Merge pull request #58 from Remi-Gau/scipy

[MAINT] follow several recommendations from the Scientific Python Library Development Guide

.github/workflows/test.yml

@@ -149,11 +149,11 @@ jobs:
     - name: Test with pytest - ignore smoke test.
       if: ${{ !contains(needs.check_skip_flags.outputs.head-commit-message, 'full_test') }}
       run: |
-        pytest -m "not smoke" --cov=giga_connectome --cov-report=xml --doctest-modules -v --pyargs giga_connectome
+        pytest -m "not smoke" --cov=giga_connectome --cov-report=xml --pyargs giga_connectome
 
     - name: Full test - run all the test to generate accurate coverage report.
       if: ${{ contains(needs.check_skip_flags.outputs.head-commit-message, 'full_test') }} || ${{ github.event.pull_request.merged }}
-      run: pytest --cov=giga_connectome --cov-report=xml --doctest-modules -v --pyargs giga_connectome
+      run: pytest --cov=giga_connectome --cov-report=xml --pyargs giga_connectome
 
     - uses: codecov/codecov-action@v4
       if: ${{ always() }}

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ repos:
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
--   repo: https://github.com/psf/black
+-   repo: https://github.com/psf/black-pre-commit-mirror
     rev: 24.3.0
     hooks:
     -   id: black

.readthedocs.yaml

@@ -1,4 +1,4 @@
-version: "2"
+version: 2
 
 build:
   os: "ubuntu-22.04"

giga_connectome/methods.py

@@ -20,7 +20,6 @@ def generate_method_section(
     average_correlation: bool,
     analysis_level: bool,
 ) -> None:
-
     env = Environment(
         loader=FileSystemLoader(Path(__file__).parent),
         autoescape=select_autoescape(),

giga_connectome/utils.py

@@ -26,7 +26,7 @@ def get_bids_images(
         root=bids_dir,
         database_path=bids_dir,
         validate=False,
-        derivatives=True,
+        derivatives=False,
         reset_database=reindex_bids,
     )
 

pyproject.toml

@@ -80,6 +80,12 @@ exclude = "giga_connectome/_version.py"
 line_length = 79
 
 [tool.pytest.ini_options]
+minversion = "7"
+log_cli_level = "INFO"
+xfail_strict = true
+testpaths = ["giga_connectome/tests"]
+addopts = ["-ra", "--strict-config", "--strict-markers", "--doctest-modules", "-v"]
 markers = [
     "smoke: smoke tests that will run on a downsampled real dataset (deselect with '-m \"not smoke\"')",
 ]
+# filterwarnings = ["error"]