diff --git a/.circleci/config.yml b/.circleci/config.yml index 16ab7299d..458a16985 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -119,25 +119,24 @@ jobs: name: Update Python install tools command: | python3 -m ensurepip - python3 -m pip install --upgrade pip setuptools wheel + python3 -m pip install --upgrade pip build - run: name: Install twine, readme renderer command: python3 -m pip install twine readme_renderer[md] - run: name: Check build and readme rendering command: | - cd bids-validator && python3 setup.py sdist bdist_wheel - twine check dist/* + python3 -m build bids-validator/ + twine check bids-validator/dist/* - run: name: Check sdist installation command: | cd bids-validator - python3 -m pip install -U virtualenv - virtualenv venv - source venv/bin/activate - python --version - pip install -U pip setuptools>=27.0 wheel - pip install dist/*.tar.gz + python3 -m venv .venv + source .venv/bin/activate + python3 --version + python3 -m pip install --upgrade pip + python3 -m pip install dist/*.tar.gz pypi_deployment: docker: - image: alpine:3.13 @@ -154,13 +153,13 @@ jobs: name: Update Python install tools command: | python3 -m ensurepip - python3 -m pip install --upgrade pip setuptools wheel + python3 -m pip install --upgrade pip build - run: name: Install twine, readme renderer command: python3 -m pip install twine readme_renderer[md] - run: git checkout -f $CIRCLE_TAG - - run: cd bids-validator && python3 setup.py sdist bdist_wheel - - run: cd bids-validator && twine upload dist/* + - run: python3 -m build bids-validator/ + - run: python3 -m twine upload bids-validator/dist/* gh-pages_deployment: docker: - image: node:18-alpine diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml index 503a963e5..a84ddbd64 100644 --- a/.github/workflows/codespell.yml +++ b/.github/workflows/codespell.yml @@ -17,7 +17,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: codespell-project/actions-codespell@master with: ignore_words_list: ro,anser,te,tage,afterall,nwe,nin,nd,falsy diff --git a/.github/workflows/deno_tests.yml b/.github/workflows/deno_tests.yml index a58604a4e..416b07705 100644 --- a/.github/workflows/deno_tests.yml +++ b/.github/workflows/deno_tests.yml @@ -16,7 +16,7 @@ jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: denoland/setup-deno@v1 with: deno-version: v1.x @@ -39,7 +39,7 @@ jobs: working-directory: ./bids-validator steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: denoland/setup-deno@v1.1.2 with: deno-version: v1.x @@ -61,7 +61,7 @@ jobs: runs-on: ubuntu-latest if: github.event_name != 'pull_request' && github.repository_owner == 'bids-standard' steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: fetch-depth: 0 token: ${{ secrets.PUSH_TOKEN }} diff --git a/.github/workflows/docker-build-push.yml b/.github/workflows/docker-build-push.yml index 0721c09fb..b7b6627a3 100644 --- a/.github/workflows/docker-build-push.yml +++ b/.github/workflows/docker-build-push.yml @@ -11,22 +11,22 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out the repo - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Log in to Docker Hub - uses: docker/login-action@v2 + uses: docker/login-action@v3 with: username: ${{ secrets.DOCKER_USERNAME }} password: ${{ secrets.DOCKER_PASSWORD }} - name: Extract metadata (tags, labels) for Docker id: meta - uses: docker/metadata-action@v4 + uses: docker/metadata-action@v5 with: images: bids/validator - name: Build and push Docker image - uses: docker/build-push-action@v4 + uses: docker/build-push-action@v5 with: context: . push: true @@ -69,10 +69,10 @@ jobs: make -C builddir && \ sudo make -C builddir install - name: Check out code for the container build - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Extract metadata (tags, labels) for Docker id: meta - uses: docker/metadata-action@v4 + uses: docker/metadata-action@v5 with: images: bids/validator - name: Build Container diff --git a/.github/workflows/node_tests.yml b/.github/workflows/node_tests.yml index 28f027a01..091da654e 100644 --- a/.github/workflows/node_tests.yml +++ b/.github/workflows/node_tests.yml @@ -25,8 +25,8 @@ jobs: run: | git config --global core.autocrlf false git config --global core.eol lf - - uses: actions/checkout@v3 - - uses: actions/setup-node@v3 + - uses: actions/checkout@v4 + - uses: actions/setup-node@v4 with: node-version: '18' cache: 'npm' diff --git a/.github/workflows/python_tests.yml b/.github/workflows/python_tests.yml index a30f9bdd1..03e61721f 100644 --- a/.github/workflows/python_tests.yml +++ b/.github/workflows/python_tests.yml @@ -21,7 +21,7 @@ jobs: runs-on: ${{ matrix.platform }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set git name/email run: | git config --global user.email "bids.maintenance@gmail.com" @@ -44,7 +44,7 @@ jobs: - name: Install git-annex windows if: matrix.platform == 'windows-latest' - uses: crazy-max/ghaction-chocolatey@v2 + uses: crazy-max/ghaction-chocolatey@v3 with: args: install git-annex --yes --ignore-checksums continue-on-error: true # This can fail for stupid reasons ¯\_(ツ)_/¯ diff --git a/.github/workflows/test-bids-examples.yml b/.github/workflows/test-bids-examples.yml index a1618ffd0..53da0011c 100644 --- a/.github/workflows/test-bids-examples.yml +++ b/.github/workflows/test-bids-examples.yml @@ -26,10 +26,10 @@ jobs: steps: - name: Set up Node.js - uses: actions/setup-node@v3 + uses: actions/setup-node@v4 with: node-version: 18 - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: recursive diff --git a/bids-validator-web/components/App.jsx b/bids-validator-web/components/App.jsx index e659de051..34ee002f2 100644 --- a/bids-validator-web/components/App.jsx +++ b/bids-validator-web/components/App.jsx @@ -1,7 +1,5 @@ import React from 'react' -import bowser from 'bowser' import Issues from '../components/Issues' -import BrowserWarning from './BrowserWarning' import Validate from '../components/Validate' import validate from '../../bids-validator' import validatorPackageJson from 'bids-validator/package.json' assert { type: 'json' } @@ -85,11 +83,6 @@ export default class App extends React.Component { } render() { - const browserUnsupported = - !bowser.chrome && - !bowser.chromium && - !bowser.firefox && - typeof window !== 'undefined' return (
-
- {browserUnsupported ? : null} -
- {!browserUnsupported ? ( - - ) : null} +
{this.state.status === 'validated' ? ( diff --git a/bids-validator-web/components/BrowserWarning.jsx b/bids-validator-web/components/BrowserWarning.jsx deleted file mode 100644 index 8624ffe1e..000000000 --- a/bids-validator-web/components/BrowserWarning.jsx +++ /dev/null @@ -1,23 +0,0 @@ -import React from 'react' - -// component setup ----------------------------------------------------------- - -class BrowserWarning extends React.Component { - render() { - return ( - - ) - } -} - -export default BrowserWarning diff --git a/bids-validator-web/package.json b/bids-validator-web/package.json index 49e135c9a..143e665d1 100644 --- a/bids-validator-web/package.json +++ b/bids-validator-web/package.json @@ -1,20 +1,19 @@ { "name": "bids-validator-web", - "version": "1.12.1-dev.0", + "version": "1.13.2-dev.0", "description": "web client for bids-validator", "main": "index.js", "license": "MIT", "dependencies": { - "@babel/runtime": "^7.16.7", - "bootstrap": "^5.3.1", - "bowser": "^2.11.0", - "eslint-config-next": "^13.4.12", - "next": "^13.4.7", + "@babel/runtime": "^7.22.10", + "bootstrap": "^5.3.2", + "eslint-config-next": "^14.0.0", + "next": "^14.0.0", "pluralize": "^8.0.0", "react": "^18.2.0", - "react-bootstrap": "^2.8.0", + "react-bootstrap": "^2.9.1", "react-dom": "^18.2.0", - "sass": "^1.63.6" + "sass": "^1.69.4" }, "scripts": { "dev": "next", @@ -22,6 +21,6 @@ "start": "next start" }, "devDependencies": { - "@next/eslint-plugin-next": "^13.4.7" + "@next/eslint-plugin-next": "^14.0.0" } } diff --git a/bids-validator/bids_validator/_version.py b/bids-validator/bids_validator/_version.py index 27f42bb3b..e1764f9b1 100644 --- a/bids-validator/bids_validator/_version.py +++ b/bids-validator/bids_validator/_version.py @@ -6,7 +6,7 @@ # that just contains the computed version number. # This file is released into the public domain. -# Generated by versioneer-0.26 +# Generated by versioneer-0.29 # https://github.com/python-versioneer/python-versioneer """Git implementation of _version.py.""" @@ -16,11 +16,11 @@ import re import subprocess import sys -from typing import Callable, Dict +from typing import Any, Callable, Dict, List, Optional, Tuple import functools -def get_keywords(): +def get_keywords() -> Dict[str, str]: """Get the keywords needed to look up the version information.""" # these strings will be replaced by git during git-archive. # setup.py/versioneer.py will grep for the variable names, so they must @@ -36,8 +36,15 @@ def get_keywords(): class VersioneerConfig: """Container for Versioneer configuration parameters.""" + VCS: str + style: str + tag_prefix: str + parentdir_prefix: str + versionfile_source: str + verbose: bool -def get_config(): + +def get_config() -> VersioneerConfig: """Create, populate and return the VersioneerConfig() object.""" # these strings are filled in when 'setup.py versioneer' creates # _version.py @@ -59,9 +66,9 @@ class NotThisMethod(Exception): HANDLERS: Dict[str, Dict[str, Callable]] = {} -def register_vcs_handler(vcs, method): # decorator +def register_vcs_handler(vcs: str, method: str) -> Callable: # decorator """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f): + def decorate(f: Callable) -> Callable: """Store f in HANDLERS[vcs][method].""" if vcs not in HANDLERS: HANDLERS[vcs] = {} @@ -70,13 +77,19 @@ def decorate(f): return decorate -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): +def run_command( + commands: List[str], + args: List[str], + cwd: Optional[str] = None, + verbose: bool = False, + hide_stderr: bool = False, + env: Optional[Dict[str, str]] = None, +) -> Tuple[Optional[str], Optional[int]]: """Call the given command(s).""" assert isinstance(commands, list) process = None - popen_kwargs = {} + popen_kwargs: Dict[str, Any] = {} if sys.platform == "win32": # This hides the console window if pythonw.exe is used startupinfo = subprocess.STARTUPINFO() @@ -92,8 +105,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, stderr=(subprocess.PIPE if hide_stderr else None), **popen_kwargs) break - except OSError: - e = sys.exc_info()[1] + except OSError as e: if e.errno == errno.ENOENT: continue if verbose: @@ -113,7 +125,11 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, return stdout, process.returncode -def versions_from_parentdir(parentdir_prefix, root, verbose): +def versions_from_parentdir( + parentdir_prefix: str, + root: str, + verbose: bool, +) -> Dict[str, Any]: """Try to determine the version from the parent directory name. Source tarballs conventionally unpack into a directory that includes both @@ -138,13 +154,13 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): @register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): +def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: """Extract version information from the given file.""" # the code embedded in _version.py can just fetch the value of these # keywords. When used from setup.py, we don't want to import _version.py, # so we do it with a regexp instead. This function is not used from # _version.py. - keywords = {} + keywords: Dict[str, str] = {} try: with open(versionfile_abs, "r") as fobj: for line in fobj: @@ -166,7 +182,11 @@ def git_get_keywords(versionfile_abs): @register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): +def git_versions_from_keywords( + keywords: Dict[str, str], + tag_prefix: str, + verbose: bool, +) -> Dict[str, Any]: """Get version information from git keywords.""" if "refnames" not in keywords: raise NotThisMethod("Short version file found") @@ -230,7 +250,12 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): @register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command): +def git_pieces_from_vcs( + tag_prefix: str, + root: str, + verbose: bool, + runner: Callable = run_command +) -> Dict[str, Any]: """Get version from 'git describe' in the root of the source tree. This only gets called if the git-archive 'subst' keywords were *not* @@ -270,7 +295,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command): raise NotThisMethod("'git rev-parse' failed") full_out = full_out.strip() - pieces = {} + pieces: Dict[str, Any] = {} pieces["long"] = full_out pieces["short"] = full_out[:7] # maybe improved later pieces["error"] = None @@ -362,14 +387,14 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command): return pieces -def plus_or_dot(pieces): +def plus_or_dot(pieces: Dict[str, Any]) -> str: """Return a + if we don't already have one, else return a .""" if "+" in pieces.get("closest-tag", ""): return "." return "+" -def render_pep440(pieces): +def render_pep440(pieces: Dict[str, Any]) -> str: """Build up version string, with post-release "local version identifier". Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you @@ -394,7 +419,7 @@ def render_pep440(pieces): return rendered -def render_pep440_branch(pieces): +def render_pep440_branch(pieces: Dict[str, Any]) -> str: """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . The ".dev0" means not master branch. Note that .dev0 sorts backwards @@ -424,7 +449,7 @@ def render_pep440_branch(pieces): return rendered -def pep440_split_post(ver): +def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]: """Split pep440 version string at the post-release segment. Returns the release segments before the post-release and the @@ -434,7 +459,7 @@ def pep440_split_post(ver): return vc[0], int(vc[1] or 0) if len(vc) == 2 else None -def render_pep440_pre(pieces): +def render_pep440_pre(pieces: Dict[str, Any]) -> str: """TAG[.postN.devDISTANCE] -- No -dirty. Exceptions: @@ -458,7 +483,7 @@ def render_pep440_pre(pieces): return rendered -def render_pep440_post(pieces): +def render_pep440_post(pieces: Dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]+gHEX] . The ".dev0" means dirty. Note that .dev0 sorts backwards @@ -485,7 +510,7 @@ def render_pep440_post(pieces): return rendered -def render_pep440_post_branch(pieces): +def render_pep440_post_branch(pieces: Dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . The ".dev0" means not master branch. @@ -514,7 +539,7 @@ def render_pep440_post_branch(pieces): return rendered -def render_pep440_old(pieces): +def render_pep440_old(pieces: Dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]] . The ".dev0" means dirty. @@ -536,7 +561,7 @@ def render_pep440_old(pieces): return rendered -def render_git_describe(pieces): +def render_git_describe(pieces: Dict[str, Any]) -> str: """TAG[-DISTANCE-gHEX][-dirty]. Like 'git describe --tags --dirty --always'. @@ -556,7 +581,7 @@ def render_git_describe(pieces): return rendered -def render_git_describe_long(pieces): +def render_git_describe_long(pieces: Dict[str, Any]) -> str: """TAG-DISTANCE-gHEX[-dirty]. Like 'git describe --tags --dirty --always -long'. @@ -576,7 +601,7 @@ def render_git_describe_long(pieces): return rendered -def render(pieces, style): +def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: """Render the given version pieces into the requested style.""" if pieces["error"]: return {"version": "unknown", @@ -612,7 +637,7 @@ def render(pieces, style): "date": pieces.get("date")} -def get_versions(): +def get_versions() -> Dict[str, Any]: """Get version information or return default if unable to do so.""" # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have # __file__, we can work backwards from there to the root. Some diff --git a/bids-validator/bids_validator/rules/file_level_rules.json b/bids-validator/bids_validator/rules/file_level_rules.json index 83f3fd4e8..a220fcb5c 100644 --- a/bids-validator/bids_validator/rules/file_level_rules.json +++ b/bids-validator/bids_validator/rules/file_level_rules.json @@ -488,6 +488,8 @@ "_events\\.tsv", "_channels\\.json", "_channels\\.tsv", + "_electrodes\\.json", + "_electrodes\\.tsv", "_meg\\.json", "_coordsystem\\.json", "_photo\\.jpg", diff --git a/bids-validator/package.json b/bids-validator/package.json index 6639a343c..206cbe093 100644 --- a/bids-validator/package.json +++ b/bids-validator/package.json @@ -1,6 +1,6 @@ { "name": "bids-validator", - "version": "1.12.1-dev.0", + "version": "1.13.2-dev.0", "description": "", "main": "./dist/commonjs/index.js", "exports": { @@ -37,23 +37,23 @@ }, "homepage": "https://github.com/bids-standard/bids-validator", "dependencies": { - "@aws-sdk/client-s3": "^3.9.0", + "@aws-sdk/client-s3": "^3.417.0", "ajv": "^6.5.2", "bytes": "^3.1.2", "colors": "^1.4.0", "cross-fetch": "^4.0.0", "date-fns": "^2.30.0", "events": "^3.3.0", - "exifreader": "^4.12.1", - "hed-validator": "^3.11.0", + "exifreader": "^4.13.2", + "hed-validator": "^3.12.0", "ignore": "^5.2.4", "is-utf8": "^0.2.1", - "jest": "^29.6.2", + "jest": "^29.7.0", "jshint": "^2.13.6", - "lerna": "^7.1.1", + "lerna": "^7.4.1", "lodash": "^4.17.21", "minimatch": "3.0.5", - "next": "13.4.12", + "next": "13.5.6", "nifti-js": "^1.0.1", "p-limit": "^2.1.0", "pako": "^1.0.6", @@ -70,12 +70,12 @@ "devDependencies": { "adm-zip": "", "chai": "", - "esbuild": "^0.18.17", + "esbuild": "^0.19.5", "esbuild-plugin-globals": "^0.2.0", "esbuild-runner": "^2.2.2", - "eslint": "^8.45.0", - "eslint-config-prettier": "^8.10.0", - "eslint-plugin-prettier": "^5.0.0", + "eslint": "^8.52.0", + "eslint-config-prettier": "^9.0.0", + "eslint-plugin-prettier": "^5.0.1", "husky": "^8.0.3", "lockfile": "^1.0.4", "sync-request": "6.1.0" diff --git a/bids-validator/pyproject.toml b/bids-validator/pyproject.toml new file mode 100644 index 000000000..dfc6b0aea --- /dev/null +++ b/bids-validator/pyproject.toml @@ -0,0 +1,39 @@ +[build-system] +requires = ["setuptools", "versioneer[toml]"] +build-backend = "setuptools.build_meta" + +[project] +name = "bids-validator" +dynamic = ["version"] +description = "Validator for the Brain Imaging Data Structure" +readme = "README.md" +license = { text = "MIT License" } +authors = [ + { name = "PyBIDS developers", email = "bids-discussion@googlegroups.com" }, +] +classifiers = [ + "Development Status :: 3 - Alpha", + "Environment :: Console", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Topic :: Scientific/Engineering", +] + +[project.urls] +Homepage = "https://github.com/bids-standard/bids-validator" + +[tool.setuptools.packages.find] +include = ["bids_validator*"] + +[tool.setuptools.package-data] +bids_validator = ["*/*.json"] + +[tool.versioneer] +VCS = "git" +style = "pep440" +versionfile_source = "bids_validator/_version.py" +versionfile_build = "bids_validator/_version.py" +tag_prefix = "v" +parentdir_prefix = "" diff --git a/bids-validator/setup.cfg b/bids-validator/setup.cfg index ef0c4de92..0c1a544d5 100644 --- a/bids-validator/setup.cfg +++ b/bids-validator/setup.cfg @@ -1,49 +1,7 @@ -[metadata] -name = bids-validator -url = https://github.com/bids-standard/bids-validator -author = PyBIDS developers -author_email = bids-discussion@googlegroups.com -maintainer = BIDS Developers -maintainer_email = bids-discussion@googlegroups.com -description = Validator for the Brain Imaging Data Structure -long_description = file:README.md -long_description_content_type = text/markdown -license = MIT -python_requires >= 3.8 -classifiers = - Development Status :: 3 - Alpha - Environment :: Console - Intended Audience :: Science/Research - License :: OSI Approved :: MIT License - Operating System :: OS Independent - Programming Language :: Python - Topic :: Scientific/Engineering - -[options] -packages = find: - -[options.package_data] -bids_validator = - rules/*.json - tsv/*.json - -[bdist_wheel] -universal=1 - [tool:pytest] ignore = - versioneer.py _version.py [flake8] exclude = - versioneer.py _version.py - -[versioneer] -VCS = git -style = pep440 -versionfile_source = bids_validator/_version.py -versionfile_build = bids_validator/_version.py -tag_prefix = v -parentdir_prefix = diff --git a/bids-validator/spec b/bids-validator/spec index d3906e286..0fc6c58a3 160000 --- a/bids-validator/spec +++ b/bids-validator/spec @@ -1 +1 @@ -Subproject commit d3906e2863136fc0ff4e6ed7952ff2a7c60c7c8d +Subproject commit 0fc6c58a35d355df83077f6790ba25afb46c2a0f diff --git a/bids-validator/src/README.md b/bids-validator/src/README.md index 1280c7aca..c9c00d5a9 100644 --- a/bids-validator/src/README.md +++ b/bids-validator/src/README.md @@ -8,9 +8,19 @@ Deno is a JavaScript and TypeScript runtime that is used to run the schema based At the root of the repository there are two directories, `bids-validator` and `bids-validator-web`. These are separate npm packages, the Deno validator lives within the bids-validator package within the `src` directory. -## Schema validator examples +## Usage -Deno by default sandboxes applications like a web browser. To validate datasets located on your local system, you need to use the --allow-read flag to read local files. --allow-env is also required to allow for detection of OS specific features. These flags are included in the script line of the `./bids-validator-deno` script. +To use the latest validator hosted at https://deno.land/x/bids_validator, use the following command: + +```console +$ deno run --allow-read --allow-env https://deno.land/x/bids_validator/bids-validator.ts path/to/dataset +``` + +Deno by default sandboxes applications like a web browser. `--allow-read` allows the validator to read local files, and `--allow-env` enables OS-specific features. + +### Development tools + +From the repository root, use `bids-validator/bids-validator-deno` to run with all permissions enabled by default: ```shell # Run from within the /bids-validator directory @@ -19,12 +29,6 @@ cd bids-validator ./bids-validator-deno path/to/dataset ``` -By default only schema derived validation rules are run. The legacy validator can be run at the same time with `--legacy` and this may improve coverage for issues not yet implemented in the schema variant. - -```shell -./bids-validator-deno --legacy path/to/dataset -``` - ## Schema validator test suite ```shell diff --git a/bids-validator/src/files/browser.test.ts b/bids-validator/src/files/browser.test.ts index 6e63bf7e9..55478cf12 100644 --- a/bids-validator/src/files/browser.test.ts +++ b/bids-validator/src/files/browser.test.ts @@ -23,9 +23,9 @@ Deno.test('Browser implementation of FileTree', async (t) => { new TestFile( ['{}'], 'dataset_description.json', - 'dataset_description.json', + 'ds/dataset_description.json', ), - new TestFile(['flat test dataset'], 'README.md', 'README.md'), + new TestFile(['flat test dataset'], 'README.md', 'ds/README.md'), ] const tree = await fileListToTree(files) const expectedTree = new FileTree('', '/', undefined) @@ -38,18 +38,22 @@ Deno.test('Browser implementation of FileTree', async (t) => { new TestFile( ['{}'], 'dataset_description.json', - 'dataset_description.json', + 'ds/dataset_description.json', ), new TestFile( ['tsv headers\n', 'column\tdata'], 'participants.tsv', - 'participants.tsv', + 'ds/participants.tsv', + ), + new TestFile( + ['single subject test dataset'], + 'README.md', + 'ds/README.md', ), - new TestFile(['single subject test dataset'], 'README.md', 'README.md'), new TestFile( ['nifti file goes here'], 'sub-01_T1w.nii.gz', - 'sub-01/anat/sub-01_T1w.nii.gz', + 'ds/sub-01/anat/sub-01_T1w.nii.gz', ), ] const tree = await fileListToTree(files) diff --git a/bids-validator/src/files/browser.ts b/bids-validator/src/files/browser.ts index fe0bacf8f..c88045697 100644 --- a/bids-validator/src/files/browser.ts +++ b/bids-validator/src/files/browser.ts @@ -21,7 +21,9 @@ export class BIDSFileBrowser implements BIDSFile { get path(): string { // @ts-expect-error webkitRelativePath is defined in the browser - return this.#file.webkitRelativePath + const relativePath = this.#file.webkitRelativePath + const prefixLength = relativePath.indexOf('/') + return relativePath.substring(prefixLength) } get size(): number { @@ -54,11 +56,11 @@ export function fileListToTree(files: File[]): Promise { for (const f of files) { const file = new BIDSFileBrowser(f, ignore) const fPath = parse(file.path) - const levels = fPath.dir.split(SEP) - if (levels[0] === '') { + if (fPath.dir === '/') { // Top level file tree.files.push(file) } else { + const levels = fPath.dir.split(SEP).slice(1) let currentLevelTree = tree for (const level of levels) { const exists = currentLevelTree.directories.find( diff --git a/bids-validator/src/files/deno.ts b/bids-validator/src/files/deno.ts index 452743ee9..ca15c4358 100644 --- a/bids-validator/src/files/deno.ts +++ b/bids-validator/src/files/deno.ts @@ -25,10 +25,10 @@ export class BIDSFileDeno implements BIDSFile { name: string path: string #fileInfo?: Deno.FileInfo - private _datasetAbsPath: string + #datasetAbsPath: string constructor(datasetPath: string, path: string, ignore: FileIgnoreRules) { - this._datasetAbsPath = datasetPath + this.#datasetAbsPath = datasetPath this.path = path this.name = basename(path) this.#ignore = ignore @@ -42,7 +42,7 @@ export class BIDSFileDeno implements BIDSFile { } private _getPath(): string { - return join(this._datasetAbsPath, this.path) + return join(this.#datasetAbsPath, this.path) } get size(): number { diff --git a/bids-validator/src/files/dwi.ts b/bids-validator/src/files/dwi.ts new file mode 100644 index 000000000..68132c94e --- /dev/null +++ b/bids-validator/src/files/dwi.ts @@ -0,0 +1,22 @@ +/* + * DWI + * Module for parsing DWI-associated files + */ +const normalizeEOL = (str: string): string => + str.replace(/\r\n/g, '\n').replace(/\r/g, '\n') + +export function parseBvalBvec(contents: string): number[][] { + // BVEC files are a matrix of numbers, with each row being + // a different axis + // BVAL files are a single row of numbers, and may contain + // trailing whitespace + return normalizeEOL(contents) + .split(/\s*\n/) + .filter((x) => x !== '') + .map((row) => + row + .split(/\s+/) + .filter((x) => x !== '') + .map((x) => Number(x)), + ) +} diff --git a/bids-validator/src/files/tsv.ts b/bids-validator/src/files/tsv.ts index 3b7370486..9689c6512 100644 --- a/bids-validator/src/files/tsv.ts +++ b/bids-validator/src/files/tsv.ts @@ -2,13 +2,15 @@ * TSV * Module for parsing TSV */ +import { ColumnsMap } from '../types/columns.ts' + const normalizeEOL = (str: string): string => str.replace(/\r\n/g, '\n').replace(/\r/g, '\n') // Typescript resolved `row && !/^\s*$/.test(row)` as `string | boolean` const isContentfulRow = (row: string): boolean => !!(row && !/^\s*$/.test(row)) export function parseTSV(contents: string) { - const columns: Record = {} + const columns = new ColumnsMap() const rows: string[][] = normalizeEOL(contents) .split('\n') .filter(isContentfulRow) @@ -20,7 +22,8 @@ export function parseTSV(contents: string) { }) for (let i = 1; i < rows.length; i++) { for (let j = 0; j < headers.length; j++) { - columns[headers[j]].push(rows[i][j]) + const col = columns[headers[j]] as string[] + col.push(rows[i][j]) } } return columns diff --git a/bids-validator/src/schema/applyRules.ts b/bids-validator/src/schema/applyRules.ts index 0e4aa7c96..c246e622d 100644 --- a/bids-validator/src/schema/applyRules.ts +++ b/bids-validator/src/schema/applyRules.ts @@ -74,7 +74,7 @@ export function evalCheck(src: string, context: BIDSContext) { return test(safeContext) } catch (error) { logger.debug(error) - return false + return null } } @@ -197,7 +197,7 @@ function evalColumns( schemaPath: string, ): void { if (!rule.columns || context.extension !== '.tsv') return - const headers = Object.keys(context.columns) + const headers = [...Object.keys(context.columns)] for (const [ruleHeader, requirement] of Object.entries(rule.columns)) { // @ts-expect-error const columnObject = schema.objects.columns[ruleHeader] @@ -211,7 +211,7 @@ function evalColumns( ]) } if (headers.includes(name)) { - for (const value of context.columns[name]) { + for (const value of context.columns[name] as string[]) { if ( !schemaObjectTypeCheck(columnObject as SchemaTypeLike, value, schema) ) { @@ -240,7 +240,7 @@ function evalInitialColumns( ): void { if (!rule?.columns || !rule?.initial_columns || context.extension !