Merge branch 'main' into il-empty-parquet

config/datasets/gcp.yaml

@@ -25,6 +25,7 @@ gene_index: ${datasets.outputs}/gene_index
 variant_annotation: ${datasets.outputs}/variant_annotation
 variant_index: ${datasets.outputs}/variant_index
 study_locus: ${datasets.outputs}/study_locus
+credible_set: ${datasets.outputs}/credible_set
 study_locus_overlap: ${datasets.outputs}/study_locus_overlap
 colocalisation: ${datasets.outputs}/colocalisation
 v2g: ${datasets.outputs}/v2g
@@ -33,6 +34,8 @@ catalog_study_index: ${datasets.outputs}/catalog_study_index
 catalog_study_locus: ${datasets.study_locus}/catalog_study_locus
 finngen_study_index: ${datasets.outputs}/finngen_study_index
 finngen_summary_stats: ${datasets.outputs}/finngen_summary_stats
+from_sumstats_study_locus: ${datasets.study_locus}/from_sumstats
+from_sumstats_pics: ${datasets.credible_set}/from_sumstats
 ukbiobank_study_index: ${datasets.outputs}/ukbiobank_study_index
 l2g_model: ${datasets.outputs}/l2g_model
 l2g_predictions: ${datasets.outputs}/l2g_predictions

config/step/pics.yaml

@@ -0,0 +1,3 @@
+_target_: otg.pics.PICSStep
+study_locus_ld_annotated_in: ${datasets.from_sumstats_study_locus}
+picsed_study_locus_out: ${datasets.from_sumstats_pics}

docs/python_api/step/pics.md

@@ -0,0 +1,4 @@
+---
+title: PICS
+---
+::: otg.pics.PICSStep

pyproject.toml

@@ -27,7 +27,7 @@ wandb = "^0.16.0"
 [tool.poetry.dev-dependencies]
 pre-commit = "^3.5.0"
 black = {version = "^22.12.0", allow-prereleases = true}
-mypy = "^1.6"
+mypy = "^1.7"
 pep8-naming = "^0.13.2"
 interrogate = "^1.5.0"
 isort = "^5.12.0"
@@ -36,7 +36,7 @@ ruff = "^0.1.3"
 
 [tool.poetry.group.docs.dependencies]
 mkdocs = "^1.5.3"
-mkdocstrings-python = "^1.7.3"
+mkdocstrings-python = "^1.7.4"
 mkdocs-material = "*"
 mkdocs-section-index = "^0.3.4"
 mkdocs-git-revision-date-localized-plugin = "^1.2.1"
@@ -61,9 +61,9 @@ pytest-xdist = "^3.4.0"
 [tool.poetry.group.dev.dependencies]
 ipython = "^8.5.0"
 ipykernel = "^6.19.0"
-google-cloud-dataproc = "^5.4.1"
+google-cloud-dataproc = "^5.7.0"
 apache-airflow = "^2.7.3"
-apache-airflow-providers-google = "^10.10.1"
+apache-airflow-providers-google = "^10.11.1"
 pydoclint = "^0.3.8"