From b1530c82484b202904143a9d60a376ec20f01bec Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Tue, 6 Aug 2024 16:19:12 +0300 Subject: [PATCH] Reformat some docs pages to render correctly (#379) Reformatting of documentation to render on mkdocs material theme --- src/docs/create-mapping-commons.md | 26 +++++++++++++++++--------- src/docs/related-documentation.md | 12 ++++++------ 2 files changed, 23 insertions(+), 15 deletions(-) diff --git a/src/docs/create-mapping-commons.md b/src/docs/create-mapping-commons.md index bd88f3ff..00e4f35b 100644 --- a/src/docs/create-mapping-commons.md +++ b/src/docs/create-mapping-commons.md @@ -1,4 +1,4 @@ -# Getting started +## Getting started - First, create a virtual environment of your choice (anaconda, venv, pyenv, poetry etc.). If you need assistance with virtual environments, [here's a guide](https://berkeleybop.github.io/best_practice/python_environments) to help you setup pyenv and use poetry with it. - Install the [cruft](https://github.com/cruft/cruft) package. Cruft enables keeping projects up-to-date with future updates made to this original template. @@ -6,12 +6,15 @@ ``` pip install cruft ``` + - Create a project using the [mapping-commons-cookiecutter](https://github.com/mapping-commons/mapping-commons-cookiecutter) template. + ``` cruft create https://github.com/mapping-commons/mapping-commons-cookiecutter ``` This kickstarts an interactive session where you declare the following: + - `project_name`: Name of the project. [defaults to: my-commons-name] - `github_org`: Name of the github org the project belongs to. [defaults to: my-org] - `project_description`: Description of the project [defaults to: 'This is the project description.'] @@ -20,13 +23,14 @@ This kickstarts an interactive session where you declare the following: - `yo`: Choose from [1]: Yes, [2]: No [**TEST OPTION FOR NOW**] - `license`: Choose from [1]: Yes, [2]: No [**TEST OPTION FOR NOW**] -# What does this do? +## What does this do? The following files and directories are autogenerated in the project: -# TODO -# Version control -## GitHub +### TODO + +## Version control +### GitHub 1. Go to [https://github.com/new] and follow the instructions, being sure to NOT add a README or .gitignore file (this cookiecutter template will take @@ -40,27 +44,31 @@ The following files and directories are autogenerated in the project: git push -u origin main ``` -## GitLab +### GitLab -### TODO +#### TODO -# Future updates to the project's boilerplate code +## Future updates to the project's boilerplate code In order to be up-to-date with the template, first check if there is a mismatch between the project's boilerplate code and the template by running: + ``` cruft check ``` This indicates if there is a difference between the current project's boilerplate code and the latest version of the project template. If the project is up-to-date with the template: + ``` SUCCESS: Good work! Project's cruft is up to date and as clean as possible :). ``` Otherwise, it will indicate that the project's boilerplate code is not up-to-date by the following: + ``` FAILURE: Project's cruft is out of date! Run `cruft update` to clean this mess up. ``` + For viewing the difference, run `cruft diff`. This shows the difference between the project's boilerplate code and the template's latest version. -After running `cruft update`, the project's boilerplate code will be updated to the latest version of the template. \ No newline at end of file +After running `cruft update`, the project's boilerplate code will be updated to the latest version of the template. diff --git a/src/docs/related-documentation.md b/src/docs/related-documentation.md index 3c78e2c4..a23b87f8 100644 --- a/src/docs/related-documentation.md +++ b/src/docs/related-documentation.md @@ -1,8 +1,8 @@ ## Related documentation -- [SSSOM Toolkit](https://mapping-commons.github.io/sssom-py/index.html#) -- [SSSOM Java](https://incenp.org/dvlpt/sssom-java/) -- Semantic Mapping Vocabulary (SEMAPV): "https://mapping-commons.github.io/semantic-mapping-vocabulary/" -- LinkML: "https://linkml.io/linkml/" -- OBO Academy: "https://oboacademy.github.io/obook/" -- Monarch Initiative: "https://monarch-initiative.github.io/monarch-documentation/" +- [SSSOM Toolkit](https://mapping-commons.github.io/sssom-py/index.html#): A toolkit and library for processing SSSOM files in Python +- [SSSOM Java](https://incenp.org/dvlpt/sssom-java/): A toolkit and library for processing SSSOM files in Java +- [Semantic Mapping Vocabulary (SEMAPV)](https://mapping-commons.github.io/semantic-mapping-vocabulary/): The mapping vocabulary used for mapping justifications and specialised mapping predicates +- [LinkML](https://linkml.io/linkml/): The modelling framework used by SSSOM +- [OBO Academy](https://oboacademy.github.io/obook/): Ontology and mapping related training materials +- [Monarch Initiative](https://monarch-initiative.github.io/monarch-documentation/): Knowledge Graph related products supported by the Monarch Initiatives, including many tools using and producing SSSOM