCAR'
-author = 'NCAR/UCAR'
+copyright = f'2024-{datetime.datetime.now().year}, NSF-NCAR/UCAR'
+author = 'NSF-NCAR/UCAR'
 
 suffix = os.getenv("SWITCHER_SUFFIX", "")
 release = f'{version}{suffix}'

pyproject.toml

@@ -21,7 +21,7 @@ classifiers = ["License :: OSI Approved :: Apache Software License"]
 dynamic = ["version", "description"]
 
 dependencies = [
-  "musica==0.8.1",
+  "musica==0.9.0",
   "xarray",
   "colorlog",
   "pandas",
@@ -41,5 +41,6 @@ waccmToMusicBox = "acom_music_box.tools.waccmToMusicBox:main"
 [project.optional-dependencies]
 dev = [
   "pytest",
-  "pytest-mock"
+  "pytest-mock",
+  "pytest-cov"
 ]

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__ = "2.5.5"
+__version__ = "2.6.0"
 
 from .utils import convert_time, convert_pressure, convert_temperature, convert_concentration
 from .model_options import BoxModelOptions
@@ -13,3 +13,5 @@
 from .evolving_conditions import EvolvingConditions
 from .music_box import MusicBox
 from .examples import Examples
+from .data_output import DataOutput
+from .plot_output import PlotOutput