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Documentation changes after Empenn Hackathon #176

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6986e90
[BUG] inside unit_tests workflow
bclenet Aug 31, 2023
d6e67f3
Merge branch 'Inria-Empenn:main' into main
bclenet Aug 31, 2023
c3bfc53
Merge branch 'Inria-Empenn:main' into main
bclenet Sep 4, 2023
4b30504
Merge branch 'Inria-Empenn:main' into main
bclenet Sep 19, 2023
fd15ffc
Merge branch 'Inria-Empenn:main' into main
bclenet Sep 21, 2023
6715950
[DOC] fix some broken links
bclenet Sep 22, 2023
57b8c86
[DOC] adding template for pipeline testing
bclenet Sep 22, 2023
2c891c2
[DOC] adding template for pipeline testing
bclenet Sep 22, 2023
552e18c
About implemented_pipelines
bclenet Sep 25, 2023
b6f21f4
Deal with test template
bclenet Sep 25, 2023
6ebe5d2
Merge branch 'Inria-Empenn:main' into main
bclenet Sep 29, 2023
0a584dd
Merge branch 'Inria-Empenn:main' into main
bclenet Sep 29, 2023
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Merge branch 'Inria-Empenn:main' into main
bclenet Sep 29, 2023
5774813
Merge branch 'Inria-Empenn:main' into main
bclenet Oct 5, 2023
8f12d3d
Merge branch 'Inria-Empenn:main' into main
bclenet Oct 5, 2023
7c3b6df
Merge branch 'main' into documentation
bclenet Oct 5, 2023
91dc744
Merge branch 'Inria-Empenn:main' into main
bclenet Oct 10, 2023
c10e3a4
Merge branch 'main' into documentation
bclenet Oct 13, 2023
0436fe4
[DOC] new readme for the doc
bclenet Oct 13, 2023
bfcf3dd
Changes in README.md
bclenet Oct 13, 2023
d212e1d
[DOC] slight changes to docs/README.md
bclenet Oct 13, 2023
c03e9d1
Merge branch 'Inria-Empenn:main' into main
bclenet Nov 20, 2023
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Merge branch 'Inria-Empenn:main' into main
bclenet Nov 22, 2023
04d5ff2
Merge branch 'Inria-Empenn:main' into main
bclenet Nov 22, 2023
6466b29
Merge branch 'main' into documentation
bclenet Nov 30, 2023
29870d5
Add links to past events
bclenet Nov 30, 2023
e4f369d
Changes in readme.md
bclenet Nov 30, 2023
142f89c
fMRI trail
bclenet Nov 30, 2023
7b7fb89
Adding trail description in contribution guide
bclenet Dec 6, 2023
23b93f6
Separate trails in contribution guide
bclenet Dec 6, 2023
6f3dd73
[TEST] Solving pytest issues with template test
bclenet Dec 6, 2023
c9ee889
Merge branch 'Inria-Empenn:main' into main
bclenet Jan 5, 2024
933e87f
Merge branch 'main' into documentation
bclenet Jan 9, 2024
5803501
Changing docker image in use
bclenet Jan 9, 2024
e297685
FSL template correction
bclenet Jan 10, 2024
9213dc4
[DOC] writing test files
bclenet Jan 10, 2024
9bfc89c
Merge branch 'Inria-Empenn:main' into main
bclenet Jan 10, 2024
d2b8452
Merge branch 'main' into documentation
bclenet Jan 10, 2024
7d5fa82
Codespell
bclenet Jan 10, 2024
11736e6
First step in writing documentation about NARPS
bclenet Jan 10, 2024
c5fd548
[DOC] completing doc about narps
bclenet Jan 11, 2024
6c9d7a3
[DOC] completing doc about narps
bclenet Jan 11, 2024
a016bdd
[DOC] completing doc about narps
bclenet Jan 11, 2024
7493f74
Merge branch 'Inria-Empenn:main' into main
bclenet Jan 11, 2024
a73f3c3
[DATALAD] change results url
bclenet Jan 11, 2024
f03f50e
Merge pull request #3 from bclenet/results
bclenet Jan 11, 2024
68ea23c
[DOC] reference to the github project for reproduction mgmt
bclenet Jan 11, 2024
f4c0c24
[DOC] adding team id choices for narps open runner
bclenet Jan 12, 2024
9120dda
Merge branch 'main' into documentation
bclenet Jan 12, 2024
6ebd536
[DOC] list of available team ids in command tools documentation
bclenet Jan 15, 2024
ecce46a
[DOC] configuration info inside INSTALL.md
bclenet Jan 16, 2024
5b46057
[DOC] configuration info inside INSTALL.md
bclenet Jan 16, 2024
a737df5
Merge branch 'Inria-Empenn:main' into main
bclenet Jan 19, 2024
b8c1fda
NARPS Exclusion comments
bclenet Jan 24, 2024
f518012
Merge branch 'main' into documentation
bclenet Jan 24, 2024
34ec585
Merge branch 'main' into documentation
bclenet Feb 14, 2024
d59c329
Empenn hackathon names
bclenet Feb 14, 2024
9f56136
Data documentation (datalad get recursive
bclenet Feb 14, 2024
d6eef33
Adjusting correlation thresholds inside testing configuration, after …
bclenet Feb 14, 2024
af709fc
Update dataset size
bclenet Feb 15, 2024
83765eb
Freeze versions
bclenet Feb 19, 2024
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7 changes: 4 additions & 3 deletions INSTALL.md
Original file line number Diff line number Diff line change
Expand Up @@ -43,15 +43,15 @@ datalad get data/original/ds001734/derivatives/fmriprep/sub-00[1-4] -J 12
[Install Docker](https://docs.docker.com/engine/install/) then pull the nipype Docker image :

```bash
docker pull nipype/nipype
docker pull nipype/nipype:py38
```

