From d404f05eaa40b3ad0bdfcd8cd80f90a8290b39f0 Mon Sep 17 00:00:00 2001 From: ckindermann Date: Wed, 1 May 2024 16:30:22 -0700 Subject: [PATCH] Update repo name after transfer --- CONTRIBUTING.md | 8 ++++---- README.md | 6 +++--- docs/odk-workflows/ManageDocumentation.md | 4 ++-- docs/odk-workflows/ReleaseWorkflow.md | 2 +- mkdocs.yaml | 4 ++-- src/metadata/gcbo.md | 9 ++++----- src/metadata/gcbo.yml | 11 +++++------ src/ontology/Makefile | 2 +- src/ontology/gcbo-odk.yaml | 2 +- 9 files changed, 23 insertions(+), 25 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 2015629..fb6eae1 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -33,7 +33,7 @@ Please carefully read our [Code of Conduct](CODE_OF_CONDUCT.md). ### Reporting problems with the ontology -Please use our [Issue Tracker](https://github.com/ckindermann/gbco/issues/) for reporting problems with the ontology. +Please use our [Issue Tracker](https://github.com/bmir-radx/gcbo/issues/) for reporting problems with the ontology. To learn how to write a good issue [see here](#great-issues). @@ -57,10 +57,10 @@ community resource, it is often necessary to do at least some of the work of add #### How to write a new term request -Request a new term _via_ the GitHub [Issue Tracker](https://github.com/ckindermann/gbco/issues/). +Request a new term _via_ the GitHub [Issue Tracker](https://github.com/bmir-radx/gcbo/issues/). It is important to remember that it takes a lot of time for curators to process issues submitted to the tracker. -To make this work easier, please always use issue templates if they are available (https://github.com/ckindermann/gbco/issues/new/choose). +To make this work easier, please always use issue templates if they are available (https://github.com/bmir-radx/gcbo/issues/new/choose). For how to write a good term request, please read the [best practices carefully](#great-issues). @@ -92,4 +92,4 @@ Please refer to the [OBO Academy term request guide](https://oboacademy.github.i ### How to create a great pull/merge request? -Please refer to the [OBO Academy best practices](https://oboacademy.github.io/obook/howto/github-create-pull-request/) \ No newline at end of file +Please refer to the [OBO Academy best practices](https://oboacademy.github.io/obook/howto/github-create-pull-request/) diff --git a/README.md b/README.md index 9add3ca..70f64e9 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ -![Build Status](https://github.com/ckindermann/gbco/actions/workflows/qc.yml/badge.svg) +![Build Status](https://github.com/bmir-radx/gcbo/actions/workflows/qc.yml/badge.svg) # Global Code Book Ontology Description: None @@ -22,8 +22,8 @@ Editors of this ontology should use the edit version, [src/ontology/gcbo-edit.ow ## Contact -Please use this GitHub repository's [Issue tracker](https://github.com/ckindermann/gbco/issues) to request new terms/classes or report errors or specific concerns related to the ontology. +Please use this GitHub repository's [Issue tracker](https://github.com/bmir-radx/gcbo/issues) to request new terms/classes or report errors or specific concerns related to the ontology. ## Acknowledgements -This ontology repository was created using the [Ontology Development Kit (ODK)](https://github.com/INCATools/ontology-development-kit). \ No newline at end of file +This ontology repository was created using the [Ontology Development Kit (ODK)](https://github.com/INCATools/ontology-development-kit). diff --git a/docs/odk-workflows/ManageDocumentation.md b/docs/odk-workflows/ManageDocumentation.md index 39f7b6b..a237c28 100644 --- a/docs/odk-workflows/ManageDocumentation.md +++ b/docs/odk-workflows/ManageDocumentation.md @@ -38,9 +38,9 @@ The documentation is _not_ automatically updated from the Markdown, and needs to If everything was successful, you will see a message similar to this one: ``` - INFO - Your documentation should shortly be available at: https://ckindermann.github.io/gbco/ + INFO - Your documentation should shortly be available at: https://bmir-radx.github.io/gbco/ ``` -3. Just to double check, you can now navigate to your documentation pages (usually https://ckindermann.github.io/gbco/). +3. Just to double check, you can now navigate to your documentation pages (usually https://bmir-radx.github.io/gbco/). Just make sure you give GitHub 2-5 minutes to build the pages! diff --git a/docs/odk-workflows/ReleaseWorkflow.md b/docs/odk-workflows/ReleaseWorkflow.md index 13f0739..bb63238 100644 --- a/docs/odk-workflows/ReleaseWorkflow.md +++ b/docs/odk-workflows/ReleaseWorkflow.md @@ -44,7 +44,7 @@ Once your [CI checks](ContinuousIntegration.md) have passed, and your reviews ar ## Create a GitHub release -1. Go to your releases page on GitHub by navigating to your repository, and then clicking on releases (usually on the right, for example: https://github.com/ckindermann/gbco/releases). Then click "Draft new release" +1. Go to your releases page on GitHub by navigating to your repository, and then clicking on releases (usually on the right, for example: https://github.com/bmir-radx/gbco/releases). Then click "Draft new release" 1. As the tag version you **need to choose the date on which your ontologies were build.