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Dev -> Master for 1.1.0 release #158

Merged
merged 341 commits into from
Jun 25, 2024
Merged

Dev -> Master for 1.1.0 release #158

merged 341 commits into from
Jun 25, 2024

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JoseEspinosa
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JoseEspinosa and others added 30 commits May 12, 2023 15:25
@JoseEspinosa
Set a default docker registry outside of profile scope
11dd9b6
@JoseEspinosa
Add dev to changelog version and document last change
43c2b11
@JoseEspinosa
Merge pull request #95 from JoseEspinosa/quay_fix
20387d3 
Set a default docker registry outside of profile scope
@athbaltzis
Change uniclust30 to uniref30 path
672a671
@athbaltzis
Update CHANGELOG
b7f59db
@JoseEspinosa
Merge pull request #97 from athbaltzis/dev
cc4145d 
Change uniclust30 to uniref30 path when using the full BFD database in Alphafold2
@athbaltzis
Update colabfold container to python 3.10 and fix bug for multimers
a9aa8a7
@athbaltzis
Update docker registry
42dc8c8
@athbaltzis
Revert default docker.registry
6b6fd50
@athbaltzis
Update container in MMSEQS_COLABFOLDSEARCH
6418f2a
@athbaltzis
Update container for RUN_ALPHAFOLD2 module
005f84d
@athbaltzis
Change file read type to any
16a0119
@athbaltzis
Fix bug with filename collision
6198d7e
@athbaltzis
Update RUN_ALPHAFOLD2_MSA and RUN_ALPHAFOLD2_PRED containers
3393d17
@athbaltzis
Update container paths and revert type of file read for alphafold dbs
23f5fb7
@athbaltzis
Add dockerfiles
aeb394a
@athbaltzis
Fix linting
868c81f
@athbaltzis
Fix linting
85574af
@athbaltzis
Fix lintint 3rd attempt
86acba0
@athbaltzis
Fix linting 4th attempt
e83e255
@athbaltzis
Update CHANGELOG
671760c
@athbaltzis
Add quay.io source for singularity pulls
b1d40d5
@athbaltzis
Merge pull request #100 from athbaltzis/dev
1080e2b 
Update containers for local modules
@athbaltzis
Update gpu flag for colabfold
2fef3ea
@JoseEspinosa
Merge pull request #101 from athbaltzis/dev
a357972 
Update gpu flag for colabfold
@athbaltzis
Update COLABFOLD_BATCH dockerfile
e071acd
@athbaltzis
Update alphafold2 full_dbs parameter description
c97eedd
@athbaltzis
Put white bg to metro map png
03a53c6
@athbaltzis
Update CHANGELOG
66507e1
@athbaltzis
Update colabfold output name pattern
7f45653
@JoseEspinosa
Merge pull request #161 from JoseEspinosa/updates
c3c748a 
Modify path to esmfold db in its test_full config
itrujnara
itrujnara approved these changes Jun 12, 2024
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LGTM!

JoseEspinosa and others added 27 commits June 17, 2024 14:55
@JoseEspinosa
Fix file staging
9065362
@JoseEspinosa
Merge remote-tracking branch 'upstream/dev' into fixes
ebe7b0a
@JoseEspinosa
Merge pull request #162 from JoseEspinosa/fixes
1e8fc3a 
Fix channel creation for pdb_mmcfiles
@JoseEspinosa
Fix full test and update release date
2b3c03a
@JoseEspinosa
Fix changelog
9ecebf2
@JoseEspinosa
Merge pull request #163 from JoseEspinosa/fixes
8a1b1a4 
Fix full test and update release date
@adamrtalbot
Always upload logs after trying to launch AWS megatests
4f89eb7
@JoseEspinosa
Fix tyop
3c642ac
@JoseEspinosa
Merge remote-tracking branch 'upstream/dev' into fixes
71ac60e
@JoseEspinosa
Merge pull request #164 from JoseEspinosa/fixes
2286292 
Fix tyop in aws full test CI
@JoseEspinosa
Merge pull request #165 from nf-core/always-upload-logs-after-megatest
d2d5ff6 
Always upload logs after trying to launch AWS megatests
@JoseEspinosa
Discriminate between num_recycles of esmfold and colabfold (default v…
11f7a93 
…alue different)
@JoseEspinosa
Update readme
ae73c37
@JoseEspinosa
Add mention to AWS Open Data Sponsorship Program
12fb738
@JoseEspinosa
Merge remote-tracking branch 'upstream/dev' into fixes
cf94e83
@JoseEspinosa
Update changelog
e30e250
@JoseEspinosa
Merge pull request #166 from JoseEspinosa/fixes
564e06a 
Create 2 different parameters for Colabfold and ESMfold number of recycles
@JoseEspinosa
Update date
0c64479
@JoseEspinosa
Merge pull request #167 from JoseEspinosa/updates
b6281b3 
Update release date
@JoseEspinosa
Final prerelease updates
0def5c7
@JoseEspinosa @mashehu
Update CHANGELOG.md
5926d82 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@JoseEspinosa
Apply suggestions review
9e62090
@JoseEspinosa
Merge pull request #168 from JoseEspinosa/updates
38e5520 
Final prerelease updates
@JoseEspinosa
Use stable version of tools for download CI
8608879
@JoseEspinosa
Merge remote-tracking branch 'upstream/dev' into updates
867d245
@JoseEspinosa
Get rid of leak
c993517
@JoseEspinosa
Merge pull request #169 from JoseEspinosa/updates
6f66cb0 
Fix download CI
@JoseEspinosa JoseEspinosa merged commit d75ade1 into master Jun 25, 2024
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@itrujnara itrujnara itrujnara approved these changes

@mirpedrol mirpedrol mirpedrol approved these changes

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8 participants
@JoseEspinosa @mirpedrol @itrujnara @athbaltzis @nf-core-bot @bjlang @ziadbkh @adamrtalbot