[ENH] add interactive figures (#439)

* use scripts to generate figure * use scripts to generate figure * refactor code openneuro data * update colormap * reset affiliations * rest affiliations and add some minimal doc * Update tools/count_citation.py Co-authored-by: Anthony Galassi <[email protected]> * Update tools/count_citation.py Co-authored-by: Anthony Galassi <[email protected]> --------- Co-authored-by: Anthony Galassi <[email protected]>
bids-standard · Jun 26, 2024 · 522d8fb · 522d8fb
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diff --git a/README.md b/README.md
@@ -27,6 +27,12 @@ Install all the dependencies.
 pip install -r requirements.txt
 ```
 
+Generate all the content require for the build.
+
+```bash
+make update
+```
+
 Serve the website with the mkdocs.
 ```bash
 mkdocs serve

diff --git a/data/beps/beps_completed.yml b/data/beps/beps_completed.yml
@@ -9,7 +9,8 @@
 #     - raw
 
 -   number: '001'
-    title: Quantitative MRI (qMRI)
+    title: Quantitative MRI
+    display: qMRI
     link: https://bids-specification.readthedocs.io/en/stable/appendices/qmri.html
     leads:
     -   name: Gilles de Hollander
@@ -22,6 +23,7 @@
 
 -   number: '002'
     title: BIDS Statistical Models Specification
+    display: stats model
     link: https://bids-standard.github.io/stats-models/
     leads:
     -   name: Tal Yarkoni
@@ -34,6 +36,7 @@
 
 -   number: '003'
     title: Common Derivatives
+    display: Common Der
     link: https://bids-specification.readthedocs.io/en/stable/derivatives/introduction.html
     leads:
     -   name: Chris Markiewicz
@@ -46,7 +49,8 @@
     pull_request_merged: 2020-06
 
 -   number: '005'
-    title: Arterial Spin Labeling (ASL)
+    title: Arterial Spin Labeling
+    display: ASL
     link: https://bids-specification.readthedocs.io/en/stable/appendices/arterial-spin-labeling.html
     leads:
     -   name: Henk-Jan Mutsaerts
@@ -60,7 +64,8 @@
     pull_request_merged: 2021-02
 
 -   number: '006'
-    title: Electroencephalography (EEG)
+    title: Electroencephalography
+    display: EEG
     link: https://bids-specification.readthedocs.io/en/stable/modality-specific-files/electroencephalography.html
     leads:
     -   name: Cyril Pernet
@@ -73,7 +78,8 @@
     pull_request_merged: 2019-03
 
 -   number: '007'
-    title: Hierarchical Event Descriptor (HED) Tags
+    title: Hierarchical Event Descriptor Tags
+    display: HED
     link: https://bids-specification.readthedocs.io/en/stable/appendices/hed.html
     leads:
     -   name: Chris Gorgolewski
@@ -84,7 +90,8 @@
     pull_request_merged: 2018-04
 
 -   number: '008'
-    title: Magnetoencephalography (MEG)
+    title: Magnetoencephalography
+    display: MEG
     link: https://bids-specification.readthedocs.io/en/stable/modality-specific-files/magnetoencephalography.html
     leads:
     -   name: Guiomar Niso
@@ -95,7 +102,8 @@
     pull_request_merged: 2018-04
 
 -   number: '009'
-    title: Positron Emission Tomography (PET)
+    title: Positron Emission Tomography
+    display: PET
     link: https://bids-specification.readthedocs.io/en/stable/modality-specific-files/positron-emission-tomography.html
     leads:
     -   name: Melanie Ganz
@@ -106,7 +114,8 @@
     pull_request_merged: 2021-04
 
 -   number: '010'
-    title: intracranial Electroencephalography (iEEG)
+    title: intracranial Electroencephalography
+    display: iEEG
     link: https://bids-specification.readthedocs.io/en/stable/modality-specific-files/intracranial-electroencephalography.html
     leads:
     -   name: Chris Holdgraf
@@ -119,6 +128,7 @@
 
 -   number: '018'
     title: Genetic information
+    display: Genetic
     link: https://bids-specification.readthedocs.io/en/stable/modality-specific-files/genetic-descriptor.html
     leads:
     -   name: Cyril Pernet
@@ -132,6 +142,7 @@
 
 -   number: '027'
     title: BIDS Applications 2.0
+    display: execution
     link: https://bids-standard.github.io/execution-spec/
     leads:
     -   name: Chris Markiewicz
@@ -144,6 +155,7 @@
 
