[ENH] organize list of tools (#338)

* list tools

* liquify rendering

_data/converters.yml

@@ -307,7 +307,7 @@
       GUI: false
 
     - name: BIDSconvertR
-      url: https://github.com/wulms/bidsconvertr
+      url: https://github.com/bidsconvertr/bidsconvertr
       comment: |
         The BIDSconvertR R package provides a user-friendly workflow with graphical user interfaces.
         It consists of the following steps:

_data/tools.yml

@@ -0,0 +1,147 @@
+# - name:
+#   url:
+#   documentation:
+#   language:
+#       -
+#   description:
+#   distribution:
+#     - name: pypi
+#       url:
+#     - name: dockerhub
+#       url:
+
+- name: babs
+  url: https://github.com/PennLINC/babs
+  documentation: https://pennlinc-babs.readthedocs.io/
+  language:
+    - Python
+  description: BIDS App Bootstrap (BABS) is a reproducible, generalizable, and scalable Python package for BIDS App analysis of large datasets. It uses DataLad and adopts FAIRly big framework.
+  distribution:
+    - name: pypi
+      url: https://pypi.org/project/babs/
+
+- name: BIDSHandler
+  url: https://github.com/Macquarie-MEG-Research/BIDSHandler
+  language:
+    -  Python
+  description: Python module allowing complete manipulation of BIDS data
+
+- name: bids-cfood
+  url: https://gitlab.indiscale.com/caosdb/src/crawler-cfoods/bids-cfood
+  language:
+    -  Python
+  description: a module to handle BIDS dataset for the caosDB data crawler
+
+- name: bids2cite
+  url: https://github.com/Remi-Gau/bids2cite
+  language:
+    -  Python
+  description: package to interactively update `dataset_description.json` and generate citation files (for example `datacite.yml`) for BIDS datasets.
+
+- name: bids-matlab
+  url: https://github.com/bids-standard/bids-matlab
+  language:
+    - MATLAB
+    - Octave
+  description: MATLAB/Octave tools to interact with datasets conforming to the BIDS format
+
+- name: BIDS-pydantic
+  url: https://github.com/gold-standard-phantoms/bids-pydantic
+  language:
+    - Python
+  description: "Pulls a specified version of the BIDS schema and creates corresponding Pydantic models, which will provide BIDS data validation using Python type annotations. See also [BIDS-pydantic-models](https://pypi.org/project/BIDS-pydantic-models/)."
+  distribution:
+    - name: pypi
+      url:  https://pypi.org/project/BIDS-pydantic/
+
+- name: bidser
+  url: https://github.com/bbuchsbaum/bidser
+  documentation: https://bbuchsbaum.github.io/bidser/
+  language:
+    - R
+  description: Working with Brain Imaging Data Structure in R
+
+- name: Brainstorm
+  url: http://neuroimage.usc.edu/brainstorm/
+  language:
+    - MATLAB
+  description: MEG/EEG analysis package
+
+- name: clpipe
+  url: https://github.com/cohenlabUNC/clpipe
+  documentation: https://clpipe.readthedocs.io/en/latest/index.html
+  language:
+    - Python
+  description: streamlined processing pipeline for MRI data centered around BIDS
+
+- name: cuBIDS
+  url: https://github.com/pennlinc/cubids
+  documentation: https://cubids.readthedocs.io/en/latest/
+  language:
+    -  Python
+  description: a Python package designed to facilitate reproducible curation of neuroimaging BIDS datasets
+  distribution:
+    - name: pypi
+      url: https://pypi.org/project/cubids/
+
+- name: GUI dataset description generator
+  url: https://github.com/tolik-g/BIDS
+  documentation:
+  language:
+    - Python
+  description: GUI form that generates `dataset_description.json`
+
+- name: Lead-DBS
+  url: https://www.lead-dbs.org/
+  language:
+    - MATLAB
+  description: A toolbox facilitating Deep Brain Stimulation electrode reconstructions  and computer simulations supports BIDS conversion and ingestion of BIDS datasets.
+
+- name: mne-bids
+  url: https://github.com/mne-tools/mne-bids
+  documentation: https://mne.tools/mne-bids/stable/index.html
+  language:
+    - Python
+  description: collection of tools for converting magnetoencephalography (MEG) data into BIDS format, as well as some helper functions for creating the folders and metadata needed for a BIDS dataset.
+
+- name: OpenNeuro
+  url: http://openneuro.org
+  description: A free and open platform for validating and sharing BIDS-compliant data.
+
+- name: PRFmodel
+  url: https://github.com/vistalab/PRFmodel
+  documentation: https://github.com/vistalab/PRFmodel/wiki
+  description: a set of tools to fit population receptive field models to BIDS datasets
+  distribution:
+    - name: dockerhub
+      url:
+        - https://hub.docker.com/r/garikoitz/prfsynth
+        - https://hub.docker.com/r/garikoitz/prfanalyze-vista
+        - https://hub.docker.com/r/garikoitz/prfanalyze-afni
+        - https://hub.docker.com/r/garikoitz/prfanalyze-aprf
+        - https://hub.docker.com/r/garikoitz/prfanalyze-popeye
+        - https://hub.docker.com/r/garikoitz/prfreport
+
+- name: PyBIDS
+  url: https://github.com/bids-standard/pybids
+  documentation:
+  language:
+    - Python
+  description: Python package to quickly parse / search the components of a BIDS dataset. It also contains functionality for running analyses on your data.
+  distribution:
+    - name: pypi
+      url: https://pypi.org/project/pybids/
+
+- name: rbids
+  url: https://github.com/mathesong/rbids
+  language:
+    - R
+  description: aims to make BIDS datasets more easily accessible for packages written in R
+
+- name: spm_2_bids
+  url: https://github.com/cpp-lln-lab/spm_2_bids
+  documentation: https://spm-2-bids.readthedocs.io/en/latest/
+  language:
+    - MATLAB
+    - Octave
+  description: a tool convert SPM preprocessed output to BIDS derivatives (trying to follow [BEP12](https://bids.neuroimaging.io/bep012))

