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Restore the edit file to its state before the 2025-08-19 release - #1676
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The file is set to its content at f945fa9, the last commit before #1631, and keeps the fix from #1657. The fix from #1644 is superseded by #1494, which corrected the same three creation_date values in 2024. Part of #1675 Co-authored-by: Chris Mungall <cjm@berkeleybop.org> Co-authored-by: Tim Alamenciak <tim.alamenciak@gmail.com> Co-authored-by: Pier Luigi Buttigieg <p.buttigieg@gmail.com> Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com> Co-authored-by: diatomsRcool <annethessen@gmail.com>
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@turbomam thanks for the PR - this is quite a profound change set - could we schedule a call to walk through it ? |
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@matentzn would be good to have you in the call too, more via email |
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Hi @pbuttigieg. @matentzn and I have already chatted this morning and I would be very happy to have a chat with both of you. I am not 100% convinced that this PR is the right first step myself. |
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I'm satisfied that this PR restores the lost classes now. The only consequences I know of are that
An alternative that preserves I think these review instructions from Claude are much more useful than the
GitHub holds no diff for Setup. Fetch the two commits being compared and the release tags. Nothing needs to be checked out: every command reads from git objects, and the only files written go to The commands pin master at a2455d1 and this pull request at 8870e81, so they give the same answers whatever branch you have checked out. Scope first. This pull request restores one file, Count the class declarations the pull request adds relative to master. This prints 145: See one of them come back, the ARMS class. The first command prints 0 on master; the second prints the class with its definition, creator, date, synonym "ARMS", label, and parent: See the change as axioms rather than lines. ROBOT needs the import lines stripped because the catalog points one module at a GitHub URL that no longer resolves: With ROBOT 1.9.10 the result is 2,806 axioms added and 1,536 removed. The additions are 2,095 annotation assertions, 284 declarations, 272 SubClassOf axioms, 127 equivalent-class axioms, 17 sub-annotation-property axioms (the NMDC subset hierarchy), 6 class assertions, 3 disjointness axioms, and 2 disjoint unions. The removals are the pre-2024 versions of things the lost pull requests changed, for example ENVO_01001243 was labelled "forest ecosystem" and is now "forest" with the old label kept as an exact synonym, and 19 old logical definitions that #1552 replaced. The removals are part of the restoration, because those 24 pull requests did not only add. Check the branch against the last good release rather than against any commit. Every ENVO class in the v2025-02-05 release is either declared in the branch's edit file or built from the DOSDP modules; the same check against master leaves 129 classes unaccounted for, and the v2025-08-19 release lacks exactly those 129: The three counts are 0, 129, and 129. The 145 restored declarations are those 129, plus 8 classes with content added between February and April 2025, plus the 8 empty declarations ENVO:03620010 to ENVO:03620017. Against f945fa9 itself, the branch differs by 17 lines, all of them the fix from #1657 that master already contains: EDITED Both CI checks passed, https://github.com/EnvironmentOntology/envo/actions/runs/39792036186 (ontology_qc) and https://github.com/EnvironmentOntology/envo/actions/runs/39792036230 (sssom_validation). The same The 145 restored classes
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matentzn
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This is exactly a revert of 1d0dd48 plus the #1657 fix. I checked it line by line, and nothing else gets lost or added.
I went through this properly this time, since I'm the one who let 1d0dd48 through. What I checked:
- 1d0dd48 is the only commit in #1631 that touched
envo-edit.owl(RC2 and theENVO_03605026commit didn't), and f945fa9 is the squash parent of 156dd8a. So going back to f945fa9 throws away nothing else from that release. git diff f945fa9 restore-envo-edit-1675is identical to the #1657 diff on master: 9 IAO_0100001 lines and the canopy boolean comment.- Every line the branch drops from master (1546) is a line from the 2024-01-23 version (e628190), except the 3 #1644 dates. Every line it adds (2980) exists in f945fa9. Nothing new sneaks in.
- @balhoff's #1644 is indeed superseded. The restored file has
2023-08-25T12:17:42.901Zfor ENVO_03600094/95/96, which #1494 had already fixed. That value looks more faithful than the17:42:00.901guess anyway. - The counts match the description: 145 ENVO classes (137 real + the 8 empty 03620010–17), 17 ENVO annotation properties, 6 individuals, 116 foreign declarations. Nothing is declared on master but not on the branch, and there are no duplicate declarations.
- All typed literals are valid (boolean, dateTime, etc.), so the restored content doesn't bring back any of the junk #1657 cleaned up.
- The 10 foreign IRIs that are newly used in logical axioms are all already in the current import modules, so the next release doesn't need an import refresh just for this.
- CI is green.
One thing the description doesn't mention: this also brings back Import(<http://purl.obolibrary.org/obo/envo/robot_templates/nmdc_env_context_subset_membership.owl>) (line 30), which 1d0dd48 dropped. That's the actual cause of the missing NMDC value sets in #1642. The catalog entry and the template file are still on master, so it resolves fine. I'd add "Part of #1642" (or closes it after the release) so people can follow it.
I agree with keeping this a plain restore and leaving the 8 empty declarations and unused foreign declarations for the follow-up PR. That's much easier to verify than redoing the cleanup in the same diff, even though #1675 originally said otherwise.
Process:
This pull request sets
src/envo/envo-edit.owlback to its content at commit f945fa9, the last commit before the 2025-08-19 release, and keeps the fix from #1657. In that release my commit 1d0dd48 replaced the edit file with its 2024-01-23 version minus 112 foreign declarations. That removed 145 classes, 17 annotation properties, 6 individuals, and every other change that 24 pull requests had made to the file between 2024-02-16 and 2025-04-02.Part of #1675
The diff against master is the mirror image of that commit, 3,308 insertions and 1,546 deletions, and nobody needs to read it. To review, compare this branch with the file it restores:
That shows the 17 lines of the fix from pull request 1657 and nothing else.
The 24 pull requests whose changes this restores