bioio-imagexpress 0.2.0__tar.gz

bioio_imagexpress-0.2.0/.cookiecutter.yaml

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+default_context:
+    author_name: "bioio-devs"
+    author_email: "brian.whitney@alleninstitute.org"
+    hosting_github_username_or_org: "bioio-devs"
+    project_name: "bioio-imagexpress"
+    project_slug: "bioio-imagexpress"
+    python_slug: "bioio_imagexpress"
+    project_short_description: "A BioIO reader plugin for reading Molecular Devices ImageXpress (multifile) images."
+    hosting_pypi_username: "bioio-devs"
+    license: "MIT License"

bioio_imagexpress-0.2.0/.editorconfig

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+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.yml]
+indent_size = 2
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

bioio_imagexpress-0.2.0/.gitattributes

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+bioio_imagexpress/tests/resources/** filter=lfs diff=lfs merge=lfs -text

bioio_imagexpress-0.2.0/.github/CODEOWNERS

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+* @bioio-devs/trusted-developers

bioio_imagexpress-0.2.0/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug Report
+about: Create a report to help us improve bioio-imagexpress
+labels: bug
+---
+
+<!--
+  ⚠️⚠️ Please do the following before submitting: ⚠️⚠️
+
+  📖 Please read our Code of Conduct.
+  🔎 Please search existing issues to avoid creating duplicates.
+-->
+
+### Describe the Bug
+
+<!-- A clear and concise description of the bug. -->
+
+### Expected Behavior
+
+<!-- What did you expect to happen instead? -->
+
+### Reproduction
+
+<!-- Steps to reproduce the behavior and/or a minimal example that exhibits the behavior. -->
+
+### Environment
+
+<!-- Any additional information about your environment. -->
+
+-   OS Version: _[e.g. macOS 11.3.1]_
+-   bioio-imagexpress Version: _[e.g. 0.5.0]_

bioio_imagexpress-0.2.0/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature Request
+about: Suggest a feature for bioio-imagexpress
+labels: enhancement
+---
+
+<!--
+  ⚠️⚠️ Please do the following before submitting: ⚠️⚠️
+
+  📖 Please read our Code of Conduct.
+  🔎 Please search existing issues to avoid creating duplicates.
+-->
+
+### Feature Description
+
+<!-- A clear and concise description of the feature you're requesting. -->
+
+### Use Case
+
+<!-- Please provide a use case to help us understand your request in context. -->
+
+### Solution
+
+<!-- Please describe your ideal solution. -->
+
+### Alternatives
+
+<!-- Please describe any alternatives you've considered, even if you've dismissed them. -->

bioio_imagexpress-0.2.0/.github/PULL_REQUEST_TEMPLATE.md

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+<!--
+  Thank you for submitting a pull request!
+
+  ⚠️⚠️ Please do the following before submitting: ⚠️⚠️
+
+  - Read the CONTRIBUTING.md guide and make sure you've followed all the steps given.
+  - Ensure that the code is up-to-date with the `main` branch.
+  - Provide or update documentation for any feature added by your pull request.
+  - Provide relevant tests for your feature or bug fix.
+
+  ❗️ Also: ❗️
+
+  Please name your pull request {development-type}/{short-description}.
+  For example: feature/read-tiff-files
+-->
+
+### Link to Relevant Issue
+
+This pull request resolves #
+
+### Description of Changes
+
+<!-- Include a description of the proposed changes. -->

bioio_imagexpress-0.2.0/.github/dependabot.yml

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+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    commit-message:
+      prefix: "ci(dependabot):"

bioio_imagexpress-0.2.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+    branches:
+      - main
+  schedule:
+    # <minute [0,59]> <hour [0,23]> <day of the month [1,31]>
+    # <month of the year [1,12]> <day of the week [0,6]>
+    # https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07
+    # Run every Monday at 10:24:00 PST
+    # (Since these CRONs are used by a lot of people -
+    # let's be nice to the servers and schedule it _not_ on the hour)
+    - cron: "24 18 * * 1"
+  workflow_dispatch:
+
+jobs:
+  # Check that all files listed in manifest make it into build
+  check-manifest:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - run: pip install check-manifest && check-manifest
+  
+  # Check tests pass on multiple Python and OS combinations
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", 3.11, 3.12, 3.13]
+        os: [ubuntu-latest, macOS-latest, windows-latest]
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        lfs: true
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - uses: extractions/setup-just@v1
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    - name: Install Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[test]
+    - name: Run Tests
+      run: just test
+    - name: Upload Codecov
+      uses: codecov/codecov-action@v3
+
+  # Check linting, formating, types, etc.
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.11"
+    - uses: extractions/setup-just@v1
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    - name: Install Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[lint]
+    - name: Lint
+      run: just lint
+
+  # Publish to PyPI if test, lint, and manifest checks passed
+  publish:
+    if: "success() && startsWith(github.ref, 'refs/tags/')"
+    needs: [check-manifest, test, lint]
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.11"
+    - name: Install Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build wheel
+    - name: Build Package
+      run: |
+        python -m build
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  # GitHub does not provide a "all status checks must pass" option
+  # in branch protection settings. Instead, you have to specify exactly
+  # what status checks want to require to pass before merging. However,
+  # naming each individual check would be effectively impossible.
+  # Therefore, by creating this stage in every repo in the org we can
+  # require "Report Result" to pass before merging and this stage can
+  # represent the result of the other checks where it only passes if
+  # all the other checks pass.
+  results:
+    if: ${{ always() && github.event_name == 'pull_request' }}
+    needs: [check-manifest, test, lint]
+    runs-on: ubuntu-latest
+    name: Report Result
+    steps:
+      - run: exit 1
+        # see https://stackoverflow.com/a/67532120/4907315
+        if: >-
+          ${{
+                contains(needs.*.result, 'failure')
+            || contains(needs.*.result, 'cancelled')
+          }}
+

