Adding testing coverage

.github/workflows/python-test.yml

@@ -2,9 +2,9 @@ name: Python Lint and Test
 
 on:
   push:
-    branches: [ main ]
+    branches: [ Adding-Testing-Coverage ]
   pull_request:
-    branches: [ main ]
+    branches: [ Adding-Testing-Coverage ]
 
 permissions:
   contents: read
@@ -25,6 +25,7 @@ jobs:
       working-directory: ./apps/backend
       run: |
         python -m pip install --upgrade pip
+        python -m pip install coverage
         pip install pipenv
         pipenv install --dev --system --deploy --ignore-pipfile
     - name: Analyze with pylint
@@ -39,4 +40,7 @@ jobs:
       run: pylint --fail-on=E --fail-under=9.0 --recursive=y app.py ./modules/ ./tests/
     - name: Test with pytest
       working-directory: ./apps/backend
-      run: pytest
+      run: coverage run -m pytest
+    - name: Printing Coverage Report
+      working-directory: ./apps/backend
+      run: coverage report -m

.vscode/extensions.json

@@ -9,6 +9,7 @@
         "wmaurer.change-case",
         "ramyaraoa.show-offset",
         "ms-vscode-remote.vscode-remote-extensionpack",
+        "ryanluker.vscode-coverage-gutters",
 
         // Frontend
         "herrmannplatz.npm-dependency-links",

.vscode/launch.json

@@ -5,7 +5,7 @@
     "version": "0.2.0",
     "configurations": [
         {
-            "name": "Debug Backend",
+            "name": "Debug Backend Locally",
             "type": "python",
             "request": "launch",
             "module": "flask",
@@ -15,10 +15,10 @@
             },
             "args": [
                 "run",
-                "--no-debugger", // I have no idea why VSCode suggested this be here, I assume it turns off flask's own debugger?
+                "--no-debugger", // no idea why VSCode suggested this be here, presumably turns off flask's own debugger?
                 "--host=0.0.0.0",
                 "-p",
-                "5050" // TODO try to read env var for BACKEND_PORT? or up to the dev to manage this?
+                "5050" // not sure how to get this to read env var for BACKEND_PORT
             ],
             "jinja": true,
             "justMyCode": false,
@@ -28,7 +28,7 @@
             },
         },
         {
-            "name": "Debug Frontend",
+            "name": "Debug Frontend Locally",
             "type": "node",
             "request": "launch",
             "runtimeArgs": [
@@ -47,7 +47,7 @@
             },
         },
         {
-            "name": "Python: Current File (in Backend App)",
+            "name": "Python: Debug Current File (in Backend App)",
             "presentation": {
                 "group": "local-debug"
             },

.vscode/tasks.json

@@ -15,19 +15,32 @@
                 "panel": "shared",
                 "showReuseMessage": true,
                 "clear": false
-            }
+            },
+            "group": "none"
         },
         {
             "label": "DEVELOPMENT Docker Compose Up (Attached)",
             "type": "shell",
             "command": "docker compose --file docker-compose.yml --file docker-compose.dev.yml up --build",
-            "problemMatcher": []
+            "problemMatcher": [],
+            "group": {
+                "kind": "build",
+                "isDefault": true
+            }
         },
         {
             "label": "PRODUCTION Docker Compose Up (Attached)",
             "type": "shell",
             "command": "docker compose up --build",
-            "problemMatcher": []
+            "problemMatcher": [],
+            "group": "build"
+        },
+        {
+            "label": "Backend Code Coverage Report",
+            "type": "shell",
+            "command": "cd ./apps/backend; source ./.venv/scripts/activate; bash ./coverage.sh",
+            "problemMatcher": [],
+            "group": "test"
         }
     ]
 }

apps/backend/.gitignore

@@ -8,4 +8,8 @@ logs/
 __pycache__
 .venv
 
+# Code Coverage reports
+.coverage
+coverage.xml
+
 # All below this point is uncategorized (categorize them!)

apps/backend/Pipfile

@@ -16,13 +16,15 @@ python-dotenv = "*"
 matplotlib = "*"
 pymongo = "*"
 pydantic = "*"
+pytest-cov = "*"
 
