Add api reference

cancervariants · Mar 31, 2024 · 5090759 · 5090759
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diff --git a/docs/source/_templates/module_summary.rst b/docs/source/_templates/module_summary.rst
@@ -0,0 +1,7 @@
+{{ fullname | underline }}
+
+.. automodule::  {{ fullname }}
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/metakb.database.rst b/docs/source/reference/api/metakb.database.rst
@@ -0,0 +1,8 @@
+metakb.database
+===============
+
+.. automodule::  metakb.database
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/metakb.exceptions.rst b/docs/source/reference/api/metakb.exceptions.rst
@@ -0,0 +1,8 @@
+metakb.exceptions
+=================
+
+.. automodule::  metakb.exceptions
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/metakb.harvesters.base.rst b/docs/source/reference/api/metakb.harvesters.base.rst
@@ -0,0 +1,8 @@
+metakb.harvesters.base
+======================
+
+.. automodule::  metakb.harvesters.base
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/metakb.harvesters.civic.rst b/docs/source/reference/api/metakb.harvesters.civic.rst
@@ -0,0 +1,8 @@
+metakb.harvesters.civic
+=======================
+
+.. automodule::  metakb.harvesters.civic
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/metakb.harvesters.moa.rst b/docs/source/reference/api/metakb.harvesters.moa.rst
@@ -0,0 +1,8 @@
+metakb.harvesters.moa
+=====================
+
+.. automodule::  metakb.harvesters.moa
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/metakb.normalizers.rst b/docs/source/reference/api/metakb.normalizers.rst
@@ -0,0 +1,8 @@
+metakb.normalizers
+==================
+
+.. automodule::  metakb.normalizers
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/metakb.query.rst b/docs/source/reference/api/metakb.query.rst
@@ -0,0 +1,8 @@
+metakb.query
+============
+
+.. automodule::  metakb.query
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/metakb.schemas.annotation.rst b/docs/source/reference/api/metakb.schemas.annotation.rst
@@ -0,0 +1,8 @@
+metakb.schemas.annotation
+=========================
+
+.. automodule::  metakb.schemas.annotation
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/metakb.schemas.api.rst b/docs/source/reference/api/metakb.schemas.api.rst
@@ -0,0 +1,8 @@
+metakb.schemas.api
+==================
+
+.. automodule::  metakb.schemas.api
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/metakb.schemas.app.rst b/docs/source/reference/api/metakb.schemas.app.rst
@@ -0,0 +1,8 @@
+metakb.schemas.app
+==================
+
+.. automodule::  metakb.schemas.app
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/metakb.schemas.categorical_variation.rst b/docs/source/reference/api/metakb.schemas.categorical_variation.rst
@@ -0,0 +1,8 @@
+metakb.schemas.categorical_variation
+====================================
+
+.. automodule::  metakb.schemas.categorical_variation
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/metakb.schemas.variation_statement.rst b/docs/source/reference/api/metakb.schemas.variation_statement.rst
@@ -0,0 +1,8 @@
+metakb.schemas.variation_statement
+==================================
+
+.. automodule::  metakb.schemas.variation_statement
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/metakb.transform.base.rst b/docs/source/reference/api/metakb.transform.base.rst
@@ -0,0 +1,8 @@
+metakb.transform.base
+=====================
+
+.. automodule::  metakb.transform.base
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/metakb.transform.civic.rst b/docs/source/reference/api/metakb.transform.civic.rst
@@ -0,0 +1,8 @@
+metakb.transform.civic
+======================
+
+.. automodule::  metakb.transform.civic
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/metakb.transform.moa.rst b/docs/source/reference/api/metakb.transform.moa.rst
@@ -0,0 +1,8 @@
+metakb.transform.moa
+====================
+
+.. automodule::  metakb.transform.moa
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/index.rst b/docs/source/reference/index.rst
@@ -0,0 +1,53 @@
+API Reference
+=============
+
+Core functions
+--------------
+
+.. autosummary::
+   :nosignatures:
+   :toctree: api/
+   :template: module_summary.rst
+
+   metakb.query
+   metakb.normalizers
+   metakb.database
+   metakb.exceptions
+
+Schemas
+-------
+
+.. autosummary::
+   :nosignatures:
+   :toctree: api/
+   :template: module_summary.rst
+
+   metakb.schemas.annotation
+   metakb.schemas.api
+   metakb.schemas.app
+   metakb.schemas.categorical_variation
+   metakb.schemas.variation_statement
+
+Data Harvesting
+---------------
+
+.. autosummary::
+   :nosignatures:
+   :toctree: api/
+   :template: module_summary.rst
+
+   metakb.harvesters.base
+   metakb.harvesters.civic
+   metakb.harvesters.moa
+
+Data Transformation
+-------------------
+
+.. autosummary::
+   :nosignatures:
+   :toctree: api/
+   :template: module_summary.rst
+
+   metakb.transform.base
+   metakb.transform.civic
+   metakb.transform.moa