Merge pull request #118 from CardiacModelling/coverage-2

Separate summarise-herg-qc script command line parsing

Author: MichaelClerx

.github/workflows/tests.yml

@@ -48,6 +48,10 @@ jobs:
         wget https://cardiac.nottingham.ac.uk/syncropatch_export/test_data.tar.xz -P tests/
         tar xvf tests/test_data.tar.xz -C tests/
 
+    - name: Install TeX dependencies for run_herg_qc test
+      timeout-minutes: 5
+      run: sudo apt-get install dvipng texlive-latex-extra texlive-fonts-recommended cm-super -y
+
     - name: Run unit tests (without coverage testing)
       if: ${{ success() && matrix.python-version != env.python-latest }}
       run: python -m unittest
@@ -56,14 +60,6 @@ jobs:
       if: ${{ success() && matrix.python-version == env.python-latest }}
       run: coverage run -m unittest
 
-    - name: Install TeX dependencies for run_herg_qc test
-      timeout-minutes: 15
-      run: sudo apt-get install dvipng texlive-latex-extra texlive-fonts-recommended cm-super -y
-
-    - name: Run `run_herg_qc` script
-      timeout-minutes: 15
-      run: pcpostprocess run_herg_qc tests/test_data/13112023_MW2_FF -w A01 A02 A03
-
     - name: Report coverage to codecov
       uses: codecov/codecov-action@v4
       if: ${{ success() && matrix.python-version == env.python-latest }}

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/__main__.py

@@ -21,7 +21,7 @@ def main():
         run_herg_qc.run_from_command_line()
 
     elif args.subcommand == "summarise_herg_export":
-        summarise_herg_export.main()
+        summarise_herg_export.run_from_command_line()
 
 
 if __name__ == "__main__":

pcpostprocess/scripts/run_herg_qc.py

@@ -11,7 +11,6 @@
 import string
 import sys
 
-import cycler
 import matplotlib
 import matplotlib.pyplot as plt
 import numpy as np
@@ -28,17 +27,11 @@
 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():
     """
-    Reads arguments from the command line and runs herg QC.
+    Reads arguments from the command line and an ``export_config.py`` and then
+    runs herg QC.
     """
 
     parser = argparse.ArgumentParser()
@@ -109,11 +102,7 @@ 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.
 
@@ -148,6 +137,9 @@ 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)]
@@ -503,8 +495,6 @@ 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
 
@@ -1255,7 +1245,7 @@ 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)]