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160 changes: 158 additions & 2 deletions bioimageio_collection_backoffice.html
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<input type="search" placeholder="Search..." role="searchbox" aria-label="search"
pattern=".+" required>

<h2>Contents</h2>
<ul>
<li><a href="#collection">collection</a>
<ul>
<li><a href="#maintaining-the-bioimageio-collection">Maintaining the bioimage.io Collection</a></li>
</ul></li>
<li><a href="#add-community-partner">Add community partner</a>
<ul>
<li><a href="#add-community-partner-compatibility-checks">Add community partner compatibility checks</a></li>
</ul></li>
</ul>


<h2>Submodules</h2>
<ul>
Expand Down Expand Up @@ -75,15 +87,159 @@ <h2>Submodules</h2>
<h1 class="modulename">
bioimageio_collection_backoffice </h1>

<div class="docstring"><p></p>
<div class="docstring"><p><a href="https://github.com/bioimage-io/collection/actions/workflows/build.yaml"><img src="https://github.com/bioimage-io/collection/actions/workflows/build.yaml/badge.svg" alt="internal tests &amp; docs" /></a>
<a href="https://github.com/bioimage-io/collection/actions/workflows/generate_collection_json.yaml"><img src="https://github.com/bioimage-io/collection/actions/workflows/generate_collection_json.yaml/badge.svg" alt="collection overview" /></a>
<a href="https://github.com/bioimage-io/collection/actions/workflows/backup.yaml"><img src="https://github.com/bioimage-io/collection/actions/workflows/backup.yaml/badge.svg" alt="backup status" /></a></p>

<p><a href="https://github.com/bioimage-io/collection/actions/workflows/stage.yaml"><img src="https://github.com/bioimage-io/collection/actions/workflows/stage.yaml/badge.svg" alt="last resource staging" /></a>
<a href="https://github.com/bioimage-io/collection/actions/workflows/test.yaml"><img src="https://github.com/bioimage-io/collection/actions/workflows/test.yaml/badge.svg" alt="last resource testing" /></a>
<a href="https://github.com/bioimage-io/collection/actions/workflows/publish.yaml"><img src="https://github.com/bioimage-io/collection/actions/workflows/publish.yaml/badge.svg" alt="last resource publishing" /></a></p>

<p><a href="https://github.com/bioimage-io/collection/actions/workflows/check_compatibility_ilastik.yaml"><img src="https://github.com/bioimage-io/collection/actions/workflows/check_compatibility_ilastik.yaml/badge.svg" alt="ilastik compatibility" /></a></p>

<p><img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="code style" /></p>

<h1 id="collection">collection</h1>

<p>This repository is used to manage the resources displayed on <a href="https://bioimage.io">bioimage.io</a>.</p>

<p>Most users will not directly dispatch the workflows defined in this reporitory, but should instead login on <a href="https://bioimage.io">bioimage.io</a> and use the front-end to interact with the bioimage.io collection.</p>

<p>We currently do not have a workflow for direct upload, but publicly available resource packages may be staged with a stage workflow dispatch.</p>

<h2 id="maintaining-the-bioimageio-collection">Maintaining the bioimage.io Collection</h2>

<p>In order to update or add new resources to the <a href="https://bioimage.io">bioimage.io</a> collection, they have to undergo review.
Current reviewers are listed in <a href="https://github.com/bioimage-io/collection/blob/main/bioimageio_collection_config.json"><code>bioimageio_collection_config.json</code></a>, under section <code>reviewers</code>.</p>

<h3 id="reviewer-onboarding">Reviewer Onboarding</h3>

<ol>
<li>Open a pull request, adding a person to the <a href="https://github.com/bioimage-io/collection/blob/main/bioimageio_collection_config.json">list of reviewers</a>, see <a href="https://github.com/bioimage-io/collection/pull/75">https://github.com/bioimage-io/collection/pull/75</a> for an example.
<ul>
<li>one public email address is required</li>
<li>github id can be found using <code>https://api.github.com/users/&lt;github_username&gt;</code></li>
</ul></li>
<li>So the changes can be applied, the service needs to be restored manually. Reach out to the team or leave an issue.</li>
<li>Once the pull request has been merged, the new reviewer can
<ul>
<li>accept resource drafts</li>
<li>request changes on resource drafts</li>
<li>upload a new version for any resource</li>
</ul></li>
</ol>

