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fee3508
Fix-GPR curation for Linoleate_metabolism and Fatty_acid_elongation_a…
JHL-452b Mar 20, 2026
1533140
feat: clearer instructions for location of test results (#997)
mihai-sysbio Mar 23, 2026
60c4f65
chore: bump memote-docker (#1008)
mihai-sysbio Mar 23, 2026
d03918f
Fix: GPR curation for acyl-CoA hydrolysis and nicotinate and nicotina…
JHL-452b Mar 24, 2026
4ba1728
Remove peroxisomal genes from mitochondrial ACAD reactions (#943)
Devlin-Moyer Mar 24, 2026
84eda78
Remove inaccurate mitochondrial nucleotide transport reactions (#944)
Devlin-Moyer Mar 24, 2026
0992401
Fix alpha-tocopheryl quinone redox reactions (#945)
Devlin-Moyer Mar 24, 2026
1ea157b
fix metabolicTasks_CellfieConsensus (#998)
edkerk Mar 24, 2026
7534584
Fix: updated lower bound of MAR04356 to make it reversible (#991)
liamkelley93 Mar 24, 2026
9318a96
chore: copy changes from main branch
edkerk Mar 26, 2026
64011af
Fix: Revise GPR of MAR06980 (#994)
JHL-452b Mar 30, 2026
a52a5d9
Feat: add MAR20191 as mitochondrial reaction of MAR03890 (#995)
JHL-452b Mar 30, 2026
8b03aff
fix: correct annotation for ISCA1 (ENSG00000135070) (#1019)
h-escoffier Jul 10, 2026
f870cbb
docs: update citation for Human2 in README.md (#1024)
mihai-sysbio Jul 10, 2026
b1c9379
refactor: macaw message template (#1025)
mihai-sysbio Jul 11, 2026
62f0b04
fix: correct invalid species cross-references (#1029)
edkerk Jul 11, 2026
dc22c97
fix: read spontaneous column as numeric in prepHumanModelForftINIT (#…
edkerk Jul 11, 2026
baeb13f
fix: correct MAR20070 subsystem casing to merge duplicate PPP group (…
edkerk Jul 11, 2026
c852d15
fix: correct cis-vaccenic acid (MAM01585) cross-references to the cis…
edkerk Jul 11, 2026
5de78d8
fix: harmonise FMN/FMNH2 annotations (#711) (#1036)
edkerk Jul 11, 2026
162326b
feat: add mass and charge balance report (#1035)
edkerk Jul 11, 2026
4e5c07b
docs: add citation.cff with the published Human2 (PNAS) citation (#30…
edkerk Jul 11, 2026
d456a30
fix: update ferrochelatase (FECH) EC number to 4.98.1.1 (#1048)
edkerk Jul 11, 2026
5f3a0e9
feat: overhaul contributor tracking (workflow, list refresh, six badg…
edkerk Jul 11, 2026
c813b92
feat: add descriptive names to all reactions (100% coverage) (#1052)
edkerk Jul 11, 2026
b90dfce
fix: fill missing and correct obsolete EC numbers (#1051)
edkerk Jul 11, 2026
2e5e5a6
Feat: add model quality-control checks workflow (#1046)
edkerk Jul 11, 2026
88ccf67
fix: ChEBI-based metabolite-name curation, first batch (#1053)
edkerk Jul 12, 2026
daba0a6
fix: normalise Title-Case metabolite (and CoA reaction) names (#1054)
edkerk Jul 12, 2026
d7ac8bd
chore: Human2 repository and code cleanup (#1055)
edkerk Jul 12, 2026
23155a1
feat: add duplicate-key QC gate to qcModelChecks (#1056)
edkerk Jul 12, 2026
ec1cefb
fix: correct malformed and cross-compartment metabolite cross-referen…
edkerk Jul 13, 2026
33bf3f5
ci: combine QC workflows, drop stamp files, modernise the comment act…
edkerk Jul 14, 2026
43308d7
feat: structure-verified annotation overhaul (metabolite + reaction c…
edkerk Jul 14, 2026
9ed8c65
Feat: convert MATLAB/RAVEN CI workflows to Python (#1027)
edkerk Jul 15, 2026
6ba2e23
ci: overhaul model-QC comment and result-file handling (#1062)
edkerk Jul 16, 2026
0cb4dfa
Merge main into develop to restore a shared ancestor
edkerk Jul 16, 2026
1ea27d8
Merge pull request #1064 from SysBioChalmers/chore/backmerge-main-int…
edkerk Jul 16, 2026
c7324a4
ci: let results reach a protected branch, and never lose a long run
edkerk Jul 16, 2026
4cc1965
chore: update model QC results [skip ci]
edkerk Jul 16, 2026
04ef04a
Merge pull request #1065 from SysBioChalmers/ci/results-push-and-salvage
edkerk Jul 16, 2026
7e13504
chore: update model QC results [skip ci]
edkerk Jul 16, 2026
73b4589
fix: install raven-toolbox for the full MEMOTE run, and stop hiding c…
edkerk Jul 16, 2026
54c02e8
Merge pull request #1066 from SysBioChalmers/fix/memote-full-raven-de…
edkerk Jul 16, 2026
3963841
chore: full MEMOTE result [skip ci]
edkerk Jul 16, 2026
b393fc1
fix: retry transient GitHub API errors when posting the QC comment
edkerk Jul 17, 2026
66bfdbb
chore: update model QC results [skip ci]
edkerk Jul 17, 2026
a81ea65
fix: fast-forward local to the remote before the MEMOTE results commit
edkerk Jul 17, 2026
3953134
Merge pull request #1067 from SysBioChalmers/fix/qc-comment-transient…
edkerk Jul 17, 2026
39dd8ca
chore: update model QC results [skip ci]
edkerk Jul 17, 2026
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253 changes: 162 additions & 91 deletions .all-contributorsrc

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7 changes: 5 additions & 2 deletions .deprecated/README.md
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@@ -1,7 +1,10 @@
# Deprecated

This directory contains old scripts, data, models, log files, etc. that are **no longer maintained or used**. They are stored here rather than deleted to maintain a historical account of repository activity in an easily accessible and searchable location.
Scripts, data, model files, and logs that were used during Human-GEM curation but are no longer maintained were once archived in this directory. They have been removed for the Human2 release (v2.0.0 and later) to keep the repository lean.

Code in this directory is **unlikely to function as expected**, and should not be modified. If a script or dataset is to be revived or updated in some way, it should be moved from this directory to the appropriate location in the repository.
These files remain fully available:

- in the git history of this repository, and
- in the last Human1 release, [v1.19.0](https://github.com/SysBioChalmers/Human-GEM/releases/tag/v1.19.0), which holds the complete set of deprecated and one-off curation files as they stood at the end of the Human1 series.

To revive a file, retrieve it from that release or from the git history and move it to the appropriate location in the repository.
24 changes: 0 additions & 24 deletions .deprecated/code/GPRs/getComplexesFromGeneRules.m

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