import mammalia toga2 annotations by emiliorighi · Pull Request #17 · guigolab/annotrieve-registry

emiliorighi · 2026-07-13T12:03:00Z

No description provided.

github-actions · 2026-07-13T13:38:17Z

Registry validation

New rows: 858 valid, 48 invalid
Manifest issues: 0
Duplicate assemblies (TSV files): 0
Duplicate URLs (TSV files): 0
Duplicate annotation files (MD5, TSV files): 0
Duplicate files vs registry index: 0
TSV header/parse errors: 0

Inline annotations on each failing row — open Files changed for details.
Updated on every push.

github-actions

Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

annotrieve-validator

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_004024985.1

download failed: ('Connection broken: IncompleteRead(130819 bytes read, 14956870 more expected)', IncompleteRead(130819 bytes read, 14956870 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 74 in f99189d

    
           GCA_004024985.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Saiga_tatarica__saiga_antelope__HLsaiTat1__GCA_004024985.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_004025025.1

download failed: ('Connection broken: IncompleteRead(294658 bytes read, 16737314 more expected)', IncompleteRead(294658 bytes read, 16737314 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 75 in f99189d

    
           GCA_004025025.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Tapirus_terrestris__Brazilian_tapir__HLtapTer1__GCA_004025025.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_004025065.1

download failed: ('Connection broken: IncompleteRead(589571 bytes read, 15127515 more expected)', IncompleteRead(589571 bytes read, 15127515 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 76 in f99189d

    
           GCA_004025065.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Semnopithecus_entellus__Hanuman_langur__HLsemEnt1__GCA_004025065.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_004025085.1

download failed: ('Connection broken: IncompleteRead(343811 bytes read, 13703956 more expected)', IncompleteRead(343811 bytes read, 13703956 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 77 in f99189d

    
           GCA_004025085.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Thryonomys_swinderianus__Greater_cane_rat__HLthrSwi1__GCA_004025085.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_004025125.1

download failed: ('Connection broken: IncompleteRead(294660 bytes read, 7714324 more expected)', IncompleteRead(294660 bytes read, 7714324 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 78 in f99189d

    
           GCA_004025125.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Tolypeutes_matacus__southern_three-banded_armadillo__HLtolMat1__GCA_004025125.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_004026525.1

download failed: ('Connection broken: IncompleteRead(163587 bytes read, 15252821 more expected)', IncompleteRead(163587 bytes read, 15252821 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 79 in f99189d

    
           GCA_004026525.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Miniopterus_schreibersii__Schreibers_long-fingered_bat__HLminSch1__GCA_004026525.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_016077325.1

download failed: ('Connection broken: IncompleteRead(4177666 bytes read, 16828067 more expected)', IncompleteRead(4177666 bytes read, 16828067 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 246 in f99189d

    
           GCA_016077325.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Equus_asinus__ass__HLequAsi3__GCA_016077325.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_049901635.1

download failed: ('Connection broken: IncompleteRead(4112130 bytes read, 14973239 more expected)', IncompleteRead(4112130 bytes read, 14973239 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 515 in f99189d

    
           GCA_049901635.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Scotinomys_teguina__Alstons_brown_mouse__HLscoTegu1__GCA_049901635.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_049997475.1

download failed: ('Connection broken: IncompleteRead(4177667 bytes read, 10392201 more expected)', IncompleteRead(4177667 bytes read, 10392201 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 516 in f99189d

    
           GCA_049997475.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Brachyteles_hypoxanthus__Northern_muriqui__HLbraHypo1__GCA_049997475.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_050000055.1

download failed: ('Connection broken: IncompleteRead(163586 bytes read, 21079611 more expected)', IncompleteRead(163586 bytes read, 21079611 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 517 in f99189d

    
           GCA_050000055.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Neotoma_floridana__Eastern_woodrat__HLneoFlor1A__GCA_050000055.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_050230965.1

download failed: ('Connection broken: IncompleteRead(163586 bytes read, 21425022 more expected)', IncompleteRead(163586 bytes read, 21425022 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 518 in f99189d

