diff --git a/.github/workflows/assign_reviewers.yml b/.github/workflows/assign_reviewers.yml index 5b5b8e57..a1316996 100644 --- a/.github/workflows/assign_reviewers.yml +++ b/.github/workflows/assign_reviewers.yml @@ -5,4 +5,4 @@ on: types: [opened, ready_for_review] jobs: assign-reviewer: - uses: khanlab/actions/.github/workflows/workflow-pr_task-assignReviewer.yml@v0.3.0 + uses: khanlab/actions/.github/workflows/workflow-pr_task-assignReviewer.yml@v0.3.4 diff --git a/.github/workflows/bump_version.yml b/.github/workflows/bump_version.yml index d675a9b2..5c0201f4 100644 --- a/.github/workflows/bump_version.yml +++ b/.github/workflows/bump_version.yml @@ -6,6 +6,6 @@ on: jobs: bump-version: if: github.event.pull_request.merged == true - uses: khanlab/actions/.github/workflows/workflow-version_task-semverGithub.yml@v0.3.0 + uses: khanlab/actions/.github/workflows/workflow-version_task-semverGithub.yml@v0.3.4 secrets: BP_PAT: ${{ secrets.BP_PAT_TOKEN }} diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index a611e705..024b4dc2 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -6,7 +6,7 @@ on: tags: [v*] jobs: deploy_docker: - uses: khanlab/actions/.github/workflows/workflow-release_task-deployDocker.yml@v0.3.0 + uses: khanlab/actions/.github/workflows/workflow-release_task-deployDocker.yml@v0.3.4 with: maximize_space: true secrets: diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 3b78f348..d7469b26 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -8,7 +8,7 @@ on: required: false jobs: release_package: - uses: khanlab/actions/.github/workflows/workflow-release_task-publishGithub.yml@v0.3.0 + uses: khanlab/actions/.github/workflows/workflow-release_task-publishGithub.yml@v0.3.4 with: comments: ${{ github.event.inputs.comments }} pipeline-description: true diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 60e326c8..bb6eb3f2 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -2,9 +2,9 @@ name: Lint and test workflow on: push: - branches: ["*", "!push-action/*"] + branches: ['*', '!push-action/*'] pull_request: - branches: ["*", "!push-action/*"] + branches: ['*', '!push-action/*'] jobs: quality: name: Lint code @@ -12,17 +12,13 @@ jobs: runs-on: ubuntu-latest steps: - name: Setup Python environment - uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.3.0 + uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.3.4 with: - python-version: "3.10" + python-version: '3.10' - name: yamlfix run: poetry run poe yamlfix-check - - name: isort - run: poetry run poe isort-check - - name: black - run: poetry run poe black-check - name: ruff - run: poetry run poe ruff-check + run: poetry run poe ruff-lint-check - name: snakefmt run: poetry run poe snakefmt-check test: @@ -30,10 +26,10 @@ jobs: needs: [quality] strategy: matrix: - python-version: ["3.8", "3.9", "3.10"] + python-version: ['3.8', '3.9', '3.10', '3.11'] steps: - name: Setup Python environments - uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.3.0 + uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.3.4 with: python-version: ${{ matrix.python-version }} install-library: true diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 1c906f0f..67d6d7c5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,4 +1,6 @@ --- +default_language_version: + python: python3.10 repos: - repo: https://github.com/pre-commit/pre-commit-hooks rev: v4.3.0 @@ -8,26 +10,21 @@ repos: - id: trailing-whitespace - repo: local hooks: - - id: yamlfix - name: yamlfix - entry: bash -c "poetry run poe yamlfix" + - name: yamlfix + id: yamlfix + entry: poetry run poe yamlfix + language: system + - name: ruff-lint + id: ruff-lint + entry: poetry run poe ruff-lint + language: system + types_or: [cython, pyi, python] + - name: ruff-format + id: ruff-format + entry: poetry run poe ruff-format + language: system + types_or: [cython, pyi, python] + - name: snakefmt + id: snakefmt + entry: poetry run poe snakefmt language: system - - repo: https://github.com/pycqa/isort - rev: 5.12.0 - hooks: - - id: isort - args: [--profile=black, --multi-line=3] - - repo: https://github.com/psf/black - rev: 22.8.0 - hooks: - - id: black - args: [--line-length=79] - - repo: https://github.com/pycqa/flake8 - rev: 5.0.4 - hooks: - - id: flake8 - - repo: https://github.com/snakemake/snakefmt - rev: 0.6.1 - hooks: - - id: snakefmt - args: [--include=\.smk$|^Snakefile, --line-length=79] diff --git a/docs/conf.py b/docs/conf.py index 613f48af..6e7411b7 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -64,4 +64,4 @@ # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ["_static"] \ No newline at end of file +html_static_path = ["_static"] diff --git a/poetry.lock b/poetry.lock index bb1d2dc2..aae7abf2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,18 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. + +[[package]] +name = "annotated-types" +version = "0.6.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, + {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, +] + +[package.dependencies] +typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} [[package]] name = "appdirs" @@ -43,47 +57,34 @@ files = [ [[package]] name = "attrs" -version = "23.1.0" +version = "23.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" files = [ - 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comments!" optional = false -python-versions = ">=3.7.2" +python-versions = ">=3.8" files = [ - {file = "yamlfix-1.15.0-py3-none-any.whl", hash = "sha256:22095f0aaa9a6c07b279385b3b567b1553d6cb12d6f2c41dd2bb0a4361efc70d"}, - {file = "yamlfix-1.15.0.tar.gz", hash = "sha256:6aa50eac3b308ef8d31f5e0d0c36aa5c5bd46de4d8f943ae6cb62df60e8e7e72"}, + {file = "yamlfix-1.16.0-py3-none-any.whl", hash = "sha256:d92bf8a6d5b6f186bd9d643d633549a1c2424555cb8d176a5d38bce3e678b2b0"}, + {file = "yamlfix-1.16.0.tar.gz", hash = "sha256:72f7990e5b2b4459ef3249df4724dacbd85ce7b87f4ea3503d8a72c48574cc32"}, ] [package.dependencies] @@ -3795,17 +3822,17 @@ ruyaml = ">=0.91.0" [[package]] name = "yte" -version = "1.5.1" +version = "1.5.4" description = "A YAML template engine with Python expressions" optional = false python-versions = ">=3.7" files = [ - {file = "yte-1.5.1-py3-none-any.whl", hash = "sha256:fd646bc47c355f202f14b7476996de4a31501cf1e107ac7ad8e19edcd786d30b"}, - {file = "yte-1.5.1.tar.gz", hash = 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include = "scattr" }] [tool.poetry.dependencies] -python = ">=3.8, <3.11" -snakebids = "^0.9.0" +python = ">=3.8, <3.12" +snakebids = "^0.10.2" +labelmerge = "^0.4.7" +matplotlib = "^3.7.1" nibabel = "^3.2.2" nilearn = "^0.10.0" -numpy = "^1.22.3" -scipy = "^1.8.0" -labelmerge = "^v0.4.6" -matplotlib = "^3.7.1" niworkflows = "^1.7.9" +numpy = "^1.22.3" pygments = "^2.15.1" +scipy = "^1.8.0" +# Required constraint for compatability with snakebids +pulp = "<2.8.0" [tool.poetry.group.dev.dependencies] pytest-console-scripts = "1.2" pytest = "^7.0.1" -black = "^22.1.0" -isort = "^5.10.1" poethepoet = "^0.13.1" pre-commit = "^2.17.0" snakefmt = "^0.6.1" yamlfix = "^1.1.0" -ruff = "^0.0.267" +ruff = "^0.1.14" [tool.poetry.scripts] scattr = 'scattr.run:main' @@ -45,22 +45,13 @@ build-backend = "poetry.core.masonry.api" [tool.poe.tasks] setup = "pre-commit install" -isort = "isort scattr" -isort-check = "isort -c scattr" -black = "black scattr" -black-check = "black --check scattr" -ruff = "ruff --fix scattr" -ruff-check = "ruff scattr" +ruff-lint = "ruff check --fix scattr" +ruff-lint-check = "ruff check scattr" +ruff-format = "ruff format ." snakefmt = "snakefmt scattr" snakefmt-check = "snakefmt --check scattr" -quality = ["yamlfix", "ruff", "isort", "black", "snakefmt"] -quality-check = [ - "ruff-check", - "yamlfix-check", - "isort-check", - "black-check", - "snakefmt-check", -] +quality = ["yamlfix", "ruff-lint", "ruff-format", "snakefmt"] +quality-check = ["yamlfix-check", "ruff-lint-check", "snakefmt-check"] test = [ "test_base", "test_freesurfer", @@ -144,15 +135,8 @@ find . -type f \\( \ \\) -exec yamlfix --check {} \\; """ -[tool.isort] -profile = "black" -multi_line_output = 3 -line_length = 79 - -[tool.black] -line-length = 79 - [tool.ruff] +select = ["E", "W", "N", "RUF", "I", "UP"] line-length = 79 builtins = ["snakemake"] diff --git a/scattr/workflow/scripts/mrtpipelines/create_exclude_mask.py b/scattr/workflow/scripts/mrtpipelines/create_exclude_mask.py index a15e9eea..8ad7e802 100644 --- a/scattr/workflow/scripts/mrtpipelines/create_exclude_mask.py +++ b/scattr/workflow/scripts/mrtpipelines/create_exclude_mask.py @@ -22,13 +22,13 @@ def create_exclude_mask( Path(out_dir).mkdir(parents=True, exist_ok=True) # Get number of labels - with open(num_labels, "r") as f: + with open(num_labels) as f: num_labels = int(f.read().strip()) node_pairs = np.triu_indices(num_labels, k=1) # Zona labels (currently misisng subjects) - lZI = expand( # noqa: F841 (used in shell call) + lZI = expand( # (used in shell call) # noqa: N806 bids( root=base_dir, datatype="roi_masks", @@ -37,7 +37,7 @@ def create_exclude_mask( **wildcards, ) ) - rZI = bids( # noqa: F841 (used in shell call) + rZI = bids( # (used in shell call) # noqa: N806 root=base_dir, datatype="roi_masks", desc="22", @@ -62,7 +62,7 @@ def create_exclude_mask( # Create masks - run sequentially due to parallelization errors for idx, mask in enumerate(out_mask): - in_roi1, in_roi2 = roi1[idx], roi2[idx] # noqa: F841 (used in shell) + in_roi1, in_roi2 = roi1[idx], roi2[idx] # (used in shell) shell( "mrcalc -nthreads {threads} " "{subcortical_seg} 0 -neq {in_roi1} -sub {in_roi2} -sub {lZI} " diff --git a/scattr/workflow/scripts/mrtpipelines/create_roi_mask.py b/scattr/workflow/scripts/mrtpipelines/create_roi_mask.py index 7d90b7b9..7f562bbc 100644 --- a/scattr/workflow/scripts/mrtpipelines/create_roi_mask.py +++ b/scattr/workflow/scripts/mrtpipelines/create_roi_mask.py @@ -2,7 +2,7 @@ from pathlib import Path from snakebids import bids -from snakemake.io import expand # noqa: F401 (used in commented command) +from snakemake.io import expand # (used in commented command) from snakemake.shell import shell @@ -19,12 +19,12 @@ def create_roi_mask( Path(out_dir).mkdir(parents=True, exist_ok=True) # Read number of labels - with open(num_labels, "r") as f: + with open(num_labels) as f: num_labels = int(f.read().strip()) # Create masks sequentially (error with trying to do it in parallel) for idx in range(1, num_labels + 1): - roi = bids( # noqa: F841 (used in shell call) + roi = bids( # (used in shell call) root=base_dir, datatype="roi_masks", desc=f"{idx}", diff --git a/scattr/workflow/scripts/qc/segmentation_qc.py b/scattr/workflow/scripts/qc/segmentation_qc.py index 788093f2..707f17a2 100644 --- a/scattr/workflow/scripts/qc/segmentation_qc.py +++ b/scattr/workflow/scripts/qc/segmentation_qc.py @@ -38,5 +38,5 @@ def segmentation_qc( seg_path=snakemake.input.qc_labels, output_path_static=snakemake.output.qc_png, output_path_html=snakemake.output.qc_html, - wildcards=snakemake.wildcards, # noqa:F821 + wildcards=snakemake.wildcards, )