== '.tsv') return - const headers = Object.keys(context.columns) + const headers = [...Object.keys(context.columns)] rule.initial_columns.map((ruleHeader: string, ruleIndex: number) => { // @ts-expect-error const ruleHeaderName = schema.objects.columns[ruleHeader].name @@ -316,11 +316,13 @@ function evalIndexColumns( ]) return } - const rowCount = context.columns[index_columns[0]].length + const rowCount = (context.columns[index_columns[0]] as string[])?.length || 0 for (let i = 0; i < rowCount; i++) { let indexValue = '' index_columns.map((col: string) => { - indexValue = indexValue.concat(context.columns[col][i]) + indexValue = indexValue.concat( + (context.columns[col] as string[])?.[i] || '', + ) }) if (uniqueIndexValues.has(indexValue)) { context.issues.addNonSchemaIssue('TSV_INDEX_VALUE_NOT_UNIQUE', [ diff --git a/bids-validator/src/schema/associations.ts b/bids-validator/src/schema/associations.ts index 1b80b0207..db42a6732 100644 --- a/bids-validator/src/schema/associations.ts +++ b/bids-validator/src/schema/associations.ts @@ -1,9 +1,13 @@ -import { ContextAssociations } from '../types/context.ts' +import { + ContextAssociations, + ContextAssociationsEvents, +} from '../types/context.ts' import { BIDSFile } from '../types/file.ts' import { FileTree } from '../types/filetree.ts' import { BIDSContext } from './context.ts' import { readEntities } from './entities.ts' import { parseTSV } from '../files/tsv.ts' +import { parseBvalBvec } from '../files/dwi.ts' // type AssociationsLookup = Record => { - return file.text().then((text) => parseTSV(text)) + load: async (file: BIDSFile): Promise => { + const text = await file.text() + const columns = parseTSV(text) + return { + path: file.path, + onset: columns.get('onset') || [], + } }, }, aslcontext: { + suffix: 'aslcontext', extensions: ['.tsv'], inherit: true, - load: (file: BIDSFile): Promise => { - return Promise.resolve({ path: file.path, n_rows: 0, volume_type: [] }) + load: async ( + file: BIDSFile, + ): Promise => { + const contents = await file.text() + const columns = parseTSV(contents) + return { + path: file.path, + n_rows: columns.get('volume_type')?.length || 0, + volume_type: columns.get('volume_type') || [], + } }, }, m0scan: { + suffix: 'm0scan', extensions: ['.nii', '.nii.gz'], inherit: false, load: (file: BIDSFile): Promise => { @@ -41,13 +61,15 @@ const associationLookup = { }, }, magnitude: { + suffix: 'magnitude', extensions: ['.nii', '.nii.gz'], inherit: false, load: (file: BIDSFile): Promise => { - return Promise.resolve({ path: file.path, onset: 'silly' }) + return Promise.resolve({ path: file.path }) }, }, magnitude1: { + suffix: 'magnitude1', extensions: ['.nii', '.nii.gz'], inherit: false, load: (file: BIDSFile): Promise => { @@ -55,24 +77,53 @@ const associationLookup = { }, }, bval: { - extensions: ['.nii', '.nii.gz'], + suffix: 'dwi', + extensions: ['.bval'], inherit: true, - load: (file: BIDSFile): Promise => { - return Promise.resolve({ path: file.path, n_cols: 0 }) + load: async (file: BIDSFile): Promise => { + const contents = await file.text() + const columns = parseBvalBvec(contents) + return { + path: file.path, + n_cols: columns ? columns[0].length : 0, + n_rows: columns ? columns.length : 0, + } }, }, bvec: { - extensions: ['.nii', '.nii.gz'], + suffix: 'dwi', + extensions: ['.bvec'], inherit: true, - load: (file: BIDSFile): Promise => { - return Promise.resolve({ path: file.path, n_cols: 0 }) + load: async (file: BIDSFile): Promise => { + const contents = await file.text() + const columns = parseBvalBvec(contents) + return { + path: file.path, + n_cols: columns ? columns[0].length : 0, + n_rows: columns ? columns.length : 0, + } }, }, channels: { + suffix: 'channels', extensions: ['.tsv'], inherit: true, - load: (file: BIDSFile): Promise => { - return file.text().then((text) => parseTSV(text)) + load: async (file: BIDSFile): Promise => { + const contents = await file.text() + const columns = parseTSV(contents) + return { + path: file.path, + type: columns.get('type') || [], + short_channel: columns.get('short_channel') || [], + } + }, + }, + coordsystem: { + suffix: 'coordsystem', + extensions: ['.json'], + inherit: true, + load: (file: BIDSFile): Promise => { + return Promise.resolve({ path: file.path }) }, }, } @@ -83,9 +134,9 @@ export async function buildAssociations( ): Promise { const associations: ContextAssociations = {} for (const key in associationLookup as typeof associationLookup) { - const { extensions, inherit } = + const { suffix, extensions, inherit } = associationLookup[key as keyof typeof associationLookup] - const paths = getPaths(fileTree, source, key, extensions) + const paths = getPaths(fileTree, source, suffix, extensions) if (paths.length === 0) { continue } diff --git a/bids-validator/src/schema/context.ts b/bids-validator/src/schema/context.ts index 22ccdcee6..284781f38 100644 --- a/bids-validator/src/schema/context.ts +++ b/bids-validator/src/schema/context.ts @@ -8,6 +8,7 @@ import { } from '../types/context.ts' import { BIDSFile } from '../types/file.ts' import { FileTree } from '../types/filetree.ts' +import { ColumnsMap } from '../types/columns.ts' import { BIDSEntities, readEntities } from './entities.ts' import { DatasetIssues } from '../issues/datasetIssues.ts' import { parseTSV } from '../files/tsv.ts' @@ -62,7 +63,7 @@ export class BIDSContext implements Context { datatype: string modality: string sidecar: object - columns: Record + columns: ColumnsMap associations: ContextAssociations nifti_header?: ContextNiftiHeader @@ -85,7 +86,7 @@ export class BIDSContext implements Context { this.datatype = '' this.modality = '' this.sidecar = {} - this.columns = {} + this.columns = new ColumnsMap() this.associations = {} as ContextAssociations } @@ -131,8 +132,21 @@ export class BIDSContext implements Context { }) if (validSidecars.length > 1) { - // two matching in one dir not allowed - } else if (validSidecars.length === 1) { + const exactMatch = validSidecars.find( + (sidecar) => + sidecar.path == this.file.path.replace(this.extension, '.json'), + ) + if (exactMatch) { + validSidecars.splice(1) + validSidecars[0] = exactMatch + } else { + logger.warning( + `Multiple sidecar files detected for '${this.file.path}'`, + ) + } + } + + if (validSidecars.length === 1) { const json = await validSidecars[0] .text() .then((text) => JSON.parse(text)) @@ -169,7 +183,7 @@ export class BIDSContext implements Context { `tsv file could not be opened by loadColumns '${this.file.path}'`, ) logger.debug(error) - return {} + return new Map() as ColumnsMap }) return } diff --git a/bids-validator/src/schema/expressionLanguage.ts b/bids-validator/src/schema/expressionLanguage.ts index c93263572..88e58e5ce 100644 --- a/bids-validator/src/schema/expressionLanguage.ts +++ b/bids-validator/src/schema/expressionLanguage.ts @@ -1,4 +1,8 @@ function exists(list: string[], rule: string = 'dataset'): number { + if (list == null) { + return 0 + } + const prefix: string[] = [] // Stimuli and subject-relative paths get prefixes @@ -31,6 +35,12 @@ export const expressionFunctions = { return index != -1 ? index : null }, intersects: (a: T[], b: T[]): boolean => { + if (!Array.isArray(a)) { + a = [a] + } + if (!Array.isArray(b)) { + b = [b] + } return a.some((x) => b.includes(x)) }, match: (target: string, regex: string): boolean => { @@ -41,16 +51,20 @@ export const expressionFunctions = { if (Array.isArray(operand)) { return 'array' } - if (typeof operand === 'undefined') { + if (typeof operand === 'undefined' || operand === null) { return 'null' } return typeof operand }, - min: (list: number[]): number => { - return Math.min(...list) + min: (list: number[]): number | null => { + return list != null + ? Math.min(...list.filter((x) => typeof x === 'number')) + : null }, - max: (list: number[]): number => { - return Math.max(...list) + max: (list: number[]): number | null => { + return list != null + ? Math.max(...list.filter((x) => typeof x === 'number')) + : null }, length: (list: T[]): number | null => { if (Array.isArray(list) || typeof list == 'string') { @@ -62,7 +76,10 @@ export const expressionFunctions = { return list.filter((x) => x === val).length }, exists: exists, - substr: (arg: string, start: number, end: number): string => { + substr: (arg: string, start: number, end: number): string | null => { + if (arg == null || start == null || end == null) { + return null + } return arg.substr(start, end - start) }, sorted: (list: T[]): T[] => { diff --git a/bids-validator/src/setup/loadSchema.ts b/bids-validator/src/setup/loadSchema.ts index 2452cb7f0..9959fff86 100644 --- a/bids-validator/src/setup/loadSchema.ts +++ b/bids-validator/src/setup/loadSchema.ts @@ -10,7 +10,8 @@ import * as schemaDefault from 'https://bids-specification.readthedocs.io/en/lat export async function loadSchema(version = 'latest'): Promise { const versionRegex = /^v\d/ let schemaUrl = version - const bidsSchema = Deno.env.get('BIDS_SCHEMA') + const bidsSchema = + typeof Deno !== 'undefined' ? Deno.env.get('BIDS_SCHEMA') : undefined if (bidsSchema !