deploy: ef0d170

.buildinfo

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+# 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: 8ee9dab2fd0e73118c4ca748e97e6dc2
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/builddoc.rst.txt

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+Build documentation
+===================
+
+This `documentation`_ was built using `Sphinx`_.
+
+
+Build locally
+-------------
+
+The following commands can be used to create a `Conda`_ environment that contains all packages needed to build the documentation.
+
+1. Install `Miniconda3`_ (Conda 23.5.2 Python 3.11.3 released July 13, 2023)
+
+2. Install dependencies
+
+   A. Option 1: install environment from `YAML environment file`_ ::
+
+         conda env create -f envs/motbxtools_doc.yml
+         conda activate motbxtools_doc
+         pip install -e .
+
+   B. Option 2: install dependencies manually using Miniconda/Anaconda Prompt or terminal::
+
+         conda create -n motbxtools_doc python=3.11
+         conda activate motbxtools_doc
+         conda install -c conda-forge furo
+         conda install -c conda-forge jsonschema
+         conda install -c conda-forge validators
+         conda install -c anaconda requests
+         conda install -c conda-forge pyyaml
+         conda install -c conda-forge sphinx
+         conda install -c conda-forge sphinx-argparse
+         conda install -c anaconda graphviz
+         pip install -e .
+
+
+The `HTML` documentation can be built using::
+
+    make html
+
+
+Deploy on GitHub pages
+----------------------
+
+A GitHub action has been defined to build the documention and deploy it on GitHub pages.
+The action is defined in `.github/workflows/documentation.yml`_ and can be manually triggered via `actions`_.
+it is also triggered when changes are made to files in `doc/`_ or `src/`_.
+
+
+.. _documentation: https://eatris.github.io/motbx/index.html
+.. _Conda: https://docs.conda.io/en/latest/
+.. _Miniconda3: https://docs.conda.io/projects/miniconda/en/latest/
+.. _Sphinx: https://www.sphinx-doc.org/en/master/
+.. _YAML environment file: https://github.com/EATRIS/motbx/blob/main/envs/motbxtools_doc.yml
+.. _.github/workflows/documentation.yml: https://github.com/EATRIS/motbx/blob/main/.github/workflows/documentation.yml
+.. _actions: https://github.com/EATRIS/motbx/actions/workflows/documentation.yml
+.. _doc/: https://github.com/EATRIS/motbx/tree/main/doc
+.. _src/: https://github.com/EATRIS/motbx/tree/main/src

