diff --git a/.github/workflows/assign_reviewers.yml b/.github/workflows/assign_reviewers.yml index 5b5b8e5..a131699 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 d675a9b..5c0201f 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 9f21b4c..a95bc7a 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -1,17 +1,16 @@ ---- -name: Deploy packages -on: - workflow_dispatch: - push: - tags: [v*] -jobs: - deploy-docker: - uses: khanlab/actions/.github/workflows/workflow-release_task-deployDocker.yml@v0.3.0 - secrets: - DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }} - DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }} - - deploy-pypi: - uses: khanlab/actions/.github/workflows/workflow-release_task-deployPypi.yml@v0.3.0 - secrets: - PYPI_API_TOKEN: ${{ secrets.PYPI_API_TOKEN }} +--- +name: Deploy packages +on: + workflow_dispatch: + push: + tags: [v*] +jobs: + deploy-docker: + uses: khanlab/actions/.github/workflows/workflow-release_task-deployDocker.yml@v0.3.4 + secrets: + DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }} + DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }} + deploy-pypi: + uses: khanlab/actions/.github/workflows/workflow-release_task-deployPypi.yml@v0.3.4 + secrets: + PYPI_API_TOKEN: ${{ secrets.PYPI_API_TOKEN }} diff --git a/.github/workflows/quality.yml b/.github/workflows/quality.yml index 375eb4e..da33802 100644 --- a/.github/workflows/quality.yml +++ b/.github/workflows/quality.yml @@ -12,16 +12,12 @@ 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" - name: yamlfix run: poetry run poe yamlfix-check - name: ruff - run: poetry run poe ruff-check - - name: isort - run: poetry run poe isort-check - - name: black - run: poetry run poe black-check + run: poetry run poe ruff-lint-check - name: snakefmt run: poetry run poe snakefmt-check diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 3b78f34..d7469b2 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: ${{ github.event.inputs.comments }} pipeline-description: true diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 1aeb387..97dca8e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,4 +1,6 @@ --- +default_language_version: + python: python3.10 repos: - repo: https://github.com/pre-commit/pre-commit-hooks rev: v4.3.0 @@ -8,26 +10,21 @@ repos: - id: trailing-whitespace - repo: local hooks: - - id: yamlfix - name: yamlfix - entry: bash -c "poetry run poe yamlfix" + - name: yamlfix + id: yamlfix + entry: poetry run poe yamlfix + language: system + - name: ruff-format + id: ruff-format + entry: poetry run ruff format labelmerge + language: system + types_or: [cython, pyi, python] + - name: ruff-lint + id: ruff-lint + entry: poetry run ruff check --fix labelmerge + language: system + types_or: [cython, pyi, python] + - name: snakefmt + id: snakefmt + entry: poetry run poe snakefmt language: system - - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.0.290 - hooks: - - id: ruff - - repo: https://github.com/pycqa/isort - rev: 5.10.1 - hooks: - - id: isort - args: [--profile=black, --multi-line=3] - - repo: https://github.com/psf/black - rev: 22.8.0 - hooks: - - id: black - args: [--line-length=79] - - repo: https://github.com/snakemake/snakefmt - rev: 0.6.1 - hooks: - - id: snakefmt - args: [--include=\.smk$|^Snakefile, --line-length=79] diff --git a/README.md b/README.md index a87f16b..b709436 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,18 @@ ## Labelmerge + ![Version](https://img.shields.io/github/v/tag/khanlab/labelmerge?label=version) -![Python3](https://img.shields.io/badge/python-3.8_|_3.9_|_3.10-blue.svg) +![Python3](https://img.shields.io/badge/python-3.8_|_3.9_|_3.10_|_3.11-blue.svg) ![Docker Pulls](https://img.shields.io/docker/pulls/khanlab/labelmerge) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7636410.svg)](https://doi.org/10.5281/zenodo.7636410) Labelmerge: A BIDS app for merging multiple label maps and metadata into a single parcellation scheme. -Examination of the brain has led to the creation and distribution of numerous parcellation schemes, studying various features or aspects including gross anatomy, cytoarchitecture, myeloarchitecture, functional connectivty, or structural connectivity. With the growing number of available schemes, there exists a need for methods