Skip to content

[FIX] no extra tab added at the end of tsv lines #179

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 8 commits into from
Oct 28, 2021
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 4 additions & 9 deletions .github/workflows/bids_validator.yml
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ on:
branches:
- master
pull_request:
branches: 'master'
branches: ['master']

env:
OCTFLAGS: --no-gui --no-window-system --silent
Expand All @@ -23,7 +23,7 @@ jobs:
- name: Make jsonread for octave
run: |
sudo apt-get -y -qq update
sudo apt-get -y install octave
sudo apt-get -y install octave
sudo apt-get -y install liboctave-dev
cd lib/JSONio
mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
Expand All @@ -32,18 +32,13 @@ jobs:
- name: Update octave path
run: |
octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'lib'))); savepath();"
octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();"
octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();"

- name: Install BIDS validator
run: |
sudo npm install -g [email protected]

- name: Create dummy dataset and validate it
- name: Create dummy dataset and validate it
run: |
cd tests/manualTests
octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/raw/ --ignoreNiftiHeaders





34 changes: 0 additions & 34 deletions .github/workflows/check_markdown.yml

This file was deleted.

4 changes: 2 additions & 2 deletions .github/workflows/check_md_links.yml
Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,11 @@ on:
branches:
- master
pull_request:
branches: '*'
branches: ['*']

jobs:
markdown-link-check:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@master
- uses: gaurav-nelson/github-action-markdown-link-check@v1
- uses: gaurav-nelson/github-action-markdown-link-check@v1
3 changes: 1 addition & 2 deletions .github/workflows/miss_hit.yml
Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,7 @@ on:
branches:
- master
pull_request:
branches: '*'

branches: ['*']
jobs:
build:

Expand Down
6 changes: 3 additions & 3 deletions .github/workflows/run_tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ on:
- master
- dev
pull_request:
branches: '*'
branches: ['*']

jobs:
build:
Expand All @@ -21,7 +21,7 @@ jobs:
- name: Make jsonread for octave
run: |
sudo apt-get -y -qq update
sudo apt-get -y install octave
sudo apt-get -y install octave
sudo apt-get -y install liboctave-dev
cd lib/JSONio
mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
Expand All @@ -30,7 +30,7 @@ jobs:
uses: joergbrech/moxunit-action@master
with:
tests: tests # files or directories containing the MOxUnit test cases
src: src # directories to be added to the Octave search path before running the tests.
src: src # directories to be added to the Octave search path before running the tests.
ext: tests/utils # External resources to add to the search put (excluded from coverage)
# data: # Directory for test data
with_coverage: true
Expand Down
44 changes: 44 additions & 0 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
repos:

- repo: local

hooks:

- id: mh_version
name: mh_version
entry: mh_style
args: [-v]
verbose: true
language: python
additional_dependencies: [miss_hit_core]

# - id: mh_style
# name: mh_style
# entry: mh_style
# args: [--process-slx, --fix]
# files: ^(.*\.(m|slx))$
# language: python
# additional_dependencies: [miss_hit_core]

# - id: mh_metric
# name: mh_metric
# entry: mh_metric
# args: [--ci]
# files: ^(.*\.(m|slx))$
# language: python
# additional_dependencies: [miss_hit_core]

# - id: mh_lint
# name: mh_lint
# entry: mh_lint
# files: ^(.*\.(m|slx))$
# language: python
# additional_dependencies: [miss_hit]

- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v2.0.0
hooks:
- id: trailing-whitespace
- id: end-of-file-fixer
- id: check-yaml
- id: check-added-large-files
2 changes: 1 addition & 1 deletion .readthedocs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -23,4 +23,4 @@ formats:
python:
version: 3.7
install:
- requirements: requirements.txt
- requirements: requirements.txt
11 changes: 0 additions & 11 deletions .remarkrc

This file was deleted.

48 changes: 0 additions & 48 deletions .travis.yml

This file was deleted.

2 changes: 1 addition & 1 deletion .zenodo.json
Original file line number Diff line number Diff line change
Expand Up @@ -32,4 +32,4 @@
],
"license": "MIT license",
"upload_type": "software"
}
}
4 changes: 0 additions & 4 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -19,10 +19,6 @@

[![codecov](https://codecov.io/gh/cpp-lln-lab/CPP_BIDS/branch/master/graph/badge.svg)](https://codecov.io/gh/cpp-lln-lab/CPP_BIDS)

**BIDS validator and linter**

[![Build Status](https://travis-ci.com/cpp-lln-lab/CPP_BIDS.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/CPP_BIDS)

**Contributors**

[![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-)
Expand Down
1 change: 0 additions & 1 deletion binder/postBuild
Original file line number Diff line number Diff line change
@@ -1,3 +1,2 @@
cd ${HOME}
cd lib/JSONio; mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS; cd ..

65 changes: 65 additions & 0 deletions checkCppBidsDependencies.m
Original file line number Diff line number Diff line change
@@ -0,0 +1,65 @@
% (C) Copyright 2020 CPP_BIDS developers

function checkCppBidsDependencies(cfg)
%
% Adds dependencies to the Matlab / Octave path and make sure we got all of them.
%
% USAGE::
%
% checkCppBidsDependencies(cfg)
%
% :param cfg: Configuration. See ``checkCFG()``.
% :type cfg: structure

if nargin < 1
cfg.verbose = 2;
end

global CPP_BIDS_INITIALIZED

if isempty(CPP_BIDS_INITIALIZED)

GITHUB_WORKSPACE = getenv('GITHUB_WORKSPACE');

if strcmp(GITHUB_WORKSPACE, '/github/workspace')

pth = GITHUB_WORKSPACE;
addpath(genpath(fullfile(pth, 'lib')));

elseif isempty(GITHUB_WORKSPACE) % local

pth = fullfile(fileparts(mfilename('fullpath')));

addpath(pth);

addpath(fullfile(pth, 'lib', 'utils'));

checkSubmodule(fullfile(pth, 'lib', 'JSONio'));
checkSubmodule(fullfile(pth, 'lib', 'bids-matlab'));

addpath(genpath(fullfile(pth, 'src')));

end

printCreditsCppBids(cfg);

CPP_BIDS_INITIALIZED = true();

else
fprintf(1, '\n\nCPP_BIDS already initialized\n\n');

end

end

function checkSubmodule(pth)
% If external dir is empty throw an exception
% and ask user to update submodules.
if numel(dir(pth)) <= 2 % Means that the external is empty
error(['Git submodules are not cloned!', ...
'Try this in your terminal:', ...
' git submodule update --recursive ']);
else
addpath(pth);
end
end
3 changes: 3 additions & 0 deletions docs/Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -18,3 +18,6 @@ help:
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc:
@$(SPHINXBUILD) -b html "$(SOURCEDIR)" "$(BUILDDIR)"
4 changes: 2 additions & 2 deletions docs/source/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'sphinxcontrib.matlab',
'sphinxcontrib.matlab',
'sphinx.ext.autodoc']
matlab_src_dir = os.path.dirname(os.path.abspath('../../src'))
primary_domain = 'mat'
Expand Down Expand Up @@ -88,4 +88,4 @@
'searchbox.html',
'donate.html',
]
}
}
5 changes: 1 addition & 4 deletions docs/source/contributing.rst
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ Template proposal

end

.. autofunction:: templateFunction
.. autofunction:: templateFunction


Example code in the help section
Expand Down Expand Up @@ -100,6 +100,3 @@ Example code in the help section
end

.. autofunction:: templateFunctionExample



Loading