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MAINT: Upgrade node for linting #1845

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merged 4 commits into from
Jun 1, 2024
Merged

MAINT: Upgrade node for linting #1845

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20d67a7
try upgrade node
sappelhoff Jun 1, 2024
48f4240
tab-size -> tab
sappelhoff Jun 1, 2024
9f93708
try pipe fix
sappelhoff Jun 1, 2024
78b7889
remaining pipe fixes
sappelhoff Jun 1, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/validation.yml
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Expand Up @@ -26,7 +26,7 @@ jobs:
- uses: actions/checkout@v4
- uses: actions/setup-node@v4
with:
node-version: 14
node-version: 22
- name: Install dependencies
run: npm install `cat npm-requirements.txt`
- name: Run style checks
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2 changes: 1 addition & 1 deletion .remarkrc
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Expand Up @@ -4,7 +4,7 @@
"preset-lint-recommended",
"remark-gfm",
["lint-no-duplicate-headings", false],
["lint-list-item-indent", "tab-size"],
["lint-list-item-indent", "tab"],
["lint-emphasis-marker", "consistent"],
["lint-maximum-line-length", false],
["lint-maximum-heading-length", false],
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8 changes: 4 additions & 4 deletions CONTRIBUTING.md
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Expand Up @@ -202,28 +202,28 @@ Don't do this:

```Markdown
| **Key name** | **Description** |
|--------------|----------------------------------------------------------|
| ------------ | -------------------------------------------------------- |
| Manufacturer | Manufacturer of the equipment, for example (`Siemens`) |
```

That would look like this:

| **Key name** | **Description** |
|--------------|----------------------------------------------------------|
| ------------ | -------------------------------------------------------- |
| Manufacturer | Manufacturer of the equipment, for example (`Siemens`) |

But do this instead:

```Markdown
| **Key name** | **Description** |
|--------------|----------------------------------------------------------|
| ------------ | -------------------------------------------------------- |
| Manufacturer | Manufacturer of the equipment, for example (`"Siemens"`) |
```

That would look like this:

| **Key name** | **Description** |
|--------------|----------------------------------------------------------|
| ------------ | -------------------------------------------------------- |
| Manufacturer | Manufacturer of the equipment, for example (`"Siemens"`) |


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4 changes: 2 additions & 2 deletions DECISION-MAKING.md
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Expand Up @@ -20,7 +20,7 @@ Current and past members of the steering group can be found
### Maintainers Group

| Name | Time commitment | Scope | Joined |
|---------------------------------------------------------------------------|-----------------|---------------------------------------|----------|
| ------------------------------------------------------------------------- | --------------- | ------------------------------------- | -------- |
| Stefan Appelhoff ([@sappelhoff](https://github.com/sappelhoff)) | 1h/week | | Mar 2020 |
| Chris Markiewicz ([@effigies](https://github.com/effigies)) | 5h/week | | Mar 2020 |
| Ross Blair ([@rwblair](https://github.com/rwblair)) | | Maintainer of the bids-validator | Mar 2020 |
Expand All @@ -46,7 +46,7 @@ is rotating among current maintainers.
#### Past maintainers group members

| Name | Duration |
|--------------------------------------------------------------------------------|---------------------|
| ------------------------------------------------------------------------------ | ------------------- |
| Franklin Feingold ([@franklin-feingold](https://github.com/franklin-feingold)) | Mar 2020 - Jul 2022 |

### BEP Leads Group
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8 changes: 4 additions & 4 deletions npm-requirements.txt
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@@ -1,5 +1,5 @@
remark-cli@9.0.0
remark-gfm@1
remark-preset-lint-recommended@5.0.0
remark-preset-lint-markdown-style-guide@4.0.0
remark-cli@12
remark-gfm@4
remark-preset-lint-recommended@7
remark-preset-lint-markdown-style-guide@6
remark-lint-no-trailing-spaces@2
4 changes: 2 additions & 2 deletions src/appendices/file-collections.md
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Expand Up @@ -47,7 +47,7 @@ and a guide for using macros can be found at
}}

