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chore: trigger release process #3

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48cf2a8
fix(susie_finemapper): fix in the fine-mapper in case of sum stat imp…
addramir May 29, 2024
b60a19f
fix(SummaryStatistics): fix in sanity_filter (#623)
addramir May 30, 2024
fa6d500
build(deps): use pandas[gcp, parquet] (#626)
tskir May 30, 2024
b22951b
fix(docs): fixed typo in l2g_prediciton schema page (#629)
project-defiant May 31, 2024
daa8331
feat(config): extract gwas_significance parameter to step configurati…
project-defiant Jun 4, 2024
95f26d0
feat(data_release): preparation for 24.06 data release (#633)
project-defiant Jun 6, 2024
027b685
build(deps): bump typing-extensions from 4.11.0 to 4.12.1 (#632)
dependabot[bot] Jun 6, 2024
947d1e6
build(deps-dev): bump pep8-naming from 0.13.3 to 0.14.1 (#616)
dependabot[bot] Jun 6, 2024
fd3154a
feat(qtl): ingest credible sets from single cell derived QTLs (#630)
ireneisdoomed Jun 6, 2024
689340c
feat(spark-helpers): enforce schema of returned objects (#617)
DSuveges Jun 6, 2024
95244fd
feat: adding locus-breaker clumping method (#634)
DSuveges Jun 7, 2024
820f921
build(deps): bump wandb from 0.16.2 to 0.17.0 (#606)
dependabot[bot] Jun 7, 2024
d1577ee
build(deps-dev): bump ipython from 8.24.0 to 8.25.0 (#636)
dependabot[bot] Jun 10, 2024
e52fd11
build(deps): bump scikit-learn from 1.4.0 to 1.5.0 (#638)
dependabot[bot] Jun 11, 2024
ca43fff
feat: enable interface with gcp secrets manager (#635)
ireneisdoomed Jun 11, 2024
45d991c
feat: credible set quality filtering (#640)
Daniel-Considine Jun 11, 2024
976ee30
build(deps-dev): bump dbldatagen from 0.3.5 to 0.4.0 (#637)
dependabot[bot] Jun 13, 2024
3c8ce58
feat(config): 24.06 data release fixes (#639)
project-defiant Jun 13, 2024
7625a79
fix(L2GPrediction): schema validation (#642)
project-defiant Jun 14, 2024
79a6cb5
feat(SusieFineMapperStep): add new function with boundaries (#645)
addramir Jun 17, 2024
d796b68
feat: exclude region for StudyLocus object (#646)
Daniel-Considine Jun 17, 2024
dc70bd8
refactor: delete unnecessary config files (#647)
d0choa Jun 18, 2024
ca377ce
build: remove python-semantic-release as project dependency (#650)
d0choa Jun 18, 2024
6d93192
feat(ld_annotator): optional r2 threshold (#648)
ireneisdoomed Jun 18, 2024
2fd6d1f
feat(stydyLocus): adding new locus collection using boundaries (#644)
addramir Jun 19, 2024
a2a7a82
chore: enable Jupyter Notebook gateway for the Dataproc cluster (#651)
tskir Jun 24, 2024
0d9160f
feat(l2g): better l2g training, evaluation, and integration (#576)
ireneisdoomed Jun 24, 2024
8ff4bfc
feat: implement UKB PPP (EUR) ingestion & harmonisation (#652)
tskir Jun 25, 2024
b839164
chore: remove the locus_radius parameter (#659)
tskir Jun 25, 2024
996e6e2
chore(deps): bump python-semantic-release/python-semantic-release (#656)
dependabot[bot] Jun 26, 2024
df4d60d
build(deps-dev): bump pydoclint from 0.4.1 to 0.5.1 (#658)
dependabot[bot] Jun 26, 2024
08eaaff
ci: pre-commit update with pydoclint adjustments (#660)
d0choa Jun 26, 2024
41cb35b
fix: remove check merge conflict from pre-commit (#661)
d0choa Jun 28, 2024
b3e89bb
fix(SusieFineMapperStep): adding filtering of NANs in LD (#654)
addramir Jun 28, 2024
f79c789
feat(datasets): adding new variant index model (#641)
DSuveges Jun 30, 2024
f0a2902
fix: typo in `cs_lbf_thr` parameter name (#667)
tskir Jul 3, 2024
3f1cbe4
fix: make extended_spark_conf an empty dict instead of None (#668)
tskir Jul 3, 2024
768b5d2
fix(finemapping): link configuration and step classes (#669)
tskir Jul 3, 2024
6487b31
feat: vep annotation (dockerised + google batch + airflow) (#608)
d0choa Jul 4, 2024
5f97232
feat: locus_breaker_clumping (#655)
Daniel-Considine Jul 8, 2024
4a5f69f
feat: add qc step (#675)
addramir Jul 9, 2024
1f1088a
feat: adding sanity filter to GWASCatalogSumstatsPreprocessStep (#677)
addramir Jul 9, 2024
