Merge pull request #132 from BIH-CEI/19-improve-gh-pages-doc-further

finally it worksss
BIH-CEI · Oct 2, 2024 · 1081663 · 1081663
2 parents 4266a41 + 7893f0d
commit 1081663
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diff --git a/docs/index.rst b/docs/index.rst
@@ -1,22 +1,18 @@
-.. phenopacket_mapper documentation master file, created by
-   sphinx-quickstart on Mon Jul 22 10:25:34 2024.
+.. Phenopacket Mapper documentation master file, created by
+   sphinx-quickstart on Thu Jan 01 2024.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-
-===========================
- Phenopacket Mapper
-===========================
-The documentation is structured as follows:
+Welcome to Phenopacket Mapper's documentation!
+===============================================
 
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
-   :numbered:
 
    installation
    quickstart
-
+   apidocs/modules
 
 Indices and tables
 ==================

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -1,12 +1,8 @@
 Installation
 ============
 
-This file is still a work in progress.
+To install the phenopacket_mapper library, run:
 
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-   :numbered:
+.. code-block:: bash
 
-   installation
-   quickstart
+   pip install phenopacket_mapper
diff --git a/docs/quickstart.rst b/docs/quickstart.rst
@@ -1,12 +1,11 @@
 Quickstart
 ==========
 
-This file is still a work in progress.
+This is a quickstart guide to help you get started with phenopacket_mapper.
 
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-   :numbered:
+Step 1: Do this...
 
-   installation
-   quickstart
+.. code-block:: python
+
+   from phenopacket_mapper import preprocess
+   preprocess(...)
diff --git a/src/phenopacket_mapper/data_standards/data_model.py b/src/phenopacket_mapper/data_standards/data_model.py
@@ -426,10 +426,9 @@ def preprocess(
         value to it. E.g.:
         ```python
         def preprocess_method(values, method, **kwargs):
-        ...
-            field1, field2 = values
-            # do something with values
-            return "preprocessed_values" + kwargs["arg1"] + kwargs["arg2"]
+        field1, field2 = values
+        # do something with values
+        return "preprocessed_values" + kwargs["arg1"] + kwargs["arg2"]
 
         dataset.preprocess(["field_1", "field_2"], preprocess_method, arg1="value1", arg2="value2")
         ```

diff --git a/src/phenopacket_mapper/mapping/mapper.py b/src/phenopacket_mapper/mapping/mapper.py
@@ -1,10 +1,9 @@
 from typing import List, Union, Dict
 
 from phenopackets import Phenopacket
-from phenopackets.schema.v2.core.base_pb2 import OntologyClass
 
-from phenopacket_mapper.data_standards import CodeSystem, Coding
-from phenopacket_mapper.data_standards.data_model import DataModel, DataSet, DataField, DataFieldValue
+from phenopacket_mapper.data_standards import CodeSystem
+from phenopacket_mapper.data_standards.data_model import DataModel, DataSet, DataField
 from phenopacket_mapper.mapping import PhenopacketElement, map_single