<h3 id="adding-a-bioimageio-resource">Adding a bioimage.io resource</h3>

<p>A bioimage.io resource is created by a user uploading a _resource package_.
Such a _resource package_ could e.g. be a newly uploaded _model package_, or _notebook package_.
Typically, uploaders would go via <a href="https://bioimage.io/#/upload">bioimage.io/upload</a>.
Alternatively, any direct link to a downloadable resource package (<code>.zip</code>-file) would work.
The latter option is reserved for members of this repository (or the bioimageio org).
Once available online the _resource package_ is staged (see <a href="#staging">Staging section</a>), tested (see <a href="#testing">Testing section</a>), and reviewed (see <a href="#review">Review section</a>).</p>

<pre class="mermaid-pre"><div class="mermaid">graph TD;
stage[stage]
test[test]
cr[request changes]
publish[accept/publish]
backup[backup to Zenodo]

stage--&gt;test
test--&gt;cr
cr--&gt;stage
test--&gt;publish
publish--&gt;backup
</div></pre>

<h4 id="staging">Staging</h4>

<p>If the _resource package_ was uploaded via the bioimage.io website, the staging of the new resource draft is initiated automatically by the uploader service.
Otherwise, given a download URL to a _resource package_, the <code>stage</code> workflow needs to be <a href="https://github.com/bioimage-io/collection/actions/workflows/stage.yaml">dispatched manually, or via github api</a> ("run workflow")<sup class="footnote-ref" id="fnref-1"><a href="#fn-1">1</a></sup>.</p>

<p>Staging unpacks the files from the zipped resource package to our public S3.
Once unpacked, the staged _resource draft_ is automatically tested (the <a href="https://github.com/bioimage-io/collection/actions/workflows/test.yaml">test workflow</a> is dispatched automatically at the end of the stage workflow).</p>

<h4 id="testing">Testing</h4>

<p>Staged resource drafts are automatically tested:</p>

<ul>
<li>Is their metadata valid?</li>
<li>Can test outputs be reproduced from test inputs?</li>
<li>Are linked URLs available?</li>
<li>...</li>
</ul>

<p>Tests can also be triggered (via github api or manually) by dispatching the <a href="https://github.com/bioimage-io/collection/actions/workflows/test.yaml">test workflow</a><sup class="footnote-ref" id="fnref-2"><a href="#fn-2">2</a></sup>.</p>

<p>Once the tests are completed, the uploader gets a notification via email that their draft is awaiting review; now a reviewer needs to take a look.</p>

<p>An overview of all pending _resource drafts_ can be found at <a href="https://bioimageio-uploader.netlify.app/#/status">https://bioimageio-uploader.netlify.app/#/status</a>.
A _draft_ is identified by its concept id (<code>id</code> from the <code>rdf.yaml</code>).</p>

<h4 id="review">Review</h4>

<p>Reviewers should check the models for technical correctness (aided by CI, see <a href="#testing">Testing section</a>) and contents/metadata of the resource.</p>

<p>To this end it can be helpful to check the logs displayed at <code>https://bioimageio-uploader.netlify.app/#/status/&lt;concept_id&gt;</code>.
There information about automated workflow steps and validation outcome is logged.
Additionally an 'error' status may be shown if an exception occured in the GitHub workflow run producing the log.
To be able to see all the packaged models along with the 'rdf.yaml' as well as covers and other documentation, go to the <a href="https://bioimage.io/#/?repo=https%3A%2F%2Fuk1s3.embassy.ebi.ac.uk%2Fpublic-datasets%2Fbioimage.io%2Fcollection_draft.json">draft collection</a> and download the model from there.</p>

<p>For models, reviewers can use <a href="https://bioimage.io/docs/#/guides/developers-guide?id=model-documentation">the model documentation</a> as a guide.</p>