a0537c2
fix: leaving only five ancestries in LD (#680)
addramir Jul 9, 2024
a9d27d7
fix: improving locus_breaker_step logic (#679)
Daniel-Considine Jul 9, 2024
8986e86
fix: reconcile changes in the finemapping step with config (#682)
tskir Jul 9, 2024
27c9b6b
feat: credible set quality control step (#681)
Daniel-Considine Jul 9, 2024
c8f26df
feat(docker): image update for new orchestration (#683)
project-defiant Jul 11, 2024
91817fd
feat(StudyIndex): validation for study type, disease, target etc (#672)
DSuveges Jul 11, 2024
b5b9c20
build(deps-dev): bump ruff from 0.4.10 to 0.5.1 (#674)
dependabot[bot] Jul 11, 2024
421a5fe
chore: pre-commit autoupdate (#676)
pre-commit-ci[bot] Jul 11, 2024
6871d7d
fix: fixed selection of major ancestry for finemapper (#685)
Daniel-Considine Jul 11, 2024
ccbadc0
build(deps): bump skops from 0.9.0 to 0.10.0 (#673)
dependabot[bot] Jul 11, 2024
2882ff7
build(deps-dev): bump google-cloud-dataproc from 5.9.3 to 5.10.1 (#684)
dependabot[bot] Jul 11, 2024
905844c
feat(variant index): calculate hash as variant id for long variants (…
DSuveges Jul 11, 2024
836bb76
build(deps-dev): bump ipython from 8.25.0 to 8.26.0 (#662)
dependabot[bot] Jul 12, 2024
3059ca4
ci: prevent user from rebasing in minimal way (#691)
project-defiant Jul 12, 2024
00361cf
feat: artifacts versionned by release (#692)
project-defiant Jul 12, 2024
c5b4385
fix: moving hl.init (#687)
Daniel-Considine Jul 12, 2024
9268279
chore(study_index): improve study definition for the eQTL Catalogue a…
ireneisdoomed Jul 12, 2024
16f3d71
feat(studyLocus validation): adding validation logic to studyLocus da…
DSuveges Jul 12, 2024
2888271
ci: revert semantic-release update (#694)
project-defiant Jul 12, 2024
9b2ba40
feat: full orchestration of the variant index dag (#678)
ireneisdoomed Jul 12, 2024
457155e
feat: explode loci to extract variants + tests
ireneisdoomed Jul 15, 2024
aa713c7
fix: fix issue with gh commit not triggering artifact workflow
Jul 15, 2024
3a51e63
chore: pre-commit autoupdate
pre-commit-ci[bot] Jul 15, 2024
c56917c
ci: authentication with github app
Jul 16, 2024
c3e9f3c
Merge pull request #698 from opentargets/il-3333-explode
DSuveges Jul 16, 2024
c7781ad
Merge branch 'dev' into pre-commit-ci-update-config
tskir Jul 16, 2024
4613609
Merge pull request #699 from opentargets/pre-commit-ci-update-config
tskir Jul 16, 2024
40c927f
feat(docker): drom jq
Jul 16, 2024
7345ff1
fix(docker): change JAVA_HOME env to `/usr`
Jul 16, 2024
b5b3555
fix: typo in artifact file
project-defiant Jul 16, 2024
380b9e0
Merge branch 'dev' into 3384-refactoring-of-the-docker-release-proces…
project-defiant Jul 16, 2024
0dc3231
fix(finemapping): typo in "elapsed_time"
tskir Jul 16, 2024
b05508e
Merge pull request #700 from opentargets/3384-refactoring-of-the-dock…
project-defiant Jul 16, 2024
adab79c
Merge branch 'dev' into tskir-fix-finemapping-typo
tskir Jul 16, 2024
ab14f8a
feat: allow image push
Jul 16, 2024
004965b
Merge pull request #701 from opentargets/tskir-fix-finemapping-typo
tskir Jul 16, 2024
499b359
Merge branch 'dev' into 3384-allow-image-push
project-defiant Jul 16, 2024
82ef4ec
Merge pull request #702 from opentargets/3384-allow-image-push
project-defiant Jul 16, 2024
fda6b5a
feat: implement reading study locus paths from the manifest (#706)
tskir Jul 17, 2024
19ca45e
ci(release): use github app token for tag push (#709)
project-defiant Jul 19, 2024
7f16bc5
build(deps-dev): bump pytest from 8.2.2 to 8.3.1 (#712)
dependabot[bot] Jul 22, 2024
64d58f5
build(deps-dev): bump deptry from 0.16.1 to 0.17.0 (#714)
dependabot[bot] Jul 22, 2024
ce8f46b
build(deps-dev): bump mypy from 1.10.0 to 1.11.0 (#713)
dependabot[bot] Jul 22, 2024
ea80fbf
feat: expose summary statistics qc and locus breaker steps to hydra c…
project-defiant Jul 25, 2024
a5c96b9
fix: change config params to match new name (#721)
project-defiant Jul 29, 2024
897ae12
chore: pre-commit autoupdate (#715)