| **Suffix** | **Linking entities** | **Application** | **Description** |
|------------|-----------------------|--------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| ---------- | --------------------- | ------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| VFA | flip | Variable flip angle | The VFA method involves at least two spoiled gradient echo (SPGR) of steady-state free precession (SSFP) images acquired at different flip angles. Depending on the provided metadata fields and the sequence type, data may be eligible for DESPOT1, DESPOT2 and their variants ([Deoni et al. 2005](https://doi.org/10.1002/mrm.20314)). |
| IRT1 | inv, part | Inversion recovery T1 mapping | The IRT1 method involves multiple inversion recovery spin-echo images acquired at different inversion times ([Barral et al. 2010](https://doi.org/10.1002/mrm.22497)). |
| MP2RAGE | flip, inv, echo, part | Magnetization prepared two gradient echoes | The MP2RAGE method is a special protocol that collects several images at different flip angles and inversion times to create a parametric T1map by combining the magnitude and phase images ([Marques et al. 2010](https://doi.org/10.1016/j.neuroimage.2009.10.002)). |
Expand Down Expand Up @@ -81,7 +81,7 @@ and a guide for using macros can be found at
}}

| **Suffix** | **Meta-data relevant entity** | **Application** | **Description** |
|------------|--------------------------------------------------------|------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| ---------- | ------------------------------------------------------ | ---------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| TB1DAM | flip | Double-angle B1+ mapping | The double-angle B1<sup>+</sup> method ([Insko and Bolinger 1993](https://doi.org/10.1006/jmra.1993.1133)) is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation flip angles. Common sequence types for this application include spin echo and echo planar imaging. |
| TB1EPI | flip, echo | B1<sup>+</sup> mapping with 3D EPI | This B1<sup>+</sup> mapping method ([Jiru and Klose 2006](https://doi.org/10.1002/mrm.21083)) is based on two EPI readouts to acquire spin echo (SE) and stimulated echo (STE) images at multiple flip angles in one sequence, used in the calculation of deviations from the nominal flip angle. |
| TB1AFI | Please see the [qMRI appendix](../appendices/qmri.md). | Actual Flip Angle Imaging (AFI) | This method ([Yarnykh 2007](https://doi.org/10.1002/mrm.21120)) calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence. |
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2 changes: 1 addition & 1 deletion src/appendices/licenses.md
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Expand Up @@ -9,7 +9,7 @@ The terms of any license should be consistent with the informed consent
obtained from participants and any institutional limitations on distribution.

| **Identifier** | **License name** | **Description** |
| ---------------| ------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------ |
| -------------- | ------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------ |
| PD | Public Domain | No license required for any purpose; the work is not subject to copyright in any jurisdiction. |
| [PDDL][pddl] | Open Data Commons Public Domain Dedication and License | License to assign public domain like permissions without giving up the copyright. |
| [CC0][cc0] | Creative Commons Zero 1.0 Universal. | Use this if you are a holder of copyright or database rights, and you wish to waive all your interests in your work worldwide. |
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2 changes: 1 addition & 1 deletion src/appendices/meg-systems.md
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Expand Up @@ -14,7 +14,7 @@ Preferred names of MEG systems comprise restricted keywords for Manufacturer fie
Restricted keywords for ManufacturersModelName field in the `*_meg.json` file:

| **System Model Name** | **Manufacturer** | **Details** |
|-------------------------- | --------- ------------| -------------------------------------------------------------------------------------------- |
| ------------------------- | --------- ----------- | -------------------------------------------------------------------------------------------- |
| CTF-64 | CTF | |
| CTF-151 | CTF | [https://www.ctf.com/products](https://www.ctf.com/products) |
| CTF-275 | CTF | CTF-275: OMEGA 2000 |
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6 changes: 3 additions & 3 deletions src/appendices/qmri.md
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Expand Up @@ -208,7 +208,7 @@ but also by which metadata fields are provided in accompanying json files.
#### Anatomy imaging data

