From 467188077687164f083b09ccaac511b02693f11d Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 17 Nov 2021 09:27:40 -0500 Subject: [PATCH 1/4] CI: Install linkchecker in a standard image --- .circleci/config.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 057dda1981..1b72ae5b15 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -21,7 +21,7 @@ jobs: linkchecker: docker: - - image: yarikoptic/linkchecker:9.4.0.anchorfix1-1 + - image: circleci/python:3.8 steps: # checkout code to default ~/project - checkout @@ -29,10 +29,10 @@ jobs: # mkdocs build outputs will be in ~/project/site at: ~/project - run: - name: install git + name: install linkchecker command: | - apt update -y - apt install git-all -y + python -m ensurepip + python -m pip install linkchecker - run: name: check links command: | From 9b71acf5f92e4e39401970f2af21ed26ca254850 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 17 Nov 2021 09:51:32 -0500 Subject: [PATCH 2/4] FIX: Use OSF archive for MEF3 spec --- .../04-intracranial-electroencephalography.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md index cd0e901282..ef3f88172d 100644 --- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md +++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md @@ -24,7 +24,7 @@ stored in one of the following formats: | [BrainVision Core Data Format](https://www.brainproducts.com/productdetails.php?id=21&tab=5) | `.vhdr`, `.vmrk`, `.eeg` | Each recording consists of a `.vhdr`, `.vmrk`, `.eeg` file triplet. | | [EEGLAB](https://sccn.ucsd.edu/eeglab) | `.set`, `.fdt` | The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab). Each recording consists of a `.set` file with an optional `.fdt` file. | | [Neurodata Without Borders](https://nwb-schema.readthedocs.io) | `.nwb` | Each recording consists of a single `.nwb` file. | -| [MEF3](https://msel.mayo.edu/files/codes/MEF%203%20Specification.pdf) | `.mefd` | Each recording consists of a `.mefd` directory. | +| [MEF3](https://osf.io/e3sf9/) | `.mefd` | Each recording consists of a `.mefd` directory. | It is RECOMMENDED to use the European data format, or the BrainVision data format. It is furthermore discouraged to use the other accepted formats over From 5db9a6ddcf661ee293cebdb67d0863058aa8a1bb Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 17 Nov 2021 10:41:49 -0500 Subject: [PATCH 3/4] FIX: Link to PDFs of Inglis article and checklist --- .../01-magnetic-resonance-imaging-data.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md index 2445a7946c..794402a2c4 100644 --- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md +++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md @@ -3,9 +3,11 @@ ## Common metadata fields MR Data described in the following sections share the following RECOMMENDED metadata -fields (stored in sidecar JSON files). MRI acquisition parameters are divided -into several categories based on -["A checklist for fMRI acquisition methods reporting in the literature"](https://thewinnower.com/papers/977-a-checklist-for-fmri-acquisition-methods-reporting-in-the-literature) +fields (stored in sidecar JSON files). +MRI acquisition parameters are divided into several categories based on +"A checklist for fMRI acquisition methods reporting in the literature" +([article](https://winnower-production.s3.amazonaws.com/papers/977/v4/pdf/977-a-checklist-for-fmri-acquisition-methods-reporting-in-the-literature.pdf), +[checklist](https://winnower-production.s3.amazonaws.com/papers/977/assets/993e199d-6bc3-4418-be3a-f620af1188b7-Parameter_Reporting_V1p3.pdf)) by Ben Inglis. ### Scanner Hardware From ddca51d13f6831b7360299004b44e1e77b6514ba Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 17 Nov 2021 12:06:37 -0500 Subject: [PATCH 4/4] MNT: Drop outdated docker recipe for linkchecker --- tools/linkchecker-docker/neurodocker-build.sh | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100755 tools/linkchecker-docker/neurodocker-build.sh diff --git a/tools/linkchecker-docker/neurodocker-build.sh b/tools/linkchecker-docker/neurodocker-build.sh deleted file mode 100755 index 8b9aa66ccc..0000000000 --- a/tools/linkchecker-docker/neurodocker-build.sh +++ /dev/null @@ -1,27 +0,0 @@ -#!/bin/bash - -# A script to build docker image with desired patched linkchecker -# using neurodocker - -# TODOs: -# - minimize image (currently >500MB) using reprozip -# see https://github.com/kaczmarj/neurodocker/#minimize-existing-docker-image -# for instructions - -# tag for patched linkchecker -- will also serve our image version -version="9.4.0.anchorfix1" -# docker image build -build=1 - -neurodocker generate docker \ - --base neurodebian:nd100 \ - --pkg-manager apt \ - --install python-pip python-requests python-dnspython python-setuptools python-wheel \ - --run "sed -e 's,^deb ,deb-src ,g' /etc/apt/sources.list > /etc/apt/sources.list.d/deb-sources.list \ - && apt-get update \ - && apt-get build-dep -y linkchecker \ - && pip install pyxdg https://github.com/yarikoptic/linkchecker/archive/$version.zip \ - && mkdir ~/.linkchecker && echo '[AnchorCheck]' > ~/.linkchecker/linkcheckerrc \ - " \ - --entrypoint /usr/local/bin/linkchecker \ -| docker build -t yarikoptic/linkchecker:$version-$build -