_includes/list_tools.html

@@ -0,0 +1,9 @@
+<div>
+  <ul>
+    {% assign tools = include.tools %}
+    {% for tool_ in tools %}
+    {% assign name = tool_.name %}
+      <li><b><a href="{{ tool_.url }}" target="_blank">{{ tool_.name }}</a>:</b>{{ tool_.description | markdownify }}</li>
+    {% endfor %}
+  </ul>
+</div>

_pages/benefits.md

@@ -30,29 +30,4 @@ A description of how to build containerized apps supporting BIDS inputs can be f
 
 ## Other Tools
 
-- [BIDSHandler](https://github.com/Macquarie-MEG-Research/BIDSHandler){:target="_blank"} (Python module allowing complete manipulation of BIDS data)
-- [bids-cfood](https://gitlab.indiscale.com/caosdb/src/crawler-cfoods/bids-cfood)
-  a module to handle BIDS dataset for the caosDB data crawler.
-- [bids2cite](https://github.com/Remi-Gau/bids2cite){:target="_blank"} a python package
-  to interactively update `dataset_description.json` and generate citation files (for example `datacite.yml`) for BIDS datasets.
-- [bids-matlab](https://github.com/bids-standard/bids-matlab){:target="_blank"}
-  (MATLAB/Octave tools to interact with datasets conforming to the BIDS format)
-- [BIDS-pydantic](https://pypi.org/project/BIDS-pydantic/) pulls a specified version of the BIDS schema
-  and creates corresponding Pydantic models, which will provide BIDS data
-  validation using Python type annotations (see also [BIDS-pydantic-models](https://pypi.org/project/BIDS-pydantic-models/)).
-- [Brainstorm](http://neuroimage.usc.edu/brainstorm/){:target="_blank"} (MEG/EEG analysis package)
-- [clpipe](https://clpipe.readthedocs.io/en/latest/index.html){:target="_blank"}
-  streamlined processing pipeline for MRI data centered around BIDS.
-- [cuBIDS](https://pypi.org/project/cubids/){:target="_blank"}
-  a Python package designed to facilitate reproducible curation of neuroimaging BIDS datasets.
-- [GUI dataset description generator](https://github.com/tolik-g/BIDS){:target="_blank"}
-  (GUI form that generates dataset_description.json)
-- [Lead-DBS](https://www.lead-dbs.org/) A toolbox facilitating Deep Brain Stimulation electrode reconstructions
-  and computer simulations supports BIDS conversion and ingestion of BIDS datasets.
-- [OpenNeuro](http://openneuro.org){:target="_blank"} (repository)
-- [PRFmodel](https://github.com/vistalab/PRFmodel){:target="_blank"} a set of tools
-  to fit population receptive field models to BIDS datasets.
-- [PyBIDS](https://github.com/bids-standard/pybids){:target="_blank"} (Python module to harmonize access and manipulation)
-- [rbids](https://github.com/mathesong/rbids) aims to make BIDS datasets more easily accessible for packages written in R.
-- [spm_2_bids](https://github.com/cpp-lln-lab/spm_2_bids){:target="_blank"} a tool convert SPM preprocessed output
-  to BIDS derivatives (trying to follow [BEP12](https://bids.neuroimaging.io/bep012){:target="_blank"})
+{% include list_tools.html tools=site.data.tools %}