Added tests for scripts. Closes #117

Author: MichaelClerx

CONTRIBUTING.md

@@ -76,6 +76,7 @@ Isort is configured in [pyproject.toml](./pyproject.toml) under the section `too
 ## Documentation
 
 Every method and every class should have a [docstring](https://www.python.org/dev/peps/pep-0257/) that describes in plain terms what it does, and what the expected input and output is.
+The only exception are unit test methods starting with `test_` - unit test classes and other methods in unit tests should all have docstrings.
 
 Each docstring should start with a one-line explanation.
 If more explanation is needed, this one-liner is followed by a blank line and more information in the following paragraphs.

pcpostprocess/scripts/run_herg_qc.py

@@ -28,13 +28,6 @@
 from pcpostprocess.leak_correct import fit_linear_leak, get_leak_corrected
 from pcpostprocess.subtraction_plots import do_subtraction_plot
 
-# TODO: Remove this
-color_cycle = ["#5790fc", "#f89c20", "#e42536", "#964a8b", "#9c9ca1", "#7a21dd"]
-plt.rcParams['axes.prop_cycle'] = cycler.cycler('color', color_cycle)
-
-# TODO: Not sure we need to explicitly set this!
-matplotlib.use('Agg')
-
 
 def run_from_command_line():
     """
@@ -110,11 +103,7 @@ def run(data_path, output_path, qc_map, wells=None,
         write_traces=False, write_failed_traces=False, write_map={},
         reversal_potential=-90, reversal_spread_threshold=10,
         max_processes=1, figure_size=None,
-        debug=False,
-
-        save_id=None,
-
-        ):
+        debug=False, save_id=None):
     """
     Imports traces and runs QC.
 
@@ -149,6 +138,9 @@ def run(data_path, output_path, qc_map, wells=None,
     # TODO Remove protocol selection here: this is done via the export file!
     #      Only protocols listed there are accepted
 
+    # TODO: Find some way around setting this?
+    matplotlib.use('Agg')
+
     # Select wells to use
     all_wells = [row + str(i).zfill(2) for row in string.ascii_uppercase[:16]
                  for i in range(1, 25)]
@@ -504,8 +496,6 @@ def agg_func(x):
     qc_df['protocol'] = ['staircaseramp1_2' if p == 'staircaseramp2' else p
                          for p in qc_df.protocol]
 
-    print(qc_df.protocol.unique())
-
     fails_dict = {}
     no_wells = 384
 
@@ -1256,7 +1246,7 @@ def fit_func(x, args=None):
     ]
 
     # TESTING ONLY
-    np.random.seed(1)
+    # np.random.seed(1)
 
     #  Repeat optimisation with different starting guesses
     x0s = [[np.random.uniform(lower_b, upper_b) for lower_b, upper_b in bounds] for i in range(100)]

pcpostprocess/scripts/summarise_herg_export.py

@@ -17,14 +17,6 @@
 from pcpostprocess.directory_builder import setup_output_directory
 from pcpostprocess.scripts.run_herg_qc import create_qc_table
 
-matplotlib.use('Agg')
-
-pool_kws = {'maxtasksperchild': 1}
-
-color_cycle = ["#5790fc", "#f89c20", "#e42536", "#964a8b", "#9c9ca1", "#7a21dd"]
-plt.rcParams['axes.prop_cycle'] = cycler.cycler('color', color_cycle)
-sns.set_palette(sns.color_palette(color_cycle))
-
 
 def get_wells_list(input_dir, experiment_name):
     regex = re.compile(f"{experiment_name}-([a-z|A-Z|0-9]*)-([A-Z][0-9][0-9])-after")
@@ -54,7 +46,6 @@ def run_from_command_line():
 
     description = ''    # TODO Describe what this does
     parser = argparse.ArgumentParser(description)
-
     parser.add_argument(
         'data_directory', help='path to the run_herg_qc results')
     parser.add_argument(
@@ -67,32 +58,27 @@ def run_from_command_line():
     parser.add_argument(
         '--figsize', type=int, nargs=2, default=(5, 3),
         help='A figure size, to pass to matplotlib')
-    parser.add_argument('--log_level', default='INFO')
     args = parser.parse_args()
 
-    # Setup logging
-    logging.basicConfig(level=args.log_level)
-    logger = logging.getLogger(__name__)
-    logger.setLevel(args.log_level)
-
     run(args.data_directory, args.output_dir, args.experiment_name,
-        logger, args.Erev, args.figsize)
+        args.Erev, args.figsize)
 
 
-def run(data_path, output_path, experiment_name, logger,
-        reversal_potential=None, figsize=None):
+def run(data_path, output_path, experiment_name, reversal_potential=None,
+        figsize=None):
     """
     Does whatever this does.
 
