ome-iris 0.0.3__tar.gz

ome_iris-0.0.3/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#   Usually these files are written by a python script from a template
+#   before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+# Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+# uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   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-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__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
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+/site
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+# mypy
+.mypy_cache/
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+dmypy.json
+
+# Pyre type checker
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+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#   JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#   be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#   and can be added to the global gitignore or merged into this file.  For a more nuclear
+#   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/
+# Temporary file for partial code execution
+tempCodeRunnerFile.py
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml
+
+# docs
+pages/
+src/OME_IRIS/_version.py

ome_iris-0.0.3/.pre-commit-config.yaml

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+# 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: "v2.21.2"
+    hooks:
+    -   id: pyproject-fmt
+-   repo: https://github.com/citation-file-format/cffconvert
+    rev: b6045d78aac9e02b039703b030588d54d53262ac
+    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: 1.0.0
+    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: "v0.15.14"
+    hooks:
+    -   id: ruff-format
+    -   id: ruff-check
+-   repo: https://github.com/rhysd/actionlint
+    rev: v1.7.12
+    hooks:
+    -   id: actionlint
+-   repo: https://github.com/jendrikseipp/vulture
+    rev: 'v2.16'
+    hooks:
+    -   id: vulture
+        args: ["src", "tests"]
+-   repo: local
+    hooks:
+    -   id: ty
+        name: ty
+        entry: bash -c "command -v uv >/dev/null 2>&1 && uv run --frozen --with ty ty check || true"
+        language: system
+        files: ^(src|tests)/.*\.py$

ome_iris-0.0.3/.python-version

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+3.11

ome_iris-0.0.3/AGENTS.md

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+# Agent Guide
+
+This repository includes local agent guidance in `.agents/skills/`.
+
+## Where agent guidance lives
+
+- Root guide: `AGENTS.md`
+- Skills directory: `.agents/skills/`
+- Skill directories:
+  - `.agents/skills/test-driven-development/SKILL.md`
+  - `.agents/skills/incremental-implementation/SKILL.md`
+  - `.agents/skills/code-review-and-quality/SKILL.md`
+  - `.agents/skills/ci-cd-and-automation/SKILL.md`
+  - `.agents/skills/debugging-and-error-recovery/SKILL.md`
+  - `.agents/skills/learning-opportunities/SKILL.md`
+
+## How to use these skills
+
+- Load relevant skill(s) before making edits.
+- Prefer small changes with frequent validation.
+- Keep work aligned with this project's `pyproject.toml`, CI workflows, and pre-commit hooks.
+
+## Default execution order
+
+1. Apply `test-driven-development` when behavior changes.
+1. Apply `incremental-implementation` for multi-file or higher-risk changes.
+1. Apply `code-review-and-quality` as the final quality gate before completion.
+1. Apply `ci-cd-and-automation` when changing checks, tasks, or pipelines.
+1. Apply `debugging-and-error-recovery` when tests, CI, or runtime behavior fails unexpectedly.
+1. Optionally apply `learning-opportunities` for 10-15 minute learning exercises after design-heavy work.
+
+## Local commands
+
+- Run tests: `uv run --frozen pytest`
+- Run lint/format hooks: `pre-commit run --all-files`
+- Run type checks via pre-commit hook: `pre-commit run ty --all-files`
+- Run full local pipeline: `uv run --frozen poe pipeline`
+
+## Scope expectations
+
+- These instructions are project-local.
+- If team standards evolve, update these files in-place.

ome_iris-0.0.3/CITATION.cff

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+cff-version: 1.2.0
+title: OME-IRIS
+message: If you use this project, please cite it using the metadata below.
+type: software
+authors:
+  - given-names: Dave
+    family-names: Bunten
+    orcid: "https://orcid.org/0000-0001-6041-3665"
+  - given-names: Gregory
+    family-names: Way
+    orcid: 'https://orcid.org/0000-0002-0503-9348'
+repository-code: https://github.com/d33bs/OME-IRIS
+license: BSD-3-Clause
+date-released: 2026-05-26
+abstract: >-
+  OME-IRIS is a minimal open bioimage dataset catalog for benchmarking image IO,
+  masks, metadata, and image-linked profile workflows.
+keywords:
+  - bioimaging
+  - benchmarking
+  - microscopy
+  - dataset catalog

ome_iris-0.0.3/CODE_OF_CONDUCT.md

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+# 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