pre-commit-ci[bot] Jul 30, 2024
397f1e9
build(deps-dev): bump pymdown-extensions from 10.8.1 to 10.9 (#720)
dependabot[bot] Jul 31, 2024
0b9af70
build(deps-dev): bump deptry from 0.17.0 to 0.18.0 (#723)
dependabot[bot] Aug 8, 2024
ae734a8
feat: notebook for locus breaker and susie finemapping benchmark (#717)
Daniel-Considine Aug 8, 2024
5b5b408
fix: updating config paths and fine-mapping methods (#725)
Daniel-Considine Aug 8, 2024
e45f295
docs: macos fix for some functions (#729)
Daniel-Considine Aug 15, 2024
f49a5c5
build(deps-dev): bump ruff from 0.5.1 to 0.6.1 (#732)
dependabot[bot] Aug 22, 2024
4169b81
chore: pre-commit autoupdate (#724)
pre-commit-ci[bot] Aug 22, 2024
02b006d
build(deps-dev): bump deptry from 0.18.0 to 0.19.1 (#728)
dependabot[bot] Aug 22, 2024
5984de9
build(deps-dev): bump lxml from 5.2.2 to 5.3.0 (#727)
dependabot[bot] Aug 23, 2024
4db64a3
build(deps-dev): bump pre-commit from 3.7.1 to 3.8.0 (#719)
dependabot[bot] Aug 23, 2024
dc8c9dc
feat(variant_index): changes for a successful run (#735)
ireneisdoomed Aug 27, 2024
348b6f0
fix: update cluster creation command (#739)
project-defiant Aug 28, 2024
b6746fb
fix: revert recursiveFileLookup to False (#738)
project-defiant Aug 28, 2024
cf1ec24
feat: Finngen r11 ingestion (#733)
project-defiant Aug 29, 2024
2612aa7
fix: using h4 instead of log2(h4/h3) (#740)
Daniel-Considine Aug 30, 2024
93a6e60
fix: adding carma_tau parameter to susie_finemapper (#743)
addramir Sep 3, 2024
bb8558c
feat: logic and airflow pipeline for validation (#730)
DSuveges Sep 3, 2024
1a7b0d7
feat(variant index): improved data structure (#710)
DSuveges Sep 3, 2024
3ea47a9
fix: remove finngen prefix from credible set (#746)
project-defiant Sep 3, 2024
12ff35b
fix(finngen_r11): preserve all studyIds (#747)
project-defiant Sep 4, 2024
15a058e
feat: adding finemapping method to studylocusid hash (#744)
Daniel-Considine Sep 9, 2024
3c1e81a
build(deps-dev): bump ipython from 8.26.0 to 8.27.0 (#741)
dependabot[bot] Sep 9, 2024
151b4ec
build(deps-dev): bump deptry from 0.19.1 to 0.20.0 (#742)
dependabot[bot] Sep 10, 2024
0b216f6
fix: validation name mapping (#753)
project-defiant Sep 10, 2024
010c881
fix: removing old functions (#752)
addramir Sep 11, 2024
feb9cad
refactor: generalise per-chromosome processing (#754)
tskir Sep 11, 2024
d10cc20
refactor: generalise the harmonisation pipeline (#755)
tskir Sep 11, 2024
a49ae9a
feat: ingest FinnGen UKB meta-analysis data (#756)
tskir Sep 11, 2024
6469bf5
feat(validation): adding credible set variant validation (#757)
DSuveges Sep 12, 2024
d3435bb
feat: drop airflow orchestration layer from gentropy (#758)
project-defiant Sep 12, 2024
d6364f8
fix: multiple fixes after debugging and test runs (#760)
tskir Sep 13, 2024
34aaaf5
build(deps-dev): bump mkdocstrings-python from 1.10.5 to 1.11.1 (#749)
dependabot[bot] Sep 13, 2024
2e0e326
build(deps): bump wandb from 0.17.2 to 0.18.0 (#763)
dependabot[bot] Sep 17, 2024
6ede736
fix: prevent multiple credible filters to override spark plan (#766)
d0choa Sep 17, 2024
8c4421a
feat: flag MHC credible sets based on lead (#767)
d0choa Sep 18, 2024
d84d43b
fix: add condition to eQTL study index and schema (#770)
vivienho Sep 18, 2024
c3651b7
fix(effect harmonisation): addressing beta harmonisation bug (#762)
DSuveges Sep 18, 2024
c292e84
perf: quickly build a Docker image for every branch (#773)
tskir Sep 19, 2024
785dad0
feat: flag all top-hits from GWAS catalog curation (#775)
d0choa Sep 20, 2024
018defa
docs: fix broken refs (#768)
d0choa Sep 20, 2024
ad3f503
feat: flag PICS top hits in studies with credset sumstats (#777)
d0choa Sep 20, 2024
58fb726
fix(ld clumping): a revised logic allows a more accurate clumping (#772)
DSuveges Sep 23, 2024
b93842a
refactor(L2GFeatureMatrix)!: streamline feature matrix management (#745)
ireneisdoomed Sep 23, 2024
a29222e
feat(dataproc): ability to version gentropy for dataproc cluster (#774)