_sources/contribute.rst.txt

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+Contribute to MOTBX
+===================
+
+
+Add a resource to MOTBX
+-----------------------
+
+The EATRIS Multi-omics Toolbox is built *with* the community, *for* the community.
+Suggestions for new resources are very welcome. You can `submit an issue`_
+to request addition of a new resource, changes to existing resources, or removal of
+a resource. We also welcome new ideas for this repository, or developers who
+want to actively contribute to it.
+
+`Contact us`_ if you have any questions.
+
+
+Information for developers
+--------------------------
+
+When making changes to this repository, we follow the `GitHub flow`_. For each issue:
+
+* Create a new branch
+* Edit the file(s)
+* Create a pull request (PR) - *automatically triggers validation checks*
+* Merge PR into `main` branch after review
+* Delete the branch after merging PR
+* Review issue and mention PR in a comment
+* Close issue
+
+Issue templates
+~~~~~~~~~~~~~~~
+
+Issue templates can be edited in `.github/ISSUE_TEMPLATE`_.
+
+
+GitHub actions
+~~~~~~~~~~~~~~
+
+Automated GitHub actions are defined in `.github/workflows`_.
+
+
+Workflow: changing a MOTBX resource
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+For each suggested edit to MOTBX resources, a GitHub issue is created.
+Changes are made based on the suggestion and a review by the MOTBX development team.
+After `resource validation`_ triggered by a pull request, changes can be accepted
+and added the resource collection.
+
+.. graphviz::
+
+   digraph add_resource {
+        fontname="Helvetica,Arial,sans-serif"
+        tooltip="Workflow: changing a MOTBX resource"
+        node [
+            fontname="Helvetica,Arial,sans-serif",
+            shape=box, style="filled"]
+        edge [fontname="Helvetica,Arial,sans-serif"]
+        issue_creation [
+            label=<<b>MOTBX community member:</b><br/>Create issue to request addition,<br/>removal or update of MOTBX resource​>,
+            color="#fa9632", tooltip="Create issue", fontcolor="#ffffff",
+            URL="https://github.com/EATRIS/motbx/issues/new/choose"];
+        first_review [
+            label=<<b>MOTBX team:</b><br/>Review request​>,
+            color="#1d2850", fontcolor="#ffffff", tooltip="Review issue",
+            URL="https://github.com/EATRIS/motbx/issues"];
+        approve_request [
+            label="Approve request?​",
+            color="#d2d2d2", shape="diamond",
+            tooltip="Should the resource be added?"];
+        request_info [
+            label="Request additional information?​",
+            color="#d2d2d2", shape="diamond",
+            tooltip="Is additional information needed?"];
+        comment_issue [
+            label=<<b>MOTBX team:</b><br/>Comment on issue to get additional details​>,
+            color="#1d2850", fontcolor="#ffffff",
+            tooltip="Request further information",
+            URL="https://github.com/EATRIS/motbx/issues"];
+        provide_info [
+            label=<<b>MOTBX community member:</b><br/>Comment on issue to provide further details​>,
+            color="#fa9632", tooltip="Provide further information",
+            fontcolor="#ffffff", URL="https://github.com/EATRIS/motbx/issues"];
+        close_reject_issue [
+            label=<<b>MOTBX team:</b><br/>Close issue​>,
+            color="#1d2850", fontcolor="#ffffff", tooltip="Close issue",
+            URL="https://github.com/EATRIS/motbx/issues"];
+        branch_creation [
+            label=<<b>MOTBX team:</b><br/>Create a new branch, add assignee>,
+            color="#1d2850", fontcolor="#ffffff", tooltip="Create branch",
+            URL="https://github.com/EATRIS/motbx/issues"];
+        branch_update [
+            label=<<b>MOTBX team:</b><br/>Add, remove, or update resource in branch​>,
+            color="#1d2850", fontcolor="#ffffff", tooltip="Update branch",
+            URL="https://github.com/EATRIS/motbx/branches"];
+        pull_request [
+            label=<<b>MOTBX team:</b><br/>Create pull request​>,
+            color="#1d2850", fontcolor="#ffffff", tooltip="Create pull request",
+            URL="https://github.com/EATRIS/motbx/branches"];
+        action_validation [
+            label=<<b>Triggered automated GitHub action:</b><br/>Perform tests validating resources in repository​>,
+            color="#6450a0", fontcolor="#ffffff",
+            tooltip="Automated resource validation",
+            URL="https://github.com/EATRIS/motbx/actions/workflows/validate_resources.yml"];
+        pull_request_review [
+            label=<<b>MOTBX team:</b><br/>Review pull request​>,
+            color="#1d2850", fontcolor="#ffffff", tooltip="Review pull request",
+            URL="https://github.com/EATRIS/motbx/pulls"];
+        validation_passed [
+            label="Did all automated checks pass?​",
