Update the test suite for cardioception.reports.report (#66)

Author: Nicolas Legrand

MANIFEST.in

@@ -7,6 +7,4 @@ include requirements.txt
 include cardioception/HRD/Images/*
 include cardioception/HRD/Sounds/*
 include cardioception/HBC/Images/*
-include cardioception/HBC/Sounds/*
-include cardioception/notebooks/data/HBC/*
-include cardioception/notebooks/data/HRD/*
+include cardioception/HBC/Sounds/*

cardioception/notebooks/HeartBeatCounting.ipynb

@@ -3,6 +3,7 @@
 import os
 import subprocess
 from os import PathLike
+from pathlib import Path
 from typing import Optional, Union
 
 import numpy as np
@@ -247,8 +248,8 @@ def report(result_path: str, report_path: Optional[str] = None, task: str = "HRD
 
     if report_path is None:
         report_path = result_path
-    temp_notebook = os.path.join(report_path, "temp.ipynb")
-    htmlreport = os.path.join(report_path, f"{task}_report.html")
+    temp_notebook = Path(report_path, "temp.ipynb")
+    htmlreport = Path(report_path, f"{task}_report.html")
 
     if task == "HRD":
         template = "HeartRateDiscrimination.ipynb"
@@ -258,11 +259,11 @@ def report(result_path: str, report_path: Optional[str] = None, task: str = "HRD
     execute_notebook(
         pkg_resources.resource_filename("cardioception.notebooks", template),
         temp_notebook,
-        parameters=dict(resultPath=result_path, reportPath=report_path),
+        parameters=dict(resultPath=str(result_path), reportPath=str(report_path)),
     )
     command = (
         "jupyter nbconvert --to html --execute "
         + f"--TemplateExporter.exclude_input=True {temp_notebook} --output {htmlreport}"
     )
-    subprocess.call(command)
+    subprocess.call(command, shell=True)
     os.remove(temp_notebook)

cardioception/notebooks/HeartRateDiscrimination.ipynb

@@ -86,18 +86,29 @@
   {
    "cell_type": "code",
    "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# ensure that the paths are pathlib instance in case they are passed through cardioception.reports.report\n",
+    "resultPath = Path(resultPath)\n",
+    "reportPath = Path(reportPath)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
    "metadata": {
     "id": "8cYkrDMvKdaY"
    },
    "outputs": [],
    "source": [
     "# Search files ending with \"final.txt\" - This is the main data frame that is saved at the end of the task\n",
-    "results_df = [file for file in Path(Path.cwd(), \"data\", \"HBC\").glob('*final.txt')]"
+    "results_df = [file for file in Path(resultPath).glob('*final.txt')]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {
     "colab": {
      "base_uri": "https://localhost:8080/",
@@ -205,7 +216,7 @@
        "5       5        23     Count        25           5         2.635"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -218,7 +229,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {
     "id": "xN2uZaX6Kdaa"
    },
@@ -228,7 +239,7 @@
     "ppg = {}\n",
     "for i in range(6):\n",
     "    ppg[str(i)] = np.load(\n",
-    "        [file for file in Path(Path.cwd(), \"data\", \"HBC\").glob(f'*_{i}.npy')][0]\n",
+    "        [file for file in resultPath.glob(f'*_{i}.npy')][0]\n",
     "        )"
    ]
   },
@@ -263,7 +274,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {
     "colab": {
      "base_uri": "https://localhost:8080/",
@@ -508,7 +519,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {
     "id": "uXUtLU1lKdad"
    },
@@ -521,7 +532,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {
     "colab": {
      "base_uri": "https://localhost:8080/",
@@ -651,7 +662,7 @@
        "5  0.916667  "
       ]
      },
-     "execution_count": 9,
+     "execution_count": 10,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -662,7 +673,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {
     "id": "-PuGeDAkKdaf"
    },

cardioception/reports.py

@@ -40,6 +40,6 @@ def get_requirements():
         package_data={
             "cardioception.HBC": ["*.wav", "*.png"],
             "cardioception.HRD": ["*.wav", "*.png"],
-            "cardioception.notebooks": ["*.ipynb", "*.npy", "*.txt"],
+            "cardioception.notebooks": ["*.ipynb"],
         },
     )

docs/source/examples/templates/HeartBeatCounting.ipynb

@@ -5,19 +5,16 @@
 from unittest import TestCase
 import pandas as pd
 from pathlib import Path
-import cardioception
 from cardioception.reports import report, preprocessing
 
 
-class TestHRD(TestCase):
+class TestReports(TestCase):
     def test_preprocessing(self):
         """Test the preprocessing function"""
         # load the main result data frame
-        results = pd.read_csv(Path(
-            Path(cardioception.__file__).parent, "notebooks", "data", "HRD", "HRD_final.txt"
-        )
-        )
-
+        results = pd.read_csv(
+            "https://raw.githubusercontent.com/embodied-computation-group/Cardioception/master/docs/source/examples/templates/data/HRD/HRD_final.txt"
+            )
         preprocessing(results=results)
 
 
@@ -27,30 +24,18 @@ def test_report(self):
         #####
         # HRD
         #####
-        hrd_resultsPath = os.path.join(
-            os.path.dirname(cardioception.__file__), "notebooks", "data", "HRD"
-        )
-
-        hrd_reportPath = os.path.join(
-            os.path.dirname(cardioception.__file__), "notebooks", "data", "HRD"
-        )
-        report(resultPath=hrd_resultsPath, reportPath=hrd_reportPath)
-
-        os.remove(os.path.join(hrd_reportPath, "HRD_report.html"))
+        hrd_results_path = Path(Path.cwd(), "docs", "source", "examples", "templates", "data", "HRD")
+        hrd_report_path = Path.cwd()
+        report(result_path=hrd_results_path, report_path=hrd_report_path)
+        #os.remove(Path(hrd_report_path, "HRD_report.html"))
 
         #####
         # HBC
         #####
-        hbc_resultsPath = os.path.join(
-            os.path.dirname(cardioception.__file__), "notebooks", "data", "HBC"
-        )
-
-        hbc_reportPath = os.path.join(
-            os.path.dirname(cardioception.__file__), "notebooks", "data", "HBC"
-        )
-        report(resultPath=hbc_resultsPath, reportPath=hbc_reportPath, task="HBC")
-
-        os.remove(os.path.join(hbc_reportPath, "HBC_report.html"))
+        hbc_results_path = Path(Path.cwd(), "docs", "source", "examples", "templates", "data", "HBC")
+        hbc_report_path = Path.cwd()
+        report(result_path=hbc_results_path, report_path=hbc_report_path, task="HBC")
+        #os.remove(Path(hbc_report_path, "HBC_report.html"))
 
 
 if __name__ == "__main__":