project-defiant Sep 23, 2024
dcacaf7
feat: add `studyType` to `StudyLocus` and `Colocalisation` (and `Stud…
vivienho Sep 24, 2024
df45a6c
feat: adding window based clumping to StudyLocus (#779)
DSuveges Sep 24, 2024
148e26e
fix: small qc flag fixes (#784)
addramir Sep 24, 2024
ccdb1f2
feat: add biosample index (#769)
Tobi1kenobi Sep 24, 2024
84d6638
feat: 99% credible set validation during `study_locus_validation` (#765)
d0choa Sep 24, 2024
2199ece
feat: flag credible sets explained by SuSiE regions (#780)
d0choa Sep 24, 2024
2010fb6
fix: remove n_eff check from qc_step (#785)
addramir Sep 24, 2024
d2a68d9
build(deps-dev): bump pymdown-extensions from 10.9 to 10.10.1 (#781)
dependabot[bot] Sep 24, 2024
95be9f6
build: updated precommits including adjustments to docstrings (#787)
d0choa Sep 24, 2024
6c4bdf5
fix(finngen_study_index): improved tests for finngen study index (#776)
project-defiant Sep 24, 2024
b525117
fix: clean unused study_locus step parameter (#786)
d0choa Sep 25, 2024
51125c7
fix(vep_parser): use nested schema for insilico predictors (#789)
project-defiant Sep 26, 2024
9f83329
fix: remove study_index_path from coloc step (#791)
project-defiant Sep 26, 2024
a135d26
fix(safe_array_union): allow for sorting nested structs (#793)
project-defiant Sep 27, 2024
26483c9
fix: fix bag in neglog_pvalue_to_mantissa_and_exponent (#795)
addramir Sep 27, 2024
88f62d4
fix(schema): recursive validation of arbitrarily deep nested structur…
DSuveges Sep 30, 2024
8b253a5
fix: adding data specific p-value filters (#788)
addramir Sep 30, 2024
5c58e58
feat: change `StudyLocusId` hashing method to md5 (and change `StudyL…
vivienho Sep 30, 2024
b7ccfae
feat: drop `v2g` and reimplement distance features (#771)
ireneisdoomed Oct 1, 2024
c3b8c2c
feat: out sample LD qc reason (#798)
d0choa Oct 1, 2024
a5588ae
chore: drop redundant parameter (#802)
project-defiant Oct 1, 2024
d4b5070
fix: align the schema of study_index for ukb ppp eur (#803)
project-defiant Oct 1, 2024
ccb484e
feat: force reinstallation of the gentropy on the cluster (#804)
project-defiant Oct 1, 2024
1c396d2
feat(validation): adding credible set confidence annotation at valida…
DSuveges Oct 1, 2024
9177dd4
chore: make the lb clumping ingest the partitionned data (#806)
project-defiant Oct 2, 2024
174f8f9
feat: adding filtering to susie finemapper (#796)
addramir Oct 2, 2024
25a4820
feat: add sumstat QC fields to schema (#809)
addramir Oct 2, 2024
70fd593
feat: fix biosample study validation (#810)
Tobi1kenobi Oct 3, 2024
c286c3b
refactor(vep_parser): store consequence to impact score as a project …
ireneisdoomed Oct 3, 2024
8876fc1
feat(l2g): implement variant consequence features from VEP (#805)
ireneisdoomed Oct 3, 2024
fca55be
feat: optimisation of qc step (#813)
addramir Oct 3, 2024
68c0168
fix(validation): add `qualityControls` column if missing in StudyLocu…
project-defiant Oct 4, 2024
b325eaa
fix: fix of type error in schema checking (#817)
addramir Oct 4, 2024
99b1d3c
fix: adding studId to FM log (#816)
addramir Oct 4, 2024
8b29168
fix: biosample id duplication (#822)
Tobi1kenobi Oct 7, 2024
27d8206
feat: change LD annotation for PICS fine-mapping to use major ancestr…
vivienho Oct 8, 2024
f3490d3
build(deps-dev): bump ipython from 8.27.0 to 8.28.0 (#819)
dependabot[bot] Oct 8, 2024
60f6bfa
build(deps-dev): bump pre-commit from 3.8.0 to 4.0.0 (#820)
dependabot[bot] Oct 9, 2024
b7dce8f
feat: decouple feature generation from L2G training step (#823)
ireneisdoomed Oct 9, 2024
9f0111c
fix: mhc flag incorrect (#825)
d0choa Oct 9, 2024
31e217b
revert: no longer rescuing variants not in LD matrix when overlapping…
d0choa Oct 10, 2024
58333c0
fix: empty inSilicoPredictors object in GnomAD variant index (#807)
DSuveges Oct 10, 2024
c7c602a
fix: write mode added to validation steps (#826)
d0choa Oct 11, 2024
e3d32ba
feat(l2g): merge sQTL and tuQTL colocalisation features (#824)
