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opentargets · Oct 16, 2023 · 33019d6 · 33019d6
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diff --git a/docs/assets/genetics_portal_logo-1.png b/docs/assets/genetics_portal_logo-1.png
diff --git a/docs/assets/imgs/GWAS_Catalog_circle_178x178.png b/docs/assets/imgs/GWAS_Catalog_circle_178x178.png
diff --git a/..._Targets_Genetics_Portal_Logo_v2_font.svg → ..._Targets_Genetics_Portal_Logo_v2_font.svg b/..._Targets_Genetics_Portal_Logo_v2_font.svg → ..._Targets_Genetics_Portal_Logo_v2_font.svg
diff --git a/docs/assets/imgs/UK_biobank_logo.png b/docs/assets/imgs/UK_biobank_logo.png
diff --git a/docs/assets/favicon.png → docs/assets/imgs/favicon.png b/docs/assets/favicon.png → docs/assets/imgs/favicon.png
diff --git a/docs/assets/imgs/finngen.svg b/docs/assets/imgs/finngen.svg
diff --git a/docs/assets/imgs/gnomad.svg b/docs/assets/imgs/gnomad.svg
diff --git a/docs/assets/imgs/open_targets_platform.svg b/docs/assets/imgs/open_targets_platform.svg
diff --git a/docs/assets/otlogo.png → docs/assets/imgs/otlogo.png b/docs/assets/otlogo.png → docs/assets/imgs/otlogo.png
diff --git a/docs/components/datasource/finngen/_finngen.md b/docs/components/datasource/finngen/_finngen.md
diff --git a/docs/components/datasource/gnomad/_gnomad.md b/docs/components/datasource/gnomad/_gnomad.md
diff --git a/docs/components/datasource/gwas_catalog/_gwas_catalog.md b/docs/components/datasource/gwas_catalog/_gwas_catalog.md
diff --git a/docs/components/datasource/open_targets/_open_targets.md b/docs/components/datasource/open_targets/_open_targets.md
diff --git a/docs/components/datasource/ukbiobank/_ukbiobank.md b/docs/components/datasource/ukbiobank/_ukbiobank.md
diff --git a/docs/components/method/_method.md b/docs/components/method/_method.md
diff --git a/docs/contributing/_contributing.md b/docs/contributing/_contributing.md
@@ -0,0 +1,3 @@
+# Contributing
+
+TBC
diff --git a/docs/contributing.md → docs/contributing/guidelines.md b/docs/contributing.md → docs/contributing/guidelines.md
@@ -1,4 +1,8 @@
-# Environment configuration and contributing changes
+---
+title: Guidelines
+---
+
+# Contributing guidelines
 
 ## One-time configuration
 The steps in this section only ever need to be done once on any particular system.

diff --git a/docs/troubleshooting.md → docs/contributing/troubleshooting.md b/docs/troubleshooting.md → docs/contributing/troubleshooting.md
@@ -1,3 +1,7 @@
+---
+title: Troubleshooting
+---
+
 # Troubleshooting
 
 ## BLAS/LAPACK

diff --git a/docs/index.md b/docs/index.md
@@ -1,6 +1,12 @@
+---
+title: Open Targets Genetics
+hide:
+  - navigation
+  - toc
+---
 
 <p align="center">
-  <img width="460" height="300" src="assets/Open_Targets_Genetics_Portal_Logo_v2_font.svg">
+  <img width="460" height="300" src="assets/imgs/Open_Targets_Genetics_Portal_Logo_v2_font.svg">
 </p>
 <style>
   .md-typeset h1,
@@ -24,4 +30,4 @@ Ingestion and analysis of genetic and functional genomic data for the identifica
 
 This project is still in experimental phase. Please refer to the [roadmap section](./roadmap/) for more information.
 
