deploy: 4caf6e5

.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: 4c76daa67fd050c88817a2421a1e7595
+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
+         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`_.
+
+
+.. _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

_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.
+
+
+Developers
+----------
+
+When making changes to this repository, we follow the `GitHub flow`_. For each issue,
+a new branch is created, files are edited, and a pull request is created. When checks are passed,
+the pull request can be merged into the `main` branch.
+
+
+Issue templates
+~~~~~~~~~~~~~~~
+
+Issue templates can be edited in `.github/ISSUE_TEMPLATE`_.
+
+
+GitHub actions
+~~~~~~~~~~~~~~
+
+Automated GitHub actions are defined in `.github/workflows`_.
+
+
+.. _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

_sources/index.rst.txt

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+.. motbxtools documentation master file, created by
+   sphinx-quickstart on Fri Nov 10 14:22:04 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to motbxtools' documentation!
+======================================
+
+.. image:: https://github.com/EATRIS/motbx/assets/1405356/8c3418b2-d67e-43d4-b204-3e086dbb9822
+  :width: 300
+  :alt: MOTBX logo
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   motbx
+   schema
+   modules
+   utilities
+   installation
+   builddoc
+   contribute
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

_sources/installation.rst.txt

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+Install `motbxtools` and use example notebooks
+==============================================
+
+Several Jupyter notebooks using the `motbxtools` Python library are provided as
+part of the `MOTBX GitHub repository`_. We make use of `Conda`_ for cross-platform
+package management.
+
+
+Install Conda environment
+-------------------------
+
+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_notebooks.yml
+         conda activate motbxtools_notebooks
+         pip install -e .
+
+   B. Option 2: install dependencies manually using Miniconda/Anaconda Prompt or terminal
+
+      i. Install `notebook` and Jupyter kernels (`nb_conda_kernels`) to Conda base environment::
+
+            conda install -c conda-forge notebook
+            conda install -c conda-forge nb_conda_kernels
+
+      ii. Create new environment and register kernel for Jupyter::
+
+            conda create -n motbxtools_notebooks python=3.11
+            conda activate motbxtools_notebooks
+            conda install ipykernel
+            python -m ipykernel install --user --name=motbxtools_notebooks --display-name "Python 3.11 (motbxtools_notebooks)"
+            conda install -c anaconda requests
+            conda install -c conda-forge pyyaml
+            conda install -c conda-forge jsonschema
+            conda install -c conda-forge validators
+            conda install -c conda-forge pygithub
+            conda install -c conda-forge keyring
+            conda install -c anaconda pandas
+            conda install -c conda-forge openpyxl
+            pip install -e .
+
+
+Run Jupyter
+-----------
+
+Jupyter can now be started from the base environment::
+
+   jupyter notebook
+
+This opens Jupyter in your default browser. Select a notebook from the
+`notebooks`_ folder to open it.
+
+
+Example Jupyter Notebooks
+-------------------------
+
+A set of `Jupyter notebooks`_ showcase how `motbxtools` can be used to create/modify
+the MOTBX resource schema and validate resources.
+Make sure to run them from the `notebooks`_ directory.
+
+
+.. _MOTBX GitHub repository: https://github.com/EATRIS/motbx
+.. _Conda: https://docs.conda.io/en/latest/
+.. _Miniconda3: https://docs.conda.io/projects/miniconda/en/latest/
+.. _YAML environment file: https://github.com/EATRIS/motbx/blob/main/envs/motbxtools_notebooks.yml
+.. _notebooks: https://github.com/EATRIS/motbx/tree/main/notebooks
+.. _Jupyter notebooks: https://github.com/EATRIS/motbx/tree/main/notebooks

