From 2f094b444c860169b5c82373802165b98316b04a Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 21 Jan 2023 17:35:03 +0100 Subject: [PATCH] [ENH] improve BEP tables (#271) * switch blocking point colum for content column * use list * css * more css * render completed BEP from yml * update css * more css * more css * more css * split css for completed beps * rm duplicate --- _data/beps.yml | 63 +++++++++++-- _data/beps_completed.yml | 88 +++++++++++++++++ _includes/beps_completed_table.html | 43 +++++++++ _includes/beps_table.html | 16 ++-- _pages/get_involved.md | 14 +-- _sass/custom.scss | 141 ++++++++++++++++++++++------ 6 files changed, 311 insertions(+), 54 deletions(-) create mode 100644 _data/beps_completed.yml create mode 100644 _includes/beps_completed_table.html diff --git a/_data/beps.yml b/_data/beps.yml index 7f5a1976..57e8f9c7 100644 --- a/_data/beps.yml +++ b/_data/beps.yml @@ -7,7 +7,7 @@ # blocking: - number: "002" - title: The BIDS Models Specification + title: BIDS Models Specification leads: - name: Tal Yarkoni - name: Chris Markiewcz @@ -16,16 +16,20 @@ - list of steps is now a directed graph, - [Model zoo](https://github.com/bids-standard/model-zoo){:target:'_blank'}, - Abstracted transformations, to ease interoperability of implementations. + content: + - file format blocking: Stat Models released v1.0.0-rc1 in June 2021 - Please review! - number: "004" title: Susceptibility Weighted Imaging (SWI) leads: update: Looking for a new leader. + content: + - raw blocking: Looking for a new leader. - number: "011" - title: The structural preprocessing derivatives + title: Structural preprocessing derivatives leads: - name: Viviana Siless update: | @@ -37,12 +41,14 @@ - morphometrics. Need to conform with final Common Derivatives and gather community feedback. + content: + - derivative blocking: | Blocked by BIDS-validator extending and PyBIDS implementation for common derivatives - number: "012" - title: The functional preprocessing derivatives + title: Functional preprocessing derivatives leads: - name: Chris Markiewicz update: | @@ -51,17 +57,21 @@ Features: - Derivative images (mean, ALFF, ReHo, etc.), - Time series (confounds, decompositions, etc.) + content: + - derivative blocking: Blocked by BIDS-validator extending and PyBIDS implementation - number: "013" - title: The resting state fMRI derivatives + title: Resting state fMRI derivatives leads: - name: Steven Giavasis update: Merged into BEP012. + content: + - derivative blocking: None - number: "014" - title: The affine transformations and nonlinear field warps + title: Affine transformations and nonlinear field warps leads: - name: Oscar Esteban update: | @@ -69,10 +79,12 @@ - [There is a software prototype - NiTransforms](https://osf.io/8aq7b/){:target:"_blank"} demonstrates implementation of this BEP. NiTransforms has been tested and integrated to work within fMRIPrep + content: + - derivative blocking: In progress. - number: "016" - title: The diffusion weighted imaging derivatives + title: Diffusion weighted imaging derivatives leads: - name: Franco Pestilli - name: Oscar Esteban @@ -81,6 +93,8 @@ - Coordinating with BEP017. - Diffusion-weighted model description merged, but must comply to [this](https://github.com/bids-standard/bids-bep016/issues/7){:target:"_blank"}. - Upcoming integration across DWI, Tractography, Tractometry, and Connectivity (from fMRI and DWI) + content: + - derivative blocking: None - number: "017" @@ -91,6 +105,8 @@ - [Current state](https://bids.neuroimaging.io/bep017){:target:"_blank}. - Intended