Deploying to pages from @ 5ad491f 🚀

main/.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 24eb0b1d90f72be96fc1686930059ce7
+tags: 645f666f9bcd5a90fca523b33c5a78b7

v0.0.11/_modules/index.html → main/_modules/index.html

@@ -77,6 +77,10 @@
 <li class="toctree-l2"><a class="reference internal" href="../examples/jump_umap_analysis_with_cosmicqc.html">JUMP UMAP analysis with coSMicQC</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="../presentations.html">Presentations</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../presentations/sbi2-2024.html">SBI2 Annual Confrerence 2024 Poster</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="../python-api.html">Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../contributing.html">Contributing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../code_of_conduct.html">Contributor Covenant Code of Conduct</a></li>
@@ -92,10 +96,11 @@
 
 <h4>Versions</h4>
 <select name="versions" id="versions" onchange="redirectToPage()">
-    <option value="index.html">v0.0.11</option>
+    <option value="../../v0.0.11/index.html">v0.0.11</option>
     <option value="../../v0.1.0/index.html">v0.1.0</option>
     <option value="../../v0.1.1/index.html">v0.1.1</option>
     <option value="../../v0.1.2/index.html">v0.1.2</option>
+    <option value="index.html">main</option>
 </select>
 <script>
 /**
@@ -190,8 +195,8 @@ <h4>Versions</h4>
 
 <p style="background:#E7C3EB;padding:5px 10px;">
 
-You're reading an old version of this documentation.
-If you want up-to-date information, please have a look at <a href="../../v0.1.2/index.html">v0.1.2</a>.
+You're reading the documentation for a development version.
+For the latest released version, please have a look at <a href="../../v0.1.2/index.html">v0.1.2</a>.
 
 </p>
 </span>
@@ -200,8 +205,6 @@ <h4>Versions</h4>
     <h1>All modules for which code is available</h1>
 <ul><li><a href="src/cosmicqc/analyze.html">src.cosmicqc.analyze</a></li>
 <li><a href="src/cosmicqc/cli.html">src.cosmicqc.cli</a></li>
-<li><a href="src/cosmicqc/frame.html">src.cosmicqc.frame</a></li>
-<li><a href="src/cosmicqc/image.html">src.cosmicqc.image</a></li>
 </ul>
 
 </main>

v0.0.11/_modules/src/cosmicqc/cli.html → main/_modules/src/cosmicqc/cli.html

@@ -78,6 +78,10 @@
 <li class="toctree-l2"><a class="reference internal" href="../../../examples/jump_umap_analysis_with_cosmicqc.html">JUMP UMAP analysis with coSMicQC</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="../../../presentations.html">Presentations</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../../presentations/sbi2-2024.html">SBI2 Annual Confrerence 2024 Poster</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="../../../python-api.html">Python API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../contributing.html">Contributing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../code_of_conduct.html">Contributor Covenant Code of Conduct</a></li>
@@ -93,10 +97,11 @@
 
 <h4>Versions</h4>
 <select name="versions" id="versions" onchange="redirectToPage()">
-    <option value="cli.html">v0.0.11</option>
+    <option value="../../../../v0.0.11/index.html">v0.0.11</option>
     <option value="../../../../v0.1.0/index.html">v0.1.0</option>
     <option value="../../../../v0.1.1/index.html">v0.1.1</option>
     <option value="../../../../v0.1.2/index.html">v0.1.2</option>
+    <option value="cli.html">main</option>
 </select>
 <script>
 /**
@@ -192,8 +197,8 @@ <h4>Versions</h4>
 
 <p style="background:#E7C3EB;padding:5px 10px;">
 
-You're reading an old version of this documentation.
-If you want up-to-date information, please have a look at <a href="../../../../v0.1.2/index.html">v0.1.2</a>.
+You're reading the documentation for a development version.
+For the latest released version, please have a look at <a href="../../../../v0.1.2/index.html">v0.1.2</a>.
 
 </p>
 </span>

main/_sources/code_of_conduct.md.txt

@@ -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 open a [new security advisory notice](https://github.com/WayScience/coSMicQC/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.
+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

main/_sources/contributing.md.txt

@@ -0,0 +1,138 @@
+# 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/WayScience/coSMicQC/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 Python [Poetry](https://python-poetry.org/).
+We leverage interactions with the Docker through Python to achieve reproducible results through containers.
+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 Poetry](https://python-poetry.org/docs/#installation)
+1. [Install Poetry Environment](https://python-poetry.org/docs/basic-usage/#installing-dependencies): `poetry install`
+
+### 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 Poetry 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
+% poetry 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/WayScience/coSMicQC/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/WayScience/coSMicQC/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 [`poetry-dynamic-versioning`](https://github.com/mtkennerly/poetry-dynamic-versioning) to help version this software through [`PEP 440`](https://peps.python.org/pep-0440/) 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.
+`poetry-dynamic-versioning` uses `git` tags to help distinguish version data.
+We also use the `__init__.py` file as a place to persist the version data for occaissions where the `git` history is unavailable or unwanted.
+
+The following command is used to add `poetry-dynamic-versioning` to Poetry for use with this project: `poetry self add "poetry-dynamic-versioning[plugin]"`.
+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/wayscience/cosmicqc/releases).
+We publish a related Python package through the [Python Packaging Index (PyPI)](https://pypi.org/) available [here](https://pypi.org/project/cosmicqc/).
+
+#### Release Publishing Process
+
+Several manual and automated steps are involved with publishing coSMicQC 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:
+coSMicQC version specifications are controlled through [`poetry-dynamic-versioning`](https://github.com/mtkennerly/poetry-dynamic-versioning) which leverages [`dunamai`](https://github.com/mtkennerly/dunamai) to create version data based on [git tags](https://git-scm.com/book/en/v2/Git-Basics-Tagging) and commits.
+coSMicQC 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-<semver release type>` to label the pull request for visibility with [`release-drafter`](https://github.com/release-drafter/release-drafter) (for example, see [coSMicQC#24](https://github.com/wayscience/cosmicqc/pull/24) as a reference of a semver patch update).
+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)
+poetry run sphinx-build docs/src docs/build
+
+# build multi-version sphinx documentation
+# (used in production)
+poetry run sphinx-multiversion docs/src docs/build
+```
+
+After the docs build, navigate the `docs/build` folder and open the HTML files with your browser.
+Opening the `index.html` file which may be found in the base of `docs/build` or `docs/build/<version>` will simulate the docsite experience through GitHub Pages.

main/_sources/examples.md.txt

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+# Examples
+
+```{toctree}
+---
+caption: "List of examples"
+maxdepth: 2
+glob:
+---
+examples/*
+```