Once it's done you can check the image is available on your system :

```bash
docker images
REPOSITORY TAG IMAGE ID CREATED SIZE
docker.io/nipype/nipype latest 0f3c74d28406 9 months ago 22.7 GB
docker.io/nipype/nipype py38 0f3c74d28406 9 months ago 22.7 GB
```

> [!NOTE]
Expand All @@ -63,10 +63,11 @@ Start a Docker container from the Docker image :

```bash
# Replace PATH_TO_THE_REPOSITORY in the following command (e.g.: with /home/user/dev/narps_open_pipelines/)
docker run -it -v PATH_TO_THE_REPOSITORY:/home/neuro/code/ nipype/nipype
docker run -it -v PATH_TO_THE_REPOSITORY:/home/neuro/code/ nipype/nipype:py38
```

Optionally edit the configuration file `narps_open/utils/configuration/default_config.toml` so that the referred paths match the ones inside the container. E.g.: if using the previous command line, the `directories` part of the configuration file should be :

```toml
# default_config.toml
# ...
Expand Down
3 changes: 2 additions & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,8 @@ This project is supported by Région Bretagne (Boost MIND) and by Inria (Explora
This project is developed in the Empenn team by Boris Clénet, Elodie Germani, Jeremy Lefort-Besnard and Camille Maumet with contributions by Rémi Gau.

In addition, this project was presented and received contributions during the following events:
- [Brainhack Marseille 2023](https://brainhack-marseille.github.io/) (December 2023):
- [Empenn team](https://team.inria.fr/empenn/) hackathon (February 2024): Mathieu Acher, Élise Bannier, Boris Clénet, Isabelle Corouge, Malo Gaubert, Élodie Germani, Gauthier Le Bartz Lyan, Jérémy Lefort-Besnard, Camille Maumet, Youenn Merel, Alexandre Pron.
- [Brainhack Marseille 2023](https://brainhack-marseille.github.io/) (December 2023)
- [ORIGAMI lab](https://neurodatascience.github.io/) hackathon (September 2023):
- [OHBM Brainhack 2023](https://ohbm.github.io/hackathon2023/) (July 2023): Arshitha Basavaraj, Boris Clénet, Rémi Gau, Élodie Germani, Yaroslav Halchenko, Camille Maumet, Paul Taylor.
- [e-ReproNim FENS NENS Cluster Brainhack](https://repro.school/2023-e-repronim-brainhack/) (June 2023) : Liz Bushby, Boris Clénet, Michael Dayan, Aimee Westbrook.
Expand Down
7 changes: 6 additions & 1 deletion docs/data.md
Original file line number Diff line number Diff line change
Expand Up @@ -20,10 +20,15 @@ Tips for people using M1 MacBooks: `git-annex` is not yet available for M1 MacBo

The `datalad install` command only downloaded the metadata associated with the dataset ; to download the actual files run the following command:

> [! WARNING]
> The following command lines will download **all** the data, which represents around :
> * 3 GB for `data/results/`
> * 880 GB for `data/original/`

