Documentation about testing (#137)

* [BUG] inside unit_tests workflow

* [DOC] fix some broken links

* [DOC] adding template for pipeline testing

* [DOC] adding template for pipeline testing

* About implemented_pipelines

* Deal with test template

* [DOC] new readme for the doc

* Changes in README.md

* [DOC] slight changes to docs/README.md

* Add links to past events

* Changes in readme.md

* fMRI trail

* Adding trail description in contribution guide

* Separate trails in contribution guide

* [TEST] Solving pytest issues with template test

* Changing docker image in use

* FSL template correction

* [DOC] writing test files

* Codespell

INSTALL.md

@@ -40,18 +40,18 @@ datalad get data/original/ds001734/derivatives/fmriprep/sub-00[1-4] -J 12
 
 ## 4 - Set up the environment
 
-[Install Docker](https://docs.docker.com/engine/install/) then pull the Docker image :
+[Install Docker](https://docs.docker.com/engine/install/) then pull the nipype Docker image :
 
 ```bash
-docker pull elodiegermani/open_pipeline:latest
+docker pull nipype/nipype
 ```
 
 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/elodiegermani/open_pipeline    latest    0f3c74d28406    9 months ago    22.7 GB
+   REPOSITORY                 TAG       IMAGE ID        CREATED         SIZE
+   docker.io/nipype/nipype    latest    0f3c74d28406    9 months ago    22.7 GB
 ```
 
 > [!NOTE]  
@@ -63,7 +63,7 @@ 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/ elodiegermani/open_pipeline
+docker run -it -v PATH_TO_THE_REPOSITORY:/home/neuro/code/ nipype/nipype
 ```
 
 Install NARPS Open Pipelines inside the container :

docs/environment.md

@@ -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 created a Docker container based on [Neurodocker](https://github.com/ReproNim/neurodocker) that contains 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` Docker image](https://hub.docker.com/r/nipype/nipype/) that contains all the required software dependencies.
 
-The simplest way to start the container using the command below :
+The simplest way to start the container is by using the command below :
 
 ```bash
-docker run -it elodiegermani/open_pipeline
+docker run -it nipype/nipype
 ```
 
 From this command line, you need to add volumes to be able to link with your local files (code repository).
@@ -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/ \
-           elodiegermani/open_pipeline
+           nipype/nipype
 ``` 
 
 ## Use Jupyter with the container
@@ -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 \
-           elodiegermani/open_pipeline
+           nipype/nipype
 ``` 
 
 Then, from inside the container :

docs/pipelines.md

@@ -149,4 +149,13 @@ First have a look at the [testing page of the documentation](/docs/testing.md).
 All tests must be contained in a single file named `tests/pipelines/test_team_<team_id>.py`. You can start by copy-pasting the template file : [tests/pipelines/templates/template_test.py](/tests/pipelines/templates/template_test.py) inside the `tests/pipelines/` directory, renaming it accordingly. Then, follow the instructions and tips inside the template and don't forget to replace `XXXX` with the actual team id, inside the document.
 
 > [!NOTE]  
-> Feel free to have a look at [tests/pipelines/test_team_2T6S.py](/tests/pipelines/test_team_2T6S.py), which is the file containing all the automatic tests for the 2T6S pipeline : it gives an example.
+> Feel free to have a look at [tests/pipelines/test_team_C88N.py](/tests/pipelines/test_team_C88N.py), which is the file containing all the automatic tests for the C88N pipeline : it gives an example.
+
+Your test file must contain the following methods:
+* one testing the execution of the pipeline and comparing the results with the original ones. This can be simply achieved with this line :
+```python
+helpers.test_pipeline_evaluation('C88N')
+```
+* one for each method you declared in the pipeline class (e.g.: testing the `get_subject_information` method)
+* one testing the instantiation of your pipeline (see `test_create` in `test_team_C88N.py`)
+* one testing the `get_*_outputs` methods of your pipeline (see `test_outputs` in `test_team_C88N.py`)