abstracting plotting (#278)

* abstracting plotting

* moving plotting code to its own file, correcting data output, readme

* correcting ci install for gnuplot

* fixing gnuplot install for linux

* running tests after installing gnuplot

* Update pep8_autoformat.yml

.github/workflows/CI_Tests.yml

@@ -29,6 +29,18 @@ jobs:
     - name: Install this package
       run: pip install -e '.[dev]'
 
+    - 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/
 

.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=2 .
 
       - name: Check for changes
         id: check-changes
@@ -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

README.md

@@ -33,13 +33,13 @@ 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 file in csv file when no `--output-format` is passed
+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 file as csv file when `--output-format` csv is passed
+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
@@ -51,13 +51,13 @@ Output can be saved to a file as netcdf file when `--output-format` netcdf is pa
 music_box --output-format netcdf -e Chapman -o output.nc
 ```
 
-Output can be saved to a file in csv file to output.csv when no output path is given but `--output-format` is csv
+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 file to output.nc when no output path is given but `--output-format` is netcdf
+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
@@ -69,10 +69,21 @@ You can also run your own configuration
 music_box -c my_config.json
 ```
 
-And, if you have gnuplot installed, some basic plots can be made to show some resulting concentrations
+## Plotting
+Some basic plots can be made to show concentrations throughout the simulation
+
+### matplotlib
+
+```
+music_box -e Chapman -o output.csv --plot O1D
+```
+
+### 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

src/acom_music_box/__init__.py

@@ -14,3 +14,4 @@
 from .music_box import MusicBox
 from .examples import Examples
 from .data_output import DataOutput
+from .plot_output import PlotOutput

src/acom_music_box/data_output.py

@@ -14,13 +14,6 @@ class DataOutput:
     This class manages file paths, unit mappings, and data output formats based on
     the provided arguments, ensuring valid paths and creating necessary directories.
 
-    Parameters
-    ----------
-    df : pandas.DataFrame
-        The DataFrame containing the data to output.
-    args : argparse.Namespace
-        Arguments specifying output path, format, and additional options.
-
     Attributes
     ----------
     df : pandas.DataFrame
@@ -64,12 +57,12 @@ def __init__(self, df, args):
             - output_format : str, optional
                 Format of the output file, either 'csv' or 'netcdf'. Defaults to 'csv'.
         """
-        self.df = df
+        self.df = df.copy(deep=True)
         self.args = args
         self.unit_mapping = {
             'ENV.temperature': 'K',
             'ENV.pressure': 'Pa',
-            'ENV.number_density_air': 'kg -m3',
+            'ENV.number_density_air': 'kg m-3',
             'time': 's'
         }
 
@@ -110,7 +103,7 @@ def _convert_to_netcdf(self):
 
         ds['ENV.temperature'].attrs = {'units': 'K'}
         ds['ENV.pressure'].attrs = {'units': 'Pa'}
-        ds['ENV.number_density_air'].attrs = {'units': 'kg -m3'}
+        ds['ENV.number_density_air'].attrs = {'units': 'kg m-3'}
         ds['time'].attrs = {'units': 's'}
 
         ds.to_netcdf(self.args.output)
@@ -146,11 +139,10 @@ def output(self):
         # Determine output type and call the respective method
         if self.args.output_format is None or self.args.output_format == 'terminal':
             self._output_terminal()
-        elif self.args.output_format is None or self.args.output_format == 'csv':
+
+        # Even if we are printing to the terminal, we still allow output to be written to csv if an output path is provided
+        if (self.args.output_format == 'csv') or (self.args.output is not None and self.args.output_format == 'terminal'):
             self._output_csv()
-        elif self.args.output_format == 'netcdf':
-            self._output_netcdf()
-        else:
-            error = f"Unsupported output format: {self.args.output_format}"
-            logger.error(error)
-            raise ValueError(error)
+
+        if self.args.output_format == 'netcdf':
+            self._output_netcdf()

src/acom_music_box/main.py

@@ -3,11 +3,8 @@
 import datetime
 import logging
 import os
-import subprocess
-import tempfile
-import matplotlib.pyplot as plt
-import mplcursors
-from acom_music_box import MusicBox, Examples, __version__, DataOutput
+import sys
+from acom_music_box import MusicBox, Examples, __version__, DataOutput, PlotOutput
 
 
 def format_examples_help(examples):
@@ -97,69 +94,6 @@ def setup_logging(verbosity, color_output):
     logging.basicConfig(level=log_level, handlers=[console_handler])
 
 
-def plot_with_gnuplot(data, species_list):
-    # Prepare columns and data for plotting
-    columns = ['time'] + species_list
-    data_to_plot = data[columns]
-
-    data_csv = data_to_plot.to_csv(index=False)
-
-    try:
-        with tempfile.NamedTemporaryFile(delete=False, suffix='.csv') as data_file:
-            data_file.write(data_csv.encode())
-            data_file_path = data_file.name
-
-        plot_commands = ',\n\t'.join(
-            f"'{data_file_path}' using 1:{i+2} with lines title '{species}'" for i,
-            species in enumerate(species_list))
-
-        gnuplot_command = f"""
-        set datafile separator ",";
-        set terminal dumb size 120,25;
-        set xlabel 'Time';
-        set ylabel 'Value';
-        set title 'Time vs Species';
-        plot {plot_commands}
-        """
-
-        subprocess.run(['gnuplot', '-e', gnuplot_command], check=True)
-    except FileNotFoundError:
-        logging.critical("gnuplot is not installed. Skipping plotting.")
-    except subprocess.CalledProcessError as e:
-        logging.error(f"Error occurred while plotting: {e}")
-    finally:
-        # Clean up the temporary file
-        if data_file_path:
-            os.remove(data_file_path)
-
-
-def plot_with_matplotlib(data, species_list):
-    # Prepare columns and data for plotting
-    indexed = data.set_index('time')
-
-    fig, ax = plt.subplots()
-    indexed[species_list].plot(ax=ax)
-
-    ax.set(xlabel='Time [s]', ylabel='Concentration [mol m-3]', title='Time vs Species')
-
-    ax.spines[:].set_visible(False)
-    ax.spines['left'].set_visible(True)
-    ax.spines['bottom'].set_visible(True)
-
-    ax.grid(alpha=0.5)
-    ax.legend()
-
-    # Enable interactive data cursors with hover functionality
-    cursor = mplcursors.cursor(hover=True)
-
-    # Customize the annotation format
-    @cursor.connect("add")
-    def on_add(sel):
-        sel.annotation.set_text(f'Time: {sel.target[0]:.2f}\nConcentration: {sel.target[1]:1.2e}')
-
-    plt.show()
-
-
 def main():
     start = datetime.datetime.now()
 
@@ -180,8 +114,6 @@ def main():
     else:
         musicBoxConfigFile = args.config
 
-    musicBoxOutputPath = args.output
-
     plot_species_list = args.plot.split(',') if args.plot else None
 
     if not musicBoxConfigFile:
@@ -200,11 +132,9 @@ def main():
     dataOutput = DataOutput(result, args)
     dataOutput.output()
 
-    if plot_species_list:
-        if args.plot_tool == 'gnuplot':
-            plot_with_gnuplot(result, plot_species_list)
-        elif args.plot_tool == 'matplotlib':
-            plot_with_matplotlib(result, plot_species_list)
+    # Create an instance of PlotOutput
+    plotOutput = PlotOutput(result, args)
+    plotOutput.plot()
 
     end = datetime.datetime.now()
     logger.info(f"End time: {end}")