as a meeting point for minimal harmonisation of connectivity-based formats across modalities. - Seeking use cases spanning modalities and input defining connectivity based formats + content: + - derivative blocking: None - number: "019" @@ -98,6 +114,8 @@ leads: - name: Satrajit Ghosh update: Not active. Could be a NIDM extension rather than in BIDS. + content: + - metadata blocking: None - number: "020" @@ -107,6 +125,8 @@ update: | - BEP close to PR submission, examples and validator under development. - Seeking additional BEP lead to help incoporate into standard contact [dejan](mailto:dejan.draschow@psy.ox.ac.uk) to get involved. + content: + - raw blocking: None - number: "021" @@ -122,6 +142,8 @@ update: | - Discussion [here](https://github.com/bids-standard/bep021){:target:"_blank"} UCSD to include head models with BIDS EEG data. - Developments of BIDS M/EEG pipelines will trigger discussion on storing derived data. + content: + - derivative blocking: Mostly on hold. - number: "022" @@ -134,6 +156,8 @@ - Group discussions [here](https://forum.mrshub.org/t/bids-for-spectroscopy/83){:target:"_blank"} and [here](https://forum.mrshub.org/t/nifti-mrs-discussion-thread/443){:target:"_blank"}. - Developed NifTI standard for MRS data - presented abstract at ISMRM; manuscript in preparation. + content: + - raw blocking: None - number: "023" @@ -147,6 +171,8 @@ - Coord. kickoff scheduled Sept. 2021 to capture various experimental designs and needs for preprocessing and pharmacokinetic modeling. - Focused on staying aligned with derivatives for MRI (structural, functional, ASL, diffusion) + content: + - derivative blocking: Progressing and soliciting input from senior PET experts. - number: "024" @@ -154,6 +180,8 @@ leads: - name: Hugo Boniface update: Lead seeking more contributors and experts. + content: + - raw blocking: None - number: "025" @@ -170,6 +198,8 @@ [BIMCV-COVID19+](https://bimcv.cipf.es/bimcv-projects/bimcv-covid19/){:target:"_blank"}, and [BIMCV-COVID19-](https://bimcv.cipf.es/bimcv-projects/bimcv-covid19/#1590859488150-148be708-c3f3){:target:"_blank"}. - Included Kaggle Challenge [SIIM-FISABIO-RSNA COVID-19 Detection](https://www.kaggle.com/c/siim-covid19-detection/overview){:target:"_blank"} + content: + - raw blocking: None - number: "026" @@ -177,6 +207,8 @@ leads: - name: update: BEP is open to new leadership, see also [BEP032 (animal electrophys)](https://bids.neuroimaging.io/bep032){:target:"_blank"} + content: + - raw blocking: Searching for a new leader. - number: "027" @@ -189,6 +221,8 @@ and common behavior (for example, exit codes for failure modes); relies upon the Boutiques standard. - Re-conception of BIDS Apps + content: + - metadata blocking: None - number: "028" @@ -203,6 +237,8 @@ - Discussions held in [this repository](https://github.com/bids-standard/BEP028_BIDSprov){:target:"_blank"}. - A set of [examples](https://github.com/bids-standard/BEP028_BIDSprov/tree/master/examples){:target:"_blank"} and [user stories](https://github.com/bids-standard/BEP028_BIDSprov/issues/48){:target:"_blank"} are being refined. + content: + - metadata blocking: None - number: "029" @@ -211,6 +247,8 @@ - name: Sein Jeung - name: Julius Welzel update: BEP is developing and starting to finalize as discussions concerning example datasets are completed. + content: + - raw blocking: None - number: "032" @@ -228,6 +266,8 @@ - Supporting early stage interaction with: [ProbeInterface & SpikeInterface](https://github.com/SpikeInterface){:target:"_blank"}, [AnDO](https://github.com/INT-NIT/AnDO){:target:"_blank"}, interoperability with NWB and NIX data/metadata formats. + content: + - raw blocking: None - number: "033" @@ -243,6 +283,8 @@ - Comments may be submitted directly on the document. - Generating example datasets [here](https://github.com/JAgho/MISP_plot/tree/main){:target:"_blank"} and determining best practice w/ vendors to record data in-sequence + content: + - raw blocking: None - number: "034" @@ -253,6 +295,9 @@ update: | BEP Computational Models: PR open for review and discussion [here](https://github.com/bids-standard/bids-specification/pull/850) + content: + - derivative + - metadata blocking: None - number: "035" @@ -265,6 +310,8 @@ - BEP revised: now collecting further comments and community feedback. - Collaborators with mega-analysis experience or with actual example use-cases (planned/ongoing/finished mega analyses) welcome! + content: + - derivative blocking: None - number: "036" @@ -277,6 +324,8 @@ - Poster presentation at OHBM 2022. - Now collecting community comments and feedback. - All collaborators are welcome. + content: + - raw blocking: More reviews and discussions are necessary. - number: "037" @@ -287,4 +336,6 @@ - name: "[Carlo Miniussi](mailto:carlo.miniussi@unitn.it)" - name: "[Marta Bortoletto](mailto:marta.bortoletto@cognitiveneuroscience.it)" update: New BEP, collecting community comments and feedback. All collaborators are welcome. + content: + - raw blocking: None diff --git a/_data/beps_completed.yml b/_data/beps_completed.yml new file mode 100644 index 00000000..85aebf2e --- /dev/null +++ b/_data/beps_completed.yml @@ -0,0 +1,88 @@ +# template +# - number: +# title: +# leads: +# - name: +# content: +# - raw + +- number: "001" + title: Quantitative MRI (qMRI) + leads: + - name: Gilles de Hollander + - name: Kirstie Whitaker + content: + - raw + +- number: "003" + title: Common Derivatives + leads: + - name: Chris Markiewicz + content: + - derivative + +- number: "005" + title: Arterial Spin Labeling (ASL) + leads: + - name: Henk-Jan Mutsaerts + - name: Patricia Clement + - name: Jan Petr + - name: Marco Castellaro + content: + - raw + +- number: "006" + title: Electroencephalography (EEG) + leads: + - name: Cyril Pernet + - name: Stefan Appelhoff + - name: Robert Oostenveld + content: + - raw + +- number: "007" + title: Hierarchical Event Descriptor (HED) Tags + leads: + - name: Chris Gorgolewski + content: + - raw + +- number: "008" + title: Positron Emission Tomography (PET) + leads: + - name: Melanie Ganz + content: + - raw + +- number: "010" + title: intracranial Electroencephalography (iEEG) + leads: + - name: Chris Holdgraf + - name: Dora Hermes + content: + - raw + +- number: "018" + title: Genetic information + leads: + - name: Cyril R Pernet + - name: Clara Moreau + - name: Thomas Nichols + content: + - raw + +- number: "030" + title: Near Infrared Spectroscopy (NIRS) + leads: + - name: Robert Luke + - name: Luca Pollonini + content: + - raw + +- number: "031" + title: Microscopy + leads: + - name: Marie-Hélène Bourget + - name: Julien Cohen-Adad + content: + - raw diff --git a/_includes/beps_completed_table.html b/_includes/beps_completed_table.html new file mode 100644 index 00000000..9ff9486e --- /dev/null +++ b/_includes/beps_completed_table.html @@ -0,0 +1,43 @@ +
+
+
+ + + + + + + + + {% assign beps = include.beps %} {% for bep in beps %} {% assign number = + bep.number %} + + + + + + + {% endfor %} +
ExtensionTitleContentLead(s)
+ BEP{{ number }} + +