-For information on how to configure the development environment, run the code, or contribute changes, see the [contributing section](./contributing/). For known technical issues and solutions to them, see the [troubleshooting section](./troubleshooting/).
+For information on how to contribute to the project see the [contributing section](./contributing).
diff --git a/docs/installation.md b/docs/installation.md
@@ -0,0 +1,9 @@
+---
+Title: Installation
+hide:
+  - navigation
+  - toc
+---
+# Installation
+
+TBC
diff --git a/docs/python_api/.pages b/docs/python_api/.pages
@@ -0,0 +1 @@
+title: Python API
diff --git a/docs/components/step/_step.md → docs/python_api/_python_api.md b/docs/components/step/_step.md → docs/python_api/_python_api.md
diff --git a/docs/components/dataset/_dataset.md → docs/python_api/dataset/_dataset.md b/docs/components/dataset/_dataset.md → docs/python_api/dataset/_dataset.md
@@ -1,2 +1,4 @@
 
+# Dataset
+
 ::: otg.dataset.dataset.Dataset
diff --git a/docs/components/dataset/colocalisation.md → docs/python_api/dataset/colocalisation.md b/docs/components/dataset/colocalisation.md → docs/python_api/dataset/colocalisation.md
@@ -1,7 +1,8 @@
-::: otg.dataset.colocalisation.Colocalisation
-
-___
+# Colocalisation
 
 ## Schema
 
 --8<-- "assets/schemas/colocalisation.md"
+
+## Class
+::: otg.dataset.colocalisation.Colocalisation
diff --git a/docs/components/dataset/gene_index.md → docs/python_api/dataset/gene_index.md b/docs/components/dataset/gene_index.md → docs/python_api/dataset/gene_index.md
@@ -1,7 +1,9 @@
-::: otg.dataset.gene_index.GeneIndex
-
-___
+# GeneIndex
 
 ## Schema
 
 --8<-- "assets/schemas/targets.md"
+
+## Class
+
+::: otg.dataset.gene_index.GeneIndex
diff --git a/docs/components/dataset/intervals.md → docs/python_api/dataset/intervals.md b/docs/components/dataset/intervals.md → docs/python_api/dataset/intervals.md
@@ -1,7 +1,9 @@
-::: otg.dataset.intervals.Intervals
-
-___
+# Intervals
 
 ## Schema
 
 --8<-- "assets/schemas/intervals.md"
+
+## Class
+
+::: otg.dataset.intervals.Intervals
diff --git a/docs/components/dataset/ld_index.md → docs/python_api/dataset/ld_index.md b/docs/components/dataset/ld_index.md → docs/python_api/dataset/ld_index.md
@@ -1,9 +1,9 @@
-# LD index
+# LDIndex
 
 ## Schema
 
 --8<-- "assets/schemas/ld_index.md"
 
-## API
+## Class
 
 ::: otg.dataset.ld_index.LDIndex
diff --git a/docs/components/dataset/study_index.md → docs/python_api/dataset/study_index.md b/docs/components/dataset/study_index.md → docs/python_api/dataset/study_index.md
@@ -1,7 +1,9 @@
-::: otg.dataset.study_index.StudyIndex
-
-___
+# StudyIndex
 
 ## Schema
 
 --8<-- "assets/schemas/studies.md"
+
+## Class
+
+::: otg.dataset.study_index.StudyIndex
diff --git a/docs/components/dataset/study_locus.md → docs/python_api/dataset/study_locus.md b/docs/components/dataset/study_locus.md → docs/python_api/dataset/study_locus.md
@@ -1,11 +1,13 @@
-# Study-locus
-
-::: otg.dataset.study_locus.StudyLocus
+# StudyLocus
 
 ## Schema
 
 --8<-- "assets/schemas/study_locus.md"
 
+## Class
+
+::: otg.dataset.study_locus.StudyLocus
+
 ___
 
 # Study-locus quality controls

diff --git a/...components/dataset/study_locus_overlap.md → ...python_api/dataset/study_locus_overlap.md b/...components/dataset/study_locus_overlap.md → ...python_api/dataset/study_locus_overlap.md
@@ -1,8 +1,9 @@
-# Study Locus Overlap
+# StudyLocusOverlap
 
