Code coverage in SonarQube (#448)

* write sounding_data.dat file in output directory instead of current working directory

* refactored plot classes - renamed logger class variables to be consistent and call utility functions to greatly simplify the main functions of each plot that are handled in the same way

* Refactored unit tests so they can be run from any directory, not just the directory containing the test. Added pytest fixtures to handle setup of environment and remove files and intermed_files directories. Set env var TEST_DIR to the current test directory and reference it in yaml files to ensure that test input/output is read/written from the correct test directory. Changed file paths to be relative to test directory instead of current working directory

* added PyCharm-generated files that shouldn't change

* run pytests from top directory and generate code coverage report to send to SonarQube server

* clone METcalcpy into different directory to prevent pytest to running its tests

* install METcalcpy into different directory

* cleanup

* remove unnecessary call to remove sounding_data.dat file that is removed when scrubbing the output dir

* remove unused variable

* removed unused variable and whitespace

* clean up linter complaints

* add prints to help debugging if test fails

* clean up tests to run faster by running plot script once and checking for all files

.coveragerc

@@ -0,0 +1,2 @@
+[run]
+relative_files = True

.github/workflows/sonarqube.yml

@@ -48,6 +48,36 @@ jobs:
         # Disable shallow clones for better analysis
         fetch-depth: 0
 
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+
+    - name: Retrieve METcalcpy repository develop branch
+      run: |
+         metcalcpy_dir="$RUNNER_WORKSPACE/METcalcpy"
+         git clone https://github.com/dtcenter/METcalcpy ${metcalcpy_dir}
+         cd ${metcalcpy_dir}
+         git -C ${metcalcpy_dir} checkout develop
+         python -m pip install -e ${metcalcpy_dir}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python -m pip install pytest-cov
+
+    - name: Run Pytests
+      run: coverage run -m pytest
+
+    - name: Output coverage report
+      run: coverage report -m
+      if: always()
+
+    - name: Generate XML coverage report
+      run: coverage xml
+      if: always()
+
     - name: Get branch name
       id: get_branch_name
       run: echo branch_name=${GITHUB_REF#refs/heads/} >> $GITHUB_OUTPUT

.github/workflows/unit_tests.yaml

@@ -39,10 +39,11 @@ jobs:
 
     - name: Retrieve METcalcpy repository develop branch
       run: |
-         /usr/bin/git clone https://github.com/dtcenter/METcalcpy
-         cd METcalcpy
-         /usr/bin/git checkout develop
-         python -m pip install -e .
+         metcalcpy_dir="$RUNNER_WORKSPACE/METcalcpy"
+         git clone https://github.com/dtcenter/METcalcpy ${metcalcpy_dir}
+         cd ${metcalcpy_dir}
+         git -C ${metcalcpy_dir} checkout develop
+         python -m pip install -e ${metcalcpy_dir}
             
     - name: Install dependencies
       run: |
@@ -55,43 +56,8 @@ jobs:
 #       run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
 #       id: extract_branch
 
-
     - name: Test with pytest
-      run: |
-          cd test
-          cd bar 
-          pytest test_bar.py
-          cd ../box
-          pytest test_box.py
-          cd ../contour
-          pytest test_contour.py
-          cd ../eclv
-          pytest test_eclv.py
-          cd ../ens_ss
-          pytest test_ens_ss.py
-          cd ../equivalence_testing_bounds
-          pytest test_equivalence_testing_bounds.py
-          cd ../line
-          pytest test_line_groups_plot.py
-          pytest test_line_plot.py
-          cd ../mpr_plot
-          pytest test_mpr_plot.py
-          cd ../performance_diagram
-          pytest test_performance_diagram.py
-          cd ../reliability_diagram
-          pytest test_reliability_diagram.py
-          cd ../roc_diagram
-          pytest test_roc_diagram.py
-          cd ../taylor_diagram
-          pytest test_taylor_diagram.py
-          cd ../wind_rose
-          pytest test_wind_rose.py
-          cd ../histogram
-          pytest test_prob_hist.py
-          pytest test_rank_hist.py
-          pytest test_rel_hist.py
-          cd ../tcmpr_plots
-          pytest --capture=fd test_tcmpr_plots.py
+      run: pytest
 
 
 

internal/scripts/sonarqube/sonar-project.properties

@@ -5,6 +5,7 @@ sonar.projectVersion=SONAR_PROJECT_VERSION
 sonar.branch.name=SONAR_BRANCH_NAME
 sonar.sources=metplotpy,test
 sonar.coverage.exclusions=test/**
+sonar.python.coverage.reportPaths=coverage.xml
 sonar.sourceEncoding=UTF-8
 
 # SonarQube server

metplotpy/plots/bar/bar.py

@@ -19,7 +19,6 @@
 
 import pandas as pd
 import plotly.graph_objects as go
-import yaml
 from plotly.graph_objects import Figure
 from plotly.subplots import make_subplots
 
