Merge branch 'main' into refactoring

.codespellrc

@@ -0,0 +1,4 @@
+[codespell]
+skip = .git,*.pdf,*.svg,analysis_pipelines_full_descriptions.tsv
+# softwares - key in data structures etc
+ignore-words-list = te,fpr,fwe,softwares

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,65 @@
+name: Bug report
+description: Create a report to help improving the project.
+title: "[BUG] "
+labels: ["\U0001F6E0 goal: fix, \U0001F6A6 status: awaiting triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for suggesting this feature! :raised_hands:
+  - type: textarea
+    id: description
+    attributes:
+      label: Describe the bug
+      description: A clear and concise description of what the bug is.
+      placeholder: ex. I cannot access the pipeline_template.py file.
+    validations:
+      required: true
+  - type: textarea
+    id: reproduction
+    attributes:
+      label: Reproduction
+      description: Describe the steps to reproduce the bug.
+      placeholder: |
+        1. Go to '...'
+        2. Click on '....'
+        3. Scroll down to '....'
+        4. See error
+    validations:
+      required: true
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected behavior
+      description: A clear and concise description of what you expected to happen.
+      placeholder: This should work like this '...'
+    validations:
+      required: true
+  - type: input
+    id: narps_open_pipelines_verion
+    attributes:
+      label: NARPS Open Pipeline version
+      placeholder: ex. 0.1.0
+    validations:
+      required: true
+  - type: input
+    id: operating_system
+    attributes:
+      label: Operating System
+      placeholder: ex. Ubuntu 22.04
+    validations:
+      required: true
+  - type: input
+    id: softwares
+    attributes:
+      label: Softwares versions
+      placeholder: ex. SPM12 - version 7219 / FSL 5.0.9 / Docker 23.0.3
+    validations:
+      required: true
+  - type: textarea
+    id: screenshot
+    attributes:
+      label: Screenshots
+      description: If applicable, add screenshots to help explain your problem.
+    validations:
+      required: false

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,49 @@
+name: Feature request
+description: Suggest an idea for the project!
+title: "[ENH] "
+labels: ["\U0001F6A6 status: awaiting triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for suggesting this feature! :raised_hands:
+  - type: input
+    id: goal
+    attributes:
+      label: Goal
+      description: Please briefly describe the purpose of your request.
+      placeholder: ex. Create a template for pipelines using AFNI.
+    validations:
+      required: true
+  - type: textarea
+    id: why-useful
+    attributes:
+      label: Why this is useful
+      description: Why you think the project could benefit from the feature.
+      placeholder: ex. This would help contributors to start writing pipeline code using AFNI.
+    validations:
+      required: true
+  - type: textarea
+    id: timeline
+    attributes:
+      label: Timeline
+      description: If there are any time limitations for the issue to be resolved, please write it here.
+      placeholder: ex. Must be done before we present the code to the AFNI convention.
+    validations:
+      required: false
+  - type: textarea
+    id: description
+    attributes:
+      label: More specifically
+      description: A clear description of what you want to happen.
+      placeholder: Add any context or screenshots about the feature request here.
+    validations:
+      required: false
+  - type: textarea
+    id: questions
+    attributes:
+      label: Open questions
+      description: Please fill this part if there are subjects left to discussion for this request. You can also describe alternatives you've considered.
+      placeholder: ex. I'm not sure which version of AFNI tu use.
+    validations:
+      required: false