 -   number: '029'
     title: Virtual and physical motion data
+    display: motion
     link: https://bids-specification.readthedocs.io/en/stable/modality-specific-files/motion.html
     leads:
     -   name: Sein Jeung
@@ -156,7 +168,8 @@
     pull_request_merged: 2023-03
 
 -   number: '030'
-    title: Near Infrared Spectroscopy (NIRS)
+    title: Near Infrared Spectroscopy
+    display: NIRS
     link: https://bids-specification.readthedocs.io/en/stable/modality-specific-files/near-infrared-spectroscopy.html
     leads:
     -   name: Robert Luke
@@ -169,6 +182,7 @@
 
 -   number: '031'
     title: Microscopy
+    display: Microscopy
     link: https://bids-specification.readthedocs.io/en/stable/modality-specific-files/microscopy.html
     leads:
     -   name: Marie-Hélène Bourget

diff --git a/data/count_citation.tsv b/data/count_citation.tsv
@@ -1,6 +1,6 @@
 papers	years	nb_citations
-fNIRS-BIDS, the Brain Imaging Data Structure Extended to Functional Near-Infrared Spectroscopy	2023	1
-ASL-BIDS, the brain imaging data structure extension for arterial spin labeling	2023	8
+fNIRS-BIDS	2023	1
+ASL-BIDS	2023	8
 Guidelines for the content and format of PET brain data in publications and archives	2021	13
 Guidelines for the content and format of PET brain data in publications and archives	2022	10
 Guidelines for the content and format of PET brain data in publications and archives	2020	6
@@ -10,36 +10,36 @@ The genetics-BIDS extension	2021	3
 The genetics-BIDS extension	2022	4
 Microscopy-BIDS	2023	5
 Microscopy-BIDS	2022	2
-PET-BIDS, an extension to the brain imaging data structure for positron emission tomography	2023	7
-PET-BIDS, an extension to the brain imaging data structure for positron emission tomography	2022	5
-MEG-BIDS, the brain imaging data structure extended to magnetoencephalography	2019	19
-MEG-BIDS, the brain imaging data structure extended to magnetoencephalography	2022	23
-MEG-BIDS, the brain imaging data structure extended to magnetoencephalography	2023	12
-MEG-BIDS, the brain imaging data structure extended to magnetoencephalography	2021	23
-MEG-BIDS, the brain imaging data structure extended to magnetoencephalography	2020	8
-MEG-BIDS, the brain imaging data structure extended to magnetoencephalography	2018	3
-iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology	2020	14
-iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology	2019	6
-iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology	2021	18
-iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology	2022	25
-iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology	2023	16
-EEG-BIDS, an extension to the brain imaging data structure for electroencephalography	2021	58
-EEG-BIDS, an extension to the brain imaging data structure for electroencephalography	2020	17
-EEG-BIDS, an extension to the brain imaging data structure for electroencephalography	2019	6
-EEG-BIDS, an extension to the brain imaging data structure for electroencephalography	2022	58
-EEG-BIDS, an extension to the brain imaging data structure for electroencephalography	2023	33
+PET-BIDS	2023	7
+PET-BIDS	2022	5
+MEG-BIDS	2019	19
+MEG-BIDS	2022	23
+MEG-BIDS	2023	12
+MEG-BIDS	2021	23
+MEG-BIDS	2020	8
+MEG-BIDS	2018	3
+iEEG-BIDS	2020	14
+iEEG-BIDS	2019	6
+iEEG-BIDS	2021	18
+iEEG-BIDS	2022	25
+iEEG-BIDS	2023	16
+EEG-BIDS	2020	17
+EEG-BIDS	2022	57
+EEG-BIDS	2021	58
+EEG-BIDS	2023	33
+EEG-BIDS	2019	6
+BIDS apps	2022	49
 BIDS apps	2021	36
-BIDS apps	2019	34
 BIDS apps	2020	26
-BIDS apps	2022	49
+BIDS apps	2019	33
 BIDS apps	2018	20
 BIDS apps	2017	12
 BIDS apps	2023	20
-The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments	2022	215
-The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments	2023	146
-The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments	2020	129
-The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments	2019	88
-The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments	2016	13
-The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments	2021	184
-The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments	2017	33
-The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments	2018	40
+The brain imaging data structure	2022	215
+The brain imaging data structure	2023	146
+The brain imaging data structure	2020	128
+The brain imaging data structure	2019	85
+The brain imaging data structure	2016	13
+The brain imaging data structure	2021	182
+The brain imaging data structure	2017	32
+The brain imaging data structure	2018	39