 ## Schema
 
 --8<-- "assets/schemas/study_locus_overlap.md"
-## API
+
+## Class
 
 ::: otg.dataset.study_locus_overlap.StudyLocusOverlap
diff --git a/.../components/dataset/summary_statistics.md → .../python_api/dataset/summary_statistics.md b/.../components/dataset/summary_statistics.md → .../python_api/dataset/summary_statistics.md
@@ -1,7 +1,9 @@
-::: otg.dataset.summary_statistics.SummaryStatistics
-
-___
+# SummaryStatistics
 
 ## Schema
 
 --8<-- "assets/schemas/summary_statistics.md"
+
+## Class
+
+::: otg.dataset.summary_statistics.SummaryStatistics
diff --git a/.../components/dataset/variant_annotation.md → .../python_api/dataset/variant_annotation.md b/.../components/dataset/variant_annotation.md → .../python_api/dataset/variant_annotation.md
@@ -1,7 +1,9 @@
-::: otg.dataset.variant_annotation.VariantAnnotation
-
-___
+# VariantAnnotation
 
 ## Schema
 
 --8<-- "assets/schemas/variant_annotation.md"
+
+## Class
+
+::: otg.dataset.variant_annotation.VariantAnnotation
diff --git a/docs/components/dataset/variant_index.md → docs/python_api/dataset/variant_index.md b/docs/components/dataset/variant_index.md → docs/python_api/dataset/variant_index.md
@@ -1,7 +1,9 @@
-::: otg.dataset.variant_index.VariantIndex
-
-___
+# VariantIndex
 
 ## Schema
 
 --8<-- "assets/schemas/variant_index.md"
+
+## Class
+
+::: otg.dataset.variant_index.VariantIndex
diff --git a/docs/components/dataset/variant_to_gene.md → docs/python_api/dataset/variant_to_gene.md b/docs/components/dataset/variant_to_gene.md → docs/python_api/dataset/variant_to_gene.md
@@ -1,7 +1,9 @@
-::: otg.dataset.v2g.V2G
-
-___
+# V2G
 