| **File collection** | **REQUIRED metadata** | **OPTIONAL metadata** |
|----------------------|------------------------------------------------------------------------------------------------------------------------------|----------------------------|
| -------------------- | ---------------------------------------------------------------------------------------------------------------------------- | -------------------------- |
| VFA | `FlipAngle`, `PulseSequenceType`, `RepetitionTimeExcitation` | `SpoilingRFPhaseIncrement` |
| IRT1 | `InversionTime` | |
| MP2RAGE<sup>\*</sup> | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreparation`, `NumberShots`,`MagneticFieldStrength` | `EchoTime` |
Expand Down Expand Up @@ -282,7 +282,7 @@ and a guide for using macros can be found at
}}

| **File collection** | **REQUIRED metadata** |
|----------------------|------------------------------------------------------------------------------------------------------|
| -------------------- | ---------------------------------------------------------------------------------------------------- |
| TB1DAM | `FlipAngle` |
| TB1EPI | `EchoTime`, `FlipAngle`, `TotalReadoutTime`, `MixingTime` |
| TB1AFI | `RepetitionTime` |
Expand Down Expand Up @@ -447,7 +447,7 @@ This approach aims at:
- keeping an inheritance track of the qMRI methods described within the specification.

| **File-collection suffix** | **If REQUIRED metadata == Value** | **OPTIONAL metadata (`entity`/`fixed`)** | **Derived application name (NOT a suffix)** |
|----------------------------|-----------------------------------|------------------------------------------|---------------------------------------------|
| -------------------------- | --------------------------------- | ---------------------------------------- | ------------------------------------------- |
| VFA | `PulseSequenceType` == `SPGR` | | DESPOT1 |
| VFA | `PulseSequenceType` == `SSFP` | `SpoilingRFPhaseIncrement` (`fixed`) | DESPOT2 |
| MP2RAGE | | `EchoTime` (`echo`) | MP2RAGE-ME |
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4 changes: 2 additions & 2 deletions src/appendices/units.md
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Expand Up @@ -47,7 +47,7 @@ Examples for CMIXF-12 (including the five unicode symbols mentioned above):
## Unit table

| **Unit name** | **Unit symbol** | **Quantity name** |
| ---------------| --------------- | ------------------------------------------ |
| -------------- | --------------- | ------------------------------------------ |
| meter | m | length |
| kilogram | kg | mass |
| liter | L | volume |
Expand Down Expand Up @@ -84,7 +84,7 @@ Examples for CMIXF-12 (including the five unicode symbols mentioned above):
### Multiples

| **Prefix name** | **Prefix symbol** | **Factor** |
| --------------------------------------------| ------------------| --------------- |
| ------------------------------------------- | ----------------- | --------------- |
| [deca](https://www.wikiwand.com/en/Deca-) | da | 10<sup>1</sup> |
| [hecto](https://www.wikiwand.com/en/Hecto-) | h | 10<sup>2</sup> |
| [kilo](https://www.wikiwand.com/en/Kilo-) | k | 10<sup>3</sup> |
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2 changes: 1 addition & 1 deletion src/derivatives/common-data-types.md
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Expand Up @@ -329,7 +329,7 @@ A guide for using macros can be found at
Contents of the `descriptions.tsv` file:

| desc_id | description |
|---------|-------------------------------------------------------------------------------------------------|
| ------- | ----------------------------------------------------------------------------------------------- |
| Filt | low-pass filtered at 30Hz |
| FiltDs | low-pass filtered at 30Hz, downsampled to 250Hz |
| preproc | low-pass filtered at 30Hz, downsampled to 250Hz, and rereferenced to a common average reference |
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2 changes: 1 addition & 1 deletion src/derivatives/introduction.md
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Expand Up @@ -108,7 +108,7 @@ The following extension table is reproduced in part from Section 9.0 of the
or combinations of data arrays.

| Intent | Extension |
|-------------|---------------|
| ----------- | ------------- |
| Coordinates | `.coord.gii` |
| Functional | `.func.gii` |
| Labels | `.label.gii` |
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