_sources/modules.rst.txt

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+`motbxtools` Python package
+===========================
+
+The `motbxtools` package provides classes and methods to read, write, validate,
+or summarise MOTBX resources. It is available in the directory `src/motbxtools`_.
+
+
+Module `motbxschema`
+--------------------
+
+.. automodule:: motbxschema
+    :members:
+    :special-members: __init__
+
+
+Unit testing
+------------
+
+The directory `tests/test_motbxtools`_ contains unit tests for the `motbxtools` package.
+The `tests`_ directory additionally contains MOTBX resource `YAML` files used by the tests.
+Unit tests can be run using the GitHub action defined in `.github/workflows/tests.yml`_ via `actions`_.
+
+
+.. _src/motbxtools: https://github.com/EATRIS/motbx/tree/main/src/motbxtools
+.. _tests/test_motbxtools: https://github.com/EATRIS/motbx/tree/main/tests/test_motbxtools
+.. _tests: https://github.com/EATRIS/motbx/tree/main/tests
+.. _.github/workflows/tests.yml: https://github.com/EATRIS/motbx/blob/main/.github/workflows/tests.yml
+.. _actions: https://github.com/EATRIS/motbx/actions/workflows/tests.yml

_sources/motbx.rst.txt

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+EATRIS Multi-omics Toolbox (MOTBX)
+==================================
+
+.. image:: https://github.com/EATRIS/.github/assets/1405356/06fb628b-13b9-4a9b-aef3-a4987d989bf6
+  :width: 200
+  :alt: EATRIS logo
+
+EATRIS is the `European infrastructure for translational medicine`_
+that brings together resources and services for research communities to translate
+scientific discoveries into benefits for patients. The organisation is a non-profit
+that provides access to a vast array of expertise and facilities from over 150
+top-tier academic centres across Europe. EATRIS focuses on improving and optimising
+preclinical and early clinical development of drugs, vaccines and diagnostics, and
+overcome barriers to health innovation. Find out more here: https://eatris.eu/
+
+.. _European infrastructure for translational medicine: https://eatris.eu/
+
+.. image:: https://github.com/EATRIS/motbx/assets/1405356/8c3418b2-d67e-43d4-b204-3e086dbb9822
+  :width: 200
+  :alt: MOTBX logo
+
+The EATRIS `Multi-omics Toolbox (MOTBX)`_ is a community-driven
+comprehensive knowledge base aimed at supporting researchers in academia and industry
+who are involved in the development, implementation, and adoption of multi-omics
+approaches for personalised medicine. MOTBX collects a rich selection of resources,
+including best practices, protocols for individual omics technologies, and tools
+for quality control and assessment. MOTBX is available at https://motbx.eatris.eu/.
+
+.. _Multi-omics Toolbox (MOTBX): https://motbx.eatris.eu/

_sources/schema.rst.txt

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+MOTBX resources and schema
+==========================
+
+MOTBX resources are stored as `YAML` files. The `YAML` file structure is defined
+using `JSON Schema`.
+
+Curated MOTBX resources are stored in the `resources/curated`_ directory, the `JSON Schema` is
+available under `schema/motbxschema.json`_. It defines the mandatory (`resourceID`,
+`resourceCategory`, `resourceSubcategory`, `resourceTitle`, `resourceDescription`, `resourceUrl`, `resourceTags`)
+and optional (`resourceKeywords`) fields describing a MOTBX resource, allowed values
+for `resourceCategory` and `resourceSubcategory`, and allowed patterns for `resourceUrl`.
+
+The `JSON Schema` file `schema/motbxschema.json`_ was created with the Jupyter notebook `notebooks/schema.ipynb`_.
+
+
+.. _resources/curated: https://github.com/EATRIS/motbx/tree/main/resources/curated
+.. _schema/motbxschema.json: https://github.com/EATRIS/motbx/blob/main/schema/motbxschema.json
+.. _notebooks/schema.ipynb: https://github.com/EATRIS/motbx/blob/main/notebooks/schema.ipynb

_sources/utilities.rst.txt

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+Scripts and GitHub Actions
+==========================
+
+Scripts for executing specific tasks are available in the `motbxtools.utils`_
+module. They can be run locally, or as automated GitHub Actions.
+
+Script `utils.summarise_resources`
+----------------------------------
+
+.. argparse::
+    :module: utils.summarise_resources
+    :func: parser
+    :prog: summarise_resources
+
+This script can be executed as GitHub Action `create_summary`_.
+
+.. _motbxtools.utils: https://github.com/EATRIS/motbx/tree/main/src/motbxtools/utils
+.. _create_summary: https://github.com/EATRIS/motbx/actions/workflows/create_summary.yml