centralize converters

data/tools/all_converters.yml

@@ -18,7 +18,7 @@
 #       GUI: false
 
 -   group:
-    name: MRI and PET converters  # <--- get rid of the groups and names. Names will be manually entered in the markdown anyway. 
+    name: MRI and PET converters  # <--- get rid of the groups and names. Names will be manually entered in the markdown anyway.
     members:
     -   name: bidsify
         url: https://github.com/NILAB-UvA/bidsify
@@ -662,7 +662,6 @@
     -   name: sim2bids
         url: https://github.com/dissagaliyeva/sim2bids
         data_types:
-        -   ther converters
         -   computational model
         expected_input:
         -   CSV/TSV/DAT/Numpy

data/tools/converters.yml

@@ -493,12 +493,13 @@
         data_types:
         -   EEG
         expected_input:
-        -   EDF, Set : EEG or sEEG
+        -   EDF, Set: EEG or sEEG
         language:
         -   Javascript
         -   Python
         documentation: https://github.com/aces/EEG2BIDS
-        comment: A tool for converting raw EEG and iEEG data into the BIDS standard data structure, prepared for LORIS (Longitudinal Online Research and Imaging System).
+        comment: A tool for converting raw EEG and iEEG data into the BIDS standard data structure, prepared for LORIS (Longitudinal Online Research and
+            Imaging System).
 
 
 # Physiological data converters
@@ -540,8 +541,8 @@
 
 
 # 'From BIDS' converters
-# Comment: Converters that take a BIDS dataset as input to convert it into something else. 
-# Not mentioned here are the many software that can import a BIDS data as data structure 
+# Comment: Converters that take a BIDS dataset as input to convert it into something else.
+# Not mentioned here are the many software that can import a BIDS data as data structure
 # they are more familiar with.
     -   name: BIDS2ISATab
         url: https://github.com/bids-standard/BIDS2ISATab

docs/tools/converters/index.md → docs/tools/converters.md

@@ -1,29 +1,40 @@
 # Converters
 
-The following list of converters is provided to help you convert your raw data into a BIDS compliant dataset. 
+The following list of converters is provided to help you convert your raw data into a BIDS compliant dataset.
+
+## MRI Converters
 
-# MRI Converters
 Converters for processing MRI data.
+
 {{ MACROS___generate_converter_table(file="converters.yml", data_type="MRI") }}
 
-# PET Converters
+## PET Converters
+
 Converters for processing PET data.
+
 {{ MACROS___generate_converter_table(file="converters.yml", data_type="PET") }}
 
-# EEG/MEEG/iEEG Converters
-Converters for processing EEG, MEEG, and/or iEEG data. 
+## EEG/MEEG/iEEG Converters
+
+Converters for processing EEG, MEEG, and/or iEEG data.
+
 {{ MACROS___generate_converter_table(file="converters.yml", data_type="EEG") }}
 
-# Physio Converters
+## Physio Converters
+
 Physiological data converters.
+
 {{ MACROS___generate_converter_table(file="converters.yml", data_type="phsyiological") }}
 
-# BIDS Converters
-Converters that take a BIDS dataset as input to convert it into something else. 
+## BIDS Converters
+
+Converters that take a BIDS dataset as input to convert it into something else.
 Not mentioned here are the many software that can import a BIDS data as data structure they are more familiar with.
+
 {{ MACROS___generate_converter_table(file="converters.yml", data_type="BIDS") }}
 
-# Miscelaneous Converters
+## Miscellaneous Converters
+
 Not exactly BIDS converters but are common tools that can used by other BIDS converters.
-{{ MACROS___generate_converter_table(file="converters.yml", data_type="MISC") }}
 
+{{ MACROS___generate_converter_table(file="converters.yml", data_type="MISC") }}

docs/tools/index.md

@@ -2,12 +2,18 @@
 
 There is a rich ecosystem of tools to help you work with BIDS datasets.
 
-- Converters: There are many [converters](./converters/index.md)
-to help you go from your sourcedata to have a BIDS dataset.
-- BIDS Validator: The [BIDS validator](./validator.md) is there to ensure that your BIDS dataset is valid and will work with BIDS Apps without any obvious issues.
-- BIDS Apps: You can use [BIDS apps](./bids-apps.md)
-(automated pipelines that can be used as Docker or Apptainer images)
-to process your BIDS datasets.
-- Misc: There are many other [tools](./others.md) to help you work with, edit, or curate BIDS datasets.
+-   Converters: There are many [converters](./converters/index.md)
+    to help you go from your sourcedata to have a BIDS dataset.
+
+-   BIDS Validator: The [BIDS validator](./validator.md) is there
+    to ensure that your BIDS dataset is valid and will work with BIDS Apps
+    without any obvious issues.
+
+-   BIDS Apps: You can use [BIDS apps](./bids-apps.md)
+    (automated pipelines that can be used as Docker or Apptainer images)
+    to process your BIDS datasets.
+
+-   Misc: There are many other [tools](./others.md)
+    to help you work with, edit, or curate BIDS datasets.
 
 <meta property="og:title" content="Tools"/>

mkdocs.yml

@@ -165,12 +165,7 @@ nav:
     -   tools/validator.md
     -   tools/bids-apps.md
     -   tools/others.md
-    -   Converters:
-        - tools/converters/index.md
-        - tools/converters/mri-pet.md
-        - tools/converters/meeg.md
-        - tools/converters/physio.md
-        - tools/converters/others.md
+    -   tools/converters.md
 -   Datasets:
     -   datasets/index.md
 -   FAQ:

templates/converters_table_md.jinja

@@ -11,4 +11,4 @@
             | [{{ converter.name }}]( {{ converter_url }} "{{ converter.comment | replace("\n", " ") }}" ) | {% for input in converter.expected_input or ["N/A"] %} {{ input }} <br> {% endfor %} | {% for lang in converter.language or ["N/A"] %} {{ lang }} <br> {% endfor %} | {% for entry in converter.distribution or [] %} {% if entry.name == "pypi" %} [![PyPI version](https://badge.fury.io/py/{{ entry.url | replace("https://pypi.org/project/", "") }}.svg)]({{ entry.url }}) <br> {% elif entry.name == "dockerhub" %} [![dockerhub pulls](https://img.shields.io/docker/pulls/{{ entry.url | replace("https://hub.docker.com/r/", "")}}.svg)]({{ entry.url }}) <br> {% elif entry.name == "conda-forge" %} [![conda forge]({{ entry.url }}badges/version.svg)]({{ entry.url }}) <br> {% else %} [entry.name](entry.url) <br> {% endif %} {% endfor %} | !["GitHub last commit"](https://img.shields.io/github/last-commit/{{ converter.url | replace("https://github.com/", "") }}?style=plastic) |
         {% endif %}
     {% endif %}
-{% endfor %}
+{% endfor %}