From 2172952dde91398f24728c60891fed34993e7b75 Mon Sep 17 00:00:00 2001 From: Dave Bunten Date: Tue, 30 Jul 2024 08:45:48 -0600 Subject: [PATCH] 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 | 5 + .pre-commit-config.yaml | 26 ++- CODE_OF_CONDUCT.md | 2 +- README.md | 6 +- logo/source/index.html | 11 -- media/coverage-badge.svg | 1 + {logo => media/logo}/just-icon.png | Bin {logo => media/logo}/just-icon.svg | 0 {logo => media/logo}/source/.gitignore | 0 {logo => media/logo}/source/README.md | 0 {logo => media/logo}/source/package.json | 0 {logo => media/logo}/source/src/Logo.jsx | 0 {logo => media/logo}/source/src/main.jsx | 0 {logo => media/logo}/source/src/styles.css | 0 {logo => media/logo}/source/vite.config.js | 0 .../logo}/with-text-for-dark-bg.png | Bin .../logo}/with-text-for-dark-bg.svg | 0 .../logo}/with-text-for-light-bg.png | Bin .../logo}/with-text-for-light-bg.svg | 0 poetry.lock | 149 +++++++++++++----- pyproject.toml | 1 + src/cosmicqc/frame.py | 2 +- 22 files changed, 146 insertions(+), 57 deletions(-) delete mode 100644 logo/source/index.html create mode 100644 media/coverage-badge.svg rename {logo => media/logo}/just-icon.png (100%) rename {logo => media/logo}/just-icon.svg (100%) rename {logo => media/logo}/source/.gitignore (100%) rename {logo => media/logo}/source/README.md (100%) rename {logo => media/logo}/source/package.json (100%) rename {logo => media/logo}/source/src/Logo.jsx (100%) rename {logo => media/logo}/source/src/main.jsx (100%) rename {logo => media/logo}/source/src/styles.css (100%) rename {logo => media/logo}/source/vite.config.js (100%) rename {logo => media/logo}/with-text-for-dark-bg.png (100%) rename {logo => media/logo}/with-text-for-dark-bg.svg (100%) rename {logo => media/logo}/with-text-for-light-bg.png (100%) rename {logo => media/logo}/with-text-for-light-bg.svg (100%) diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index dbfc25a..927c6f5 100644 --- a/.github/workflows/run-tests.yml +++ b/.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/action@v3.0.1 run_tests: strategy: diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f2b1cb5..72b4c72 100644 --- a/.pre-commit-config.yaml +++ b/.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"] diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 77ea94d..dc9d40a 100644 --- a/CODE_OF_CONDUCT.md +++ b/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. diff --git a/README.md b/README.md index e773fd4..7077d74 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,12 @@ - + # 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) diff --git a/logo/source/index.html b/logo/source/index.html deleted file mode 100644 index 4d7b594..0000000 --- a/logo/source/index.html +++ /dev/null @@ -1,11 +0,0 @@ - - - - - - - -
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