ome_iris-0.0.3/CONTRIBUTING.md

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+# Contributing to OME-IRIS
+
+Thanks for contributing to OME-IRIS.
+
+This project is intentionally small: a lightweight bioimage dataset catalog with fetch/verify tooling. Keep changes simple, readable, and easy to validate.
+
+## Development setup
+
+1. Install dependencies:
+
+```bash
+uv sync
+```
+
+2. Run the test suite:
+
+```bash
+uv run --frozen pytest
+```
+
+3. Run pre-commit checks:
+
+```bash
+pre-commit run --all-files
+```
+
+4. (Optional) build docs:
+
+```bash
+uv sync --group docs
+uv run --frozen sphinx-build docs/src docs/build
+```
+
+## Repository orientation
+
+- Keep changes aligned with the project goal: a small, easy-to-use bioimage dataset catalog.
+- Prefer working through the unified CLI and tests rather than relying on fixed internal paths.
+- Treat schema, manifests, and validation tooling as evolving components.
+
+## Common workflows
+
+### Update or add a dataset
+
+1. Add or edit a dataset manifest in the current manifest location.
+1. Update the catalog metadata index used by the project.
+1. Validate locally:
+
+```bash
+uv run ome-iris verify
+uv run --frozen pytest
+```
+
+To generate a starter manifest + CSV row from a source path:
+
+```bash
+uv run ome-iris scaffold --source-path /path/to/dataset
+uv run ome-iris scaffold --source-path /path/to/dataset --append-csv
+uv run ome-iris scaffold --source-path /path/to/dataset --include-directory-entry --directory-path images --archive-format zip
+```
+
+### Use a custom data directory
+
+```bash
+uv run ome-iris fetch --data-dir /tmp/ome-iris-data
+uv run ome-iris verify --data-dir /tmp/ome-iris-data
+```
+
+### Check fetch behavior
+
+```bash
+uv run ome-iris fetch --tier small
+uv run ome-iris fetch --dataset <dataset-id>
+uv run ome-iris export-rocrate --dataset <dataset-id>
+```
+
+If URLs are missing, fetch should report them clearly instead of failing silently.
+Each fetched dataset directory includes `ro-crate-metadata.json` for provenance and relationship metadata.
+
+For mixed-source datasets, add multiple `files` entries with per-file URLs. If a source is provided as an archive, you can use:
+
+- `kind: directory`
+- `archive_format: zip` or `archive_format: tar`
+- required top-level `source_identifier` to define the local dataset root under `data/`
+- `files[].path` relative to `data/<source_identifier>/`
+- directory traversal is supported for GitHub `tree` URLs and local directories
+
+`sha256` is optional, but recommended when URLs are stable.
+
+You can also define top-level `relationships` entries to link components.
+`from` and `to` must reference existing `files[].path` values.
+Prefer standard relationship fields (`via_columns`, `filename_patterns`, `derived_from_columns`) before using `custom_metadata`.
+Set `rocrate_predicate` on every relationship using an explicit absolute JSON-LD predicate URI (required).
+
+## Custom metadata support
+
+Custom metadata is first-class and validated.
+
+- Use `custom_metadata` at manifest, source, or file level.
+- `custom_metadata` must be an object/map.
+- Supported value types: string, number, boolean, null, list, and nested objects.
+
+If `custom_metadata` is not an object or contains unsupported types, `ome-iris verify` reports an error.
+
+## Testing expectations
+
+- Add or update tests for behavior changes.
+- Prefer small, focused tests over broad integration tests.
+- Keep the suite fast.
+
+Recommended test loop:
+
+```bash
+uv run --frozen pytest -k fetch -q
+uv run --frozen pytest -k verify -q
+uv run --frozen pytest
+```
+
+## Pull request guidelines
+
+- Keep PR scope tight and purpose-specific.
+- Include a short summary of what changed and why.
+- Include validation evidence (tests/checks run).
+- Do not commit large data files.
+
+## Style and design principles
+
+- Prefer plain Python and minimal dependencies.
+- Avoid adding workflow orchestration tools (DVC, Snakemake, Nextflow, Docker) for core functionality.
+- Preserve the project goal: "a tiny data catalog with fetch and verify."

ome_iris-0.0.3/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2025, 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:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

ome_iris-0.0.3/MANIFEST.in

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+include LICENSE
+include README.md
+include pyproject.toml
+
+graft src
+
+prune tests
+prune docs
+prune pages
+prune .github
+prune .agents
+
+global-exclude __pycache__ *.py[cod] .DS_Store