     @param data_path The path to read data from
     @param output_path A root path, will be appended with "summarise_herg_export"
     @param experiment_name
-    @param logger
     @param reversal_potential The calculated reversal potential, or ``None``
     @param figsize The matplotlib figure size, or ``None``.
-
     """
-    output_path = setup_output_directory(output_path, 'summarise_herg_export')
+    # TODO: Find some way around setting this
+    matplotlib.use('Agg')
+
+    output_path = setup_output_directory(output_path)
 
     leak_parameters_df = pd.read_csv(os.path.join(data_path, 'subtraction_qc.csv'))
 
@@ -113,8 +99,6 @@ def run(data_path, output_path, experiment_name, logger,
     leak_parameters_df.protocol = ['staircaseramp1_2' if protocol == 'staircaseramp_2' else protocol
                                    for protocol in leak_parameters_df.protocol]
 
-    print(leak_parameters_df.protocol.unique())
-
     with open(os.path.join(data_path, 'passed_wells.txt')) as fin:
         passed_wells = fin.read().splitlines()
 
@@ -138,8 +122,6 @@ def run(data_path, output_path, experiment_name, logger,
 
         leak_parameters_df.sort_values(['protocol', 'sweep'], inplace=True)
     except FileNotFoundError as exc:
-        logging.warning(str(exc))
-        logger.warning('no chronological information provided. Sorting alphabetically')
         leak_parameters_df.sort_values(['protocol', 'sweep'])
 
     scatterplot_timescale_E_obs(output_path, leak_parameters_df, passed_wells, figsize)
@@ -171,13 +153,6 @@ def run(data_path, output_path, experiment_name, logger,
     # do_scatter_matrices(leak_parameters_df, qc_vals_df, output_path, reversal_potential)
     plot_histograms(leak_parameters_df, output_path, reversal_potential, figsize)
 
-    # Don't work
-    # wells = leak_parameters_df.well.unique()
-    # overlay_reversal_plots(data_path, output_path, experiment_name,
-    #                       leak_parameters_df, wells, reversal_potential, figsize)
-    # do_combined_plots(data_path, output_path, experiment_name,
-    #                  leak_parameters_df, passed_wells, logger, figsize)
-
 
 def compute_leak_magnitude(df, lims=[-120, 60]):
     def compute_magnitude(g, E, lims=lims):
@@ -371,7 +346,7 @@ def label_func(p, s):
 
 
 def do_combined_plots(data_path, output_path, experiment_name,
-                      leak_parameters_df, passed_wells, logger, figsize=None):
+                      leak_parameters_df, passed_wells, figsize=None):
     """
     ???
 
@@ -380,7 +355,6 @@ def do_combined_plots(data_path, output_path, experiment_name,
     @param experiment_name
     @param leak_parameters_df
     @param passed_wells
-    @param logger
     @param figsize
 
     """
@@ -389,8 +363,6 @@ def do_combined_plots(data_path, output_path, experiment_name,
 
     wells = [well for well in leak_parameters_df.well.unique() if well in passed_wells]
 
-    logger.info(f"passed wells are {passed_wells}")
-
     protocol_overlaid_dir = os.path.join(output_path, 'overlaid_by_protocol')
     if not os.path.exists(protocol_overlaid_dir):
         os.makedirs(protocol_overlaid_dir)
@@ -456,8 +428,6 @@ def do_combined_plots(data_path, output_path, experiment_name,
     if not os.path.exists(wells_overlaid_dir):
         os.makedirs(wells_overlaid_dir)
 
-    logger.info('overlaying traces by well')
-
     for well in passed_wells:
         i = 0
         for sweep in leak_parameters_df.sweep.unique():
@@ -728,6 +698,7 @@ def func(protocol, sweep):
         ax = fig.subplots()
         # add black color for NaNs
 
+        color_cycle = ["#5790fc", "#f89c20"]
         cmap = matplotlib.colors.ListedColormap([color_cycle[0], color_cycle[1]], 'indexed')
         ax.pcolormesh(zs, edgecolors='white', cmap=cmap,
                       linewidths=1, antialiased=True)
@@ -776,6 +747,7 @@ def plot_spatial_passed(df, output_path, passed_wells):
 
     zs = np.array(zs).reshape(16, 24)
 
+    color_cycle = ["#5790fc", "#f89c20"]
     cmap = matplotlib.colors.ListedColormap([color_cycle[0], color_cycle[1]], 'indexed')
     _ = ax.pcolormesh(zs, edgecolors='white',
                       linewidths=1, antialiased=True, cmap=cmap

tests/__init__.py

@@ -0,0 +1,5 @@
+#
+#
+# Unit tests for pcpostproces
+#
+#

tests/test_scripts.py

@@ -0,0 +1,43 @@
+#!/usr/bin/env python3
+import os
+import tempfile
+import unittest
+
+from pcpostprocess.scripts.run_herg_qc import run as run_herg_qc
+from pcpostprocess.scripts.summarise_herg_export import run as run_summarise
+
+store_output = False
+
+
+class TestScripts(unittest.TestCase):
+    """
+    Tests the scripts bundled with pcpostprocess.
+    """
+
+    def test_run_herg_qc_and_summarise_herg_export(self):
+        # Test run_herg_qc_, then summarise_herg_export
+
+        data = os.path.join('tests', 'test_data', '13112023_MW2_FF')
+        with tempfile.TemporaryDirectory() as d:
+            if store_output:
+                d = 'test_output'
+            d1 = os.path.join(d, 'run_herg_qc')
+            d2 = os.path.join(d, 'summarise_herg_export')
+
+            # Test run herg qc
+            erev = -90.71
+            qc_map = {'staircaseramp (2)_2kHz': 'staircaseramp'}
+            write_map = {'staircaseramp2': 'staircaseramp2'}
+            run_herg_qc(
+                data, d1, qc_map, ('A03', 'A20', 'D16'),
+                write_traces=True, write_map=write_map,
+                save_id='13112023_MW2', reversal_potential=erev)
+
+            # Test summarise herg export
+            run_summarise(d1, d2, '13112023_MW2', reversal_potential=erev)
+
+
+if __name__ == '__main__':
+    store_output=True
+    unittest.main()
+