** You can find this, for example, by looking at the `gcbo.obo` file and check the `data-version:` property. The date needs to be prefixed with a `v`, so, for example `v2020-02-06`. 1. You can write whatever you want in the release title, but we typically write the date again. The description underneath should contain a concise list of changes or term additions. 1. Click "Publish release". Done. diff --git a/mkdocs.yaml b/mkdocs.yaml index 8de9b7a..2d2a4d5 100644 --- a/mkdocs.yaml +++ b/mkdocs.yaml @@ -18,8 +18,8 @@ markdown_extensions: - pymdownx.mark - pymdownx.tilde -site_url: https://ckindermann.github.io/gbco/ -repo_url: https://github.com/ckindermann/gbco/ +site_url: https://bmir-radx.github.io/gbco/ +repo_url: https://github.com/bmir-radx/gcbo nav: - Getting started: index.md diff --git a/src/metadata/gcbo.md b/src/metadata/gcbo.md index c922213..83d29e5 100644 --- a/src/metadata/gcbo.md +++ b/src/metadata/gcbo.md @@ -3,10 +3,10 @@ layout: ontology_detail id: gcbo title: Global Code Book Ontology jobs: - - id: https://travis-ci.org/ckindermann/gbco + - id: https://travis-ci.org/bmir-radx/gbco type: travis-ci build: - checkout: git clone https://github.com/ckindermann/gbco.git + checkout: git clone https://github.com/bmir-radx/gbco.git system: git path: "." contact: @@ -15,7 +15,7 @@ contact: github: description: Global Code Book Ontology is an ontology... domain: stuff -homepage: https://github.com/ckindermann/gbco +homepage: https://github.com/bmir-radx/gbco products: - id: gcbo.owl name: "Global Code Book Ontology main release in OWL format" @@ -32,7 +32,7 @@ products: dependencies: - id: symp -tracker: https://github.com/ckindermann/gbco/issues +tracker: https://github.com/bmir-radx/gbco/issues license: url: http://creativecommons.org/licenses/by/3.0/ label: CC-BY @@ -41,4 +41,3 @@ activity_status: active Enter a detailed description of your ontology here. You can use arbitrary markdown and HTML. You can also embed images too. - diff --git a/src/metadata/gcbo.yml b/src/metadata/gcbo.yml index 26c3404..3bf8f59 100644 --- a/src/metadata/gcbo.yml +++ b/src/metadata/gcbo.yml @@ -4,8 +4,8 @@ idspace: GCBO base_url: /obo/gcbo products: -- gcbo.owl: https://raw.githubusercontent.com/ckindermann/gbco/main/gcbo.owl -- gcbo.obo: https://raw.githubusercontent.com/ckindermann/gbco/main/gcbo.obo +- gcbo.owl: https://raw.githubusercontent.com/bmir-radx/gbco/main/gcbo.owl +- gcbo.obo: https://raw.githubusercontent.com/bmir-radx/gbco/main/gcbo.obo term_browser: ontobee example_terms: @@ -14,15 +14,14 @@ example_terms: entries: - prefix: /releases/ - replacement: https://raw.githubusercontent.com/ckindermann/gbco/v + replacement: https://raw.githubusercontent.com/bmir-radx/gbco/v - prefix: /tracker/ - replacement: https://github.com/ckindermann/gbco/issues + replacement: https://github.com/bmir-radx/gbco/issues - prefix: /about/ replacement: http://www.ontobee.org/ontology/GCBO?iri=http://purl.obolibrary.org/obo/ ## generic fall-through, serve direct from github by default - prefix: / - replacement: https://raw.githubusercontent.com/ckindermann/gbco/main/ - + replacement: https://raw.githubusercontent.com/bmir-radx/gbco/main/ diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 43ea056..8f06fc2 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -10,7 +10,7 @@ # More information: https://github.com/INCATools/ontology-development-kit/ # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= fd4792a5b818d4783baec205d067e9cc25f438ab4ff94e3526180e316dbf5f78 +CONFIG_HASH= f813d9da4a727cc003bd735e994a9613b8874d6f64229bd624878dba7214969e # ---------------------------------------- diff --git a/src/ontology/gcbo-odk.yaml b/src/ontology/gcbo-odk.yaml index 5b33f18..5d73986 100644 --- a/src/ontology/gcbo-odk.yaml +++ b/src/ontology/gcbo-odk.yaml @@ -1,6 +1,6 @@ id: gcbo title: "Global Code Book Ontology" -github_org: ckindermann +github_org: bmir-radx repo: gbco use_dosdps: true dosdp_tools_options: "--obo-prefixes=true --prefixes=config/prefixes.yaml"