ireneisdoomed Oct 11, 2024
fb6111d
fix: adding single point statistics to pics loci (#832)
DSuveges Oct 11, 2024
9f446e8
fix(find_overlap): missing right study type in output (#828)
DSuveges Oct 11, 2024
c4520aa
feat: enhance variant index partitioning (#834)
d0choa Oct 12, 2024
e77abf4
feat: adding new LD interface (#759)
addramir Oct 14, 2024
38d4cb5
ci: configure java v8 (#840)
ireneisdoomed Oct 14, 2024
d461e38
fix(trainer): drop `studyLocusId` from training sets (#837)
ireneisdoomed Oct 14, 2024
6817aad
fix(l2g): remove custom session params + other fixes (#841)
ireneisdoomed Oct 14, 2024
44f05c4
build(deps-dev): bump pymdown-extensions from 10.10.1 to 10.11.2 (#815)
dependabot[bot] Oct 14, 2024
7fa85b2
build(deps-dev): bump mkdocs-git-committers-plugin-2 from 2.3.0 to 2.…
dependabot[bot] Oct 14, 2024
c50f660
build(deps-dev): bump pyparsing from 3.1.2 to 3.2.0 (#836)
dependabot[bot] Oct 14, 2024
6da92ce
build(deps-dev): bump mkdocstrings-python from 1.11.1 to 1.12.1 (#842)
dependabot[bot] Oct 14, 2024
e34e0c9
chore: adding priors to coloc step (#830)
addramir Oct 15, 2024
0a6d57b
fix: fix ukbppp studindex (#839)
addramir Oct 15, 2024
84a7a0d
fix: l2g fixes (#844)
d0choa Oct 15, 2024
172cedf
chore: remove h4/h3 ratio (#829)
addramir Oct 15, 2024
97a8873
fix: updating the susie_finemapper init (#846)
Daniel-Considine Oct 16, 2024
6a059d0
feat(coloc): step refactoring (#845)
project-defiant Oct 17, 2024
9bbbc02
test: skip `fetch_coordinates_from_rsids` (#850)
ireneisdoomed Oct 17, 2024
5cbf5ed
fix(eqtl): deduplicating credible set loci (#849)
DSuveges Oct 17, 2024
3ef43a9
chore: adding logging even when no CS in locus (#848)
addramir Oct 17, 2024
d33f66a
feat(l2g): limit colocalisation neighbourhood to protein coding genes…
ireneisdoomed Oct 17, 2024
9c52397
fix: filter nan in CSs (#855)
addramir Oct 17, 2024
c68a144
revert(finngen): restore the studyId prefix in finngen cs and si (#856)
project-defiant Oct 17, 2024
d650a29
feat(susie_finemapper): allow for extraction of the log file from man…
project-defiant Oct 18, 2024
333facb
chore(coloc): changing the content of `numberColocalisingVariants` fi…
DSuveges Oct 18, 2024
f93a9d3
fix: susie credible sets with unknown confidence (#862)
d0choa Oct 18, 2024
40a582c
fix: adding beta for lead variant (#863)
addramir Oct 21, 2024
13c2040
fix: biosample index add efo cell types (#853)
Tobi1kenobi Oct 21, 2024
7b20d55
feat(l2g): extend colocalisation neighbourhood metrics to missing gen…
ireneisdoomed Oct 21, 2024
de4627f
fix: add scQTLs into coloc features (#833)
addramir Oct 22, 2024
782a458
chore: pre-commit autoupdate (#866)
pre-commit-ci[bot] Oct 22, 2024
df220e9
feat: gwas catalog top-hit + study step (#808)
d0choa Oct 22, 2024
a78bae3
build(deps-dev): bump mypy from 1.11.0 to 1.12.1 (#865)
dependabot[bot] Oct 22, 2024
34a4e61
feat: adding desision tree to fine-mapper (#860)
addramir Oct 22, 2024
c5adb75
build(deps-dev): bump ruff from 0.6.1 to 0.7.0 (#864)
dependabot[bot] Oct 22, 2024
6e6687b
fix: logging of finemamper (#870)
addramir Oct 23, 2024
52da70f
chore: add chromosome validation (#869)
addramir Oct 23, 2024
9fe77ca
feat: add gene count features to l2g (#852)
xyg123 Oct 24, 2024
e233dac
feat: change betas to posterior mean from susie for Finngen credible …
Daniel-Considine Oct 24, 2024
d4b91d6
feat: step to export disease/target evidence (#867)
DSuveges Oct 24, 2024
c252dcb
feat(variant_index): hash variants at the time of instance creation (…
ireneisdoomed Oct 24, 2024
b694d80
fix: fix in calculate_credible_set_log10bf (#868)
addramir Oct 24, 2024
4c1013e
feat(l2g_feature_matrix): add `credibleSetConfidence` to L2G (#875)
ireneisdoomed Oct 25, 2024
3e61996
feat(l2g): normalise distance features (#878)
ireneisdoomed Oct 25, 2024
ee96c11
feat: l2g feature to indicate if gene is protein-coding or not (#873)
xyg123 Oct 25, 2024
85be796
feat: making credset qc have an option to coalsce and deduplicate cre…
