Feat: changes some doc files

ylemarechal · Aug 30, 2023 · 34b6ec9 · 34b6ec9
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diff --git a/docs/citation.md b/docs/citation.md
@@ -1,2 +1,3 @@
+# Citation
 If you publish using PyOrthanc, we kindly ask that you credit us. PyOrthanc can be found on Zenodo :
 [https://doi.org/10.5281/zenodo.3387551](https://doi.org/10.5281/zenodo.3387551).
diff --git a/docs/contributing.md b/docs/contributing.md
@@ -1,3 +1,5 @@
+# Contribute 
+
 You can contribute to this project with the following steps:
 
 1. First, fork the project on Github

diff --git a/docs/index.md b/docs/index.md
@@ -1,12 +1,39 @@
-# **Presentation**
-Python library that wraps the Orthanc REST API and facilitates the manipulation
-of data with several cool utilities.
+<!-- ====================== TOC ====================== -->
+<!-- Generated by mkdocs-toc-md plugin -->
+<!-- ================================================= -->
 
-## **What for ?**
+# PyOrthanc
 
-The aim of the PyOrthanc module is to easy use the Orthanc Dicom server API. 
+Python library that wraps the Orthanc REST API and facilitates the manipulation of data with several cool utilities.
+What for ?
+
+The aim of the PyOrthanc module is to easy use the Orthanc Dicom server API.
 
 It has access to the full available Orthanc API and get the useful return without dealing with http requests.
 
-It also allows you to find specifics series/studies/patients 
-according to complex filters 
+It also allows you to find specifics series/studies/patients according to complex filters
+
+## [First steps](tutorial/quickstart.md#first-steps)
+### [Requirements](tutorial/quickstart.md#requirements)
+### [Installation](tutorial/quickstart.md#installation)
+### [Getting started](tutorial/quickstart.md#getting-started)
+* [Import pyorthanc library](tutorial/quickstart.md#import-pyorthanc-library)
+* [Connect to Orthanc](tutorial/quickstart.md#connect-to-orthanc)
+* [Upload DICOM files to Orthanc:](tutorial/quickstart.md#upload-dicom-files-to-orthanc)
+* [Getting list of connected remote modalities:](tutorial/quickstart.md#getting-list-of-connected-remote-modalities)
+* [Find and download patients according to criteria:](tutorial/quickstart.md#find-and-download-patients-according-to-criteria)
+* [Query (C-Find) and Retrieve (C-Move) from remote modality:](tutorial/quickstart.md#query-c-find-and-retrieve-c-move-from-remote-modality)
+### [Full basic examples](tutorial/quickstart.md#full-basic-examples)
+* [Access instance informations](tutorial/quickstart.md#access-instance-informations)
+### [Some useful commands](tutorial/quickstart.md#some-useful-commands)
+* [Docker commands](tutorial/quickstart.md#docker-commands)
+### [Advanced examples](tutorial/advanced.md)
+* [Transfer data from a PACS to a Orthanc server](tutorial/advanced.md#transfer-data-from-a-pacs-to-a-orthanc-server)
+### [Releases](releases/releases.md)
+* [Lastest release : 1.12.1](releases/releases.md#lastest-release-1121)
+* [Release 1.11.5](releases/releases.md#release-1115)
+## [Contribute](contributing.md#contribute)
+## [Contacts](contacts.md#contacts)
+* [Maintainers Team](contacts.md#maintainers-team)
+* [Useful links](contacts.md#useful-links)
+## [Citation](citation.md#citation)
diff --git a/docs/purpose.md b/docs/purpose.md
diff --git a/docs/releases/releases.md b/docs/releases/releases.md
@@ -1,5 +1,6 @@
-Lastest release : 1.12.1
-------------
+# Releases 
+
+## Lastest release : 1.12.1
 
 The Orthanc client has been regenerated on the Orthanc 1.12.1 version (source of the [changelist](https://hg.orthanc-server.com/orthanc/file/Orthanc-1.12.1/NEWS)).
 
@@ -30,8 +31,8 @@ Details:
 
     - All tests made with unittest has been refactored to use pytest
 
-Release 1.11.5 
-------------
+## Release 1.11.5 
+
 
 PyOrthanc v1.11.5 follow Orthanc version 1.11.3.
 

diff --git a/docs/to-start.md b/docs/to-start.md
diff --git a/docs/tutorial/advanced.md b/docs/tutorial/advanced.md
@@ -1,9 +1,8 @@
-Example of usage
-----------------
+# Advanced examples 
 
 Here is a list of complete examples with pyorthanc
 
-| code                                                                                                            | 
-|-----------------------------------------------------------------------------------------------------------------|
-| [Transfer data from a PACS to a Orthanc server](https://github.com/ylemarechal/dicom-transfer)                  |
+## Transfer data from a PACS to a Orthanc server
+
+[Transfer data from a PACS to a Orthanc server](https://github.com/ylemarechal/dicom-transfer)   
 
diff --git a/docs/tutorial/quickstart.md b/docs/tutorial/quickstart.md
@@ -109,15 +109,15 @@ orthanc.post_patients_id_anonymize(patient_identifier)
 #  'Type': 'Patient'}
 ```
 
-Example of usage
-----------------
+## Full basic examples
+
 Be sure that Orthanc is running. The default URL (if running locally) is `http://localhost:8042`.
 
 Here is a list of examples to helps you getting started with pyorthanc
 
-| code                                                                                                            | 
-|-----------------------------------------------------------------------------------------------------------------|
-| [Access instance informations](https://github.com/ylemarechal/pyorthanc-examples/tree/main/basic/access_informations) |
+### Access instance informations
+
+[Get instance informations](https://github.com/ylemarechal/pyorthanc-examples/tree/main/basic/access_informations)
 
 ## Some useful commands
 

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -51,3 +51,9 @@ plugins:
           options:
             docstring_style: numpy
       default_handler: python
+#  - toc-md:
+#      header_level:
+#      pickup_description_class: false
+#      ignore_page_pattern: api/*
+#      remove_navigation_page_pattern: api/*
+