to robustly merge different these different atlases from numerous sources depending on the aims of the specific study. +Examination of the brain has led to the creation and distribution of numerous parcellation schemes, studying various features or aspects including gross anatomy, cytoarchitecture, myeloarchitecture, functional connectivty, or structural connectivity. With the growing number of available schemes, there exists a need for methods to robustly merge different these different atlases from numerous sources depending on the aims of the specific study. Currently, combining multiple atlases requires image-processing tools to manually remove and add the regions of interest from the respective atlases. While effective, this task becomes inefficient and is prone to error when looking to combine specific labels of interest from multiple atlases or across a group of subjects. To that end we developed Labelmerge, a Brain Imaging Data Structure (BIDS) app that combines the parcellations of multiple atlases into a single parcellation scheme that can be applied towards downstream analysis. - ### Contributing + Clone the git repository. Labelmerge dependencies are managed with Poetry (version 1.2.x), which you'll need installed on your machine. You can find instructions on the Poetry @@ -34,10 +35,8 @@ poetry run poe If you wish, you can also run poe [command] directly by installing poethepoet on your system. Follow the install instructions at the link above. -Labelmerge uses pre-commit hooks (installed via the poe setup command above) to +Labelmerge uses pre-commit hooks (installed via the poe setup command above) to lint and format code (we use black, isort, flake8). By default, these hooks are run on every commit. Please be sure they all pass before making a PR. - - diff --git a/poetry.lock b/poetry.lock index b194726..4ce68fa 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" @@ -36,25 +50,6 @@ files = [ {file = "astor-0.8.1.tar.gz", hash = "sha256:6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e"}, ] -[[package]] -name = "astroid" -version = "2.15.6" -description = "An abstract syntax tree for Python with inference support." -optional = false -python-versions = ">=3.7.2" -files = [ - {file = "astroid-2.15.6-py3-none-any.whl", hash = "sha256:389656ca57b6108f939cf5d2f9a2a825a3be50ba9d589670f393236e0a03b91c"}, - {file = "astroid-2.15.6.tar.gz", hash = "sha256:903f024859b7c7687d7a7f3a3f73b17301f8e42dfd9cc9df9d4418172d3e2dbd"}, -] - -[package.dependencies] -lazy-object-proxy = ">=1.4.0" -typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} -wrapt = [ - {version = ">=1.11,<2", markers = "python_version < \"3.11\""}, - {version = ">=1.14,<2", markers = "python_version >= \"3.11\""}, -] - [[package]] name = "attrs" version = "23.1.0" @@ -84,20 +79,6 @@ files = [ {file = "bids_validator-1.13.1-py2.py3-none-any.whl", hash = "sha256:da6edf5e76ef86c8a63b3fcee1dbfb039a16a9ef63cb0d2d05312c200d4607f7"}, ] -[[package]] -name = "binaryornot" -version = "0.4.4" -description = "Ultra-lightweight pure Python package to check if a file is binary or text." -optional = false -python-versions = "*" -files = [ - {file = "binaryornot-0.4.4-py2.py3-none-any.whl", hash = "sha256:b8b71173c917bddcd2c16070412e369c3ed7f0528926f70cac18a6c97fd563e4"}, - {file = "binaryornot-0.4.4.tar.gz", hash = "sha256:359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061"}, -] - -[package.dependencies] -chardet = ">=3.0.2" - [[package]] name = "black" version = "22.12.0" @@ -155,17 +136,6 @@ simplejson = "*" tabulate = "*" termcolor = "*" -[[package]] -name = "cached-property" -version = "1.5.2" -description = "A decorator for caching properties in classes." -optional = false -python-versions = "*" -files = [ - {file = "cached-property-1.5.2.tar.gz", hash = "sha256:9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130"}, - {file = "cached_property-1.5.2-py2.py3-none-any.whl", hash = "sha256:df4f613cf7ad9a588cc381aaf4a512d26265ecebd5eb9e1ba12f1319eb85a6a0"}, -] - [[package]] name = "certifi" version = "2023.7.22" @@ -188,17 +158,6 @@ files = [ {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"}, ] -[[package]] -name = "chardet" -version = "5.2.0" -description = "Universal encoding detector for Python 3" -optional = false -python-versions = ">=3.7" -files = [ - {file = "chardet-5.2.0-py3-none-any.whl", hash = "sha256:e1cf59446890a00105fe7b7912492ea04b6e6f06d4b742b2c788469e34c82970"}, - {file = "chardet-5.2.0.tar.gz", hash = "sha256:1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7"}, -] - [[package]] name = "charset-normalizer" version = "3.2.0" @@ -334,25 +293,32 @@ files = [ ] [[package]] -name = "cookiecutter" -version = "2.3.0" -description = "A command-line utility that creates projects from project templates, e.g. creating a Python package project from a Python package project template." +name = "copier" +version = "9.1.0" +description = "A library for rendering project templates." optional = false -python-versions = ">=3.7" +python-versions = ">=3.8,<4.0" files = [ - {file = "cookiecutter-2.3.0-py3-none-any.whl", hash = "sha256:7e87944757c6e9f8729cf89a4139b6a35ab4d6dcbc6ae3e7d6360d44ad3ad383"}, - {file = "cookiecutter-2.3.0.tar.gz", hash = "sha256:942a794981747f6d7f439d6e49d39dc91a9a641283614160c93c474c72c29621"}, + {file = "copier-9.1.0-py3-none-any.whl", hash = "sha256:a7c8ce77e0efcf5d6605ebbf9049577534e4ed87f9964fe928d491c56c69b0f9"}, + {file = "copier-9.1.0.tar.gz", hash = "sha256:0810134f0bf3ce72b402480d1420ab7e773c1c9ce719a923e1584cb69f97dacb"}, ] [package.dependencies] -arrow = "*" -binaryornot = ">=0.4.4" -click = ">=7.0,<9.0.0" -Jinja2 = ">=2.7,<4.0.0" -python-slugify = ">=4.0.0" +colorama = ">=0.4.6" +decorator = ">=5.1.1" +dunamai = ">=1.7.0" +funcy = ">=1.17" +jinja2 = ">=3.1.1" +jinja2-ansible-filters = ">=1.3.1" +packaging = ">=23.0" +pathspec = ">=0.9.0" +plumbum = ">=1.6.9" +pydantic = ">=2.4.2" +pygments = ">=2.7.1" pyyaml = ">=5.3.1" -requests = ">=2.23.0" -rich = "*" +pyyaml-include = ">=1.2" +questionary = ">=1.8.1" +typing-extensions = {version = ">=3.7.4,<5.0.0", markers = "python_version < \"3.9\""} [[package]] name = "datrie" @@ -389,19 +355,16 @@ files = [ ] [[package]] -name = "dill" -version = "0.3.7" -description = "serialize all of Python" +name = "decorator" +version = "5.1.1" +description = "Decorators for Humans" optional = false -python-versions = ">=3.7" +python-versions = ">=3.5" files = [ - 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Lau", - "Ali R. Khan" + "Ali R. Khan", ] readme = "README.md" -packages = [ - { include = "labelmerge" } -] +packages = [{ include = "labelmerge" }] [tool.poetry.dependencies] python = ">=3.8,<3.12" -snakebids = "^0.9.0" +snakebids = "^0.10.2" nibabel = "^3.2.2" numpy = "^1.22.3" xarray = "^2022.11.0" +# Newer versions of pulp incompatible with snakebids +pulp = "<2.8.0" [tool.poetry.group.dev.dependencies] pytest-console-scripts = "1.2" pytest = "^7.0.1" -black = "^22.1.0" -pylint = "^2.12.2" -isort = "^5.10.1" poethepoet = "^0.13.1" pre-commit = "^2.17.0" snakefmt = "^0.6.1" yamlfix = "^1.1.0" mypy = "^0.991" -ruff = "^0.0.290" +ruff = "^0.1.14" [tool.poetry.scripts] labelmerge = 'labelmerge.run:main' @@ -47,34 +44,19 @@ build-backend = "poetry.core.masonry.api" setup = "pre-commit install" yamlfix = { shell = "find . -type f \\( -iname \\*.yaml -o -iname \\*.yml ! -iname snakemake* ! -iname snakebids* \\) -exec yamlfix {} \\;" } yamlfix-check = { shell = "find . -type f \\( -iname \\*.yaml -o -iname \\*.yml ! -iname snakemake* ! -iname snakebids* \\) -exec yamlfix --check {} \\;" } -isort = "isort labelmerge" -isort-check = "isort -c labelmerge" -black = "black labelmerge" -black-check = "black --check labelmerge" -ruff = "ruff --fix labelmerge" -ruff-check = "ruff labelmerge" +ruff-format = "ruff format labelmerge" +ruff-lint = "ruff --fix labelmerge" +ruff-lint-check = "ruff labelmerge" snakefmt = "snakefmt labelmerge" snakefmt-check = "snakefmt --check labelmerge" -quality = ["yamlfix", "ruff", "isort", "black", "snakefmt"] -quality-check = [ - "yamlfix-check", - "ruff-check", - "isort-check", - "black-check", - "snakefmt-check", -] - -[tool.isort] -profile = "black" -multi_line_output = 3 - -[tool.black] -line-length = 79 +quality = ["yamlfix", "ruff-format", "ruff-lint", "snakefmt"] +quality-check = ["yamlfix-check", "ruff-lint-check", "snakefmt-check"] [tool.snakefmt] line_length = 79 include = '\.smk$|^Snakefile' [tool.ruff] +select = ["E", "W", "N", "RUF", "I", "UP"] line-length = 79 -builtins = [ "snakemake" ] +builtins = ["snakemake"]