ODK upgrade && odkrunner

README.md

@@ -14,6 +14,9 @@ Python is a dev dependency. It's not needed to run the docker containers, but ne
   One or both of the following, depending on if you want to run the stable build `latest` or `dev`:
     - a. `docker pull obolibrary/odkfull:latest`
     - b. `docker pull obolibrary/odkfull:dev`
+4. Optional: [`odkrunner`](https://github.com/gouttegd/odkrunner): Alternative to `run.sh`. If using this, you would run
+    like `odkrun make build-mondo-ingest` instead of `sh run.sh make build-mondo-ingest`. Suggestion: rename the binary 
+    to `odk`; this is the convention of `mondo-ingest` developers. 
 
 ## Running
 ### Full build

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://monarch-initiative.github.io/noname/ 
+   INFO    -  Your documentation should shortly be available at: https://monarch-initiative.github.io/mondo-ingest/ 
    ```
-3. Just to double check, you can now navigate to your documentation pages (usually https://monarch-initiative.github.io/noname/). 
+3. Just to double check, you can now navigate to your documentation pages (usually https://monarch-initiative.github.io/mondo-ingest/). 
    Just make sure you give GitHub 2-5 minutes to build the pages!
 
 

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/monarch-initiative/noname/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/monarch-initiative/mondo-ingest/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 `mondo-ingest.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.

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for mondo-ingest
 # Generated using ontology-development-kit
-# ODK Version: v1.5.3
+# ODK Version: v1.5.4
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use mondo-ingest.Makefile instead
 
@@ -47,7 +47,7 @@ REPORT_PROFILE_OPTS =       --profile $(ROBOT_PROFILE)
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  properties-as-annotation-and-object ordo-mapping-annotations 
 SPARQL_EXPORTS =            basic-report 
-ODK_VERSION_MAKEFILE =      v1.5.3
+ODK_VERSION_MAKEFILE =      v1.5.4
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')

src/ontology/run.sh.conf

@@ -1,3 +1,3 @@
 ODK_IMAGE=odkfull
-ODK_TAG=v1.5.3
+ODK_TAG=v1.5.4
 ODK_DEBUG=yes