{{ bep.title }}

+ 		+
    + {% for x in bep.content %} +
  • {{ x | markdownify }}
    • + {% endfor %} +
+ 		+
    + {% for person in bep.leads %} +
  • {{ person.name | markdownify }}
    • + {% endfor %} +
+
+
+ +
+
diff --git a/_includes/beps_table.html b/_includes/beps_table.html index dee0d00d..75f90e64 100644 --- a/_includes/beps_table.html +++ b/_includes/beps_table.html @@ -5,9 +5,9 @@ Extension Title + Content Lead(s) Last update - Blocking point(s) {% assign beps = include.beps %} {% for bep in beps %} {% assign number = @@ -21,19 +21,23 @@

{{ bep.title }}

- + + + +

{{ bep.update | markdownify }}

- -

{{ bep.blocking | markdownify }}

- {% endfor %} diff --git a/_pages/get_involved.md b/_pages/get_involved.md index 280c2711..cf6c6d11 100644 --- a/_pages/get_involved.md +++ b/_pages/get_involved.md @@ -66,19 +66,7 @@ Below is a table of BEPs that have been merged. The references of the final publication for those BEPS can be found in the BIDS [specification](https://bids-specification.readthedocs.io/en/latest/01-introduction.html#datatype-specific-publications). -| Extension label | Title | Moderators/leads | -| --------------------------------------------------------------- | ------------------------------------------ | -------------------------------------------------------------------- | -| [BEP001](https://bids.neuroimaging.io/bep001){:target:"_blank"} | Quantitative MRI (qMRI) | Gilles de Hollander and Kirstie Whitaker | -| [BEP003](https://bids.neuroimaging.io/bep003){:target:"_blank"} | Common Derivatives | Chris Markiewicz | -| [BEP005](https://bids.neuroimaging.io/bep005){:target:"_blank"} | Arterial Spin Labeling (ASL) | Henk-Jan Mutsaerts, Patricia Clement, Jan Petr, and Marco Castellaro | -| [BEP006](https://bids.neuroimaging.io/bep006){:target:"_blank"} | Electroencephalography (EEG) | Cyril Pernet, Stefan Appelhoff, and Robert Oostenveld | -| [BEP007](https://bids.neuroimaging.io/bep007){:target:"_blank"} | Hierarchical Event Descriptor (HED) Tags | Chris Gorgolewski | -| [BEP008](https://bids.neuroimaging.io/bep008){:target:"_blank"} | Magnetoencephalography (MEG) | Guiomar Niso | -| [BEP009](https://bids.neuroimaging.io/bep009){:target:"_blank"} | Positron Emission Tomography (PET) | Melanie Ganz | -| [BEP010](https://bids.neuroimaging.io/bep010){:target:"_blank"} | intracranial Electroencephalography (iEEG) | Chris Holdgraf and Dora Hermes | -| [BEP018](https://bids.neuroimaging.io/bep018){:target:"_blank"} | Genetic information | Cyril R Pernet, Clara Moreau, and Thomas Nichols | -| [BEP030](https://bids.neuroimaging.io/bep030){:target:"_blank"} | Near Infrared Spectroscopy (NIRS) | Robert Luke and Luca Pollonini | -| [BEP031](https://bids.neuroimaging.io/bep031){:target:"_blank"} | Microscopy | Marie-Hélène Bourget and Julien Cohen-Adad | +{% include beps_completed_table.html beps=site.data.beps_completed %}
diff --git a/_sass/custom.scss b/_sass/custom.scss index 8ccf9a91..9a7968d7 100644 --- a/_sass/custom.scss +++ b/_sass/custom.scss @@ -45,6 +45,70 @@ padding: 1rem; } + .completed-bep-table-container { + + overflow: auto; + padding: 0; + + width: 100%; + + margin-left: 0%; + margin-right: 0%; + + padding: 0; + + text-align: left; + + vertical-align: middle; + + @include tablesmall { + width: 100%; + margin-left: 0%; + } + + table { + + .bep-number { + width: 8%; + } + + .bep-title { + width: 22%; + p{ + text-align: left; + white-space: wrap; + }; + } + + .bep-content { + width:10%; + ul { + margin: 0; + padding-left: 15px; + li { + margin: 0; + padding: 0; + margin-top: 2px; + } + } + } + + .bep-leads { + width:18%; + ul { + margin: 0; + padding-left: 15px; + li { + margin: 0; + padding: 0; + margin-top: 2px; + } + } + } + } + } + + .table-container { overflow: auto; @@ -54,12 +118,12 @@ margin-left: -10%; margin-right: 0%; - + padding: 0; text-align: left; - vertical-align: middle; + vertical-align: middle; @include tablesmall { width: 100%; @@ -69,40 +133,75 @@ table { .bep-title { - width: 15%; + width: 22%; p{ text-align: left; white-space: wrap; }; } - .leads { - width:15%; - padding: 0; - margin: 0; - p{margin: 0;} + .bep-content { + width:10%; + ul { + margin: 0; + padding-left: 15px; + li { + margin: 0; + padding: 0; + margin-top: 2px; + } + } + } + + .bep-leads { + width:18%; + ul { + margin: 0; + padding-left: 15px; + li { + margin: 0; + padding: 0; + margin-top: 2px; + } + } + } + + .bep-comment { + p { + margin: 0; + margin-top: 5px; + } + ul { + margin: 0; + padding-left: 15px; + li { + margin: 0; + padding: 0; + margin-top: 2px; + } + } } .comment { width:25% - } + } .shield-badge{ - display: flex; + display: flex; flex-direction: column; align-items: center; width: 180px } .distribution { - display: flex; + display: flex; flex-direction: column; align-items: center; justify-content: center; align-content: center; gap: 5px; width: 160px - } + } .converter-ul { p { @@ -118,22 +217,6 @@ margin-top: 2px; } } - } - - .bep-comment { - p { - margin: 0; - margin-top: 5px; - } - ul { - margin: 0; - padding-left: 15px; - li { - margin: 0; - padding: 0; - margin-top: 2px; - } - } } } @@ -157,7 +240,7 @@ } @include small { background-size: 90%; - } + } } .election-banner {