[MAINT] Update packaging

.github/workflows/pipeline_status.yml

@@ -56,7 +56,7 @@ jobs:
         git config user.name github-actions
         git config user.email [email protected]
 
-        # Test if there are changes in the repository before commiting
+        # Test if there are changes in the repository before committing
         if [[ $(git diff --name-only) ]]; then
           git add .
           git commit -m "Pipeline status updated"

.github/workflows/pipeline_tests.yml

@@ -56,6 +56,11 @@ jobs:
     - name: Checkout PR branch
       uses: actions/checkout@v3
 
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.9
+
     - name: Load configuration for self-hosted runner
       run: cp /home/neuro/local_testing_config.toml narps_open/utils/configuration/testing_config.toml
 

.github/workflows/test_changes.yml

@@ -23,6 +23,11 @@ jobs:
       with:
         fetch-depth: 0
 
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.9
+
     - name: Create a list of tests for changed tests
       id: identify
       run: |

.github/workflows/unit_tests.yml

@@ -34,6 +34,11 @@ jobs:
     - name: Checkout repository
       uses: actions/checkout@v3
 
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.9
+
     - name: Load configuration for self-hosted runner
       run: cp /home/neuro/local_testing_config.toml narps_open/utils/configuration/testing_config.toml
 

MANIFEST.in

@@ -0,0 +1,2 @@
+include narps_open/utils/configuration/*.toml
+include narps_open/data/description/*.tsv

environment.yml

@@ -4,12 +4,7 @@ channels:
   - defaults
 dependencies:
   - python=3.8.0
-  - pip
-  - traits 
-  - jupyter 
-  - nilearn 
-  - graphviz 
-  - nipype 
-  - scikit-image
+  - pip==23.2.1
   - pip:
-    - matplotlib
+    - .
+

pyproject.toml

@@ -0,0 +1,59 @@
+[build-system]
+build-backend = "hatchling.build"
+requires = ["hatchling"]
+
+
+[project]
+name = 'narps_open'
+version = '0.1.0'
+description = 'The NARPS open pipelines project: a codebase reproducing the 70 pipelines of the NARPS study (Botvinik-Nezer et al., 2020).'
+readme = "README.md"
+classifiers = [
+    'Programming Language :: Python',
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3.8'
+]
+requires-python = '>=3.8,<3.12'
+dependencies = [
+    'importlib_resources>=5.10.2,<5.11',
+    'tomli>=2.0.1,<2.1',
+    'nilearn==0.10.1',
+    'jupyterlab',
+    'graphviz',
+    'traits==6.3.0',
+    'nipype==1.8.6',
+    'scikit-image==0.21.0',
+    'matplotlib==3.7.3',
+]
+
+
+[project.urls]
+Homepage = 'https://github.com/Inria-Empenn/narps_open_pipelines'
+"Bug trakcer" = 'https://github.com/Inria-Empenn/narps_open_pipelines/issues'
+Source = 'https://github.com/Inria-Empenn/narps_open_pipelines'
+
+
+[project.optional-dependencies]
+tests= [
+        'pylint',
+        'pytest',
+        'pytest-cov',
+        'pytest-helpers-namespace',
+        'pytest-mock',
+        'checksumdir'
+]
+
+
+[tool.pytest.ini_options]
+addopts = "--strict-markers"
+testpaths =["tests"]
+markers = [
+    "pipeline_test: marks tests that execute complete pipelines",
+    "unit_test: marks unit tests"
+]
+
+
+[tool.codespell]
+skip = ".git,*.pdf,*.svg,analysis_pipelines_full_descriptions.tsv,data,env,run"
+# softwares - key in data structures etc
+ignore-words-list = "te,fpr,fwe,softwares"