<p>Reviewers can:</p>

<ul>
<li>_request changes_:
A contributor is expected to upload an updated (fixed) draft (which overwrites the current draft).
This can be done either by the website, or the stage workflow.
Important is to keep the <code>id</code> the same.</li>
<li>_apply minor changes_:
For minor changes it is often not necessary to involve the contributor directly.
Such changes could be e.g. obvious typos in some of the fields.
Reviewers can apply changes locally to the _resource package_ and re-upload (using the same <code>id</code>), or, given S3 credentials, files could also be changed in place.
Latter way of changing requires manually triggering the tests (see <a href="#testing">Testing section</a>).</li>
<li>_accept_:
Accepting the _resource draft_ via the web interface triggers the <a href="https://github.com/bioimage-io/collection/actions/workflows/publish.yaml">publish workflow</a>, which creates a new unique _resource version_.
As a result, the resource is published, the draft deleted and, thus, the _resource_ is available via the <a href="https://bioimage.io">bioimage.io</a> website.
The <a href="https://github.com/bioimage-io/collection/actions/workflows/backup.yaml">backup workflow</a> will upload/publish the _resource version_ to zenodo using the bioimage.io bot account (tagged with <a href="https://zenodo.org/search?q=metadata.subjects.subject%3A%22backup.bioimage.io%22&amp;l=list&amp;p=1&amp;s=10&amp;sort=bestmatch"><code>backup.bioimage.io</code></a>).</li>
</ul>

<h1 id="add-community-partner">Add community partner</h1>

<p>To link yourself as a community partner, please create a PR to insert relevant metadata into <a href="https://github.com/bioimage-io/collection/blob/4087336ad00bff0198f5de83c94aa13be357840d/bioimageio_collection_config.json">bioimageio_collection_config.json</a> under <code>"partners"</code>.
Checkout <a href="https://github.com/bioimage-io/collection/blob/4087336ad00bff0198f5de83c94aa13be357840d/bioimageio_collection_config.json#L283-L301">ilastik partner entry</a> for an example.</p>

<h2 id="add-community-partner-compatibility-checks">Add community partner compatibility checks</h2>

<p>Any community partner is invited to add a GitHub Actions workflow in this repo (please make a PR) that generates reports on its software compatibility with new and updated resources in the bioimage.io collection.
See <a href="https://github.com/bioimage-io/collection/blob/main/.github/workflows/check_compatibility_ilastik.yaml">ilastik compatibility checks workflow</a> for an example.</p>

<p>If you are not familiar with GitHub Actions workflows, we can help you to set this up analog to our existing community partner compatibility checks.
Ideally you can provide a script to create a compatibility report (a relativley simple json file) for a given resource description. see <a href="https://github.com/bioimage-io/collection/blob/main/scripts/check_compatibility_ilastik.py">this Python script as an example</a>.</p>

<div class="footnotes">
<hr />
<ol>
<li id="fn-1">
<p>Parameters to this workflow are <code>bioimage.io resource concept ID</code> (<code>id</code> from the <code>rdf.yaml</code>), and <code>Download URL of the resource package zip-file</code>, which should contain a publicly reachable URL to a _resource package_ <code>.zip</code>-file.&#160;<a href="#fnref-1" class="footnoteBackLink" title="Jump back to footnote 1 in the text.">&#8617;</a></p>
</li>

<li id="fn-2">
<p>Parameters to this workflow are <code>Bioimage.io resource concept ID</code> (<code>id</code> from the <code>rdf.yaml</code>), and <code>Published version or 'draft'</code> (optional, usually <code>draft</code>).&#160;<a href="#fnref-2" class="footnoteBackLink" title="Jump back to footnote 2 in the text.">&#8617;</a></p>
</li>
</ol>
</div>
</div>

<input id="mod-bioimageio_collection_backoffice-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">

<label class="view-source-button" for="mod-bioimageio_collection_backoffice-view-source"><span>View Source</span></label>