 [dev-packages]
 # libmagic dlls for windows hosts https://pypi.org/project/python-magic/ (when missing, vague errors and it crashes)
 python-magic-bin = {version = "*", markers = "platform_system == 'Windows'"}
 yapf = "*"
 pylint = "*"
 pytest = "*"
+coverage = "*"
 
 [requires]
 python_version = "3.8"

apps/backend/coverage.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+# Avoid pollution from past runs
+rm -f .coverage
+rm -f coverage.xml
+
+# Can't find docs on how to automatically detect subdirectories?
+# https://pytest-cov.readthedocs.io/en/latest/config.html
+
+pytest --cov-report xml:coverage.xml \
+    --cov-branch \
+    --cov . \
+    --cov modules/ \
+    --cov modules/data/ \
+    --cov modules/db/ \
+    --cov modules/logging/ \
+    --cov modules/output/
+
+# Print information in the console for the user as well
+coverage report -m
+
+echo "Use the VSCode action 'Coverage Gutters: Display Coverage' to see coverage in the editor"

apps/backend/pytest.ini

@@ -1,3 +1,4 @@
+; TODO from old team, axe?
 [pytest]
 markers =
     should_fail: marks a set of test that should throw an error when run

apps/backend/tox.ini

@@ -1,3 +1,4 @@
+; TODO from old team, axe?
 [tox]
 envlist = py{35,36}-pytest{3,4,5,6}
 

apps/frontend/.eslintrc.json

@@ -38,7 +38,7 @@
         ],
         "prefer-template": "error",
         "no-tabs": "off",
-        "space-before-function-paren": "off",
+        "space-before-function-paren": "off", // cspell:disable-line
         "comma-dangle": "warn",
         "object-curly-spacing": [
             "warn",

example_experiments/python/addNums.py

@@ -31,6 +31,7 @@
 y, 1, 1, 10, 1
 """
 
+# pylint: disable=glados-print-used
 
 def main():
     config = configparser.ConfigParser()

example_experiments/python/addNumsFailsOnXis1Yis5.py

@@ -20,6 +20,7 @@
 y, default: 1, min: 1, max: 10, step: 1
 """
 
+# pylint: disable=glados-print-used
 
 def main():
     config = configparser.ConfigParser()

example_experiments/python/addNumsTimeOutOnXis1Yis5.py

@@ -28,6 +28,7 @@
 waitTime = 2
 """
 
+# pylint: disable=glados-print-used
 
 def main():
     config = configparser.ConfigParser()

example_experiments/python/addNumsTimed.py

@@ -29,6 +29,7 @@
 waitTime = 3
 """
 
+# pylint: disable=glados-print-used
 
 def main():
     config = configparser.ConfigParser()

example_experiments/python/addNumsWithConstants.py

@@ -36,6 +36,7 @@
 c = Test String
 """
 
+# pylint: disable=glados-print-used
 
 def shuffle_word(word):
     word = list(word)

example_experiments/python/alwaysFail.py

@@ -19,7 +19,7 @@
 """
 
 # There is intentionally unreachable code in this example
-# pylint: disable=unreachable
+# pylint: disable=unreachable glados-print-used
 
 
 def main():

example_experiments/python/genetic_algorithm.py

@@ -9,7 +9,7 @@
 #sample experiment that runs a truncation generational loop with a genome represented by a list of 0s and 1s. fitness is measured by number of 1s
 #in genome. maximum fitness is measured at the given generation number.
 #number of population, genome length, and mutation rate are given. a number can be given for seed or an r can be given for a random seed
-# pylint: disable = W0612
+
 # pylint: disable-next=pointless-string-statement
 """
 This experiment demonstrates doing things with Post Processing.
@@ -39,13 +39,15 @@
 
 """
 
+# pylint: disable = unused-variable glados-print-used
+# cspell:ignore chrom
 
 class Chromosome:
     genome = []
     fitness = 0
 
     #determine fitness of chromosome
-    def chromFitness(self):
+    def chromosomeFitness(self):
         self.fitness = 0
         for bit in self.genome:
             if bit == 1: