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update the commit hash of mist2templateflow (#98) #2

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Mar 25, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/run_precommit.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,4 +11,4 @@ jobs:
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
- uses: pre-commit/[email protected].0
- uses: pre-commit/[email protected].1
8 changes: 4 additions & 4 deletions .github/workflows/test.yml
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ jobs:
- uses: actions/setup-python@v5
- name: install tox
run: pip install tox
- uses: actions/cache@v3
- uses: actions/cache@v4
id: cache
env:
cache-name: ds000017
Expand Down Expand Up @@ -136,7 +136,7 @@ jobs:

- name: Restore cached data ds000017
id: cache
uses: actions/cache/restore@v3
uses: actions/cache/restore@v4
with:
path: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data
key: ds000017
Expand All @@ -155,7 +155,7 @@ jobs:
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

- uses: codecov/codecov-action@v3
- uses: codecov/codecov-action@v4
if: ${{ always() }}
with:
token: ${{ secrets.CODECOV_TOKEN }}
Expand All @@ -176,7 +176,7 @@ jobs:

- name: Restore cached data ds000017
id: cache
uses: actions/cache/restore@v3
uses: actions/cache/restore@v4
with:
path: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data
key: ds000017
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/update_precommit_hooks.yml
Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ jobs:
- name: Update pre-commit hooks
run: pre-commit autoupdate
- name: Create Pull Request
uses: peter-evans/create-pull-request@v5
uses: peter-evans/create-pull-request@v6
with:
commit-message: pre-commit hooks auto-update
base: main
Expand Down
2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ repos:
- id: check-yaml
- id: check-added-large-files
- repo: https://github.com/psf/black
rev: 23.12.1
rev: 24.3.0
hooks:
- id: black
- repo: https://github.com/codespell-project/codespell
Expand Down
1 change: 1 addition & 0 deletions giga_connectome/logger.py
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
"""General logger for the cohort_creator package."""

from __future__ import annotations

import logging
Expand Down
6 changes: 3 additions & 3 deletions giga_connectome/methods.py
Original file line number Diff line number Diff line change
Expand Up @@ -40,9 +40,9 @@ def generate_method_section(
"atlas": atlas,
"smoothing_fwhm": smoothing_fwhm,
"strategy": strategy,
"standardize": "percent signal change"
if standardize == "psc"
else standardize,
"standardize": (
"percent signal change" if standardize == "psc" else standardize
),
"mni_space": mni_space,
"average_correlation": average_correlation,
"analysis_level": analysis_level,
Expand Down
1 change: 1 addition & 0 deletions giga_connectome/tests/test_cli.py
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
"""
Simple code to smoke test the functionality.
"""

from pathlib import Path
from pkg_resources import resource_filename
from giga_connectome.run import main
Expand Down
8 changes: 5 additions & 3 deletions giga_connectome/utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -90,9 +90,11 @@ def _filter_pybids_none_any(dct: dict) -> dict:
import bids

return {
k: bids.layout.Query.NONE
if v is None
else (bids.layout.Query.ANY if v == "*" else v)
k: (
bids.layout.Query.NONE
if v is None
else (bids.layout.Query.ANY if v == "*" else v)
)
for k, v in dct.items()
}

Expand Down
1 change: 1 addition & 0 deletions giga_connectome/workflow.py
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
"""
Process fMRIPrep outputs to timeseries based on denoising strategy.
"""

from __future__ import annotations

from giga_connectome import (
Expand Down
1 change: 1 addition & 0 deletions tools/download_templates.py
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
Set up templateflow with customised altases.
Download atlases that are relevant.
"""

from pathlib import Path

from giga_connectome.logger import gc_logger
Expand Down
2 changes: 1 addition & 1 deletion tools/mist2templateflow
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