Daniel-Considine Oct 25, 2024
5d9d7cb
test(study_locus) credible_set_qc step integration test (#880)
project-defiant Oct 25, 2024
cbbf3c5
feat: flagging duplicated entries while keeping one of the duplicates…
DSuveges Oct 26, 2024
d12d65d
feat: flag and filter credible sets (#879)
Tobi1kenobi Oct 28, 2024
1596c4c
build(deps-dev): bump ipython from 8.28.0 to 8.29.0 (#883)
dependabot[bot] Oct 28, 2024
31d8716
build(deps-dev): bump mypy from 1.12.1 to 1.13.0 (#884)
dependabot[bot] Oct 28, 2024
759857e
feat(trainer): log model explanation with shap (#886)
ireneisdoomed Oct 31, 2024
7bb74a5
chore: pre-commit autoupdate (#885)
pre-commit-ci[bot] Oct 31, 2024
fa38ca6
fix(distance_features): correct mean distance equation and correct ro…
ireneisdoomed Oct 31, 2024
b812f67
feat: add step to generate association data (#888)
vivienho Nov 1, 2024
c599856
fix: revert distinct for associations input file (#871)
vivienho Nov 1, 2024
9295d58
feat: add effect size direction to coloc output (#854)
Tobi1kenobi Nov 1, 2024
9237d73
refactor(convert to vcf): allow multiple input sources (#891)
project-defiant Nov 4, 2024
e0304fc
feat: deconvolute studies upon ingestion of GWAS Catalog datasets (#…
DSuveges Nov 4, 2024
3639b23
fix(`credibleSetConfidence`): inner join between study locus and vari…
ireneisdoomed Nov 4, 2024
04b1e22
feat(feature_matrix): impute values for gene attribute cols (#895)
ireneisdoomed Nov 5, 2024
94abc79
feat: adding l2g features to prediction table (#899)
DSuveges Nov 5, 2024
4d8e7c4
fix: ensure the #CHROM is not quoted (#896)
project-defiant Nov 5, 2024
2af1074
feat(feature_matrix): extract features for gwas associations only (#901)
ireneisdoomed Nov 5, 2024
6ec0d45
fix: do not impute `isProteinCoding` (#902)
addramir Nov 5, 2024
c305dbe
fix: reclassify eqtl catalogue sc datasets (#894)
Tobi1kenobi Nov 6, 2024
ebde0da
feat: improve partitioning of credible sets (#900)
d0choa Nov 6, 2024
0d3c01b
fix: using the 99% PIP cs column, (#904)
Daniel-Considine Nov 7, 2024
93de448
chore: add `hf_model_commit_message` to `LocusToGeneStep` (#905)
ireneisdoomed Nov 7, 2024
b5b71f0
refactor: finemapping method enum (#897)
d0choa Nov 8, 2024
0e7e815
chore(l2g): parametrise score threshold when writing predictions (#907)
ireneisdoomed Nov 11, 2024
bb609cb
chore: validate chromosome (#906)
DSuveges Nov 11, 2024
10b4be0
feat: extract pos and chromosome from variantid (#909)
project-defiant Nov 11, 2024
e5b3c9e
feat: changes to PICS credible sets (OUT_OF_SAMPLE_LD QC flag and cap…
vivienho Nov 12, 2024
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63 changes: 63 additions & 0 deletions .github/labeler.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,63 @@
version: 1
labels:
- label: "size-XS"
size:
exclude-files: ["poetry.lock"]
below: 10
- label: "size-S"
size:
exclude-files: ["poetry.lock"]
above: 9
below: 100
- label: "size-M"
size:
exclude-files: ["poetry.lock"]
above: 100
below: 500
- label: "size-L"
size:
exclude-files: ["poetry.lock"]
above: 499
below: 1000
- label: "size-XL"
size:
exclude-files: ["poetry.lock"]
above: 999
- label: "airflow"
files:
- "^src/airflow/.*"
- label: "Documentation"
files:
- "^docs/.*"
- label: "Dataset"
files:
- "^src/gentropy/dataset/.*"
- label: "Method"
files:
- "^src/gentropy/method/.*"
- label: "Datasource"
files:
- "^src/gentropy/datasource/.*"
- label: "Step"
files:
- "^src/gentropy/[a-zA-Z]\\w+\\.py"
- label: "Feature"
title: "^feat.*"
- label: "Bug"
title: "^fix.*"
- label: "Refactor"
title: "^refactor.*"
- label: "Chore"
title: "^chore.*"
- label: "CI"
title: "^ci.*"
- label: "Test"
title: "^test.*"
- label: "Documentation"
title: "^docs.*"
- label: "Performance"
title: "^perf.*"
- label: "Build"
title: "^build.*"
- label: "Revert"
title: "^revert.*"
28 changes: 28 additions & 0 deletions .github/pull_request_template.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
## ✨ Context

<!---
Congratulations! You've made it this far!
Once merged, your PR is going to appear in the release notes with the title you set, so make sure it's a great title that fully reflects the extent of your contribution.
What's the context for the changes? If the changes are related to a specific issue, please [link](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue) to it:
-->

## 🛠 What does this PR implement

<!--- _Detailed description of the changes introduced, Give examples of the changes you've made in this pull request, include an itemized list if you can and
add diagrams or images if necessary. It'll help the reviewer_ -->

## 🙈 Missing

<!--- If there are things that are requested in the task and were not implemented, list them here -->

## 🚦 Before submitting

- [ ] Do these changes cover one single feature (one change at a time)?
- [ ] Did you read the [contributor guideline](https://opentargets.github.io/gentropy/development/contributing/#contributing-checklist)?
- [ ] Did you make sure to update the documentation with your changes?
- [ ] Did you make sure there is no commented out code in this PR?
- [ ] Did you follow [conventional commits](https://www.conventionalcommits.org/en/v1.0.0/) standards in PR title and commit messages?
- [ ] Did you make sure the branch is up-to-date with the `dev` branch?
- [ ] Did you write any new necessary tests?
- [ ] Did you make sure the changes pass local tests (`make test`)?
- [ ] Did you make sure the changes pass pre-commit rules (e.g `poetry run pre-commit run --all-files`)?
85 changes: 85 additions & 0 deletions .github/workflows/artifact.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,85 @@
name: Build and Push to Artifact Registry

"on":
push:
branches: ["*"]
tags: ["*"]

env:
PROJECT_ID: open-targets-genetics-dev
REGION: europe-west1
GAR_LOCATION: europe-west1-docker.pkg.dev/open-targets-genetics-dev
REPOSITORY: gentropy-app
PYTHON_VERSION_DEFAULT: "3.10.8"

jobs:
build-push-artifact:
runs-on: ubuntu-latest
steps:
- name: "Checkout"
uses: "actions/checkout@v3"

- name: "auth"
uses: "google-github-actions/auth@v2"
with:
credentials_json: "${{ secrets.SERVICE_ACCOUNT_KEY }}"

- name: "Set up Cloud SDK"
uses: "google-github-actions/setup-gcloud@v2"

- name: "Use gcloud CLI"
run: "gcloud info"

- name: Set up QEMU
uses: docker/setup-qemu-action@v3

- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3

- name: "Docker auth"
run: |-
gcloud auth configure-docker ${{ env.REGION }}-docker.pkg.dev --quiet

- name: Quick Docker build (gentropy only, AMD64 only, with layer cache)
uses: docker/build-push-action@v6
with:
platforms: linux/amd64
push: true
tags: "${{ env.GAR_LOCATION }}/${{ env.REPOSITORY }}/gentropy:${{ github.ref_name }}"
context: .
cache-from: type=gha
cache-to: type=gha,mode=max

- name: Build and push gentropy image
if: github.ref == 'refs/heads/dev' || startsWith(github.ref, 'refs/tags/v')
uses: docker/build-push-action@v6
with:
platforms: linux/amd64,linux/arm64
push: true
tags: "${{ env.GAR_LOCATION }}/${{ env.REPOSITORY }}/gentropy:${{ github.ref_name }}"
context: .

- name: Build and push VEP image
if: github.ref == 'refs/heads/dev' || startsWith(github.ref, 'refs/tags/v')
uses: docker/build-push-action@v6
with:
platforms: linux/amd64
push: true
tags: "${{ env.GAR_LOCATION }}/${{ env.REPOSITORY }}/custom_ensembl_vep:${{ github.ref_name }}"
context: .
file: "src/vep/Dockerfile"

- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: ${{ env.PYTHON_VERSION_DEFAULT }}
- name: Install and configure Poetry
uses: snok/install-poetry@v1
with:
virtualenvs-create: true
virtualenvs-in-project: true
installer-parallel: true

- name: Build and push spark cluster dependencies
run: |
make build
14 changes: 14 additions & 0 deletions .github/workflows/labeler.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
name: Label PRs

"on":
- pull_request
- issues

jobs:
build:
runs-on: ubuntu-latest

steps:
- uses: srvaroa/labeler@master
env:
GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
5 changes: 5 additions & 0 deletions .github/workflows/pr.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,11 @@ jobs:
uses: actions/setup-python@v5
with:
python-version: 3.10.8
- name: Set up Java
uses: actions/setup-java@v4
with:
java-version: "8"
distribution: "temurin"
- name: Install and configure Poetry
uses: snok/install-poetry@v1
with:
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/pr_release_trigger.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ jobs:
source_branch: "dev"
destination_branch: "main"
pr_title: "chore: trigger release process"
pr_body: ":warning: *This PR requires a MERGE or REBASE COMMIT (Don't squash!)*"
pr_body: ":warning: *This PR requires a MERGE COMMIT (Don't squash!)*"
pr_label: "auto-pr"
pr_draft: false
pr_allow_empty: true
Expand Down
17 changes: 15 additions & 2 deletions .github/workflows/release.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -23,22 +23,35 @@ jobs:
contents: write

steps:
# NOTE: commits using GITHUB_TOKEN does not trigger workflows
- uses: actions/create-github-app-token@v1
id: trigger-token
with:
app-id: ${{ vars.TRIGGER_WORKFLOW_GH_APP_ID}}
private-key: ${{ secrets.TRIGGER_WORKFLOW_GH_APP_KEY }}
- uses: actions/checkout@v4
with:
fetch-depth: 0
repository: opentargets/gentropy
token: ${{ secrets.GITHUB_TOKEN }}
persist-credentials: false