 ## Schema
 
 --8<-- "assets/schemas/v2g.md"
+
+## Class
+
+::: otg.dataset.v2g.V2G
diff --git a/docs/python_api/datasource/_datasource.md b/docs/python_api/datasource/_datasource.md
@@ -0,0 +1,3 @@
+# Datasource
+
+TBC
diff --git a/docs/python_api/datasource/finngen/_finngen.md b/docs/python_api/datasource/finngen/_finngen.md
@@ -0,0 +1,15 @@
+---
+title: FinnGen
+---
+
+<p align="center">
+  <img width="300" height="200" src="/assets/imgs/finngen.svg">
+</p>
+<style>
+  .md-typeset h1,
+  .md-content__button {
+    display: none;
+  }
+</style>
+
+[TOC]
diff --git a/...ponents/datasource/finngen/study_index.md → ...hon_api/datasource/finngen/study_index.md b/...ponents/datasource/finngen/study_index.md → ...hon_api/datasource/finngen/study_index.md
diff --git a/docs/python_api/datasource/gnomad/_gnomad.md b/docs/python_api/datasource/gnomad/_gnomad.md
@@ -0,0 +1,9 @@
+<p align="center">
+  <img width="300" height="200" src="/assets/imgs/gnomad.svg">
+</p>
+<style>
+  .md-typeset h1,
+  .md-content__button {
+    display: none;
+  }
+</style>
diff --git a/...components/datasource/gnomad/gnomad_ld.md → ...python_api/datasource/gnomad/gnomad_ld.md b/...components/datasource/gnomad/gnomad_ld.md → ...python_api/datasource/gnomad/gnomad_ld.md
diff --git a/...ents/datasource/gnomad/gnomad_variants.md → ..._api/datasource/gnomad/gnomad_variants.md b/...ents/datasource/gnomad/gnomad_variants.md → ..._api/datasource/gnomad/gnomad_variants.md
diff --git a/docs/python_api/datasource/gwas_catalog/_gwas_catalog.md b/docs/python_api/datasource/gwas_catalog/_gwas_catalog.md
@@ -0,0 +1,6 @@
+<div align="center">
+  <img width="100" height="100" src="/assets/imgs/GWAS_Catalog_circle_178x178.png">
+  <h1>GWAS Catalog</h1>
+</div>
+
+[TOC]
diff --git a/...s/datasource/gwas_catalog/associations.md → ...i/datasource/gwas_catalog/associations.md b/...s/datasource/gwas_catalog/associations.md → ...i/datasource/gwas_catalog/associations.md
diff --git a/...ts/datasource/gwas_catalog/study_index.md → ...pi/datasource/gwas_catalog/study_index.md b/...ts/datasource/gwas_catalog/study_index.md → ...pi/datasource/gwas_catalog/study_index.md
diff --git a/...datasource/gwas_catalog/study_splitter.md → ...datasource/gwas_catalog/study_splitter.md b/...datasource/gwas_catalog/study_splitter.md → ...datasource/gwas_catalog/study_splitter.md
diff --git a/...source/gwas_catalog/summary_statistics.md → ...source/gwas_catalog/summary_statistics.md b/...source/gwas_catalog/summary_statistics.md → ...source/gwas_catalog/summary_statistics.md
diff --git a/...onents/datasource/intervals/_intervals.md → ...on_api/datasource/intervals/_intervals.md b/...onents/datasource/intervals/_intervals.md → ...on_api/datasource/intervals/_intervals.md
diff --git a/...ponents/datasource/intervals/andersson.md → ...hon_api/datasource/intervals/andersson.md b/...ponents/datasource/intervals/andersson.md → ...hon_api/datasource/intervals/andersson.md
diff --git a/...mponents/datasource/intervals/javierre.md → ...thon_api/datasource/intervals/javierre.md b/...mponents/datasource/intervals/javierre.md → ...thon_api/datasource/intervals/javierre.md
diff --git a/docs/components/datasource/intervals/jung.md → docs/python_api/datasource/intervals/jung.md b/docs/components/datasource/intervals/jung.md → docs/python_api/datasource/intervals/jung.md
diff --git a/...omponents/datasource/intervals/thurman.md → ...ython_api/datasource/intervals/thurman.md b/...omponents/datasource/intervals/thurman.md → ...ython_api/datasource/intervals/thurman.md
diff --git a/docs/python_api/datasource/open_targets/_open_targets.md b/docs/python_api/datasource/open_targets/_open_targets.md
@@ -0,0 +1,9 @@
+<p align="center">
+  <img width="400" height="200" src="/assets/imgs/open_targets_platform.svg">
+</p>
+<style>
+  .md-typeset h1,
+  .md-content__button {
+    display: none;
+  }
+</style>