.github/ISSUE_TEMPLATE/pipeline_reproduction.yml

@@ -0,0 +1,61 @@
+name: Pipeline reproduction
+description: Select this when you are about to start a pipeline reproduction.
+title: "[team_id] Pipeline reproduction"
+labels: ["\U0001F6A6 status: awaiting triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thank you for starting this pipeline reproduction! :tada:
+        Please make sure there is no concurrent issue about it : have a look [here](https://github.com/Inria-Empenn/narps_open_pipelines/wiki/pipeline_status).
+        Once it's ok, start by changing the `team_id` in the title of this issue, then fill the form.
+
+        :warning: Please do not reference any other team IDs in the following, unless the issue is actually related these IDs.
+
+  - type: textarea
+    id: softwares
+    attributes:
+      label: Softwares
+      description: Which softwares are used by the pipeline ?
+      placeholder: Basically, this is the `general.software` column of the pipeline description.
+    validations:
+      required: true
+
+  - type: dropdown
+    id: data
+    attributes:
+      label: Input data
+      description: Which data used the team ?
+      options:
+        - raw data
+        - derivatives (fMRIprep)
+    validations:
+      required: true
+
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional context
+      description: Any supplementary information you find relevant about the pipeline, that would help reproducing it.
+      placeholder: ex. This pipeline uses a run level analysis.
+    validations:
+      required: true
+
+  - type: textarea
+    id: tasks
+    attributes:
+      label: List of tasks
+      description: Please keep the following tasks, as they are common to all pipeline reproduction. Feel free to add other tasks.
+      value: |
+        Please tick the boxes below once the corresponding task is finished. :+1:
+        - [ ] :ok_hand: A maintainer of the project approved the issue, by assigning a :checkered_flag:`status: ready for dev` label to it.
+        - [ ] :deciduous_tree: Create a branch on your fork to start the reproduction.
+        - [ ] :sunrise: Create a file `team_{team_id}.py` inside the [`narps_open/pipelines/`](https://github.com/Inria-Empenn/narps_open_pipelines/blob/main/narps_open/pipelines) directory. You can use a file inside [`narps_open/pipelines/templates`](https://github.com/Inria-Empenn/narps_open_pipelines/blob/main/narps_open/pipelines/templates) as a template if needed.
+        - [ ] :inbox_tray: Create a [pull request](https://github.com/Inria-Empenn/narps_open_pipelines/blob/main/CONTRIBUTING.md#pull_requests) as soon as you completed the previous task.
+        - [ ] :brain: Write the code for the pipeline, using Nipype and the file architecture described in [docs/pipelines.md](https://github.com/Inria-Empenn/narps_open_pipelines/blob/main/docs/pipelines.md).
+        - [ ] :blue_book: Make sure your code is documented enough.
+        - [ ] :snake: Make sure your code is explicit and conforms with PEP8.
+        - [ ] :microscope: Create tests for your pipeline. You can use files in [`tests/pipelines/test_team_*`](https://github.com/Inria-Empenn/narps_open_pipelines/blob/main/tests/pipelines/) as examples.
+        - [ ] :microscope: Make sure your code passes all the tests you created (see [docs/testing.md](https://github.com/Inria-Empenn/narps_open_pipelines/blob/main/docs/testing.md)).
+    validations:
+      required: true

.github/pull_request_template.md

@@ -0,0 +1,20 @@
+This Pull Request is related to issue [#](add a link to the issue here).
+
+Before reviewing this Pull Request, please review Pull Request [#](add a link to the Pull Request here).
+
+Changes proposed in this Pull Request:
+
+- 
+- 
+- 
+
+Checklist:
+
+- [ ] Descriptive title
+- [ ] Targets the `main` branch
+- [ ] Changes are functional
+- [ ] My code is explicit and comments were added to it
+- [ ] Code conforms with PEP8
+- [ ] Tests were added for the changes and they complete successfully
+- [ ] Existing tests were updated (if needed) and they complete successfully
+- [ ] Documentation was updated

.github/workflows/code_quality.yml

@@ -8,9 +8,11 @@ on:
   push:
     paths:
       - '**.py'
+      - '.github/workflows/code_quality.yml'
   pull_request:
     paths:
       - '**.py'
+      - '.github/workflows/code_quality.yml'
 
 # Jobs that define the workflow
 jobs:
@@ -33,22 +35,23 @@ jobs:
     - uses: actions/cache@v3
       with:
         path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-pylint
+        key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}
         restore-keys: |
-          ${{ runner.os }}-pip-pylint
+          ${{ runner.os }}-pip-
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pylint
+        pip install .[tests]
 
     - name: Analyse the code with pylint
       run: |
-        pylint --exit-zero narps_open > pylint_report_narps_open.txt
-        pylint --exit-zero tests > pylint_report_narps_open.txt
+        pylint --fail-under 8 --ignore-paths narps_open/pipelines/ narps_open > pylint_report_narps_open.txt
+        pylint --fail-under 8 tests > pylint_report_tests.txt
 
     - name: Archive pylint results
       uses: actions/upload-artifact@v3
+      if: failure() # Only if previous step failed
       with:
         name: pylint-reports-python
         path: |

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+## Disclaimer - This GitHub Actions workflow performs a check for spelling errors inside code comments and documentation
+name: codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2