@@ -53,11 +52,11 @@ def __init__(self, parameters: dict) -> None:
         # the
         # config file that represents the BasePlot object (Bar).
         self.config_obj = BarConfig(self.parameters)
-        self.bar_logger = self.config_obj.logger
-        self.bar_logger.info(f"Start bar plot: {datetime.now()}")
+        self.logger = self.config_obj.logger
+        self.logger.info(f"Start bar plot: {datetime.now()}")
         # Check that we have all the necessary settings for each series
-        self.bar_logger.info(f"Consistency checking of config settings for colors, "
-                        f"legends, etc.")
+        self.logger.info("Consistency checking of config settings for colors, "
+                         "legends, etc.")
         is_config_consistent = self.config_obj._config_consistency_check()
         if not is_config_consistent:
             value_error_msg = ("ValueError: The number of series defined by series_val_1 and "
@@ -66,20 +65,19 @@ def __init__(self, parameters: dict) -> None:
                                "check the number of your configuration file's "
                                "plot_i, plot_disp, series_order, user_legend, show_legend and "
                                "colors settings.")
-            self.bar_logger.error(value_error_msg)
+            self.logger.error(value_error_msg)
             raise ValueError(value_error_msg)
 
-
         # Read in input data, location specified in config file
-        self.bar_logger.info(f"Begin reading input data: {datetime.now()}")
+        self.logger.info(f"Begin reading input data: {datetime.now()}")
         self.input_df = self._read_input_data()
 
         # Apply event equalization, if requested
         if self.config_obj.use_ee is True:
-            self.bar_logger.info(f"Performing event equalization: {datetime.now()}")
+            self.logger.info(f"Performing event equalization: {datetime.now()}")
             self.input_df = calc_util.perform_event_equalization(self.parameters,
                                                                  self.input_df)
-            self.bar_logger.info(f"End event equalization: {datetime.now()}")
+            self.logger.info(f"End event equalization: {datetime.now()}")
 
         # Create a list of series objects.
         # Each series object contains all the necessary information for plotting,
@@ -91,9 +89,9 @@ def __init__(self, parameters: dict) -> None:
         # Need to have a self.figure that we can pass along to
         # the methods in base_plot.py (BasePlot class methods) to
         # create binary versions of the plot.
-        self.bar_logger.info(f"Begin creating the figure: {datetime.now()}")
+        self.logger.info(f"Begin creating the figure: {datetime.now()}")
         self._create_figure()
-        self.bar_logger.info(f"End creating the figure: {datetime.now()}")
+        self.logger.info(f"End creating the figure: {datetime.now()}")
 
     def __repr__(self):
         """ Implement repr which can be useful for debugging this
@@ -114,7 +112,7 @@ def _read_input_data(self):
             Returns:
 
         """
-        self.bar_logger.info(f"Finished reading input data: "
+        self.logger.info(f"Finished reading input data: "
                                     f"{datetime.now()}")
         return pd.read_csv(self.config_obj.parameters['stat_input'], sep='\t',
                            header='infer', float_precision='round_trip')
@@ -516,28 +514,7 @@ def main(config_filename=None):
                 @param config_filename: default is None, the name of the custom
                 config file to apply
         """
-
-    # Retrieve the contents of the custom config file to over-ride
-    # or augment settings defined by the default config file.
-    if not config_filename:
-        config_file = util.read_config_from_command_line()
-    else:
-        config_file = config_filename
-    with open(config_file, 'r') as stream:
-        try:
-            docs = yaml.load(stream, Loader=yaml.FullLoader)
-        except yaml.YAMLError as exc:
-            print(exc)
-
-    try:
-        plot = Bar(docs)
-        plot.save_to_file()
-        # plot.show_in_browser()
-        plot.write_html()
-        plot.write_output_file()
-        plot.bar_logger.info(f"Finished bar plot at {datetime.now()}")
-    except ValueError as val_er:
-        print(val_er)
+    util.make_plot(config_filename, Bar)
 
 
 if __name__ == "__main__":

metplotpy/plots/base_plot.py

@@ -74,7 +74,6 @@ def __init__(self, parameters, default_conf_filename):
         self.remove_file()
         self.config_obj = Config(self.parameters)
 
-
     def get_image_format(self):
         """Reads the image format type from user provided image name.
         Uses file extension as a type. If the file extension is not valid -
@@ -340,8 +339,6 @@ def save_to_file(self):
         Returns:
 
         """
-
-
         image_name = self.get_config_value('plot_filename')
 
         # Suppress deprecation warnings from third-party packages that are not in our control.
@@ -388,8 +385,8 @@ def show_in_browser(self):
         if self.figure:
             self.figure.show()
         else:
-            self.logger.error(f" Figure not created. Nothing to show in the "
-                              f"browser. ")
+            self.logger.error(" Figure not created. Nothing to show in the "
+                              "browser. ")
             print("Oops!  The figure was not created. Can't show")
 
     def _add_lines(self, config_obj: Config, x_points_index: Union[list, None] = None) -> None: