diff --git a/.github/ISSUE_TEMPLATE/issue.yml b/.github/ISSUE_TEMPLATE/issue.yml new file mode 100644 index 0000000..4e449ed --- /dev/null +++ b/.github/ISSUE_TEMPLATE/issue.yml @@ -0,0 +1,46 @@ +# GitHub Issue template for bug reports +name: Open a GitHub issue +description: > + Please use this form to send along new ideas for content or + changes that might be helpful! + +body: + - type: checkboxes + attributes: + label: Is this a duplicate of an existing idea for this project? + description: > + Please make sure to search the existing issues first + to see whether the same issue was reported already. + If you find an existing issue, please don't hesitate to comment + on it or add a reaction to existing content! + options: + - label: > + I found no existing covering this topic. + required: true + + - type: textarea + id: description + attributes: + label: What is your idea? + description: > + Please provide a specific description of what you'd like to see + including the context and what the result might look like. + placeholder: > + For example: "When x happens I see y. + The following might be a good way to address this ..." + validations: + required: true + + - type: checkboxes + attributes: + label: Would you like to work on a solution for this? + description: > + This is a community-driven project and we + love new contributors (including through opening or adding to issues)! + This is an optional check to help us understand your interest to be + involved (especially if you already have a good understanding + of how to implement it). + We are happy to guide you in the contribution process and please + don't hesitate to reach out for help along the way. + options: + - label: Yes I am willing to submit a PR for this! diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 0000000..66a3c90 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,37 @@ + + +# Description + + + +## What kind of change(s) are included? + +- [ ] Documentation (changes docs or other related content) +- [ ] Bug fix (fixes an issue). +- [ ] Enhancement (adds functionality). +- [ ] Breaking change (these changes would cause existing functionality to not work as expected). + +# Checklist + +Please ensure that all boxes are checked before indicating that this pull request is ready for review. + +- [ ] I have read and followed the [CONTRIBUTING.md](CONTRIBUTING.md) guidelines. +- [ ] I have searched for existing content to ensure this is not a duplicate. +- [ ] I have performed a self-review of these additions (including spelling, grammar, and related). +- [ ] These changes pass all pre-commit checks. +- [ ] I have added comments to my code to help provide understanding +- [ ] I have added a test which covers the code changes found within this PR +- [ ] I have deleted all non-relevant text in this pull request template. diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..fb147fa --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,36 @@ +--- +# GitHub Dependabot configuration +# Note: there is no interaction between this +# configuration and dependabot security updates. +# See here for more information: +# https://docs.github.com/en/code-security/dependabot/dependabot-security-updates/about-dependabot-security-updates#about-dependabot-security-updates + +version: 2 +updates: + # GitHub Actions checks + # See here for more information: + # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuring-dependabot-version-updates + - package-ecosystem: "github-actions" + directory: "/" + schedule: + # Check for updates to GitHub Actions every week + interval: "monthly" + groups: + github-actions: + patterns: + - "*" + + # Perform checks and updates for python uv environment. + # This depends on changes to dependabot via: + # https://github.com/dependabot/dependabot-core/pull/10040 + # See here for more information: + # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file#pip-and-pip-compile + - package-ecosystem: "uv" + directory: "/" + schedule: + # Check for updates to uv environment files every week + interval: "monthly" + groups: + python-packages: + patterns: + - "*" diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml new file mode 100644 index 0000000..3d8f4ed --- /dev/null +++ b/.github/release-drafter.yml @@ -0,0 +1,21 @@ +--- +# template configuration for release-drafter +# see: https://github.com/release-drafter/release-drafter +name-template: 'v$RESOLVED_VERSION' +tag-template: 'v$RESOLVED_VERSION' +version-resolver: + major: + labels: + - 'release-major' + minor: + labels: + - 'release-minor' + patch: + labels: + - 'release-patch' + default: patch +change-template: '- $TITLE (@$AUTHOR via #$NUMBER)' +template: | + ## Changes + + $CHANGES diff --git a/.github/workflows/draft-release.yml b/.github/workflows/draft-release.yml new file mode 100644 index 0000000..4847e3e --- /dev/null +++ b/.github/workflows/draft-release.yml @@ -0,0 +1,23 @@ +--- +# workflow for drafting releases on GitHub +# see: https://github.com/release-drafter/release-drafter +name: release drafter + +on: + push: + branches: + - main + +jobs: + draft_release: + permissions: + # write permission is required to create a github release + contents: write + # write permission is required for autolabeler + # otherwise, read permission is required at least + pull-requests: write + runs-on: ubuntu-latest + steps: + - uses: release-drafter/release-drafter@v6 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/publish-docs.yml b/.github/workflows/publish-docs.yml new file mode 100644 index 0000000..e4c7fdf --- /dev/null +++ b/.github/workflows/publish-docs.yml @@ -0,0 +1,41 @@ +--- +# used for publishing documentation on push to main or published release +name: publish docs + +on: + push: + branches: + - main + release: + types: + - published + +jobs: + build: + # only build and deploy docs if the actor is not dependabot + if: ${{ github.actor != 'dependabot[bot]' }} + runs-on: ubuntu-22.04 + steps: + - name: Checkout + uses: actions/checkout@v4 + with: + fetch-depth: 0 + - uses: actions/setup-python@v5 + with: + python-version: "3.11" + - name: Install the latest version of uv + uses: astral-sh/setup-uv@v6 + - name: Build documentation + run: | + mkdir pages + touch pages/.nojekyll + cd docs + uv run --frozen sphinx-build src build + # remove any doctrees dirs which aren't needed for publishing + find ./build -type d -name '.doctrees' -exec rm -rf {} + + cp -r build/* ../pages/ + - name: Deploy documentation + uses: JamesIves/github-pages-deploy-action@v4 + with: + branch: pages + folder: pages diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml new file mode 100644 index 0000000..71b18e5 --- /dev/null +++ b/.github/workflows/publish-pypi.yml @@ -0,0 +1,33 @@ +--- +# used for publishing packages to pypi on release +name: publish pypi release + +on: + release: + types: + - published + +jobs: + publish_pypi: + runs-on: ubuntu-latest + environment: release + permissions: + # IMPORTANT: this permission is mandatory for trusted publishing + id-token: write + steps: + - name: Checkout + uses: actions/checkout@v4 + with: + fetch-depth: 0 + - name: Fetch tags + run: git fetch --all --tags + - name: Python setup + uses: actions/setup-python@v5 + with: + python-version: "3.11" + - name: Install the latest version of uv + uses: astral-sh/setup-uv@v6 + - name: uv build distribution content + run: uv build + - name: Publish package distributions to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml new file mode 100644 index 0000000..668b9b5 --- /dev/null +++ b/.github/workflows/run-tests.yml @@ -0,0 +1,66 @@ +--- +# used for running tests +name: tests + +"on": + push: + branches: [main] + pull_request: + branches: [main] + +jobs: + pre_commit_checks: + runs-on: ubuntu-24.04 + steps: + # checks out the repo + - uses: actions/checkout@v4 + # run pre-commit + - name: Python setup + uses: actions/setup-python@v5 + with: + python-version: "3.11" + - name: Install the latest version of uv + uses: astral-sh/setup-uv@v6 + - uses: pre-commit/action@v3.0.1 + # run pre-commit ci lite for automated fixes + - uses: pre-commit-ci/lite-action@v1.1.0 + if: ${{ !cancelled() }} + run_tests: + strategy: + matrix: + python_version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"] + os: [ubuntu-24.04, macos-14] + runs-on: ${{ matrix.os }} + env: + OS: ${{ matrix.os }} + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Python setup + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python_version }} + - name: Install the latest version of uv + uses: astral-sh/setup-uv@v6 + - name: Run pytest + run: uv run --frozen pytest + coverage_and_badge: + runs-on: ubuntu-24.04 + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Python setup + uses: actions/setup-python@v5 + with: + python-version: "3.11" + - name: Install the latest version of uv + uses: astral-sh/setup-uv@v6 + - name: Run coverage check and update badge + run: just coverage-check + - name: Verify coverage badge is up to date + run: | + git diff --exit-code README.md || { + echo "README coverage badge is out of date."; + echo "Run 'just coverage-check' and commit changes."; + exit 1; + } diff --git a/.gitignore b/.gitignore index b7faf40..cdf09d1 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,6 @@ # Byte-compiled / optimized / DLL files __pycache__/ -*.py[codz] +*.py[cod] *$py.class # C extensions @@ -46,7 +46,7 @@ htmlcov/ nosetests.xml coverage.xml *.cover -*.py.cover +*.py,cover .hypothesis/ .pytest_cache/ cover/ @@ -106,24 +106,17 @@ ipython_config.py # commonly ignored for libraries. # https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control #poetry.lock -#poetry.toml # pdm # Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. -# pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python. -# https://pdm-project.org/en/latest/usage/project/#working-with-version-control #pdm.lock -#pdm.toml +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/latest/usage/project/#working-with-version-control +.pdm.toml .pdm-python .pdm-build/ -# pixi -# Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control. -#pixi.lock -# Pixi creates a virtual environment in the .pixi directory, just like venv module creates one -# in the .venv directory. It is recommended not to include this directory in version control. -.pixi - # PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm __pypackages__/ @@ -136,7 +129,6 @@ celerybeat.pid # Environments .env -.envrc .venv env/ venv/ @@ -175,33 +167,11 @@ cython_debug/ # option (not recommended) you can uncomment the following to ignore the entire idea folder. #.idea/ -# Abstra -# Abstra is an AI-powered process automation framework. -# Ignore directories containing user credentials, local state, and settings. -# Learn more at https://abstra.io/docs -.abstra/ - -# Visual Studio Code -# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore -# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore -# and can be added to the global gitignore or merged into this file. However, if you prefer, -# you could uncomment the following to ignore the entire vscode folder -# .vscode/ - # Ruff stuff: .ruff_cache/ # PyPI configuration file .pypirc -# Cursor -# Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to -# exclude from AI features like autocomplete and code analysis. Recommended for sensitive data -# refer to https://docs.cursor.com/context/ignore-files -.cursorignore -.cursorindexingignore - -# Marimo -marimo/_static/ -marimo/_lsp/ -__marimo__/ +# project-specific ignores +_version.py diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..fea72da --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,71 @@ +# See https://pre-commit.com for more information +# See https://pre-commit.com/hooks.html for more hooks +repos: +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v6.0.0 + hooks: + - id: trailing-whitespace + - id: end-of-file-fixer + - id: check-yaml + - id: detect-private-key +- repo: https://github.com/tox-dev/pyproject-fmt + rev: "v2.21.1" + hooks: + - id: pyproject-fmt +- repo: https://github.com/citation-file-format/cffconvert + rev: 5295f87c0e261da61a7b919fc754e3a77edd98a7 + hooks: + - id: validate-cff +- repo: https://github.com/codespell-project/codespell + rev: v2.4.2 + hooks: + - id: codespell + exclude: | + (?x)^( + .*\.lock | + .*\.csv | + .*\.cff | + .*\.ipynb + )$ +- repo: https://github.com/executablebooks/mdformat + rev: 0.7.21 + hooks: + - id: mdformat + additional_dependencies: + - mdformat-gfm +- repo: https://github.com/adrienverge/yamllint + rev: v1.38.0 + hooks: + - id: yamllint + exclude: pre-commit-config.yaml +- repo: https://github.com/astral-sh/ruff-pre-commit + rev: "v0.15.10" + hooks: + - id: ruff-format + - id: ruff-check +- repo: https://github.com/rhysd/actionlint + rev: v1.7.12 + hooks: + - id: actionlint +- repo: https://gitlab.com/vojko.pribudic.foss/pre-commit-update + rev: v0.6.0 + hooks: + - id: pre-commit-update + args: ["--keep", "mdformat", "--keep", "pre-commit-update", "--keep", "cffconvert"] +- repo: https://github.com/jendrikseipp/vulture + rev: 'v2.16' + hooks: + - id: vulture +- repo: https://github.com/koalaman/shellcheck-precommit + rev: v0.11.0 + hooks: + - id: shellcheck +# args: ["--severity=warning"] # Optionally only show errors and warnings +- repo: local + hooks: + - id: coverage-check + name: coverage-check-and-badge-update + entry: just coverage-check + language: system + pass_filenames: false + always_run: true diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..2c07333 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.11 diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..b9aaab4 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,45 @@ +# This CITATION.cff file was generated with cffinit. +# Visit https://bit.ly/cffinit to generate yours today! +--- +cff-version: 1.2.0 +title: ZedProfiler +message: >- + If you use this software, please cite it using the + metadata from the CITATION.cff file. +type: software +authors: + - given-names: Michael J. + family-names: Lippincott + orcid: "https://orcid.org/0000-0002-8637-1448" + - given-names: Dave + family-names: Bunten + orcid: "https://orcid.org/0000-0001-6041-3665" + - given-names: Gregory P. + family-names: Way + orcid: "https://orcid.org/0000-0002-0503-9348" + +repository-code: "https://github.com/WayScience/ZedProfiler" +abstract: >- + CPU-first handcrafted 3D featurization toolkit for high-throughput profiling +keywords: + - python + - image-based profiling + - high-content screening + - high-throughput screening + - microscopy + - volumetric image analysis + - image feature extraction + - feature engineering +license: BSD-3-Clause + +references: + - url: "https://github.com/WayScience/ZedProfiler" + type: software-code + title: "ZedProfiler: A CPU-first 3D image feature extraction toolkit for high-content and high-throughput image-based profiling" + authors: + - given-names: Michael J. + family-names: Lippincott + - given-names: Dave + family-names: Bunten + - given-names: Gregory P. + family-names: Way diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..bde3cb7 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,132 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +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, socioeconomic status, +nationality, personal appearance, race, caste, color, religion, or sexual +identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +- Demonstrating empathy and kindness toward other people +- Being respectful of differing opinions, viewpoints, and experiences +- Giving and gracefully accepting constructive feedback +- Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +- Focusing on what is best not just for us as individuals, but for the overall + community + +Examples of unacceptable behavior include: + +- The use of sexualized language or imagery, and sexual attention or advances of + any kind +- Trolling, insulting or derogatory comments, and personal or political attacks +- Public or private harassment +- Publishing others' private information, such as a physical or email address, + without their explicit permission +- Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official email address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to community leaders responsible for enforcement. +Please reach out to the maintainers of this repository by using their GitHub profile email address contact information to privately notify us of any incidents of this nature. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.1, available at +[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1]. + +Community Impact Guidelines were inspired by +[Mozilla's code of conduct enforcement ladder][mozilla coc]. + +For answers to common questions about this code of conduct, see the FAQ at +[https://www.contributor-covenant.org/faq][faq]. Translations are available at +[https://www.contributor-covenant.org/translations][translations]. + +[faq]: https://www.contributor-covenant.org/faq +[homepage]: https://www.contributor-covenant.org +[mozilla coc]: https://github.com/mozilla/diversity +[translations]: https://www.contributor-covenant.org/translations +[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..4ef5b53 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,129 @@ +# Contributing + +First of all, thank you so much for contributing! 🎉 💯 + +This document contains guidelines on how to most effectively contribute within this repository. + +If you are stuck, please feel free to ask any questions or ask for help. + +## Code of conduct + +This project is governed by our [code of conduct](code_of_conduct.md). By participating, you are expected to uphold this code. +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to community leaders responsible for enforcement. +Please open a [new security advisory notice](https://github.com/org/repohttps://github.com/WayScience/ZedProfiler/security/advisories/new) (using defaults or "n/a" where unable to fill in the form) to privately notify us of any incidents of this nature. + +## Development + +This project leverages development environments managed by [uv](https://docs.astral.sh/uv/). +We use [pytest](https://docs.pytest.org/) for testing and [GitHub actions](https://docs.github.com/en/actions) for automated tests. + +### Development setup + +Perform the following steps to setup a Python development environment. + +1. [Install Python](https://www.python.org/downloads/) (we recommend using [`pyenv`](https://github.com/pyenv/pyenv) or similar) +1. [Install uv](https://docs.astral.sh/uv/getting-started/installation/) + +### Linting + +Work added to this project is automatically checked using [pre-commit](https://pre-commit.com/) via [GitHub Actions](https://docs.github.com/en/actions). +Pre-commit can work alongside your local [git with git-hooks](https://pre-commit.com/index.html#3-install-the-git-hook-scripts) + +After [installing pre-commit](https://pre-commit.com/#installation) within your development environment, the following command also can perform the same checks within your local development environment: + +```sh +% pre-commit run --all-files +``` + +We use these same checks within our automated tests which are managed by [GitHub Actions workflows](https://docs.github.com/en/actions/using-workflows). +These automated tests generally must pass in order to merge work into this repository. + +### Testing + +Work added to this project is automatically tested using [pytest](https://docs.pytest.org/) via [GitHub Actions](https://docs.github.com/en/actions). +Pytest is installed through the uv environment for this project. +We recommend testing your work before opening pull requests with proposed changes. + +You can run pytest on your work using the following example: + +```sh +% uv run pytest +``` + +## Making changes to this repository + +We welcome anyone to use [GitHub issues](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues) (requires a GitHub login) or create [pull requests](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests) (to directly make changes within this repository) to modify content found within this repository. + +Specifically, there are several ways to suggest or make changes to this repository: + +1. Open a GitHub issue: https://github.com/org/repohttps://github.com/WayScience/ZedProfiler/issues +1. Create a pull request from a forked branch of the repository + +### Creating a pull request + +### Pull requests + +After you’ve decided to contribute code and have written it up, please file a pull request. +We specifically follow a [forked pull request model](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request-from-a-fork). +Please create a fork of this repository, clone the fork, and then create a new, feature-specific branch. +Once you make the necessary changes on this branch, you should file a pull request to incorporate your changes into this (fork upstream) repository. + +The content and description of your pull request are directly related to the speed at which we are able to review, approve, and merge your contribution. +To ensure an efficient review process please perform the following steps: + +1. Follow all instructions in the [pull request template](https://github.com/org/repohttps://github.com/WayScience/ZedProfiler/blob/main/.github/PULL_REQUEST_TEMPLATE.md) +1. Triple check that your pull request is adding _one_ specific feature or additional group of content. + Small, bite-sized pull requests move so much faster than large pull requests. +1. After submitting your pull request, ensure that your contribution passes all status checks (e.g. passes all tests) + +Pull request review and approval is required by at least one project maintainer to merge. +We will do our best to review the code addition in a timely fashion. +Ensuring that you follow all steps above will increase our speed and ability to review. +We will check for accuracy, style, code coverage, and scope. + +## Versioning + +We use [`setuptools-scm`](https://github.com/pypa/setuptools-scm) to help version this software through [`PEP 440`](https://peps.python.org/pep-0440/) standards and [semver.org](https://semver.org/) standards. +Configuration for versioning is found within the `pyproject.toml` file. +All builds for packages include dynamic version data to help label distinct versions of the software. +`setuptools-scm` uses `git` tags to help distinguish version data. +We also use the `_version.py` file as a place to persist the version data for occaissions where the `git` history is unavailable or unwanted (this file is only present in package builds). +Versioning for the project is intended to align with GitHub Releases which provide `git` tag capabilities. + +### Releases + +We publish source code by using [GitHub Releases](https://docs.github.com/en/repositories/releasing-projects-on-github/about-releases) available [here](https://github.com/org/repohttps://github.com/WayScience/ZedProfiler/releases). + +#### Release Publishing Process + +Several manual and automated steps are involved with publishing releases. +See below for an overview of how this works. + +Notes about [semantic version](https://en.wikipedia.org/wiki/Software_versioning#Semantic_versioning) (semver) specifications: version specifications are controlled through [`setuptools-scm`](https://github.com/pypa/setuptools-scm) to create version data based on [git tags](https://git-scm.com/book/en/v2/Git-Basics-Tagging) and commits. +Release git tags are automatically applied through [GitHub Releases](https://docs.github.com/en/repositories/releasing-projects-on-github/about-releases) and related inferred changes from [`release-drafter`](https://github.com/release-drafter/release-drafter). + +1. Open a pull request and use a repository label for `release-` to label the pull request for visibility with [`release-drafter`](https://github.com/release-drafter/release-drafter). +1. On merging the pull request for the release, a [GitHub Actions workflow](https://docs.github.com/en/actions/using-workflows) defined in `draft-release.yml` leveraging [`release-drafter`](https://github.com/release-drafter/release-drafter) will draft a release for maintainers. +1. The draft GitHub release will include a version tag based on the GitHub PR label applied and `release-drafter`. +1. Make modifications as necessary to the draft GitHub release, then publish the release (the draft release does not normally need additional modifications). +1. On publishing the release, another GitHub Actions workflow defined in `publish-pypi.yml` will run to build and deploy the Python package to PyPI (utilizing the earlier modified `pyproject.toml` semantic version reference for labeling the release). + +## Documentation + +Documentation for this project is published using [Sphinx](https://www.sphinx-doc.org) with markdown and Jupyter notebook file compatibility provided by [myst-parser](https://myst-parser.readthedocs.io/en/latest/) and [myst-nb](https://myst-nb.readthedocs.io/en/latest/) to create a "documentation website" (also known as "docsite"). +The docsite is hosted through [GitHub Pages](https://pages.github.com/) and deployed through automated [GitHub Actions](https://docs.github.com/en/actions) jobs which trigger on pushes to the main branch or the publishing of a new release on GitHub. +Documentation is versioned as outlined earlier sections covering versioning details to help ensure users are able to understand each release independently of one another. + +It can sometimes be useful to test documentation builds locally before proposing changes within a pull request. +See below for some examples of how to build documentation locally. + +```shell +# build single-version sphinx documentation +# (useful for troubleshooting potential issues) +uv run sphinx-build docs/src docs/build + +# build multi-version sphinx documentation +# (used in production) +uv run sphinx-multiversion docs/src docs/build +``` diff --git a/LICENSE b/LICENSE index a66a34f..5087a77 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ BSD 3-Clause License -Copyright (c) 2026, The Way Lab +Copyright (c) 2026, the Regents of the University of Colorado Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: diff --git a/README.md b/README.md index 08b3e64..5240a92 100644 --- a/README.md +++ b/README.md @@ -1 +1,54 @@ -# ZedProfiler \ No newline at end of file +# ZedProfiler + +[![Coverage](https://img.shields.io/badge/coverage-88%25-green)](#quality-gates) + +CPU-first 3D image feature extraction toolkit for high-content and high-throughput image-based profiling. + +This repository is used for image-based feature extraction of objects in 3D microscopy images. +In this use case we extract freatures from single cells in 3D volumetric microscopy images. +We developmed ZedProfiler to be used on high-content and high-throughput microscopy images, which are often large in size and require efficient processing. +ZedProfiler is extensible to any fluorescence microscopy image modality, and is designed to be modular. + +## Install environment (development) + +```bash +just env +``` + +## Quick usage (API shape) + +```python +from zedprofiler import colocalization # promoted convenience import +from zedprofiler.featurization import texture # stays in feature namespace + +# Implementation is scaffolded in PR 1 and will be completed in module PRs. +result = colocalization.compute() +texture_result = texture.compute() +``` + +## Data Contract + +Where: + +- `x` is the width of the image in pixels +- `y` is the height of the image in pixels +- `z` is the depth of the image in pixels +- `c` is the number of channels + +Though I have reservations about width, height, and depth being used to describe the dimensions of an image. +Different fields use different dimensions for different meanings. +We use `x` and `y` to refer to the same dimensions captured in a 2D image, and `z` to refer to the "depth" dimension in a 3D image if looking down into the image stack. +The `x`, `y`, and `z` dimensions are less description and more absolute while `depth` is relative to angle of observation. + +Accepted image formats (order matters): + +- Single channel: `(z, y, x)` +- Multi channel: `(c, z, y, x)` + +## Quality Gates + +We lint and format code with our pre-commit configuration. + +## Roadmap + +The roadmap is maintained in `ROADMAP.md`. diff --git a/ROADMAP.md b/ROADMAP.md new file mode 100644 index 0000000..322b3a2 --- /dev/null +++ b/ROADMAP.md @@ -0,0 +1,113 @@ +# ZedProfiler Roadmap + +This file is for planning of new modules, features, and PRs that are needed the release(s) of ZedProfiler. +The roadmap is organized into phases, with each phase containing a set of PRs that build upon each other. +The roadmap is intended to be a living document and may be updated as needed. + +## Scope for current release + +### In scope + +- [ ] Handcrafted featurization modules: + - [ ] AreaSizeShape + - [ ] Colocalization + - [ ] Intensity + - [ ] Granularity + - [ ] Neighbors + - [ ] Texture +- [ ] Featurization helper utilities needed by the modules +- [ ] Full test suite with coverage gate (>=85%) +- [ ] Sphinx documentation +- [ ] Example notebooks for module usage +- [ ] Our [RFC2119-specification](./docs/src/RFC-2119-Feature-Naming-Convention.md) driven feature naming policy + +## Architecture and Product Decisions + +- [ ] Linux-first, CPU-only, low RAM usage for the current release. +- [ ] File-format agnostic APIs operating on NumPy arrays. +- [ ] Input contracts: + - [ ] Single-channel arrays: (z, y, x) + - [ ] Multi-channel arrays: (c, z, y, x) +- [ ] Modules are intentionally small and composable for external parallel orchestration. + +## PR Plan + +### Phase 1: Foundation (PR 1-3) + +1. PR 1: Packaging and environment baseline + +- [ ] Python package scaffold, uv dependency management, version metadata 0.0.1, lint/test tooling, CI skeleton. +- [ ] Linux support and CPU-only scope statements in metadata and docs. + +2. PR 2: Core data model and API contracts + +- [ ] Canonical input contracts, loader interfaces, common error types. +- [ ] Return schema contract (required keys, types, deterministic ordering). + +3. PR 3: RFC2119 naming specification and validators + +- [ ] Port and adapt naming conventions into this repository. +- [ ] Add runtime and CI naming validation helpers and conformance tests. + +### Phase 2: Feature modules and tests (PR 4-9) + +4. PR 4: AreaSizeShape module and tests + +- [ ] CPU implementation, anisotropy handling, edge cases. + +5. PR 5: Colocalization module and tests + +- [ ] Metrics API, threshold options, schema and naming compliance. + +6. PR 6: Intensity module and tests + +- [ ] Object-level intensity features and required helpers. + +7. PR 7: Granularity module and tests + +- [ ] CPU granularity spectrum, subsampling behavior, parameter validation. + +8. PR 8: Neighbors module and tests + +- [ ] Neighbor counting APIs, distance threshold and anisotropy handling. + +9. PR 9: Texture module and tests + +- [ ] Haralick-style texture API, scaling helper, deterministic output ordering. + +### Phase 3: Integration, docs, release (PR 10-13) + +10. PR 10: Integration matrix and parallelization guidance + +- [ ] Cross-module integration tests and explicit non-goal docs for internal parallelization. + +11. PR 11: Example notebooks and public dataset references + +- [ ] One notebook per module plus one end-to-end chaining notebook. + +12. PR 12: Sphinx docs, logo, API docs + +- [ ] API pages, architecture and scope pages, docs build checks in CI. + +13. PR 13: Release v0.0.1 and publish workflow + +- [ ] Changelog, semantic tag, PyPI publish automation, README install updates. + +## Verification Gates + +- [ ] Run full unit and integration tests on Linux with coverage >=85%. +- [ ] Run naming validation tests for all emitted feature names. +- [ ] Build Sphinx docs in CI with warnings treated as errors. +- [ ] Execute example notebooks in a clean environment. +- [ ] Validate install/import from both wheel and sdist. +- [ ] Perform release dry-run before publishing. + +## v0.0.2 Backlog (Planned) + +- [ ] Nucleocentric featurization. +- [ ] Optional mask output mode. +- [ ] Expanded benchmark strategy. + +## v0.0.3 Backlog (Planned) + +- [ ] Potential Arrow Flight handoff experiments. diff --git a/docs/src/RFC-2119-Feature-Naming-Convention.md b/docs/src/RFC-2119-Feature-Naming-Convention.md new file mode 100644 index 0000000..935b0f0 --- /dev/null +++ b/docs/src/RFC-2119-Feature-Naming-Convention.md @@ -0,0 +1,223 @@ +# Feature naming convention and schema specification + +**Status:** experimental +**Version:** 0.0.1 +**Date:** April 9th, 2026 +**Authors:** ZedProfiler development team +**Keywords:** feature naming, schema, morphology, 3D image analysis, standardization, interoperability, RFC 2119 + +______________________________________________________________________ + +## Abstract + +This document specifies the naming convention and schema for morphological features extracted using ZedProfiler. The specification defines requirements for feature identifiers, data structures, and formatting rules to ensure consistency, interoperability, and maintainability across pipelines. + +______________________________________________________________________ + +## 1. Introduction + +### 1.1 Purpose + +This specification establishes a standardized feature naming convention and data schema. Standardization enables: + +- Consistent feature identification across analysis stages +- Automated feature parsing and metadata extraction +- Integration with downstream analysis tools +- Reproducible research outputs + +### 1.2 Scope + +This specification applies to all feature extraction modules within the pipeline, including but not limited to: + +- Area, size, and shape measurements +- Colocalization analysis +- Granularity features +- Intensity measurements +- Neighbor relationships +- Deep learning features (sammed3d) +- Texture features + +### 1.3 Key words + +The key words "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT", "SHOULD", "SHOULD NOT", "RECOMMENDED", "MAY", and "OPTIONAL" in this document are to be interpreted as described in [RFC 2119](https://www.ietf.org/rfc/rfc2119.txt). + +______________________________________________________________________ + +## 2A. feature name format specification + +### 2.1 General structure + +Feature names MUST conform to the following structure: + +``` +___ +``` + +Where each component is separated by a single underscore character (`_`). + +### 2.2 Component definitions + +#### 2.2.1 Compartment component + +The `` component: + +- MUST identify the cellular or spatial compartment from which the feature is extracted +- MUST be one of the following enumerated values: + - `Nuclei` - nuclear compartment + - `Cell` - whole cell compartment + - `Cytoplasm` - cytoplasmic compartment (cell excluding nucleus) + - `Organoid` - organoid-level compartment +- MUST NOT contain whitespace or special characters +- MUST use pascalcase capitalization + +**Example:** `Nuclei`, `Cytoplasm`, `Organoid` + +#### 2.2.2 Channel component + +The `` component: + +- MUST identify the imaging channel or fluorophore used for the measurement +- MUST be one of the following values: + - `DNA` - DAPI/hoechst nuclear stain (405nm excitation) + - `AGP` - AGP marker (488nm excitation) + - `ER` - endoplasmic reticulum marker (555nm excitation) + - `Mito` - mitochondrial marker (640nm excitation) + - `BF` - brightfield/transmitted light +- MUST NOT contain whitespace +- MAY use pascalcase capitalization +- MAY use hyphen-separated channel combinations for colocalization features (e.g., `DNA-mito`) +- MUST list channels in alphabetical order when combined (e.g., `DNA-mito` not `mito-DNA`) +- MUST be set to `NoChannel` for channel-independent features (e.g., areasizeshape) + +**Example:** `DNA`, `Mito`, `DNA-Mito` + +#### 2.2.3 Featuretype component + +The `` component: + +- MUST identify the category or method of feature extraction +- MUST be one of the following enumerated values: + - `Areasizeshape` - morphological measurements (area, volume, shape descriptors) + - `Colocalization` - channel colocalization metrics + - `Granularity` - granular spectrum and texture-at-scale features + - `Intensity` - pixel intensity statistics + - `Neighbors` - spatial relationship and neighbor counting + - `SAMMed3D` - deep learning features from SAM-med3d model + - `Texture` - haralick texture features +- MUST NOT contain whitespace +- MUST use pascalcase capitalization +- MUST NOT include version numbers or implementation details + +**Example:** `Intensity`, `Texture`, `Colocalization` + +#### 2.2.4 Measurement component + +The `` component: + +- MUST identify the specific measurement or metric +- MUST NOT contain underscores, periods, spaces, or forward slashes +- MUST replace prohibited characters with hyphens (`-`) +- SHOULD use pascalcase for measurement names to maintain consistency +- MAY include parameter values appended with hyphens (e.g., `entropy-256-3`) +- MUST be descriptive and unambiguous + +**Character replacement rules:** + +- Underscore (`_`) → hyphen (`-`) +- Period (`.`) → hyphen (`-`) +- Space (` `) → hyphen (`-`) +- Forward slash (`/`) → hyphen (`-`) + +**Example:** `meanintensity`, `entropy-256-3`, `angularsecondmoment` + +### 2.3 Complete feature name examples + +Valid feature names conforming to this specification: + +``` +Nuclei_DNA_Intensity_MeanIntensity +Cytoplasm_Mito_Texture_Entropy-256-3 +Cell_DNA-Mito_Colocalization_Correlation +Organoid_NoChannel_AreaSizeShape_Volume +Nuclei_NoChannel_Neighbors_AdjacentCount +Cell_Mito_Granularity_Spectrum-10 +Nuclei_DNA_SAMMed3D_CLSFeature-512 +``` + +______________________________________________________________________ + +## 2B. metadata naming convention + +### 2.1 General structure + +Metadata are non morphology feature values that provide contextual information about the sample, experiment, or imaging conditions, or objects in the dataset. +Metadata are used to capture information that may be relevant for analysis, interpretation, or downstream processing but do not represent morphological measurements of the objects themselves. + +Metadata names MUST conform to the following structure: + +``` +Metadata__ +``` + +Where each component is separated by a single underscore character (`_`). +The `Metadata_` prefix is used to clearly distinguish metadata features from morphological features in the dataset. +Each category metadata name MUST be in pascalcase and MUST NOT contain whitespace or special characters. the `` component MUST be descriptive and unambiguous, following the same character restrictions as morphological feature names. + +### 2.2 Metadata category definitions + +The `` component MUST identify the type (category) of metadata and MUST be one of the following enumerated values: + +- `Storage` - metadata related to data storage and file management. +- `Biology` - metadata related to biological characteristics of the sample. +- `Experiment` - metadata related to experimental conditions and treatments. +- `Imaging` - metadata related to imaging parameters and conditions. +- `Microscopy` - metadata related to microscopy settings and configurations. +- `Object` - metadata related to specific objects (e.g., nuclei) or regions of interest in the dataset. +- `Neighbors` - metadata related to spatial relationships and neighbor counts of objects in the dataset. +- `Location` - metadata related to spatial information and coordinates. +- `Other` - this is a place holder for any metadata that might be used in the future that does not fit into the above categories. new categories can be added as needed, but the `other` category provides a catch-all for any metadata that does not fit into the predefined categories. + +### 2.3 Complete metadata name examples + +Valid metadata names conforming to this specification: + +``` +Metadata_Storage_FilePath +Metadata_Biology_PatientID +Metadata_Experiment_Treatment +Metadata_Imaging_ExposureTime +Metadata_Microscopy_Magnification +Metadata_Object_ObjectID +Metadata_Neighbors_AdjacentCount +Metadata_Location_Cell_CentroidX +``` + +## 3. References + +### 3.1 Normative references + +- **RFC 2119**: key words for use in rfcs to indicate requirement levels + Https://www.ietf.org/rfc/rfc2119.txt + +- **Apache parquet format specification** + Https://parquet.apache.org/docs/file-format/ + +### 3.2 Informative references + +- **Cellprofiler feature naming convention** + Influenced naming structure for biological image analysis + +- **OME data model** + Open microscopy environment standards for microscopy data + +______________________________________________________________________ + +## Copyright notice + +Copyright (c) 2026 way science lab. all rights reserved. + +This document may be freely distributed and used for implementation purposes within the NF1 3D organoid profiling pipeline project and related research activities. the license for this document is the covered under the license of ZedProfiler, which is available at [LICENSE](../LICENSE). + +______________________________________________________________________ + +**END OF SPECIFICATION** diff --git a/docs/src/conf.py b/docs/src/conf.py new file mode 100644 index 0000000..ae9fc89 --- /dev/null +++ b/docs/src/conf.py @@ -0,0 +1,85 @@ +# Configuration file for the Sphinx documentation builder. +# +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Path setup -------------------------------------------------------------- + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +# +import pathlib +import sys + +basedir = str(pathlib.Path(__file__).parent.parent.parent.resolve()) + +sys.path.insert(0, basedir) + +# -- Project information ----------------------------------------------------- + +project = "ZedProfiler" +# is used here due to sphinx decision-making: https://github.com/sphinx-doc/sphinx/issues/8132 +copyright = "2024, DBMI Community" # noqa: A001 +author = "DBMI Community" + +# -- General configuration --------------------------------------------------- + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + "myst_nb", + "sphinx.ext.autodoc", + "sphinx.ext.napoleon", + "sphinx.ext.viewcode", + "pydata_sphinx_theme", +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns = [] # type: ignore + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = "pydata_sphinx_theme" + +html_theme_options = { + "header_links_before_dropdown": 5, + "icon_links": [ + { + "name": "GitHub", + "url": "https://github.com/WayScience/ZedProfiler", + "icon": "fa-brands fa-github", + }, + ], + "logo": {"text": "ZedProfiler"}, + "use_edit_page_button": False, + "show_toc_level": 1, + "navbar_align": "left", + "navbar_center": ["navbar-nav"], + "footer_start": ["copyright"], + "footer_center": ["sphinx-version"], + "secondary_sidebar_items": { + "**/*": ["page-toc", "edit-this-page", "sourcelink"], + }, +} + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ["_static"] +html_css_files = ["custom.css"] + +# set option to avoid rendering default variables +autodoc_preserve_defaults = True + +# enable anchor creation +myst_heading_anchors = 3 diff --git a/docs/src/index.md b/docs/src/index.md new file mode 100644 index 0000000..e811a07 --- /dev/null +++ b/docs/src/index.md @@ -0,0 +1,16 @@ + + +```{include} ../../README.md +--- +relative-docs: docs/src/ +relative-images: +--- +``` + +```{toctree} +--- +caption: 'Contents:' +maxdepth: 3 +--- +python-api +``` diff --git a/docs/src/python-api.md b/docs/src/python-api.md new file mode 100644 index 0000000..c995fcb --- /dev/null +++ b/docs/src/python-api.md @@ -0,0 +1,11 @@ +# Python API + +```{eval-rst} +ZedProfiler.main +------------------- +.. automodule:: src.ZedProfiler.main + :members: + :private-members: + :undoc-members: + :show-inheritance: +``` diff --git a/justfile b/justfile new file mode 100644 index 0000000..fc6f117 --- /dev/null +++ b/justfile @@ -0,0 +1,32 @@ +set shell := ["bash", "-cu"] + +# Create and sync the local uv environment with all project extras. +env: + uv sync --extra dev --extra docs --extra featurization + +# Re-sync environment after dependency changes. +sync: + uv sync --extra dev --extra docs --extra featurization + +# Run tests with coverage gate from pyproject settings. +test: + uv run python -m pytest + +# Generate coverage reports (terminal, XML, and HTML). +coverage: + uv run python -m pytest --cov=zedprofiler --cov-report=term-missing --cov-report=xml --cov-report=html --cov-fail-under=85 + +# Update README coverage badge from the generated coverage.xml report. +coverage-badge: + uv run python scripts/update_coverage_badge.py --coverage-file coverage.xml --readme README.md + +# Run coverage check and refresh coverage badge in one command. +coverage-check: coverage + just coverage-badge + +# Run lint checks. +lint: + uv run ruff check . + +# Run the full project workflow (env sync, lint, tests, and coverage). +all: sync lint test coverage-check diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..bcccdcd --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,100 @@ +[build-system] +build-backend = "setuptools.build_meta" +requires = [ "setuptools>=64", "setuptools-scm>=8" ] + +[project] +name = "zedprofiler" +version = "0.0.1" +description = "CPU-first handcrafted 3D featurization toolkit for high-throughput profiling" +readme = "README.md" +authors = [ + { name = "Your NameWay Lab" }, +] +requires-python = ">=3.11" +classifiers = [ + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", +] +dependencies = [ + "fire>=0.7", + "jinja2>=3.1.6", + "pandas>=2.2.3", +] +scripts.ZedProfiler = "ZedProfiler.cli:trigger" + +[dependency-groups] +dev = [ + "poethepoet>=0.34", + "pytest>=8.3.5", + "pytest-cov>=5", +] +docs = [ + "myst-nb>=1.2", + "pydata-sphinx-theme>=0.16.1", + "sphinx>=8.2.3", +] +notebooks = [ + "black>=25.1", + "isort>=6.0.1", + "jupyterlab>=4.4.2", + "jupyterlab-code-formatter>=3.0.2", + "jupytext>=1.17.1", +] + +[tool.setuptools_scm] +root = "." +version_scheme = "no-guess-dev" +local_scheme = "no-local-version" +version_file = "src/ZedProfiler/_version.py" + +[tool.ruff] +target-version = "py311" +line-length = 88 +fix = true +lint.select = [ + # flake8-builtins + "A", + # flake8-annotations + "ANN", + # flake8-comprehensions + "C4", + # mccabe + "C90", + # pycodestyle + "E", + # pyflakes + "F", + # isort + "I", + # pylint + "PL", + # ruff + "RUF", + # flake8-simplify + "SIM", + "W", +] +# Ignore `F401` (unused imports) for `__init__.py` file +lint.per-file-ignores."__init__.py" = [ "F401" ] + +[tool.pytest] +ini_options.pythonpath = [ "." ] + +[tool.jupytext] +formats = "ipynb,py:light" + +[tool.vulture] +min_confidence = 90 +paths = [ "src/zedprofiler", "tests" ] + +[tool.poe] +# tasks for development environments +tasks.test.shell = """ +pytest +""" +tasks.jupyter.shell = """ +jupyter lab +""" diff --git a/scripts/update_coverage_badge.py b/scripts/update_coverage_badge.py new file mode 100644 index 0000000..4057310 --- /dev/null +++ b/scripts/update_coverage_badge.py @@ -0,0 +1,109 @@ +"""Update the README coverage badge from a coverage.py XML report.""" + +from __future__ import annotations + +import argparse +import re +import xml.etree.ElementTree as ET +from pathlib import Path + +BADGE_PATTERN = re.compile( + r"\[!\[Coverage\]\(https://img\.shields\.io/badge/coverage-[^)]+\)\]\(#quality-gates\)" +) +BRIGHTGREEN_THRESHOLD = 90 +GREEN_THRESHOLD = 80 +YELLOWGREEN_THRESHOLD = 70 +YELLOW_THRESHOLD = 60 +ORANGE_THRESHOLD = 50 + + +def choose_color(percent: int) -> str: + """Pick a simple badge color based on rounded percentage coverage.""" + if percent >= BRIGHTGREEN_THRESHOLD: + return "brightgreen" + if percent >= GREEN_THRESHOLD: + return "green" + if percent >= YELLOWGREEN_THRESHOLD: + return "yellowgreen" + if percent >= YELLOW_THRESHOLD: + return "yellow" + if percent >= ORANGE_THRESHOLD: + return "orange" + return "red" + + +def read_percent_from_coverage_xml(coverage_file: Path) -> int: + """Parse overall line-rate from coverage XML and return rounded percent.""" + root = ET.parse(coverage_file).getroot() + line_rate = root.attrib.get("line-rate") + if line_rate is None: + msg = f"Missing 'line-rate' attribute in {coverage_file}" + raise ValueError(msg) + + return round(float(line_rate) * 100) + + +def update_readme_badge(readme_file: Path, percent: int) -> bool: + """Update badge in README and return True when file content changed.""" + color = choose_color(percent) + badge = ( + f"[![Coverage](https://img.shields.io/badge/coverage-{percent}%25-{color})]" + "(#quality-gates)" + ) + + original = readme_file.read_text(encoding="utf-8") + + if BADGE_PATTERN.search(original): + updated = BADGE_PATTERN.sub(badge, original, count=1) + else: + lines = original.splitlines() + if not lines: + msg = f"README file is empty: {readme_file}" + raise ValueError(msg) + lines.insert(1, "") + lines.insert(2, badge) + updated = "\n".join(lines) + if original.endswith("\n"): + updated += "\n" + + if updated == original: + return False + + readme_file.write_text(updated, encoding="utf-8") + return True + + +def parse_args() -> argparse.Namespace: + """Parse command line arguments.""" + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument( + "--coverage-file", + default="coverage.xml", + type=Path, + help="Path to coverage.py XML report (default: coverage.xml)", + ) + parser.add_argument( + "--readme", + default="README.md", + type=Path, + help="Path to README file (default: README.md)", + ) + return parser.parse_args() + + +def main() -> int: + """Update README badge and print a small status message.""" + args = parse_args() + percent = read_percent_from_coverage_xml(args.coverage_file) + changed = update_readme_badge(args.readme, percent) + + if changed: + print(f"Updated coverage badge to {percent}% in {args.readme}") + else: + print(f"Coverage badge already up to date at {percent}%") + + return 0 + + +if __name__ == "__main__": + raise SystemExit(main()) diff --git a/src/zedprofiler/__init__.py b/src/zedprofiler/__init__.py new file mode 100644 index 0000000..914fce3 --- /dev/null +++ b/src/zedprofiler/__init__.py @@ -0,0 +1,37 @@ +"""Top-level package for ZedProfiler. + +Selected featurizers are promoted for convenient imports, while the full +module tree remains available under ``zedprofiler.featurization``. +""" + +from __future__ import annotations + +from importlib import import_module +from types import ModuleType +from typing import TYPE_CHECKING + +from zedprofiler._version import __version__ + +if TYPE_CHECKING: + from zedprofiler.featurization import colocalization, intensity + +_PROMOTED_MODULES = { + "colocalization": "zedprofiler.featurization.colocalization", + "intensity": "zedprofiler.featurization.intensity", +} + +__all__ = ["__version__", "colocalization", "intensity"] + + +def __getattr__(name: str) -> ModuleType: + """Lazily load promoted modules on first access.""" + if name in _PROMOTED_MODULES: + module = import_module(_PROMOTED_MODULES[name]) + globals()[name] = module + return module + raise AttributeError(f"module 'zedprofiler' has no attribute '{name}'") + + +def __dir__() -> list[str]: + """Include lazy exports in interactive completion.""" + return sorted(set(globals()) | set(__all__)) diff --git a/src/zedprofiler/contracts.py b/src/zedprofiler/contracts.py new file mode 100644 index 0000000..ea4a654 --- /dev/null +++ b/src/zedprofiler/contracts.py @@ -0,0 +1,31 @@ +"""Core data contracts shared across featurizers. + +The package accepts either: +- Single-channel 3D arrays shaped (z, y, x) +- Multi-channel 4D arrays shaped (c, z, y, x) +""" + +from __future__ import annotations + +from dataclasses import dataclass +from typing import Literal + +import numpy as np +import numpy.typing as npt + +DimensionOrder = Literal["zyx", "czyx"] + + +@dataclass(frozen=True) +class ImageArrayContract: + """Document expected dimensionality and ordering for input arrays.""" + + dimensions: int + order: DimensionOrder + + +FloatArray = npt.NDArray[np.floating] +IntArray = npt.NDArray[np.integer] + +SINGLE_CHANNEL_CONTRACT = ImageArrayContract(dimensions=3, order="zyx") +MULTI_CHANNEL_CONTRACT = ImageArrayContract(dimensions=4, order="czyx") diff --git a/src/zedprofiler/exceptions.py b/src/zedprofiler/exceptions.py new file mode 100644 index 0000000..d1fc6b9 --- /dev/null +++ b/src/zedprofiler/exceptions.py @@ -0,0 +1,9 @@ +"""Custom exception types for ZedProfiler.""" + + +class ZedProfilerError(Exception): + """Base exception for package-level failures.""" + + +class ContractError(ZedProfilerError): + """Raised when an input violates a documented data contract.""" diff --git a/src/zedprofiler/featurization/__init__.py b/src/zedprofiler/featurization/__init__.py new file mode 100644 index 0000000..df017b7 --- /dev/null +++ b/src/zedprofiler/featurization/__init__.py @@ -0,0 +1,16 @@ +"""Featurization modules. + +Keep feature families grouped under this namespace while allowing select +modules to be promoted at the package top-level. +""" + +from . import areasizeshape, colocalization, granularity, intensity, neighbors, texture + +__all__ = [ + "areasizeshape", + "colocalization", + "granularity", + "intensity", + "neighbors", + "texture", +] diff --git a/src/zedprofiler/featurization/areasizeshape.py b/src/zedprofiler/featurization/areasizeshape.py new file mode 100644 index 0000000..f482c3a --- /dev/null +++ b/src/zedprofiler/featurization/areasizeshape.py @@ -0,0 +1,10 @@ +"""Area/size/shape featurization module scaffold.""" + +from __future__ import annotations + +from zedprofiler.exceptions import ZedProfilerError + + +def compute() -> dict[str, list[float]]: + """Placeholder for area/size/shape computation implementation.""" + raise ZedProfilerError("areasizeshape.compute is not implemented yet") diff --git a/src/zedprofiler/featurization/colocalization.py b/src/zedprofiler/featurization/colocalization.py new file mode 100644 index 0000000..3f798c8 --- /dev/null +++ b/src/zedprofiler/featurization/colocalization.py @@ -0,0 +1,10 @@ +"""Colocalization featurization module scaffold.""" + +from __future__ import annotations + +from zedprofiler.exceptions import ZedProfilerError + + +def compute() -> dict[str, list[float]]: + """Placeholder for colocalization computation implementation.""" + raise ZedProfilerError("colocalization.compute is not implemented yet") diff --git a/src/zedprofiler/featurization/granularity.py b/src/zedprofiler/featurization/granularity.py new file mode 100644 index 0000000..958ff14 --- /dev/null +++ b/src/zedprofiler/featurization/granularity.py @@ -0,0 +1,10 @@ +"""Granularity featurization module scaffold.""" + +from __future__ import annotations + +from zedprofiler.exceptions import ZedProfilerError + + +def compute() -> dict[str, list[float]]: + """Placeholder for granularity computation implementation.""" + raise ZedProfilerError("granularity.compute is not implemented yet") diff --git a/src/zedprofiler/featurization/intensity.py b/src/zedprofiler/featurization/intensity.py new file mode 100644 index 0000000..dd65a0e --- /dev/null +++ b/src/zedprofiler/featurization/intensity.py @@ -0,0 +1,10 @@ +"""Intensity featurization module scaffold.""" + +from __future__ import annotations + +from zedprofiler.exceptions import ZedProfilerError + + +def compute() -> dict[str, list[float]]: + """Placeholder for intensity computation implementation.""" + raise ZedProfilerError("intensity.compute is not implemented yet") diff --git a/src/zedprofiler/featurization/neighbors.py b/src/zedprofiler/featurization/neighbors.py new file mode 100644 index 0000000..44dac09 --- /dev/null +++ b/src/zedprofiler/featurization/neighbors.py @@ -0,0 +1,10 @@ +"""Neighbors featurization module scaffold.""" + +from __future__ import annotations + +from zedprofiler.exceptions import ZedProfilerError + + +def compute() -> dict[str, list[float]]: + """Placeholder for neighbors computation implementation.""" + raise ZedProfilerError("neighbors.compute is not implemented yet") diff --git a/src/zedprofiler/featurization/texture.py b/src/zedprofiler/featurization/texture.py new file mode 100644 index 0000000..a6df7e3 --- /dev/null +++ b/src/zedprofiler/featurization/texture.py @@ -0,0 +1,10 @@ +"""Texture featurization module scaffold.""" + +from __future__ import annotations + +from zedprofiler.exceptions import ZedProfilerError + + +def compute() -> dict[str, list[float]]: + """Placeholder for texture computation implementation.""" + raise ZedProfilerError("texture.compute is not implemented yet") diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..72658c5 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,10 @@ +""" +conftest.py for pytest configuration. +""" + +import pytest + + +@pytest.fixture +def my_data() -> str: + return "Hello, differently!" diff --git a/tests/test_cli.py b/tests/test_cli.py new file mode 100644 index 0000000..4f9aeed --- /dev/null +++ b/tests/test_cli.py @@ -0,0 +1,8 @@ +"""Package namespace tests replacing obsolete template CLI checks.""" + +from zedprofiler.featurization import texture + + +def test_feature_namespace_import() -> None: + """Lower-level feature namespace remains importable.""" + assert texture.__name__ == "zedprofiler.featurization.texture" diff --git a/tests/test_contracts.py b/tests/test_contracts.py new file mode 100644 index 0000000..b454645 --- /dev/null +++ b/tests/test_contracts.py @@ -0,0 +1,39 @@ +"""Tests for core data contracts.""" + +from __future__ import annotations + +from dataclasses import FrozenInstanceError + +import numpy as np +import pytest + +from zedprofiler.contracts import ( + MULTI_CHANNEL_CONTRACT, + SINGLE_CHANNEL_CONTRACT, + FloatArray, + ImageArrayContract, + IntArray, +) + + +def test_contract_constants_have_expected_values() -> None: + """Single- and multi-channel constants should match documented shapes.""" + assert ImageArrayContract(dimensions=3, order="zyx") == SINGLE_CHANNEL_CONTRACT + assert ImageArrayContract(dimensions=4, order="czyx") == MULTI_CHANNEL_CONTRACT + + +def test_image_array_contract_is_frozen() -> None: + """Contracts are immutable to prevent accidental mutation in pipelines.""" + contract = ImageArrayContract(dimensions=3, order="zyx") + + with pytest.raises(FrozenInstanceError): + contract.dimensions = 4 # type: ignore[misc] + + +def test_array_type_aliases_accept_numpy_ndarray_runtime_values() -> None: + """Type aliases should correspond to ndarray values at runtime.""" + float_values: FloatArray = np.array([1.0, 2.0, 3.0], dtype=float) + int_values: IntArray = np.array([1, 2, 3], dtype=int) + + assert isinstance(float_values, np.ndarray) + assert isinstance(int_values, np.ndarray) diff --git a/tests/test_main.py b/tests/test_main.py new file mode 100644 index 0000000..0a4d27e --- /dev/null +++ b/tests/test_main.py @@ -0,0 +1,15 @@ +"""Smoke tests for top-level package access.""" + +import zedprofiler +from zedprofiler import colocalization + + +def test_package_version_is_exposed() -> None: + """The package should expose a string version.""" + assert isinstance(zedprofiler.__version__, str) + assert zedprofiler.__version__ + + +def test_promoted_feature_module_is_accessible() -> None: + """Promoted feature modules should be importable from top-level.""" + assert colocalization.__name__ == "zedprofiler.featurization.colocalization" diff --git a/tests/test_package_exports.py b/tests/test_package_exports.py new file mode 100644 index 0000000..27c1f46 --- /dev/null +++ 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