Add code coverage badge through coverage.py (#63)

* add code coverage badge thru pre-commit

* update pre-commit config

* linting post pre-commit updates

* add poetry setup for pre-commit runs in ci

.github/workflows/run-tests.yml

@@ -19,6 +19,11 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: "3.11"
+      - name: Setup for poetry
+        run: |
+          python -m pip install poetry
+      - name: Install environment
+        run: poetry install --no-interaction --no-ansi
       - uses: pre-commit/[email protected]
   run_tests:
     strategy:

.pre-commit-config.yaml

@@ -8,15 +8,19 @@ repos:
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
+        exclude: |
+          (?x)^(
+              .*\.svg
+          )$
       - id: check-yaml
       - id: check-added-large-files
       - id: detect-private-key
   - repo: https://github.com/python-poetry/poetry
-    rev: "1.5.1"
+    rev: "1.8.0"
     hooks:
       - id: poetry-check
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         exclude: |
@@ -41,11 +45,25 @@ repos:
     hooks:
       - id: yamllint
   - repo: https://github.com/rhysd/actionlint
-    rev: v1.7.0
+    rev: v1.7.1
     hooks:
       - id: actionlint
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.4.4"
+    rev: "v0.5.5"
     hooks:
       - id: ruff
       - id: ruff-format
+  - repo: local
+    hooks:
+      - id: code-cov-gen
+        name: Generate code coverage
+        language: system
+        entry: poetry run coverage run -m pytest
+        pass_filenames: false
+        always_run: true
+  - repo: https://github.com/Weird-Sheep-Labs/coverage-pre-commit
+    rev: 0.1.1
+    hooks:
+      - id: coverage-xml
+      - id: coverage-badge
+        args: ["-o", "media/coverage-badge.svg"]

CODE_OF_CONDUCT.md

@@ -5,7 +5,7 @@
 We as members, contributors, and leaders pledge to make participation in our
 community a harassment-free experience for everyone, regardless of age, body
 size, visible or invisible disability, ethnicity, sex characteristics, gender
-identity and expression, level of experience, education, socio-economic status,
+identity and expression, level of experience, education, socioeconomic status,
 nationality, personal appearance, race, caste, color, religion, or sexual
 identity and orientation.
 

README.md

@@ -1,11 +1,12 @@
-<img height="200" src="https://raw.githubusercontent.com/WayScience/coSMicQC/main/logo/with-text-for-light-bg.png?raw=true">
+<img height="200" src="https://raw.githubusercontent.com/WayScience/coSMicQC/main/media/logo/with-text-for-light-bg.png?raw=true">
 
 # Single cell Morphology Quality Control
 
+![PyPI - Version](https://img.shields.io/pypi/v/cosmicqc)
 [![Build Status](https://github.com/WayScience/coSMicQC/actions/workflows/run-tests.yml/badge.svg?branch=main)](https://github.com/WayScience/coSMicQC/actions/workflows/run-tests.yml?query=branch%3Amain)
+![Coverage Status](./media/coverage-badge.svg)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![Poetry](https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json)](https://python-poetry.org/)
-![PyPI - Version](https://img.shields.io/pypi/v/cosmicqc)
 
 > :stars: Navigate the cosmos of single-cell morphology with confidence — coSMicQC keeps your data on course!
 
@@ -35,6 +36,7 @@ pip install git+https://github.com/WayScience/coSMicQC.git
 ## Contributing, Development, and Testing
 
 Please see [CONTRIBUTING.md](CONTRIBUTING.md) for more details on contributions, development, and testing.
+
 ## References
 
 - [pycytominer](https://github.com/cytomining/pycytominer)