<div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos">1</span></a><span class="sd">&quot;&quot;&quot;</span>
</span><span id="L-2"><a href="#L-2"><span class="linenos">2</span></a><span class="sd">.. include:: ./README.md</span>
</span><span id="L-2"><a href="#L-2"><span class="linenos">2</span></a><span class="sd">.. include:: ../README.md</span>
</span><span id="L-3"><a href="#L-3"><span class="linenos">3</span></a><span class="sd">&quot;&quot;&quot;</span>
</span><span id="L-4"><a href="#L-4"><span class="linenos">4</span></a>
</span><span id="L-5"><a href="#L-5"><span class="linenos">5</span></a><span class="kn">from</span> <span class="nn">._backoffice</span> <span class="kn">import</span> <span class="n">BackOffice</span> <span class="k">as</span> <span class="n">BackOffice</span>
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2 changes: 1 addition & 1 deletion bioimageio_collection_backoffice/_settings.html
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<div class="attr variable">
<span class="name">settings</span> =
<input id="settings-view-value" class="view-value-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<label class="view-value-button pdoc-button" for="settings-view-value"></label><span class="default_value">Settings(github_output=&#39;/home/runner/work/_temp/_runner_file_commands/set_output_47653a43-679f-41ff-8ecf-3dbfd4d0ae9c&#39;, collection_config=&#39;https://raw.githubusercontent.com/bioimage-io/collection/main/bioimageio_collection_config.json&#39;, run_url=None, s3_host=&#39;uk1s3.embassy.ebi.ac.uk&#39;, s3_bucket=&#39;public-datasets&#39;, s3_folder=&#39;testing.bioimage.io/runner/instance&#39;, s3_pytest_folder=&#39;testing.bioimage.io/runner/pytest&#39;, s3_sandbox_folder=&#39;sandbox.bioimage.io&#39;, s3_test_folder=&#39;testing.bioimage.io/runner/sandbox&#39;, test_package_id=&#39;frank-water-buffalo&#39;, test_package_url=&#39;https://uk1s3.embassy.ebi.ac.uk/public-datasets/examples.bioimage.io/frank-water-buffalo_v1.zip&#39;, zenodo_test_url=&#39;https://sandbox.zenodo.org&#39;, zenodo_url=&#39;https://sandbox.zenodo.org&#39;, bioimageio_user_id=None, mail_password=SecretStr(&#39;&#39;), s3_access_key_id=SecretStr(&#39;&#39;), s3_secret_access_key=SecretStr(&#39;&#39;), zenodo_api_access_token=SecretStr(&#39;&#39;), zenodo_test_api_access_token=SecretStr(&#39;&#39;), github_pat=SecretStr(&#39;&#39;))</span>
<label class="view-value-button pdoc-button" for="settings-view-value"></label><span class="default_value">Settings(github_output=&#39;/home/runner/work/_temp/_runner_file_commands/set_output_7e5b8508-8489-44dc-a986-812d3b24967e&#39;, collection_config=&#39;https://raw.githubusercontent.com/bioimage-io/collection/main/bioimageio_collection_config.json&#39;, run_url=None, s3_host=&#39;uk1s3.embassy.ebi.ac.uk&#39;, s3_bucket=&#39;public-datasets&#39;, s3_folder=&#39;testing.bioimage.io/runner/instance&#39;, s3_pytest_folder=&#39;testing.bioimage.io/runner/pytest&#39;, s3_sandbox_folder=&#39;sandbox.bioimage.io&#39;, s3_test_folder=&#39;testing.bioimage.io/runner/sandbox&#39;, test_package_id=&#39;frank-water-buffalo&#39;, test_package_url=&#39;https://uk1s3.embassy.ebi.ac.uk/public-datasets/examples.bioimage.io/frank-water-buffalo_v1.zip&#39;, zenodo_test_url=&#39;https://sandbox.zenodo.org&#39;, zenodo_url=&#39;https://sandbox.zenodo.org&#39;, bioimageio_user_id=None, mail_password=SecretStr(&#39;&#39;), s3_access_key_id=SecretStr(&#39;&#39;), s3_secret_access_key=SecretStr(&#39;&#39;), zenodo_api_access_token=SecretStr(&#39;&#39;), zenodo_test_api_access_token=SecretStr(&#39;&#39;), github_pat=SecretStr(&#39;&#39;))</span>