+            color="#d2d2d2", shape="diamond",
+            tooltip="Could resources be validated?"];
+        expectations_met [
+            label="Do the implemented changes\nmeet expectations?​",
+            color="#d2d2d2", shape="diamond",
+            tooltip="Is resource described as expected?"];
+        pull_request_merge [
+            label=<<b>MOTBX team:</b><br/>Merge pull request and close issue​>,
+            color="#1d2850", fontcolor="#ffffff", tooltip="Merge pull request",
+            URL="https://github.com/EATRIS/motbx/pulls"];
+        pull_request_draft [
+            label=<<b>MOTBX team:</b><br/>Convert pull request to draft,<br/>comment on issue to request edit​>,
+            color="#1d2850", fontcolor="#ffffff", tooltip="Edits required",
+            URL="https://github.com/EATRIS/motbx/pulls"];
+        issue_creation -> first_review -> approve_request;
+        approve_request -> request_info [label=<<i>Reject</i>>, style="dotted"];
+        request_info -> comment_issue [label=<<i>Yes</i>>, style="dotted"];
+        comment_issue -> provide_info -> first_review [style="dotted"];
+        request_info -> close_reject_issue [label=<<i>No</i>>, style="dotted"];
+        approve_request -> branch_creation [label=<<i>Approve</i>>];
+        branch_creation -> branch_update -> pull_request -> action_validation;
+        action_validation -> pull_request_review -> validation_passed;
+        validation_passed -> expectations_met [label=<<i>Yes</i>>];
+        expectations_met -> pull_request_merge [label=<<i>Yes</i>>];
+        validation_passed -> pull_request_draft [label=<<i>No</i>>, style="dotted"];
+        expectations_met -> pull_request_draft [label=<<i>No</i>>, style="dotted"];
+        pull_request_draft -> branch_update [style="dotted"];
+
+   }
+
+
+Workflow: summarise changes
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+While individual resources can be continuously edited, updates to the MOTBX website
+are made in regular time intervals. For this purpose, summaries of all resources
+and changes made compared to a previous summary are made.
+
+.. graphviz::
+
+   digraph summarise_resources {
+        fontname="Helvetica,Arial,sans-serif"
+        tooltip="Workflow: summarise MOTBX resource and changes"
+        node [
+            fontname="Helvetica,Arial,sans-serif",
+            shape=box, style="filled"]
+        edge [fontname="Helvetica,Arial,sans-serif"]
+        action_summary [
+            label=<<b>GitHub action:</b><br/>Create resource summary>,
+            fontcolor="#ffffff",
+            color="#6450a0", tooltip="Manually triggered GitHub action",
+            URL="https://github.com/EATRIS/motbx/actions/workflows/create_summary.yml"];
+        send_for_approval [
+            label=<<b>MOTBX team:</b><br/>Send change summary to<br/>MOTBX content committee​>,
+            color="#1d2850", tooltip="Send summary for approval",
+            fontcolor="#ffffff",
+            URL="https://github.com/EATRIS/motbx/tree/main/resources/summary"]
+        content_review [
+            label=<<b>MOTBX content committee:</b><br/>Review changes​>,
+            color="#00b4b4", tooltip="Changes are reviwed by content committee",
+            URL="https://motbx.eatris.eu/motbx-team/", fontcolor="#ffffff"]
+        changes_approved [
+            label="Are all changes approved?",
+            color="#d2d2d2", shape="diamond",
+            tooltip="Does the content committee approve resource changes?"]
+        publish_changes [
+            label=<<b>MOTBX team:</b><br/>Publish changes on MOTBX website>,
+            color="#1d2850", tooltip="Publish changes on MOTBX website",
+            URL="https://motbx.eatris.eu/", fontcolor="#ffffff"]
+        resolve_issues [
+            label=<<b>MOTBX team:</b><br/>Follow the above workflow <i>changing a<br/>MOTBX resource </i> to resolve approval issues>,
+            tooltip="Create issue per resource and make edits",
+            color="#1d2850", fontcolor="#ffffff",
+            URL="https://github.com/EATRIS/motbx/issues"
+        ]
+
+        action_summary -> send_for_approval -> content_review -> changes_approved;
+        changes_approved -> publish_changes [label=<<i>Yes</i>>];
+        changes_approved -> resolve_issues [label=<<i>No</i>>, style="dotted"];
+        resolve_issues -> action_summary [style="dotted"];
+
+   }
+
+
+.. _submit an issue: https://github.com/EATRIS/motbx/issues/new/choose
+.. _Contact us: https://motbx.eatris.eu/contact/
+.. _GitHub flow: https://docs.github.com/en/get-started/quickstart/github-flow
+.. _.github/ISSUE_TEMPLATE: https://github.com/EATRIS/motbx/tree/main/.github/ISSUE_TEMPLATE
+.. _.github/workflows: https://github.com/EATRIS/motbx/tree/main/.github/workflows
+.. _resource validation: https://github.com/EATRIS/motbx/actions/workflows/validate_resources.yml