fix(docs): rearrange structure + update ci workflow deps (#362)

cancervariants · Jul 15, 2024 · cbc4499 · cbc4499
1 parent 7b4aaa4
commit cbc4499
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Showing 14 changed files with 12 additions and 8 deletions.
diff --git a/.github/workflows/checks.yaml b/.github/workflows/checks.yaml
@@ -47,7 +47,7 @@ jobs:
 
       - name: Run tests
         run: python3 -m pytest
-  
+
   lint:
     runs-on: ubuntu-latest
     steps:
@@ -79,7 +79,7 @@ jobs:
       - name: Install dependencies
         run: |
           python3 -m pip install --upgrade pip
-          python3 -m pip install '.[docs]'
+          python3 -m pip install '.[docs,pg,etl]'
 
       - name: Attempt docs build
         working-directory: ./docs

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -56,7 +56,7 @@ The Gene Normalizer was created to support the `Knowledgebase Integration Projec
     Usage<usage>
     Normalizing data<normalizing_data/index>
     Managing data<managing_data/index>
-    API Reference<api/index>
+    API Reference<reference/index>
     Changelog<changelog>
     Contributing<contributing>
     License<license>
diff --git a/...source/api/api/gene.database.database.rst → ...e/api/database/gene.database.database.rst b/...source/api/api/gene.database.database.rst → ...e/api/database/gene.database.database.rst
diff --git a/...source/api/api/gene.database.dynamodb.rst → ...e/api/database/gene.database.dynamodb.rst b/...source/api/api/gene.database.dynamodb.rst → ...e/api/database/gene.database.dynamodb.rst
diff --git a/...urce/api/api/gene.database.postgresql.rst → ...api/database/gene.database.postgresql.rst b/...urce/api/api/gene.database.postgresql.rst → ...api/database/gene.database.postgresql.rst
diff --git a/docs/source/api/api/gene.etl.base.rst → ...ource/reference/api/etl/gene.etl.base.rst b/docs/source/api/api/gene.etl.base.rst → ...ource/reference/api/etl/gene.etl.base.rst
diff --git a/docs/source/api/api/gene.etl.ensembl.rst → ...ce/reference/api/etl/gene.etl.ensembl.rst b/docs/source/api/api/gene.etl.ensembl.rst → ...ce/reference/api/etl/gene.etl.ensembl.rst
diff --git a/docs/source/api/api/gene.etl.exceptions.rst → ...reference/api/etl/gene.etl.exceptions.rst b/docs/source/api/api/gene.etl.exceptions.rst → ...reference/api/etl/gene.etl.exceptions.rst
diff --git a/docs/source/api/api/gene.etl.hgnc.rst → ...ource/reference/api/etl/gene.etl.hgnc.rst b/docs/source/api/api/gene.etl.hgnc.rst → ...ource/reference/api/etl/gene.etl.hgnc.rst
diff --git a/docs/source/api/api/gene.etl.merge.rst → ...urce/reference/api/etl/gene.etl.merge.rst b/docs/source/api/api/gene.etl.merge.rst → ...urce/reference/api/etl/gene.etl.merge.rst
diff --git a/docs/source/api/api/gene.etl.ncbi.rst → ...ource/reference/api/etl/gene.etl.ncbi.rst b/docs/source/api/api/gene.etl.ncbi.rst → ...ource/reference/api/etl/gene.etl.ncbi.rst
diff --git a/docs/source/api/api/gene.query.rst → docs/source/reference/api/gene.query.rst b/docs/source/api/api/gene.query.rst → docs/source/reference/api/gene.query.rst
diff --git a/docs/source/api/api/gene.schemas.rst → docs/source/reference/api/gene.schemas.rst b/docs/source/api/api/gene.schemas.rst → docs/source/reference/api/gene.schemas.rst
diff --git a/docs/source/api/index.rst → docs/source/reference/index.rst b/docs/source/api/index.rst → docs/source/reference/index.rst
@@ -1,7 +1,9 @@
+.. _api_reference:
+
 API Reference
 =============
 
-Core functions
+Core Modules
 --------------
 
 .. autosummary::
@@ -12,24 +14,26 @@ Core functions
    gene.query
    gene.schemas
 
-Database connections
+Database Modules
 --------------------
 
 .. autosummary::
    :nosignatures:
-   :toctree: api/
+   :toctree: api/database
    :template: module_summary.rst
 
    gene.database.database
    gene.database.dynamodb
    gene.database.postgresql
 
-Source ETL
+.. _etl-api:
+
+ETL Modules
 ----------
 
 .. autosummary::
    :nosignatures:
-   :toctree: api/
+   :toctree: api/etl
    :template: module_summary.rst
 
    gene.etl.base