== undefined) { schemaUrl = bidsSchema } else if (version === 'latest' || versionRegex.test(version)) { diff --git a/bids-validator/src/summary/summary.ts b/bids-validator/src/summary/summary.ts index 1135d152d..1e96f8d15 100644 --- a/bids-validator/src/summary/summary.ts +++ b/bids-validator/src/summary/summary.ts @@ -1,5 +1,4 @@ import { collectSubjectMetadata } from './collectSubjectMetadata.ts' -import { readAll, readerFromStreamReader } from '../deps/stream.ts' import { SummaryOutput, SubjectMetadata } from '../types/validation-result.ts' import { BIDSContext } from '../schema/context.ts' @@ -66,7 +65,7 @@ export class Summary { pet: Record modalitiesCount: Record secondaryModalitiesCount: Record - datatypes: Set + dataTypes: Set schemaVersion: string constructor() { this.dataProcessed = false @@ -77,7 +76,7 @@ export class Summary { this.subjectMetadata = [] this.tasks = new Set() this.pet = {} - this.datatypes = new Set() + this.dataTypes = new Set() this.modalitiesCount = { mri: 0, pet: 0, @@ -120,7 +119,7 @@ export class Summary { } if (context.datatype.length) { - this.datatypes.add(context.datatype) + this.dataTypes.add(context.datatype) } if (context.extension === '.json') { @@ -162,7 +161,7 @@ export class Summary { size: this.size, dataProcessed: this.dataProcessed, pet: this.pet, - datatypes: Array.from(this.datatypes), + dataTypes: Array.from(this.dataTypes), schemaVersion: this.schemaVersion, } } diff --git a/bids-validator/src/tests/local/bids_examples.test.ts b/bids-validator/src/tests/local/bids_examples.test.ts index 31d8fb80c..14df7e3cb 100644 --- a/bids-validator/src/tests/local/bids_examples.test.ts +++ b/bids-validator/src/tests/local/bids_examples.test.ts @@ -42,6 +42,12 @@ Deno.test('validate bids-examples', async (t) => { continue } const path = `${prefix}/${dirEntry.name}` + + try { + if (Deno.statSync(`${path}/.SKIP_VALIDATION`).isFile) { + continue + } + } catch (e) {} const { tree, result } = await validatePath(t, path, options) const output = result.issues.formatOutput() output.errors = output.errors.filter((x) => useIssue(x)) diff --git a/bids-validator/src/tests/schema-expression-language.test.ts b/bids-validator/src/tests/schema-expression-language.test.ts index cc9b50e0c..798f640bf 100644 --- a/bids-validator/src/tests/schema-expression-language.test.ts +++ b/bids-validator/src/tests/schema-expression-language.test.ts @@ -4,10 +4,18 @@ import { colors } from '../deps/fmt.ts' import { BIDSContext } from '../schema/context.ts' import { assert, assertEquals } from '../deps/asserts.ts' import { evalCheck } from '../schema/applyRules.ts' +import { expressionFunctions } from '../schema/expressionLanguage.ts' const schema = await loadSchema() const pretty_null = (x: string | null): string => (x === null ? 'null' : x) +const equal = (a: T, b: T): boolean => { + if (Array.isArray(a) && Array.isArray(b)) { + return a.length === b.length && a.every((val, idx) => val === b[idx]) + } + return a === b +} + Deno.test('validate schema expression tests', async (t) => { const results: string[][] = [] const header = ['expression', 'desired', 'actual', 'result'].map((x) => @@ -15,8 +23,10 @@ Deno.test('validate schema expression tests', async (t) => { ) for (const test of schema.meta.expression_tests) { await t.step(`${test.expression} evals to ${test.result}`, () => { - const actual_result = evalCheck(test.expression, {} as BIDSContext) - if (actual_result == test.result) { + // @ts-expect-error + const context = expressionFunctions as BIDSContext + const actual_result = evalCheck(test.expression, context) + if (equal(actual_result, test.result)) { results.push([ colors.cyan(test.expression), pretty_null(test.result), diff --git a/bids-validator/src/types/columns.test.ts b/bids-validator/src/types/columns.test.ts new file mode 100644 index 000000000..0b99e007e --- /dev/null +++ b/bids-validator/src/types/columns.test.ts @@ -0,0 +1,33 @@ +import { assertEquals } from '../deps/asserts.ts' +import { ColumnsMap } from './columns.ts' + +Deno.test('ColumnsMap', async (t) => { + await t.step('get is accessible with square bracket notation', () => { + const columns = new ColumnsMap() + columns['a'] = ['0'] + assertEquals(columns['a'], ['0']) + }) + await t.step('preserves insertion order with property access', () => { + const columns = new ColumnsMap() + columns['a'] = ['0'] + columns[2] = ['1'] + columns[1] = ['2'] + columns['b'] = ['3'] + + // Check that the order is still correct with iteration + let iteration = 0 + for (const [_, val] of columns) { + assertEquals(val, [iteration.toString()]) + iteration += 1 + } + assertEquals(columns.a, ['0']) + }) + await t.step('keys are accessible with Object.keys', () => { + const columns = new ColumnsMap() + columns['a'] = ['0'] + columns['b'] = ['1'] + columns[0] = ['2'] + assertEquals(Object.keys(columns), ['a', 'b', '0']) + assertEquals(Object.getOwnPropertyNames(columns), ['a', 'b', '0']) + }) +}) diff --git a/bids-validator/src/types/columns.ts b/bids-validator/src/types/columns.ts new file mode 100644 index 000000000..6227b5cf9 --- /dev/null +++ b/bids-validator/src/types/columns.ts @@ -0,0 +1,40 @@ +// Allow ColumnsMap to be accessed as an object too +export class ColumnsMap extends Map { + [key: string]: Map[keyof Map] | string[] + constructor() { + super() + const columns = new Map() as ColumnsMap + return new Proxy(columns, columnMapAccessorProxy) + } +} + +// Proxy handler to implement ColumnsMap type +export const columnMapAccessorProxy = { + get: function ( + target: ColumnsMap, + prop: symbol | string, + receiver: ColumnsMap, + ) { + const value = Reflect.get(target, prop, receiver) + if (typeof value === 'function') return value.bind(target) + if (prop === Symbol.iterator) return target[Symbol.iterator].bind(target) + if (value === undefined) return target.get(prop as string) + return value + }, + set: function (target: ColumnsMap, prop: string, value: string[]) { + target.set(prop, value) + return true + }, + has: function (target: ColumnsMap, prop: string) { + return Reflect.has(target, prop) + }, + ownKeys: function (target: ColumnsMap) { + return Array.from(target.keys()) + }, + getOwnPropertyDescriptor: function ( + target: ColumnsMap, + prop: string, + ): PropertyDescriptor { + return { enumerable: true, configurable: true, value: target.get(prop) } + }, +} diff --git a/bids-validator/src/types/context.ts b/bids-validator/src/types/context.ts index 5849d6e31..4b03fcbee 100644 --- a/bids-validator/src/types/context.ts +++ b/bids-validator/src/types/context.ts @@ -43,10 +43,20 @@ export interface ContextAssociationsMagnitude1 { export interface ContextAssociationsBval { path: string n_cols: number + n_rows: number } export interface ContextAssociationsBvec { path: string n_cols: number + n_rows: number +} +export interface ContextAssociationsChannels { + path?: string + type?: string[] + short_channel?: string[] +} +export interface ContextAssociationsCoordsystem { + path: string } export interface ContextAssociations { events?: ContextAssociationsEvents @@ -56,6 +66,8 @@ export interface ContextAssociations { magnitude1?: ContextAssociationsMagnitude1 bval?: ContextAssociationsBval bvec?: ContextAssociationsBvec + channels?: ContextAssociationsChannels + coordsystem?: ContextAssociationsCoordsystem } export interface ContextNiftiHeaderDimInfo { freq: number diff --git a/bids-validator/src/types/validation-result.ts b/bids-validator/src/types/validation-result.ts index fb2985777..3113cd375 100644 --- a/bids-validator/src/types/validation-result.ts +++ b/bids-validator/src/types/validation-result.ts @@ -24,7 +24,7 @@ export interface SummaryOutput { size: number dataProcessed: boolean pet: Record - datatypes: string[] + dataTypes: string[] schemaVersion: string } diff --git a/bids-validator/tests/data/bids-examples b/bids-validator/tests/data/bids-examples index c557d1f33..633d96425 160000 --- a/bids-validator/tests/data/bids-examples +++ b/bids-validator/tests/data/bids-examples @@ -1 +1 @@ -Subproject commit c557d1f33a8168c21126419f7033f8aa9c809e0c +Subproject commit 633d96425594af70718e34cd29bb3682d6f3c1d3 diff --git a/bids-validator/tests/events.spec.js b/bids-validator/tests/events.spec.js index bf01681d5..19ac4b0f7 100644 --- a/bids-validator/tests/events.spec.js +++ b/bids-validator/tests/events.spec.js @@ -1,5 +1,5 @@ import assert from 'assert' -import validate from '../index' +import validateEvents from '../validators/events/validate' describe('Events', function () { const headers = [ @@ -21,12 +21,9 @@ describe('Events', function () { events: ['/stimuli/images/red-square.jpg'], directory: [{ relativePath: '/stimuli/images/blue-square.jpg' }], } - return validate.Events.validateEvents([], stimuli, [], {}).then( - (issues) => { - assert.strictEqual(issues.length, 1) - assert.strictEqual(issues[0].code, 77) - }, - ) + const issues = validateEvents([], stimuli, [], {}) + assert.strictEqual(issues.length, 1) + assert.strictEqual(issues[0].code, 77) }) it('should not throw issues if all files in the /stimuli folder are included in an _events.tsv file', () => { @@ -34,11 +31,8 @@ describe('Events', function () { events: ['/stimuli/images/red-square.jpg'], directory: [{ relativePath: '/stimuli/images/red-square.jpg' }], } - return validate.Events.validateEvents([], stimuli, [], {}, []).then( - (issues) => { - assert.deepStrictEqual(issues, []) - }, - ) + const issues = validateEvents([], stimuli, [], {}) + assert.deepStrictEqual(issues, []) }) it('should throw an issue if the onset of the last event in _events.tsv is more than TR * number of volumes in corresponding nifti header', () => { @@ -54,24 +48,10 @@ describe('Events', function () { RepetitionTime: 1, }, } - const jsonFiles = [ - { - relativePath: '/sub01/sub01_task-test_events.json', - path: '/sub01/sub01_task-test_events.json', - }, - ] - return validate.Events.validateEvents( - events, - [], - headers, - jsonDictionary, - jsonFiles, - '', - ).then((issues) => { - assert.strictEqual(issues.length, 1) - assert.strictEqual(issues[0].code, 85) - }) + const issues = validateEvents(events, [], headers, jsonDictionary) + assert.strictEqual(issues.length, 1) + assert.strictEqual(issues[0].code, 85) }) it('should throw an issue if the onset of the last event in _events.tsv is less than .5 * TR * number of volumes in corresponding nifti header', () => { @@ -87,24 +67,10 @@ describe('Events', function () { RepetitionTime: 1, }, } - const jsonFiles = [ - { - relativePath: '/sub01/sub01_task-test_events.json', - path: '/sub01/sub01_task-test_events.json', - }, - ] - return validate.Events.validateEvents( - events, - [], - headers, - jsonDictionary, - jsonFiles, - '', - ).then((issues) => { - assert.strictEqual(issues.length, 1) - assert.strictEqual(issues[0].code, 86) - }) + const issues = validateEvents(events, [], headers, jsonDictionary) + assert.strictEqual(issues.length, 1) + assert.strictEqual(issues[0].code, 86) }) it('should not throw any issues if the onset of the last event in _events.tsv is a reasonable value', () => { @@ -120,244 +86,8 @@ describe('Events', function () { RepetitionTime: 1, }, } - const jsonFiles = [ - { - relativePath: '/sub01/sub01_task-test_events.json', - path: '/sub01/sub01_task-test_events.json', - }, - ] - - return validate.Events.validateEvents( - events, - [], - headers, - jsonDictionary, - jsonFiles, - '', - ).then((issues) => { - assert.deepStrictEqual(issues, []) - }) - }) - - describe('HED event strings', () => { - const jsonFiles = [ - { - relativePath: '/sub01/sub01_task-test_events.json', - path: '/sub01/sub01_task-test_events.json', - }, - { - relativePath: '/dataset_description.json', - path: '/dataset_description.json', - }, - ] - - it('should not throw an issue if the HED data is valid', () => { - const events = [ - { - file: { path: '/sub01/sub01_task-test_events.tsv' }, - path: '/sub01/sub01_task-test_events.tsv', - contents: - 'onset\tduration\ttest\tHED\n' + - '7\tsomething\tone\tSpeed/30 mph\n', - }, - ] - const jsonDictionary = { - '/sub01/sub01_task-test_events.json': { - myCodes: { - HED: { - one: 'Duration/5 s', - }, - }, - }, - '/dataset_description.json': { HEDVersion: '8.0.0' }, - } - - return validate.Events.validateEvents( - events, - [], - headers, - jsonDictionary, - jsonFiles, - '', - ).then((issues) => { - assert.deepStrictEqual(issues, []) - }) - }) - - it('should not throw an issue if a value column is annotated', () => { - const events = [ - { - file: { path: '/sub01/sub01_task-test_events.tsv' }, - path: '/sub01/sub01_task-test_events.tsv', - contents: - 'onset\tduration\ttest\tHED\n' + '7\t3.0\tone\tSpeed/30 mph\n', - }, - ] - const jsonDictionary = { - '/sub01/sub01_task-test_events.json': { - myCodes: { - test: { - HED: { - one: 'Label/#', - }, - }, - }, - }, - '/dataset_description.json': { HEDVersion: '8.0.0' }, - } - - return validate.Events.validateEvents( - events, - [], - headers, - jsonDictionary, - jsonFiles, - '', - ).then((issues) => { - assert.deepStrictEqual(issues, []) - }) - }) - - it('should not throw an issue if a library schema is included', () => { - const events = [ - { - file: { path: '/sub01/sub01_task-test_events.tsv' }, - path: '/sub01/sub01_task-test_events.tsv', - contents: - 'onset\tduration\ttest\tHED\n' + '7\t3.0\tone\tSpeed/30 mph\n', - }, - ] - - const jsonDictionary = { - '/sub01/sub01_task-test_events.json': { - myCodes: { - test: { - HED: { - one: 'ts:Sensory-presentation, Label/#', - }, - }, - }, - }, - '/dataset_description.json': { - HEDVersion: ['8.0.0', 'ts:testlib_1.0.2'], - }, - } - - return validate.Events.validateEvents( - events, - [], - headers, - jsonDictionary, - jsonFiles, - '', - ).then((issues) => { - assert.deepStrictEqual(issues, []) - }) - }) - - it('should throw an issue if the HED data is invalid', () => { - const events = [ - { - file: { path: '/sub01/sub01_task-test_events.tsv' }, - path: '/sub01/sub01_task-test_events.tsv', - contents: - 'onset\tduration\ttest\tHED\n' + - '7\tsomething\tone\tDuration/5 s\n', - }, - ] - const jsonDictionary = { - '/sub01/sub01_task-test_events.json': { - test: { - HED: { - one: 'Speed/5 ms', - }, - }, - }, - '/dataset_description.json': { HEDVersion: '8.0.0' }, - } - - return validate.Events.validateEvents( - events, - [], - headers, - jsonDictionary, - jsonFiles, - '', - ).then((issues) => { - assert.strictEqual(issues.length, 1) - assert.strictEqual(issues[0].code, 104) - }) - }) - - it('should not throw an issue if multiple library schemas are included', () => { - const events = [ - { - file: { path: '/sub01/sub01_task-test_events.tsv' }, - path: '/sub01/sub01_task-test_events.tsv', - contents: - 'onset\tduration\ttest\tHED\n' + '7\t3.0\tone\tSpeed/30 mph\n', - }, - ] - - const jsonDictionary = { - '/sub01/sub01_task-test_events.json': { - myCodes: { - test: { - HED: { - one: 'ts:Sensory-presentation, Label/#, sc:Sleep-deprivation', - }, - }, - }, - }, - '/dataset_description.json': { - HEDVersion: ['8.0.0', 'ts:testlib_1.0.2', 'sc:score_1.0.0'], - }, - } - - return validate.Events.validateEvents( - events, - [], - headers, - jsonDictionary, - jsonFiles, - '', - ).then((issues) => { - assert.deepStrictEqual(issues, []) - }) - }) - - it('should properly issue warnings when appropriate', () => { - const events = [ - { - file: { path: '/sub01/sub01_task-test_events.tsv' }, - path: '/sub01/sub01_task-test_events.tsv', - contents: - 'onset\tduration\ttest\tHED\n' + - '7\tsomething\tone\tHuman/Driver\n', - }, - ] - const jsonDictionary = { - '/sub01/sub01_task-test_events.json': { - test: { - HED: { - one: 'Train/Maglev', - }, - }, - }, - '/dataset_description.json': { HEDVersion: '8.0.0' }, - } - return validate.Events.validateEvents( - events, - [], - headers, - jsonDictionary, - jsonFiles, - '', - ).then((issues) => { - assert.strictEqual(issues.length, 1) - assert.strictEqual(issues[0].code, 105) - }) - }) + const issues = validateEvents(events, [], headers, jsonDictionary) + assert.deepStrictEqual(issues, []) }) }) diff --git a/bids-validator/tests/hed.spec.js b/bids-validator/tests/hed.spec.js new file mode 100644 index 000000000..295a3b4bc --- /dev/null +++ b/bids-validator/tests/hed.spec.js @@ -0,0 +1,198 @@ +import assert from 'assert' +import validateHed from '../validators/hed' + +describe('HED', function () { + const jsonFiles = [ + { + relativePath: '/sub01/sub01_task-test_events.json', + path: '/sub01/sub01_task-test_events.json', + }, + { + relativePath: '/dataset_description.json', + path: '/dataset_description.json', + }, + ] + + it('should not throw an issue if the HED data is valid', () => { + const events = [ + { + file: { + path: '/sub01/sub01_task-test_events.tsv', + relativePath: '/sub01/sub01_task-test_events.tsv', + }, + path: '/sub01/sub01_task-test_events.tsv', + contents: + 'onset\tduration\ttest\tHED\n' + '7\tsomething\tone\tSpeed/30 mph\n', + }, + ] + const jsonDictionary = { + '/sub01/sub01_task-test_events.json': { + myCodes: { + HED: { + one: 'Duration/5 s', + }, + }, + }, + '/dataset_description.json': { HEDVersion: '8.0.0' }, + } + + return validateHed(events, jsonDictionary, jsonFiles, '').then((issues) => { + assert.deepStrictEqual(issues, []) + }) + }) + + it('should not throw an issue if a value column is annotated', () => { + const events = [ + { + file: { + path: '/sub01/sub01_task-test_events.tsv', + relativePath: '/sub01/sub01_task-test_events.tsv', + }, + path: '/sub01/sub01_task-test_events.tsv', + contents: + 'onset\tduration\ttest\tHED\n' + '7\t3.0\tone\tSpeed/30 mph\n', + }, + ] + const jsonDictionary = { + '/sub01/sub01_task-test_events.json': { + myCodes: { + test: { + HED: { + one: 'Label/#', + }, + }, + }, + }, + '/dataset_description.json': { HEDVersion: '8.0.0' }, + } + + return validateHed(events, jsonDictionary, jsonFiles, '').then((issues) => { + assert.deepStrictEqual(issues, []) + }) + }) + + it('should not throw an issue if a library schema is included', () => { + const events = [ + { + file: { + path: '/sub01/sub01_task-test_events.tsv', + relativePath: '/sub01/sub01_task-test_events.tsv', + }, + path: '/sub01/sub01_task-test_events.tsv', + contents: + 'onset\tduration\ttest\tHED\n' + '7\t3.0\tone\tSpeed/30 mph\n', + }, + ] + + const jsonDictionary = { + '/sub01/sub01_task-test_events.json': { + myCodes: { + test: { + HED: { + one: 'ts:Sensory-presentation, Label/#', + }, + }, + }, + }, + '/dataset_description.json': { + HEDVersion: ['8.0.0', 'ts:testlib_1.0.2'], + }, + } + + return validateHed(events, jsonDictionary, jsonFiles, '').then((issues) => { + assert.deepStrictEqual(issues, []) + }) + }) + + it('should throw an issue if the HED data is invalid', () => { + const events = [ + { + file: { + path: '/sub01/sub01_task-test_events.tsv', + relativePath: '/sub01/sub01_task-test_events.tsv', + }, + path: '/sub01/sub01_task-test_events.tsv', + contents: + 'onset\tduration\ttest\tHED\n' + '7\tsomething\tone\tDuration/5 s\n', + }, + ] + const jsonDictionary = { + '/sub01/sub01_task-test_events.json': { + test: { + HED: { + one: 'Speed/5 ms', + }, + }, + }, + '/dataset_description.json': { HEDVersion: '8.0.0' }, + } + + return validateHed(events, jsonDictionary, jsonFiles, '').then((issues) => { + assert.strictEqual(issues.length, 1) + assert.strictEqual(issues[0].code, 104) + }) + }) + + it('should not throw an issue if multiple library schemas are included', () => { + const events = [ + { + file: { + path: '/sub01/sub01_task-test_events.tsv', + relativePath: '/sub01/sub01_task-test_events.tsv', + }, + path: '/sub01/sub01_task-test_events.tsv', + contents: + 'onset\tduration\ttest\tHED\n' + '7\t3.0\tone\tSpeed/30 mph\n', + }, + ] + + const jsonDictionary = { + '/sub01/sub01_task-test_events.json': { + myCodes: { + test: { + HED: { + one: 'ts:Sensory-presentation, Label/#, sc:Sleep-deprivation', + }, + }, + }, + }, + '/dataset_description.json': { + HEDVersion: ['8.0.0', 'ts:testlib_1.0.2', 'sc:score_1.0.0'], + }, + } + + return validateHed(events, jsonDictionary, jsonFiles, '').then((issues) => { + assert.deepStrictEqual(issues, []) + }) + }) + + it('should properly issue warnings when appropriate', () => { + const events = [ + { + file: { + path: '/sub01/sub01_task-test_events.tsv', + relativePath: '/sub01/sub01_task-test_events.tsv', + }, + path: '/sub01/sub01_task-test_events.tsv', + contents: + 'onset\tduration\ttest\tHED\n' + '7\tsomething\tone\tHuman/Driver\n', + }, + ] + const jsonDictionary = { + '/sub01/sub01_task-test_events.json': { + test: { + HED: { + one: 'Train/Maglev', + }, + }, + }, + '/dataset_description.json': { HEDVersion: '8.0.0' }, + } + + return validateHed(events, jsonDictionary, jsonFiles, '').then((issues) => { + assert.strictEqual(issues.length, 2) + assert.strictEqual(issues[0].code, 105) + assert.strictEqual(issues[1].code, 105) + }) + }) +}) diff --git a/bids-validator/validators/bids/fullTest.js b/bids-validator/validators/bids/fullTest.js index 955b6f642..867c7b941 100644 --- a/bids-validator/validators/bids/fullTest.js +++ b/bids-validator/validators/bids/fullTest.js @@ -8,6 +8,7 @@ import bval from '../bval' import bvec from '../bvec' import microscopy from '../microscopy' import Events from '../events' +import hed from '../hed' import { session } from '../session' import checkAnyDataPresent from '../checkAnyDataPresent' import headerFields from '../headerFields' @@ -214,17 +215,15 @@ const fullTest = (fileList, options, annexed, dir, schema, callback) => { // Events validation stimuli.directory = files.stimuli - return Events.validateEvents( - events, - stimuli, - headers, - jsonContentsDict, - jsonFiles, - dir, + self.issues = self.issues.concat( + Events.validateEvents(events, stimuli, headers, jsonContentsDict), ) + + // check the HED strings + return hed(tsvs, jsonContentsDict, jsonFiles, dir) }) - .then((eventsIssues) => { - self.issues = self.issues.concat(eventsIssues) + .then((hedIssues) => { + self.issues = self.issues.concat(hedIssues) // Validate custom fields in all TSVs and add any issues to the list self.issues = self.issues.concat( diff --git a/bids-validator/validators/events/events.js b/bids-validator/validators/events/events.js index 94cf4a709..8df4fe372 100644 --- a/bids-validator/validators/events/events.js +++ b/bids-validator/validators/events/events.js @@ -1,28 +1,16 @@ /* eslint-disable no-unused-vars */ -import hed from './hed' import utils from '../../utils' const Issue = utils.issues.Issue -export default function ( - events, - stimuli, - headers, - jsonContents, - jsonFiles, - dir, -) { - const issues = [] +export default function (events, stimuli, headers, jsonContents) { // check that all stimuli files present in /stimuli are included in an _events.tsv file const stimuliIssues = checkStimuli(stimuli) // check the events file for suspiciously long or short durations const designIssues = checkDesignLength(events, headers, jsonContents) - // check the HED strings - return hed(events, jsonContents, jsonFiles, dir).then((hedIssues) => { - return issues.concat(stimuliIssues, designIssues, hedIssues) - }) + return [].concat(stimuliIssues, designIssues) } const checkStimuli = function (stimuli) { diff --git a/bids-validator/validators/events/index.js b/bids-validator/validators/events/index.js index 970f96b09..7e19d4c85 100644 --- a/bids-validator/validators/events/index.js +++ b/bids-validator/validators/events/index.js @@ -1,9 +1,7 @@ import events from './events' -import hed from './hed' import validate from './validate' export default { events: events, - hed: hed, validateEvents: validate, } diff --git a/bids-validator/validators/events/hed.js b/bids-validator/validators/hed.js similarity index 63% rename from bids-validator/validators/events/hed.js rename to bids-validator/validators/hed.js index cb159353f..34383e1cc 100644 --- a/bids-validator/validators/events/hed.js +++ b/bids-validator/validators/hed.js @@ -1,14 +1,14 @@ import hedValidator from 'hed-validator' +import cloneDeep from 'lodash/cloneDeep' import intersection from 'lodash/intersection' -import utils from '../../utils' -import parseTsv from '../tsv/tsvParser' +import utils from '../utils' const Issue = utils.issues.Issue -export default function checkHedStrings(events, jsonContents, jsonFiles, dir) { - const eventData = constructEventData(events, jsonContents) - const sidecarData = constructSidecarData(events, jsonContents, jsonFiles) - const hedDataExists = detectHed(eventData, sidecarData) +export default function checkHedStrings(tsvs, jsonContents, jsonFiles, dir) { + const tsvData = constructTsvData(tsvs, jsonContents) + const sidecarData = constructSidecarData(tsvData, jsonContents, jsonFiles) + const hedDataExists = detectHed(tsvData, sidecarData) if (!hedDataExists) { return Promise.resolve([]) } @@ -16,11 +16,11 @@ export default function checkHedStrings(events, jsonContents, jsonFiles, dir) { const datasetDescription = jsonContents['/dataset_description.json'] const datasetDescriptionData = new hedValidator.validator.BidsJsonFile( '/dataset_description.json', - datasetDescription, + cloneDeep(datasetDescription), getSidecarFileObject('/dataset_description.json', jsonFiles), ) const dataset = new hedValidator.validator.BidsDataset( - eventData, + tsvData, sidecarData, datasetDescriptionData, dir, @@ -43,61 +43,65 @@ export default function checkHedStrings(events, jsonContents, jsonFiles, dir) { } } -function constructEventData(events, jsonContents) { - return events.map((eventFile) => { +function constructTsvData(tsvFiles, jsonContents) { + return tsvFiles.map((tsvFile) => { const potentialSidecars = utils.files.potentialLocations( - eventFile.path.replace('.tsv', '.json'), + tsvFile.file.relativePath.replace('.tsv', '.json'), ) const mergedDictionary = utils.files.generateMergedSidecarDict( potentialSidecars, jsonContents, ) - const parsedTsv = parseTsv(eventFile.contents) - const file = eventFile.file - return new hedValidator.validator.BidsEventFile( - eventFile.path, + let TsvFileClass + if (tsvFile.file.relativePath.endsWith('_events.tsv')) { + TsvFileClass = hedValidator.bids.BidsEventFile + } else { + TsvFileClass = hedValidator.bids.BidsTabularFile + } + return new TsvFileClass( + tsvFile.path, potentialSidecars, mergedDictionary, - parsedTsv, - file, + tsvFile.contents, + tsvFile.file, ) }) } -function constructSidecarData(eventData, jsonContents, jsonFiles) { +function constructSidecarData(tsvData, jsonContents, jsonFiles) { const actualSidecarNames = Object.keys(jsonContents) - let potentialEventSidecars = [] - for (const eventFileData of eventData) { - potentialEventSidecars = potentialEventSidecars.concat( - eventFileData.potentialSidecars, - ) + const potentialSidecars = [] + for (const tsvFileData of tsvData) { + potentialSidecars.push(...tsvFileData.potentialSidecars) } const actualEventSidecars = intersection( actualSidecarNames, - potentialEventSidecars, + potentialSidecars, ) return actualEventSidecars.map((sidecarName) => { - return new hedValidator.validator.BidsSidecar( + return new hedValidator.bids.BidsSidecar( sidecarName, - jsonContents[sidecarName], + cloneDeep(jsonContents[sidecarName]), getSidecarFileObject(sidecarName, jsonFiles), ) }) } function getSidecarFileObject(sidecarName, jsonFiles) { - return jsonFiles.filter((file) => { - return file.relativePath === sidecarName - })[0] + return cloneDeep( + jsonFiles.filter((file) => { + return file.relativePath === sidecarName + })[0], + ) } -function detectHed(eventData, sidecarData) { +function detectHed(tsvData, sidecarData) { return ( sidecarData.some((sidecarFileData) => { return Object.values(sidecarFileData.sidecarData).some(sidecarValueHasHed) }) || - eventData.some((eventFileData) => { - return eventFileData.parsedTsv.headers.indexOf('HED') !== -1 + tsvData.some((tsvFileData) => { + return tsvFileData.parsedTsv.headers.indexOf('HED') !