Simple release procedure (obsolete) - pombase/fypo GitHub Wiki
- do editing on laptop in Protégé
| Command (on laptop) | Notes |
|---|---|
% scp src/ontology/fypo-edit.obo curation.pombase.org:pombase-fypo/src/ontology/ |
copy changes to server |
- change to server
- run ODK commands in the
pombase-fypodirectory oncuration.pombase.org/oliver1:
| Command (on server) | Notes |
|---|---|
% git pull |
- |
% cd src/ontology |
- |
% sh run.sh make synonyms -B |
adds synonyms from .tsv file |
% sh run.sh make fix_quality_issue -B |
don't have to do this every time, but it fixes BFO:quality to PATO:quality, so do it every so often (especially if you've added "normal" or "abnormal" terms) |
% sh run.sh make clear_obsoletes -B |
only if anything has just gone obsolete |
% sh run.sh make prepare_release -B |
runs release (takes a while) (minus B =report all problems) |
% cd ../.. |
go back to the pombase-fypo directory |
- if there's an error, go back to first step - edit in Protégé
| Command (on server) | Notes |
|---|---|
% git add . |
- |
% git commit -m 'commit message' |
"closes #123; closes #124;" will link the commit to, and automagically close, the ticket(s) |
% git push origin master |
Push changes to GitHub |
- wait for CI checks (can see in GitHub under "Actions")
- if there's an error, go back to first step - edit in Protégé
- make a release:
| Action | Notes |
|---|---|
| Go to https://github.com/pombase/fypo/releases/new | - |
| Code -> Releases (right-hand panel) -> "Draft a new release" (button on right, near top) | - |
| Click "Choose a tag", type vyyyy-mm-dd click "Create new tag" (appears below the text box) | - |
| Add: Release title | (comments optional) |
| Click "Publish release" | (button near the bottom) |
| Return to your command line on server | - |
% git pull |