Merge pull request #253 from mcwdsi/update-qc-yml

Update qc yml

.github/workflows/qc.yml

@@ -19,15 +19,15 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.4
+    container: obolibrary/odkfull:v1.5.2
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Run ontology QC checks
         env:
           DEFAULT_BRANCH: main
-        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false
+        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false
 

docs/odk-workflows/ManageDocumentation.md

@@ -38,9 +38,10 @@ 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://ufbmi.github.io/OMRSE/ 
+   INFO    -  Your documentation should shortly be available at: https://mcwdsi.github.io/OMRSE/ 
    ```
-3. Just to double check, you can now navigate to your documentation pages (usually https://ufbmi.github.io/OMRSE/). 
+3. Just to double check, you can now navigate to your documentation pages (usually https://mcwdsi.github.io/OMRSE/). 
    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/ufbmi/OMRSE/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/mcwdsi/OMRSE/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 `omrse.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.

docs/odk-workflows/RepoManagement.md

@@ -2,7 +2,7 @@
 
 ## Updating your ODK repository
 
-Your ODK repositories configuration is managed in `src/ontology/omrse-odk.yaml`. Once you have made your changes, you can run the following to apply your changes to the repository:
+Your ODK repositories configuration is managed in `src/ontology/omrse-odk.yaml`. The [ODK Project Configuration Schema](https://github.com/INCATools/ontology-development-kit/blob/master/docs/project-schema.md) defines all possible parameters that can be used in this config YAML. Once you have made your changes, you can run the following to apply your changes to the repository:
 
 
 ```

docs/odk-workflows/RepositoryFileStructure.md

@@ -28,7 +28,7 @@ These are the current imports in OMRSE
 | oostt | http://purl.obolibrary.org/obo/oostt.owl | None |
 | omo | http://purl.obolibrary.org/obo/omo.owl | mirror |
 | pno | http://purl.obolibrary.org/obo/iao/pno.owl | mirror |
-| d-acts | http://purl.obolibrary.org/obo/iao/d-acts.owl | mirror |
+| d-acts | http://purl.obolibrary.org/obo/iao/d-acts.owl | filter |
 | geo | http://purl.obolibrary.org/obo/geo.owl | None |
 | mf | http://purl.obolibrary.org/obo/mf.owl | None |