From 837c3e7d84b62b3585f2caa826f8576996ed8811 Mon Sep 17 00:00:00 2001 From: Hao-Ting Wang Date: Tue, 23 Jan 2024 14:38:18 -0500 Subject: [PATCH 1/8] update the commit hash of mist2templateflow (#98) * update the commit hash of mist2templateflow * full_test --- tools/mist2templateflow | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/mist2templateflow b/tools/mist2templateflow index 4e0a2a3..e9c6b20 160000 --- a/tools/mist2templateflow +++ b/tools/mist2templateflow @@ -1 +1 @@ -Subproject commit 4e0a2a3688f344d197e6e753ca4c9bdc9b8ed5a4 +Subproject commit e9c6b2087ce698c873fea21433f1c7ed1fe762f0 From 5a84e6a2a8e428a4fb6c582800d8db8f2d3c16f0 Mon Sep 17 00:00:00 2001 From: htwangtw Date: Mon, 29 Jan 2024 00:54:45 +0000 Subject: [PATCH 2/8] pre-commit hooks auto-update --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index faf8fab..117b292 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -9,7 +9,7 @@ repos: - id: check-yaml - id: check-added-large-files - repo: https://github.com/psf/black - rev: 23.12.1 + rev: 24.1.1 hooks: - id: black - repo: https://github.com/codespell-project/codespell From e7cc0e60cf9ad2bc155c26389149f1d4afb60934 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Mon, 29 Jan 2024 09:04:49 +0100 Subject: [PATCH 3/8] [STY] apply the new black --- giga_connectome/logger.py | 1 + giga_connectome/methods.py | 6 +++--- giga_connectome/tests/test_cli.py | 1 + giga_connectome/utils.py | 8 +++++--- giga_connectome/workflow.py | 1 + tools/download_templates.py | 1 + 6 files changed, 12 insertions(+), 6 deletions(-) diff --git a/giga_connectome/logger.py b/giga_connectome/logger.py index e859451..6a9e9b2 100644 --- a/giga_connectome/logger.py +++ b/giga_connectome/logger.py @@ -1,4 +1,5 @@ """General logger for the cohort_creator package.""" + from __future__ import annotations import logging diff --git a/giga_connectome/methods.py b/giga_connectome/methods.py index 10cf984..c2f9a5f 100644 --- a/giga_connectome/methods.py +++ b/giga_connectome/methods.py @@ -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, diff --git a/giga_connectome/tests/test_cli.py b/giga_connectome/tests/test_cli.py index 710ed08..fead8b5 100644 --- a/giga_connectome/tests/test_cli.py +++ b/giga_connectome/tests/test_cli.py @@ -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 diff --git a/giga_connectome/utils.py b/giga_connectome/utils.py index e439172..58eaf0c 100644 --- a/giga_connectome/utils.py +++ b/giga_connectome/utils.py @@ -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() } diff --git a/giga_connectome/workflow.py b/giga_connectome/workflow.py index 5fbada5..034e910 100644 --- a/giga_connectome/workflow.py +++ b/giga_connectome/workflow.py @@ -1,6 +1,7 @@ """ Process fMRIPrep outputs to timeseries based on denoising strategy. """ + from __future__ import annotations from giga_connectome import ( diff --git a/tools/download_templates.py b/tools/download_templates.py index d79a421..20ee80a 100644 --- a/tools/download_templates.py +++ b/tools/download_templates.py @@ -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 From 23a02ed3d094620fbec77f59360c3315909295a4 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 1 Feb 2024 22:36:39 +0000 Subject: [PATCH 4/8] Bump codecov/codecov-action from 3 to 4 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/v3...v4) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 735a460..526d182 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -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 }} From 867602864ab49456a31059170b1335f6a8f468d9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 1 Feb 2024 22:36:44 +0000 Subject: [PATCH 5/8] Bump peter-evans/create-pull-request from 5 to 6 Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 5 to 6. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](https://github.com/peter-evans/create-pull-request/compare/v5...v6) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/update_precommit_hooks.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/update_precommit_hooks.yml b/.github/workflows/update_precommit_hooks.yml index a0cf4bf..cdacc3c 100644 --- a/.github/workflows/update_precommit_hooks.yml +++ b/.github/workflows/update_precommit_hooks.yml @@ -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 From 3ffe04b5fa72b24fa75073bca30803eb679f6625 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 1 Feb 2024 22:36:48 +0000 Subject: [PATCH 6/8] Bump actions/cache from 3 to 4 Bumps [actions/cache](https://github.com/actions/cache) from 3 to 4. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/test.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 735a460..eaff926 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -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 @@ -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 @@ -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 From a89e23a6f55d8ee9635acc2c5f32b0afc7728558 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 1 Mar 2024 23:00:14 +0000 Subject: [PATCH 7/8] Bump pre-commit/action from 3.0.0 to 3.0.1 Bumps [pre-commit/action](https://github.com/pre-commit/action) from 3.0.0 to 3.0.1. - [Release notes](https://github.com/pre-commit/action/releases) - [Commits](https://github.com/pre-commit/action/compare/v3.0.0...v3.0.1) --- updated-dependencies: - dependency-name: pre-commit/action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- .github/workflows/run_precommit.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_precommit.yml b/.github/workflows/run_precommit.yml index a100dcb..65947d3 100644 --- a/.github/workflows/run_precommit.yml +++ b/.github/workflows/run_precommit.yml @@ -11,4 +11,4 @@ jobs: steps: - uses: actions/checkout@v4 - uses: actions/setup-python@v5 - - uses: pre-commit/action@v3.0.0 + - uses: pre-commit/action@v3.0.1 From bfd81a4bb89fb7c17854b3029958953dcce8057d Mon Sep 17 00:00:00 2001 From: htwangtw <13743617+htwangtw@users.noreply.github.com> Date: Mon, 18 Mar 2024 00:55:10 +0000 Subject: [PATCH 8/8] pre-commit hooks auto-update --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 117b292..9b63cd7 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -9,7 +9,7 @@ repos: - id: check-yaml - id: check-added-large-files - repo: https://github.com/psf/black - rev: 24.1.1 + rev: 24.3.0 hooks: - id: black - repo: https://github.com/codespell-project/codespell