diff --git a/...ponents/datasource/open_targets/target.md → ...hon_api/datasource/open_targets/target.md b/...ponents/datasource/open_targets/target.md → ...hon_api/datasource/open_targets/target.md
diff --git a/docs/python_api/datasource/ukbiobank/_ukbiobank.md b/docs/python_api/datasource/ukbiobank/_ukbiobank.md
@@ -0,0 +1,9 @@
+<p align="center">
+  <img width="400" height="200" src="/assets/imgs/UK_biobank_logo.png">
+</p>
+<style>
+  .md-typeset h1,
+  .md-content__button {
+    display: none;
+  }
+</style>
diff --git a/...nents/datasource/ukbiobank/study_index.md → ...n_api/datasource/ukbiobank/study_index.md b/...nents/datasource/ukbiobank/study_index.md → ...n_api/datasource/ukbiobank/study_index.md
diff --git a/docs/python_api/method/_method.md b/docs/python_api/method/_method.md
@@ -0,0 +1 @@
+TBC
diff --git a/docs/components/method/clumping.md → docs/python_api/method/clumping.md b/docs/components/method/clumping.md → docs/python_api/method/clumping.md
diff --git a/docs/components/method/coloc.md → docs/python_api/method/coloc.md b/docs/components/method/coloc.md → docs/python_api/method/coloc.md
diff --git a/docs/components/method/ecaviar.md → docs/python_api/method/ecaviar.md b/docs/components/method/ecaviar.md → docs/python_api/method/ecaviar.md
diff --git a/docs/components/method/ld_annotator.md → docs/python_api/method/ld_annotator.md b/docs/components/method/ld_annotator.md → docs/python_api/method/ld_annotator.md
diff --git a/docs/components/method/pics.md → docs/python_api/method/pics.md b/docs/components/method/pics.md → docs/python_api/method/pics.md
diff --git a/...omponents/method/window_based_clumping.md → ...ython_api/method/window_based_clumping.md b/...omponents/method/window_based_clumping.md → ...ython_api/method/window_based_clumping.md
diff --git a/docs/python_api/step/_step.md b/docs/python_api/step/_step.md
@@ -0,0 +1,3 @@
+# Step
+
+TBC
diff --git a/docs/components/step/colocalisation.md → docs/python_api/step/colocalisation.md b/docs/components/step/colocalisation.md → docs/python_api/step/colocalisation.md
diff --git a/docs/components/step/finngen.md → docs/python_api/step/finngen.md b/docs/components/step/finngen.md → docs/python_api/step/finngen.md
diff --git a/docs/components/step/gene_index.md → docs/python_api/step/gene_index.md b/docs/components/step/gene_index.md → docs/python_api/step/gene_index.md
diff --git a/docs/components/step/gwas_catalog.md → docs/python_api/step/gwas_catalog.md b/docs/components/step/gwas_catalog.md → docs/python_api/step/gwas_catalog.md
diff --git a/...s/step/gwas_catalog_sumstat_preprocess.md → ...i/step/gwas_catalog_sumstat_preprocess.md b/...s/step/gwas_catalog_sumstat_preprocess.md → ...i/step/gwas_catalog_sumstat_preprocess.md
diff --git a/docs/components/step/ld_index.md → docs/python_api/step/ld_index.md b/docs/components/step/ld_index.md → docs/python_api/step/ld_index.md
diff --git a/docs/components/step/ukbiobank.md → docs/python_api/step/ukbiobank.md b/docs/components/step/ukbiobank.md → docs/python_api/step/ukbiobank.md
diff --git a/...omponents/step/variant_annotation_step.md → ...ython_api/step/variant_annotation_step.md b/...omponents/step/variant_annotation_step.md → ...ython_api/step/variant_annotation_step.md
diff --git a/docs/components/step/variant_index_step.md → docs/python_api/step/variant_index_step.md b/docs/components/step/variant_index_step.md → docs/python_api/step/variant_index_step.md
diff --git a/docs/components/step/variant_to_gene_step.md → docs/python_api/step/variant_to_gene_step.md b/docs/components/step/variant_to_gene_step.md → docs/python_api/step/variant_to_gene_step.md
diff --git a/docs/roadmap.md b/docs/roadmap.md
@@ -1,4 +1,9 @@
-
+---
+title: Roadmap
+hide:
+  - navigation
+  - toc
+---
 # Roadmap
 
 The Open Targets core team is working on refactoring Open Targets Genetics, aiming to:

diff --git a/docs/usage.md b/docs/usage.md
@@ -0,0 +1,10 @@
+---
+Title: How-to
+hide:
+  - navigation
+  - toc
+---
+
+# How-to
+
+TBC