Update the usage guide#227
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domgz merged 26 commits intorelease/4/devfrom Sep 9, 2022
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* New "Ontology management" section that agglomerates several pages. * Updated "Included ontologies" page. * Dedicated page for `pico`. Removed related content from "Utilities" page. * Updated "Working with ontologies" page and renamed to "Ontology packages". * Moved supported ontology languages and formats to a new dedicated page. * Removed YAML ontology format documentation, as it is not longed supported. * Moved all pages from the "Working with Ontologies" sections to the usage guide.
Remember that the pico part of the utils page was moved to the ontology management section earlier.
* Create dedicated section for sessions. * Add introductory page to sessions. * Add page on managing the session contents. * Add page on queries using the session object. * Add page on queries using the search module (WIP). * Add page on queries using SPARQL (blueprint). * Rename the import/export tutorial to RDF Import and export (no other changes yet). * Remove sessions_and_vars.ipynb * Remove multiple_wrappers.ipynb
* Create dedicated section for wrappers. * Rename existing page to be the introductory page for wrappers (changes yet to be done). * Move SimLAMMPS and Quantum Espresso wrapper pages. * Add blueprint pages for wrappers included with SimPhoNy.
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@pablo-de-andres The whole PR is not ready but all sections in the usage guide from the beginning up to "Queries: using the session object" can be reviewed.
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* Finish the page on queries using the search module.
* Finish the page on queries using SPARQL.
* Minor changes to the page on queries using the session object.
* Minor changes to the page on managing the session contents.
* Minor changes to the introductory page to sessions.
* Adapt the import/export tutorial to SimPhoNy v4.
* Add introduction. * Fill SQLite wrapper page. * Fill SQLAlchemy wrapper page.
* Update introduction.ipynb.
* Update sqlite.ipynb.
* Update sqlalchemy.ipynb.
* Fill dataspace.ipynb
* Fill remote.ipynb
* Remove Quantum espresso tutorial. * Remove SimLAMMPS tutorial.
* Hide the wrapper development tutorials (to be reincorporated later).
… they were not part of the public API.
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New "Ontology management" section that agglomerates several pages.
Updated "Included ontologies" page.
Dedicated page for
pico. Removed related content from "Utilities" page.Updated "Working with ontologies" page and renamed to "Ontology packages".
Moved supported ontology languages and formats to a new dedicated page.
Removed YAML ontology format documentation, as it is not longed supported.
Removed "Introduction to ontologies" section.
Moved all pages from the "Working with Ontologies" sections to the usage guide.
Changed title "Supported languages" to "supported formats" on supported_formats.md
Remove the "Detailed design" section
Update panels on the main page
Replace ontology_interface.ipynb with terminological_knowledge.ipynb
Replace cuds_api.ipynb with assertional_knowledge.ipynb
Replace utils.md with visualization.ipynb (just a placeholder for now).
Create dedicated section for sessions.
Add introductory page to sessions.
Add page on managing the session contents.
Add page on queries using the session object.
Add page on queries using the search module (WIP).
Add page on queries using SPARQL (placeholder).
Rename the import/export tutorial to RDF Import and export (no other changes yet).
Remove sessions_and_vars.ipynb
Remove multiple_wrappers.ipynb
Create dedicated section for wrappers.
Rename existing page to be the introductory page for wrappers (changes yet to be done).
Move SimLAMMPS and Quantum Espresso wrapper pages.
Add placeholder pages for wrappers included with SimPhoNy.
Add page on queries using the search module.
Add page on queries using SPARQL.
Adapt the import/export tutorial to SimPhoNy v4.
Add introduction (wrappers section).
Fill SQLite wrapper page.
Fill SQLAlchemy wrapper page.
Fill Dataspace wrapper page.
Fill Remote wrapper page.
Remove Quantum Espresso tutorial.
Remove SimLAMMPS tutorial.
Hide the wrapper development tutorials (to be reincorporated later).
Add visualization section.