- name: Python Semantic Release
id: semrelease
uses: python-semantic-release/python-semantic-release@master
# v9.6.0 is required due to the python v3.12 in the newer version of semantic release action which
# breaks the poetry build command.
uses: python-semantic-release/[email protected]
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
github_token: ${{ steps.trigger-token.outputs.token }}

- name: Publish package to GitHub Release
uses: python-semantic-release/upload-to-gh-release@main
if: ${{ steps.semrelease.outputs.released }} == 'true'
with:
# NOTE: allow to start the workflow when push action on tag gets executed
# requires using GH_APP to authenitcate, otherwise push authorised with
# the GITHUB_TOKEN does not trigger the tag artifact workflow.
# see https://github.com/actions/create-github-app-token
github_token: ${{ secrets.GITHUB_TOKEN }}
tag: ${{ steps.semrelease.outputs.tag }}

Expand Down
3 changes: 3 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -11,3 +11,6 @@ src/airflow/logs/*
!src/airflow/logs/.gitkeep
site/
.env
.coverage*
wandb/
hail*.log
25 changes: 17 additions & 8 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -1,9 +1,12 @@
default_language_version:
python: python3.10
ci:
autoupdate_commit_msg: "chore: pre-commit autoupdate"
autofix_commit_msg: "chore: pre-commit auto fixes [...]"
skip: [poetry-lock]
repos:
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.2.2
rev: v0.7.1
hooks:
- id: ruff
args:
Expand All @@ -12,13 +15,12 @@ repos:
files: ^((gentropy|utils|tests)/.+)?[^/]+\.py$

- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.5.0
rev: v5.0.0
hooks:
- id: trailing-whitespace
- id: end-of-file-fixer
exclude: "CHANGELOG.md"
- id: debug-statements
- id: check-merge-conflict
- id: check-case-conflict
- id: check-json
exclude: (.vscode|.devcontainer)
Expand Down Expand Up @@ -56,14 +58,14 @@ repos:
exclude: "CHANGELOG.md"

- repo: https://github.com/alessandrojcm/commitlint-pre-commit-hook
rev: v9.11.0
rev: v9.18.0
hooks:
- id: commitlint
additional_dependencies: ["@commitlint/config-conventional"]
additional_dependencies: ["@commitlint/config-conventional@18.6.3"]
stages: [commit-msg]

- repo: https://github.com/pre-commit/mirrors-mypy
rev: "v1.8.0"
rev: "v1.13.0"
hooks:
- id: mypy
args:
Expand All @@ -79,7 +81,7 @@ repos:
- "--disallow-untyped-defs"

- repo: https://github.com/econchick/interrogate
rev: 1.5.0
rev: 1.7.0
hooks:
- id: interrogate
args: [--verbose]
Expand All @@ -96,6 +98,13 @@ repos:
- id: beautysh

- repo: https://github.com/jsh9/pydoclint
rev: 0.4.1
rev: 0.5.9
hooks:
- id: pydoclint

- repo: https://github.com/python-poetry/poetry
rev: "1.8.0"
hooks:
- id: poetry-check
- id: poetry-lock
args: ["--no-update"]
5 changes: 4 additions & 1 deletion .vscode/settings.json
Original file line number Diff line number Diff line change
Expand Up @@ -25,5 +25,8 @@
"python.testing.pytestEnabled": true,
"mypy-type-checker.severity": {
"error": "Information"
}
},
"yaml.extension.recommendations": false,
"workbench.remoteIndicator.showExtensionRecommendations": false,
"extensions.ignoreRecommendations": true
}
27 changes: 27 additions & 0 deletions Dockerfile
Original file line number Diff line number Diff line change
@@ -0,0 +1,27 @@
FROM python:3.10-bullseye

RUN apt-get update \
&& apt-get clean \
&& apt-get install -y openjdk-11-jdk \
&& rm -rf /var/lib/apt/lists/*

ENV POETRY_NO_INTERACTION=1 \
POETRY_VIRTUALENVS_IN_PROJECT=1 \
POETRY_VIRTUALENVS_CREATE=1 \
POETRY_CACHE_DIR=/tmp/poetry_cache \
JAVA_HOME=/usr

RUN pip install poetry==1.7.1
WORKDIR /app

COPY pyproject.toml poetry.lock ./
RUN touch README.md

RUN poetry config installer.max-workers 10
RUN poetry install --without dev,docs,tests --no-root --no-interaction --no-ansi -vvv && rm -rf $POETRY_CACHE_DIR

COPY src ./src

RUN poetry install --without dev,docs,tests

ENTRYPOINT ["poetry", "run", "gentropy"]
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