</div>
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46 changes: 23 additions & 23 deletions bioimageio_collection_backoffice/collection_config.html
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<p>A base class for creating Pydantic models.</p>

<p>Attributes:
__class_vars__: The names of the class variables defined on the model.
__private_attributes__: Metadata about the private attributes of the model.
__signature__: The synthesized <code><a href="#CollectionConfig.__init__">__init__</a></code> [<code>Signature</code>][inspect.Signature] of the model.</p>

<pre><code>__pydantic_complete__: Whether model building is completed, or if there are still undefined fields.
__pydantic_core_schema__: The core schema of the model.
__pydantic_custom_init__: Whether the model has a custom `__init__` function.
__pydantic_decorators__: Metadata containing the decorators defined on the model.
This replaces `Model.__validators__` and `Model.__root_validators__` from Pydantic V1.
__pydantic_generic_metadata__: Metadata for generic models; contains data used for a similar purpose to
__args__, __origin__, __parameters__ in typing-module generics. May eventually be replaced by these.
__pydantic_parent_namespace__: Parent namespace of the model, used for automatic rebuilding of models.
__pydantic_post_init__: The name of the post-init method for the model, if defined.
__pydantic_root_model__: Whether the model is a [`RootModel`][pydantic.root_model.RootModel].
__pydantic_serializer__: The `pydantic-core` `SchemaSerializer` used to dump instances of the model.
__pydantic_validator__: The `pydantic-core` `SchemaValidator` used to validate instances of the model.

__pydantic_extra__: A dictionary containing extra values, if [`extra`][pydantic.config.ConfigDict.extra]
is set to `'allow'`.
__pydantic_fields_set__: The names of fields explicitly set during instantiation.
__pydantic_private__: Values of private attributes set on the model instance.
</code></pre>
<h6 id="attributes">Attributes:</h6>

<ul>
<li><strong>__class_vars__:</strong> The names of the class variables defined on the model.</li>
<li><strong>__private_attributes__:</strong> Metadata about the private attributes of the model.</li>
<li><strong>__signature__:</strong> The synthesized <code><a href="#CollectionConfig.__init__">__init__</a></code> [<code>Signature</code>][inspect.Signature] of the model.</li>
<li><strong>__pydantic_complete__:</strong> Whether model building is completed, or if there are still undefined fields.</li>
<li><strong>__pydantic_core_schema__:</strong> The core schema of the model.</li>
<li><strong>__pydantic_custom_init__:</strong> Whether the model has a custom <code><a href="#CollectionConfig.__init__">__init__</a></code> function.</li>
<li><strong>__pydantic_decorators__:</strong> Metadata containing the decorators defined on the model.
This replaces <code>Model.__validators__</code> and <code>Model.__root_validators__</code> from Pydantic V1.</li>
<li><strong>__pydantic_generic_metadata__:</strong> Metadata for generic models; contains data used for a similar purpose to
__args__, __origin__, __parameters__ in typing-module generics. May eventually be replaced by these.</li>
<li><strong>__pydantic_parent_namespace__:</strong> Parent namespace of the model, used for automatic rebuilding of models.</li>
<li><strong>__pydantic_post_init__:</strong> The name of the post-init method for the model, if defined.</li>
<li><strong>__pydantic_root_model__:</strong> Whether the model is a [<code>RootModel</code>][pydantic.root_model.RootModel].</li>
<li><strong>__pydantic_serializer__:</strong> The <code>pydantic-core</code> <code>SchemaSerializer</code> used to dump instances of the model.</li>
<li><strong>__pydantic_validator__:</strong> The <code>pydantic-core</code> <code>SchemaValidator</code> used to validate instances of the model.</li>
<li><strong>__pydantic_extra__:</strong> A dictionary containing extra values, if [<code>extra</code>][pydantic.config.ConfigDict.extra]
is set to <code>'allow'</code>.</li>
<li><strong>__pydantic_fields_set__:</strong> The names of fields explicitly set during instantiation.</li>
<li><strong>__pydantic_private__:</strong> Values of private attributes set on the model instance.</li>
</ul>
</div>


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