Merge pull request #17 from CardiacModelling/make-scripts-modules

Make scripts modules

.github/workflows/pytest.yml

@@ -37,15 +37,16 @@ jobs:
         python -m pip install -e .
         python -m pytest --cov --cov-config=.coveragerc
     - name: Run export with test data
+      timeout-minutes: 15
       run: |
         sudo apt-get install dvipng texlive-latex-extra texlive-fonts-recommended cm-super -y
-        python3 scripts/run_herg_qc.py tests/test_data/13112023_MW2_FF
+        pcpostprocess run_herg_qc tests/test_data/13112023_MW2_FF -w A01 A02 A03
     - uses: codecov/codecov-action@v1
       with:
         token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
     - name: Lint with flake8
       run: |
-        python -m flake8 pcpostprocess/*.py tests/*.py scripts/*.py
+        python -m flake8 pcpostprocess/*.py tests/*.py pcpostprocess/scripts/*.py
     - name: Import sorting with isort
       run: |
         python -m isort --verbose --check-only --diff pcpostprocess tests setup.py

README.md

@@ -90,6 +90,75 @@ Then you can run the tests.
 python3 -m unittest
 ```
 
+
+<!-- USAGE -->
+## Usage
+
+### Running QC and post-processing
+
+```
+$ pcpostprocess run_herg_qc --help
+
+usage: pcpostprocess run_herg_qc [-h] [-c NO_CPUS]
+                      [--output_dir OUTPUT_DIR] [-w WELLS [WELLS ...]]
+                      [--protocols PROTOCOLS [PROTOCOLS ...]]
+                      [--reversal_spread_threshold REVERSAL_SPREAD_THRESHOLD] [--export_failed]
+                      [--selection_file SELECTION_FILE] [--subtracted_only]
+                      [--figsize FIGSIZE FIGSIZE]
+                      [--debug] [--log_level LOG_LEVEL] [--Erev EREV]
+                      data_directory
+
+positional arguments:
+  data_directory
+
+options:
+  -h, --help            show this help message and exit
+  -c NO_CPUS, --no_cpus NO_CPUS
+  --output_dir OUTPUT_DIR
+  -w WELLS [WELLS ...], --wells WELLS [WELLS ...]
+  --protocols PROTOCOLS [PROTOCOLS ...]
+  --reversal_spread_threshold REVERSAL_SPREAD_THRESHOLD
+  --export_failed
+  --selection_file SELECTION_FILE
+  --subtracted_only
+  --figsize FIGSIZE FIGSIZE
+  --debug
+  --log_level LOG_LEVEL
+  --Erev EREV
+```
+
+
+### Exporting Summary
+
+```
+$ pcpostprocess summarise_herg_export --help
+
+usage: pcpostprocess summarise_herg_export [-h] [--cpus CPUS]
+                      [--wells WELLS [WELLS ...]] [--output OUTPUT]
+                      [--protocols PROTOCOLS [PROTOCOLS ...]] [-r REVERSAL]
+                      [--experiment_name EXPERIMENT_NAME]
+                      [--figsize FIGSIZE FIGSIZE] [--output_all]
+                      [--log_level LOG_LEVEL]
+                      data_dir qc_estimates_file
+
+positional arguments:
+  data_dir           path to the directory containing the subtract_leak results
+  qc_estimates_file
+
+options:
+  -h, --help            show this help message and exit
+  --cpus CPUS, -c CPUS
+  --wells WELLS [WELLS ...], -w WELLS [WELLS ...]
+  --output OUTPUT, -o OUTPUT
+  --protocols PROTOCOLS [PROTOCOLS ...]
+  -r REVERSAL, --reversal REVERSAL
+  --experiment_name EXPERIMENT_NAME
+  --figsize FIGSIZE FIGSIZE
+  --output_all
+  --log_level LOG_LEVEL
+```
+
+
 <!-- CONTRIBUTING -->
 ## Contributing
 

pcpostprocess/scripts/__main__.py

@@ -0,0 +1,28 @@
+import argparse
+import sys
+
+from . import run_herg_qc, summarise_herg_export
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        usage="pcpostprocess (run_herg_qc | summarise_herg_export) [<args>]",
+    )
+    parser.add_argument(
+        "subcommand",
+        choices=["run_herg_qc", "summarise_herg_export"],
+    )
+    args = parser.parse_args(sys.argv[1:2])
+
+    sys.argv[0] = f"pcpostprocess {args.subcommand}"
+    sys.argv.pop(1)  # Subcommand's argparser shouldn't see this
+
+    if args.subcommand == "run_herg_qc":
+        run_herg_qc.main()
+
+    elif args.subcommand == "summarise_herg_export":
+        summarise_herg_export.main()
+
+
+if __name__ == "__main__":
+    main()

scripts/summarise_herg_export.py → pcpostprocess/scripts/summarise_herg_export.py

@@ -12,10 +12,11 @@
 import regex as re
 import scipy
 import seaborn as sns
-from run_herg_qc import create_qc_table
 from syncropatch_export.voltage_protocols import VoltageProtocol
 
-matplotlib.rcParams['figure.dpi'] = 300
+from pcpostprocess.scripts.run_herg_qc import create_qc_table
+
+matplotlib.use('Agg')
 
 pool_kws = {'maxtasksperchild': 1}
 

setup.py

@@ -29,7 +29,7 @@
 
     # Packages to include
     packages=find_packages(
-        include=('pcpostprocess', 'pcpostprocess.*')),
+        include=('pcpostprocess', 'pcpostprocess.scripts', 'pcpostprocess.*')),
 
     # Include non-python files (via MANIFEST.in)
     include_package_data=True,
@@ -46,6 +46,7 @@
         'regex>=2023.12.25',
         'openpyxl>=3.1.2',
         'jinja2>=3.1.0',
+        'seaborn>=0.12.2'
     ],
     extras_require={
         'test': [
@@ -58,4 +59,10 @@
             'syncropatch_export @ git+ssh://[email protected]/CardiacModelling/syncropatch_export@main'
         ],
     },
+    entry_points={
+        'console_scripts': [
+            'pcpostprocess='
+            'pcpostprocess.scripts.__main__:main',
+        ],
+    },
 )