bioio_imagexpress-0.2.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# OS generated files
+.DS_Store
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# Dask
+dask-worker-space
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# VSCode
+.vscode

bioio_imagexpress-0.2.0/.pre-commit-config.yaml

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+files: bioio_imagexpress
+repos:
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/myint/autoflake
+    rev: v2.2.0
+    hooks:
+      - id: autoflake
+        args: ["--in-place", "--remove-all-unused-imports"]
+
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        additional_dependencies:
+          - flake8-typing-imports>=1.9.0
+          - flake8-pyprojecttoml
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.4.1
+    hooks:
+      - id: mypy

bioio_imagexpress-0.2.0/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+-   Using welcoming and inclusive language
+-   Being respectful of differing viewpoints and experiences
+-   Gracefully accepting constructive criticism
+-   Focusing on what is best for the community
+-   Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+-   The use of sexualized language or imagery and unwelcome sexual attention or
+    advances
+-   Trolling, insulting/derogatory comments, and personal or political attacks
+-   Public or private harassment
+-   Publishing others' private information, such as a physical or electronic
+    address, without explicit permission
+-   Other conduct which could reasonably be considered inappropriate in a
+    professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers 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, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting any of the maintainers of this project and
+we will attempt to resolve the issues with respect and dignity.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

bioio_imagexpress-0.2.0/CONTRIBUTING.md

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+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+## Developer Installation
+
+If something goes wrong at any point during installing the library please see how
+[our CI/CD on GitHub Actions](.github/workflows/build-main.yml) installs and builds the
+project as it will always be the most up-to-date.
+
+## Get Started!
+
+Ready to contribute? Here's how to set up `bioio-imagexpress` for local development.
+
+1. Fork the `bioio-imagexpress` repo on GitHub.
+
+2. Clone your fork locally:
+
+    ```bash
+    git clone git@github.com:{your_name_here}/bioio-imagexpress.git
+    ```
+
+3. Install the project in editable mode. (It is also recommended to work in a virtualenv or anaconda environment):
+
+    ```bash
+    cd bioio-imagexpress/
+    just install
+    ```
+
+4. Create a branch for local development:
+
+    ```bash
+    git checkout -b {your_development_type}/short-description
+    ```
+
+    Ex: feature/read-tiff-files or bugfix/handle-file-not-found<br>
+    Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass linting and
+   tests with [just](https://github.com/casey/just):
+
+    ```bash
+    just build
+    ```
+
+6. Commit your changes and push your branch to GitHub:
+
+    ```bash
+    git add .
+    git commit -m "Your detailed description of your changes."
+    git push origin {your_development_type}/short-description
+    ```
+
+7. Submit a pull request through the GitHub website.
+
+## Just Commands
+
+For development commands we use [just](https://github.com/casey/just).
+
+```bash
+just
+```
+```
+Available recipes:
+    build                    # run lint and then run tests
+    clean                    # clean all build, python, and lint files
+    default                  # list all available commands
+    install                  # install with all deps
+    lint                     # lint, format, and check all files
+    release                  # release a new version
+    tag-for-release version  # tag a new version
+    test                     # run tests
+    update-from-cookiecutter # update this repo using latest cookiecutter-bioio-reader
+```
+
+## Deploying
+
+A reminder for the maintainers on how to deploy.
+Make sure the main branch is checked out and all desired changes
+are merged. Then run:
+
+```bash
+just tag-for-release "vX.Y.Z"
+just release
+```
+
+The presence of a tag starting with "v" will trigger the `publish` step in the
+main github workflow, which will build the package and upload it to PyPI. The
+version will be injected into the package metadata by
+[`setuptools-scm`](https://github.com/pypa/setuptools_scm)

bioio_imagexpress-0.2.0/Justfile

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+# list all available commands
+default:
+  just --list
+
+# clean all build, python, and lint files
+clean:
+	rm -fr build
+	rm -fr dist
+	rm -fr .eggs
+	find . -name '*.egg-info' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -f {} +
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+	rm -fr .coverage
+	rm -fr coverage.xml
+	rm -fr htmlcov
+	rm -fr .pytest_cache
+	rm -fr .mypy_cache
+
+# install with all deps
+install:
+	pip install -e .[lint,test]
+	pre-commit install
+
+# lint, format, and check all files
+lint:
+	pre-commit run --all-files
+
+# run tests
+test:
+	pytest --cov-report xml --cov-report html --cov=bioio_imagexpress bioio_imagexpress/tests
+
+# run lint and then run tests
+build:
+	just lint
+	just test
+
+# tag a new version
+tag-for-release version:
+	git tag -a "{{version}}" -m "{{version}}"
+	echo "Tagged: $(git tag --sort=-version:refname| head -n 1)"
+
+# release a new version
+release:
+	git push --follow-tags
+
+# update this repo using latest cookiecutter-bioio-reader
+update-from-cookiecutter:
+	pip install cookiecutter
+	cookiecutter gh:bioio-devs/cookiecutter-bioio-reader --config-file .cookiecutter.yaml --no-input --overwrite-if-exists --output-dir ..

bioio_imagexpress-0.2.0/LICENSE

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+MIT License
+
+Copyright (c) 2026, bioio-devs
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

bioio_imagexpress-0.2.0/MANIFEST.in

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+exclude bioio_imagexpress/tests/**