```bash
# To get all the data
cd data/
datalad get ./*
datalad get --recursive ./*
```

If you only want parts of the data, replace the `./*` by the paths to the desired files.
Expand Down
10 changes: 5 additions & 5 deletions docs/environment.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,12 @@

## The Docker container :whale:

The NARPS Open Pipelines project is build upon several dependencies, such as [Nipype](https://nipype.readthedocs.io/en/latest/) but also the original software packages used by the pipelines (SPM, FSL, AFNI...). Therefore we recommend to use the [`nipype/nipype` Docker image](https://hub.docker.com/r/nipype/nipype/) that contains all the required software dependencies.
The NARPS Open Pipelines project is build upon several dependencies, such as [Nipype](https://nipype.readthedocs.io/en/latest/) but also the original software packages used by the pipelines (SPM, FSL, AFNI...). Therefore we recommend to use the [`nipype/nipype:py38` Docker image](https://hub.docker.com/r/nipype/nipype/) that contains all the required software dependencies.

The simplest way to start the container is by using the command below :

```bash
docker run -it nipype/nipype
docker run -it nipype/nipype:py38
```

From this command line, you need to add volumes to be able to link with your local files (code repository).
Expand All @@ -16,7 +16,7 @@ From this command line, you need to add volumes to be able to link with your loc
# Replace PATH_TO_THE_REPOSITORY in the following command (e.g.: with /home/user/dev/narps_open_pipelines/)
docker run -it \
-v PATH_TO_THE_REPOSITORY:/home/neuro/code/ \
nipype/nipype
nipype/nipype:py38
```

## Use Jupyter with the container
Expand All @@ -27,7 +27,7 @@ If you wish to use [Jupyter](https://jupyter.org/) to run the code, a port forwa
docker run -it \
-v PATH_TO_THE_REPOSITORY:/home/neuro/code/ \
-p 8888:8888 \
nipype/nipype
nipype/nipype:py38
```

Then, from inside the container :
Expand Down Expand Up @@ -81,7 +81,7 @@ To use SPM inside the container, use this command at the beginning of your scrip
```python
from nipype.interfaces import spm

matlab_cmd = '/opt/spm12-r7771/run_spm12.sh /opt/matlabmcr-2010a/v713/ script'
matlab_cmd = '/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713/ script'

spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
```
30 changes: 30 additions & 0 deletions narps_open/pipelines/__main__.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,30 @@
#!/usr/bin/python
# coding: utf-8

""" Provide a command-line interface for the package narps_open.pipelines """

from argparse import ArgumentParser

from narps_open.pipelines import get_implemented_pipelines

def main():
""" Entry-point for the command line tool narps_open_pipeline """

# Parse arguments
parser = ArgumentParser(description='Get description of a NARPS pipeline.')
parser.add_argument('-v', '--verbose', action='store_true',
help='verbose mode')
arguments = parser.parse_args()

# Print header
print('NARPS Open Pipelines')

# Print general information about NARS Open Pipelines
print('A codebase reproducing the 70 pipelines of the NARPS study (Botvinik-Nezer et al., 2020) shared as an open resource for the community.')

# Print pipelines
implemented_pipelines = get_implemented_pipelines()
print(f'There are currently {len(implemented_pipelines)} implemented pipelines: {implemented_pipelines}')

if __name__ == '__main__':
main()
2 changes: 1 addition & 1 deletion narps_open/utils/configuration/testing_config.toml
Original file line number Diff line number Diff line change
Expand Up @@ -23,4 +23,4 @@ neurovault_naming = true # true if results files are saved using the neurovault

[testing.pipelines]
nb_subjects_per_group = 4 # Compute first level analyses by subgroups of N subjects, to avoid lacking of disk and memory
correlation_thresholds = [0.30, 0.70, 0.79, 0.85, 0.93] # Correlation between reproduced hypotheses files and results, respectively for [20, 40, 60, 80, 108] subjects.
correlation_thresholds = [0.30, 0.70, 0.78, 0.85, 0.93] # Correlation between reproduced hypotheses files and results, respectively for [20, 40, 60, 80, 108] subjects.
18 changes: 9 additions & 9 deletions setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -18,18 +18,18 @@
'tomli>=2.0.1,<2.1',
'networkx>=2.0,<3.0', # a workaround to nipype's bug (issue 3530)
'nilearn>=0.10.0,<0.11',
'nipype',
'pandas'
'nipype>=1.8.6,<1.9',
'pandas>=1.5.2,<1.6'
]
extras_require = {
'tests': [
'pathvalidate',
'pylint',
'pytest',
'pytest-cov',
'pytest-helpers-namespace',
'pytest-mock',
'checksumdir'
'pathvalidate>=3.2.0,<3.3',
'pylint>=3.0.3,<3.1',
'pytest>=7.2.0,<7.3',
'pytest-cov>=2.10.1,<2.11',
'pytest-helpers-namespace>=2021.12.29,<2021.13',
'pytest-mock>=3.12.0,<3.13',
'checksumdir>=1.2.0,<1.3'
]
}

Expand Down
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