    
           GCA_050230965.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Bettongia_gaimardi__Tasmanian_bettong__HLbetGaim1A__GCA_050230965.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_050320145.1

download failed: ('Connection broken: IncompleteRead(163586 bytes read, 19452151 more expected)', IncompleteRead(163586 bytes read, 19452151 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 519 in f99189d

    
           GCA_050320145.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Hydrurga_leptonyx__Leopard_seal__HLhydLept1__GCA_050320145.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_050436925.1

download failed: ('Connection broken: IncompleteRead(2342658 bytes read, 17929367 more expected)', IncompleteRead(2342658 bytes read, 17929367 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 520 in f99189d

    
           GCA_050436925.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Pseudoryx_nghetinhensis__Saola__HLpseNghe1__GCA_050436925.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_050578075.1

download failed: ('Connection broken: IncompleteRead(311043 bytes read, 14154051 more expected)', IncompleteRead(311043 bytes read, 14154051 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 521 in f99189d

    
           GCA_050578075.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Holochilus_nanus__Neotropical_marsh_rat__HLholNanu1__GCA_050578075.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_050624465.1

download failed: ('Connection broken: IncompleteRead(4112130 bytes read, 15180240 more expected)', IncompleteRead(4112130 bytes read, 15180240 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 522 in f99189d

    
           GCA_050624465.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Tenrec_ecaudatus__Tailless_tenrec__HLtenEcau2B__GCA_050624465.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_050655435.1

download failed: ('Connection broken: IncompleteRead(753410 bytes read, 18655090 more expected)', IncompleteRead(753410 bytes read, 18655090 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 523 in f99189d

    
           GCA_050655435.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Gardnerycteris_keenani__Keenans_Hairy-nosed_Bat__HLgarKeen1A__GCA_050655435.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_050655445.1

download failed: ('Connection broken: IncompleteRead(163586 bytes read, 18708939 more expected)', IncompleteRead(163586 bytes read, 18708939 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 524 in f99189d

    
           GCA_050655445.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Gardnerycteris_keenani__Keenans_Hairy-nosed_Bat__HLgarKeen1B__GCA_050655445.1/query_annotation.gff.gz

🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCF_002288905.1

download failed: ('Connection broken: IncompleteRead(4177666 bytes read, 15769498 more expected)', IncompleteRead(4177666 bytes read, 15769498 more expected))

annotrieve-registry/TOGA2/annotations.tsv

Line 797 in f99189d

    
           GCF_002288905.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Enhydra_lutris_kenyoni__sea_otter__enhLutKen1__GCF_002288905.1/query_annotation.gff.gz

github-actions · 2026-07-13T13:38:19Z

+GCA_003327715.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Puma_concolor__puma__HLpumCon1__GCA_003327715.1/query_annotation.gff.gz
+GCA_003336285.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Mus_spicilegus__steppe_mouse__HLmusSpi1__GCA_003336285.1/query_annotation.gff.gz
+GCA_003426925.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Urocitellus_parryii__Arctic_ground_squirrel__HLuroPar1__GCA_003426925.1/query_annotation.gff.gz
+GCA_003668045.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Cricetulus_griseus__Chinese_hamster__HLcriGri3__GCA_003668045.1/query_annotation.gff.gz


🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_003668045.1

download failed: ('Connection broken: IncompleteRead(4112130 bytes read, 17504481 more expected)', IncompleteRead(4112130 bytes read, 17504481 more expected))

github-actions · 2026-07-13T13:38:19Z

+GCA_003336285.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Mus_spicilegus__steppe_mouse__HLmusSpi1__GCA_003336285.1/query_annotation.gff.gz
+GCA_003426925.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Urocitellus_parryii__Arctic_ground_squirrel__HLuroPar1__GCA_003426925.1/query_annotation.gff.gz
+GCA_003668045.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Cricetulus_griseus__Chinese_hamster__HLcriGri3__GCA_003668045.1/query_annotation.gff.gz
+GCA_003676075.2	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Marmota_flaviventris__yellow-bellied_marmot__HLmarFla1__GCA_003676075.2/query_annotation.gff.gz


🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_003676075.2

download failed: ('Connection broken: IncompleteRead(130818 bytes read, 19033891 more expected)', IncompleteRead(130818 bytes read, 19033891 more expected))

github-actions · 2026-07-13T13:38:19Z

+GCA_003426925.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Urocitellus_parryii__Arctic_ground_squirrel__HLuroPar1__GCA_003426925.1/query_annotation.gff.gz
+GCA_003668045.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Cricetulus_griseus__Chinese_hamster__HLcriGri3__GCA_003668045.1/query_annotation.gff.gz
+GCA_003676075.2	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Marmota_flaviventris__yellow-bellied_marmot__HLmarFla1__GCA_003676075.2/query_annotation.gff.gz
+GCA_003697995.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Taxidea_taxus_jeffersonii__American_badger__HLtaxTax1__GCA_003697995.1/query_annotation.gff.gz


🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_003697995.1

download failed: ('Connection broken: IncompleteRead(294659 bytes read, 14434072 more expected)', IncompleteRead(294659 bytes read, 14434072 more expected))

github-actions · 2026-07-13T13:38:19Z

+GCA_003668045.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Cricetulus_griseus__Chinese_hamster__HLcriGri3__GCA_003668045.1/query_annotation.gff.gz
+GCA_003676075.2	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Marmota_flaviventris__yellow-bellied_marmot__HLmarFla1__GCA_003676075.2/query_annotation.gff.gz
+GCA_003697995.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Taxidea_taxus_jeffersonii__American_badger__HLtaxTax1__GCA_003697995.1/query_annotation.gff.gz
+GCA_003704035.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Peromyscus_maniculatus_bairdii__prairie_deer_mouse__HLperManBai2__GCA_003704035.1/query_annotation.gff.gz


🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_003704035.1

download failed: ('Connection broken: IncompleteRead(4112130 bytes read, 17318898 more expected)', IncompleteRead(4112130 bytes read, 17318898 more expected))

github-actions · 2026-07-13T13:38:19Z

+GCA_003676075.2	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Marmota_flaviventris__yellow-bellied_marmot__HLmarFla1__GCA_003676075.2/query_annotation.gff.gz
+GCA_003697995.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Taxidea_taxus_jeffersonii__American_badger__HLtaxTax1__GCA_003697995.1/query_annotation.gff.gz
+GCA_003704035.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Peromyscus_maniculatus_bairdii__prairie_deer_mouse__HLperManBai2__GCA_003704035.1/query_annotation.gff.gz
+GCA_003704135.2	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Peromyscus_polionotus_subgriseus__oldfield_mouse__HLperPol1__GCA_003704135.2/query_annotation.gff.gz


🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_003704135.2

download failed: ('Connection broken: IncompleteRead(294658 bytes read, 20478843 more expected)', IncompleteRead(294658 bytes read, 20478843 more expected))

github-actions · 2026-07-13T13:38:21Z

+GCA_004024805.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Xerus_inauris__South_African_ground_squirrel__HLxerIna1__GCA_004024805.1/query_annotation.gff.gz
+GCA_004024825.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Pygathrix_nemaeus__Red_shanked_douc_langur__HLpygNem1__GCA_004024825.1/query_annotation.gff.gz
+GCA_004024845.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Tonatia_bakeri__stripe-headed_round-eared_bat__HLtonSau1__GCA_004024845.1/query_annotation.gff.gz
+GCA_004024885.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Saguinus_imperator__tamarin__HLsagImp1__GCA_004024885.1/query_annotation.gff.gz


🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_004024885.1

download failed: ('Connection broken: IncompleteRead(81666 bytes read, 17111731 more expected)', IncompleteRead(81666 bytes read, 17111731 more expected))

github-actions · 2026-07-13T13:38:21Z

+GCA_004024825.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Pygathrix_nemaeus__Red_shanked_douc_langur__HLpygNem1__GCA_004024825.1/query_annotation.gff.gz
+GCA_004024845.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Tonatia_bakeri__stripe-headed_round-eared_bat__HLtonSau1__GCA_004024845.1/query_annotation.gff.gz
+GCA_004024885.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Saguinus_imperator__tamarin__HLsagImp1__GCA_004024885.1/query_annotation.gff.gz
+GCA_004024905.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Tapirus_indicus__Asiatic_tapir__HLtapInd1__GCA_004024905.1/query_annotation.gff.gz


🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_004024905.1

download failed: ('Connection broken: IncompleteRead(261890 bytes read, 17039062 more expected)', IncompleteRead(261890 bytes read, 17039062 more expected))

github-actions · 2026-07-13T13:38:21Z

+GCA_004024845.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Tonatia_bakeri__stripe-headed_round-eared_bat__HLtonSau1__GCA_004024845.1/query_annotation.gff.gz
+GCA_004024885.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Saguinus_imperator__tamarin__HLsagImp1__GCA_004024885.1/query_annotation.gff.gz
+GCA_004024905.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Tapirus_indicus__Asiatic_tapir__HLtapInd1__GCA_004024905.1/query_annotation.gff.gz
+GCA_004024925.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Scalopus_aquaticus__eastern_mole__HLscaAqu1__GCA_004024925.1/query_annotation.gff.gz


🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_004024925.1

download failed: ('Connection broken: IncompleteRead(294659 bytes read, 15708075 more expected)', IncompleteRead(294659 bytes read, 15708075 more expected))

github-actions · 2026-07-13T13:38:21Z

+GCA_004024885.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Saguinus_imperator__tamarin__HLsagImp1__GCA_004024885.1/query_annotation.gff.gz
+GCA_004024905.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Tapirus_indicus__Asiatic_tapir__HLtapInd1__GCA_004024905.1/query_annotation.gff.gz
+GCA_004024925.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Scalopus_aquaticus__eastern_mole__HLscaAqu1__GCA_004024925.1/query_annotation.gff.gz
+GCA_004024945.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Uropsilus_gracilis__gracile_shrew_mole__HLuroGra1__GCA_004024945.1/query_annotation.gff.gz


🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_004024945.1

download failed: ('Connection broken: IncompleteRead(737027 bytes read, 14012282 more expected)', IncompleteRead(737027 bytes read, 14012282 more expected))

github-actions · 2026-07-13T13:38:21Z

+GCA_004024905.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Tapirus_indicus__Asiatic_tapir__HLtapInd1__GCA_004024905.1/query_annotation.gff.gz
+GCA_004024925.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Scalopus_aquaticus__eastern_mole__HLscaAqu1__GCA_004024925.1/query_annotation.gff.gz
+GCA_004024945.1	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Uropsilus_gracilis__gracile_shrew_mole__HLuroGra1__GCA_004024945.1/query_annotation.gff.gz
+GCA_004024965.2	https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Mammalia/Tragulus_javanicus__Java_mouse-deer__HLtraJav1__GCA_004024965.2/query_annotation.gff.gz


🚫 [annotrieve-validator] _{reported by reviewdog 🐶}
GCA_004024965.2

download failed: ('Connection broken: IncompleteRead(163586 bytes read, 20521647 more expected)', IncompleteRead(163586 bytes read, 20521647 more expected))

emiliorighi · 2026-07-13T14:49:35Z

Accepting PR: manual step to fix connection errors: switch to master, remove lines 44-73 (Chinese hamster to Java deer), switch to toga2 branch remove lines, re-add lines and reopen PR

import mammalia toga2 annotations

f99189d

github-actions Bot reviewed Jul 13, 2026

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emiliorighi merged commit d849e51 into master Jul 13, 2026
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emiliorighi commented Jul 13, 2026

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github-actions Bot commented Jul 13, 2026

Registry validation

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emiliorighi commented Jul 13, 2026

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