== -1 }) ) } diff --git a/bids-validator/validators/json/json.js b/bids-validator/validators/json/json.js index bf0c8aa65..2f0e63445 100644 --- a/bids-validator/validators/json/json.js +++ b/bids-validator/validators/json/json.js @@ -161,6 +161,8 @@ const selectSchema = (file) => { schema = require('./schemas/beh.json') } else if (file.name.endsWith('_motion.json')) { schema = require('./schemas/motion.json') + } else if (file.name.endsWith('_channels.json')) { + schema = require('./schemas/channels.json') } } return schema diff --git a/bids-validator/validators/json/schemas/channels.json b/bids-validator/validators/json/schemas/channels.json new file mode 100644 index 000000000..e4be45d89 --- /dev/null +++ b/bids-validator/validators/json/schemas/channels.json @@ -0,0 +1,47 @@ +{ + "$schema": "http://json-schema.org/draft-06/schema#", + "allOf": [ + { + "type": "object", + "properties": { + "reference_frame": { + "title": "Reference Frame", + "type": "object", + "properties": { + "Levels": { + "type": "object", + "patternProperties": { + "^.+$": { + "type": "object", + "properties": { + "RotationOrder": { + "description": "The sequence in which the extrinsic rotations are applied around the three axes.", + "type": "string", + "enum": ["XYZ", "XZY", "YXZ", "YZX", "ZXY", "ZYX"] + }, + "RotationRule": { + "description": "The direction of rotation around each axis.", + "type": "string", + "enum": ["left-hand", "right-hand"] + }, + "SpatialAxes": { + "description": "The coordinate system in which the motion data are to be interpreted. A sequence of characters from the set `{'A', 'P', 'L', 'R', 'S', 'I', '_'}` indicating the direction of each axis. For example `\"ARS\"` indicates positive values in the X, Y, Z axes are respectively anterior, right, and superior of the origin, while `\"PLI\"` indicates positive values are posterior, left, and inferior of the origin. The `\"_\"` character may be used for unused axes.", + "type": "string", + "pattern": "^[APLRSI_]{3}$" + } + } + } + } + } + } + } + } + }, + { + "type": "object", + "patternProperties": { + "^.+$": { "$ref": "common_definitions.json#/definitions/ColumnDescription" } + } + } + ] +} diff --git a/bids-validator/validators/json/schemas/common_definitions.json b/bids-validator/validators/json/schemas/common_definitions.json index ad0e9bf40..5980ca3c2 100644 --- a/bids-validator/validators/json/schemas/common_definitions.json +++ b/bids-validator/validators/json/schemas/common_definitions.json @@ -122,6 +122,73 @@ "SoftwareVersions": { "type": "string" }, "TaskDescription": { "type": "string" }, "TaskName": { "type": "string", "minLength": 1 }, - "TriggerChannelCount": { "type": "integer", "minimum": 0 } + "TermURL": { + "title": "TermURL", + "description": "URL pointing to a formal definition in an ontology available on the web.", + "type": "string", + "format": "uri" + }, + "TriggerChannelCount": { "type": "integer", "minimum": 0 }, + "ColumnDescription": { + "type": "object", + "title": "Column", + "description": "Column of a corresponding tabular file.", + "properties": { + "LongName": { + "title": "LongName", + "description": " Long (unabbreviated) name of column.", + "type": "string" + }, + "Description": { + "title": "Description", + "description": "Description of the column.", + "type": "string" + }, + "Units": { + "title": "Units", + "description": "Measurement units.", + "type": "string" + }, + "Levels": { + "type": "object", + "title": "Levels", + "description": "For categorical variables: a dictionary of possible values (keys) and their descriptions (values).", + "patternProperties": { + "^.+$": { + "anyOf": [ + { "type": "string" }, + { + "type": "object", + "properties": { + "Description": { "type": "string" }, + "TermURL": { "$ref": "#/definitions/TermURL" } + } + } + ] + } + } + }, + "TermURL": { "$ref": "#/definitions/TermURL" }, + "HED": { + "anyOf": [ + { + "type": "object", + "title": "HED", + "description": "For categorical variables: a dictionary of possible values (keys) and their HED strings (values).", + "patternProperties": { + "^.+$": { + "type": "string" + } + } + }, + { + "type": "string", + "title": "HED", + "description": "For value variables: a string with a single '#' character where the cell value is to be interpolated." + } + ] + } + } + } } } diff --git a/bids-validator/validators/json/schemas/data_dictionary.json b/bids-validator/validators/json/schemas/data_dictionary.json index 6873ca56b..f3bfc1921 100644 --- a/bids-validator/validators/json/schemas/data_dictionary.json +++ b/bids-validator/validators/json/schemas/data_dictionary.json @@ -1,62 +1,6 @@ { "type": "object", "patternProperties": { - "^.+$": { - "type": "object", - "title": "Column", - "description": "Column of a corresponding tabular file.", - "properties": { - "LongName": { - "title": "LongName", - "description": " Long (unabbreviated) name of column.", - "type": "string" - }, - "Description": { - "title": "Description", - "description": "Description of the column.", - "type": "string" - }, - "Units": { - "title": "Units", - "description": "Measurement units.", - "type": "string" - }, - "Levels": { - "type": "object", - "title": "Levels", - "description": "For categorical variables: a dictionary of possible values (keys) and their descriptions (values).", - "patternProperties": { - "^.+$": { - "type": "string" - } - } - }, - "TermURL": { - "title": "TermURL", - "description": "URL pointing to a formal definition in an ontology available on the web.", - "type": "string", - "format": "uri" - }, - "HED": { - "anyOf": [ - { - "type": "object", - "title": "HED", - "description": "For categorical variables: a dictionary of possible values (keys) and their HED strings (values).", - "patternProperties": { - "^.+$": { - "type": "string" - } - } - }, - { - "type": "string", - "title": "HED", - "description": "For value variables: a string with a single '#' character where the cell value is to be interpolated." - } - ] - } - } - } + "^.+$": { "$ref": "common_definitions.json#/definitions/ColumnDescription" } } } diff --git a/bids-validator/validators/json/schemas/eeg.json b/bids-validator/validators/json/schemas/eeg.json index 2a0cdaf74..14ed03748 100644 --- a/bids-validator/validators/json/schemas/eeg.json +++ b/bids-validator/validators/json/schemas/eeg.json @@ -74,7 +74,9 @@ "EpochLength": { "$ref": "common_definitions.json#/definitions/EpochLength" }, - "SubjectArtefactDescription": { "type": "string" } + "SubjectArtefactDescription": { "type": "string" }, + "ElectricalStimulation": { "type": "boolean" }, + "ElectricalStimulationParameters": { "type": "string" } }, "required": [ "TaskName", diff --git a/bids-validator/validators/json/schemas/events.json b/bids-validator/validators/json/schemas/events.json index 208b941fe..bace2aa3a 100644 --- a/bids-validator/validators/json/schemas/events.json +++ b/bids-validator/validators/json/schemas/events.json @@ -1,57 +1,7 @@ { "type": "object", "patternProperties": { - "^.+$": { - "type": "object", - "title": "Column", - "description": "Column of a corresponding tabular file.", - "properties": { - "LongName": { - "title": "LongName", - "description": " Long (unabbreviated) name of column.", - "type": "string" - }, - "Description": { - "title": "Description", - "description": "Description of the column.", - "type": "string" - }, - "Units": { - "title": "Units", - "description": "Measurement units.", - "type": "string" - }, - "Levels": { - "type": "object", - "title": "Levels", - "description": "For categorical variables: a dictionary of possible values (keys) and their descriptions (values).", - "patternProperties": { - "^.+$": { - "type": "string" - } - } - }, - "HED": { - "anyOf": [ - { - "type": "object", - "title": "HED", - "description": "For categorical variables: a dictionary of possible values (keys) and their HED strings (values).", - "patternProperties": { - "^.+$": { - "type": "string" - } - } - }, - { - "type": "string", - "title": "HED", - "description": "For value variables: a string with a single '#' character where the cell value is to be interpolated." - } - ] - } - } - } + "^.+$": { "$ref": "common_definitions.json#/definitions/ColumnDescription" } }, "properties": { "StimulusPresentation": { diff --git a/bids-validator/validators/json/schemas/meg.json b/bids-validator/validators/json/schemas/meg.json index 11bc5bbe4..b2da2d3fa 100644 --- a/bids-validator/validators/json/schemas/meg.json +++ b/bids-validator/validators/json/schemas/meg.json @@ -102,7 +102,9 @@ "MaxMovement": { "type": "number" }, "SubjectArtefactDescription": { "type": "string" }, "DigitizedLandmarks": { "type": "boolean" }, - "DigitizedHeadPoints": { "type": "boolean" } + "DigitizedHeadPoints": { "type": "boolean" }, + "ElectricalStimulation": { "type": "boolean" }, + "ElectricalStimulationParameters": { "type": "string" } }, "required": [ "TaskName", diff --git a/bids-validator/validators/json/schemas/motion.json b/bids-validator/validators/json/schemas/motion.json index 9a4d2c34b..3db7717a8 100644 --- a/bids-validator/validators/json/schemas/motion.json +++ b/bids-validator/validators/json/schemas/motion.json @@ -27,7 +27,6 @@ }, "SubjectArtefactDescription": { "type": "string" }, "MotionChannelCount": { "type": "number" }, - "TrackingSystemCount": { "type": "number" }, "TrackingSystemName": { "type": "string" }, "DeviceSerialNumber": { "$ref": "common_definitions.json#/definitions/DeviceSerialNumber" @@ -56,21 +55,12 @@ "GYROChannelCount": { "type": "number" }, "JNTANGChannelCount": { "type": "number" }, "MAGNChannelCount": { "type": "number" }, - "MISChannelCount": { "type": "number" }, + "MISCChannelCount": { "type": "number" }, "ORNTChannelCount": { "type": "number" }, "POSChannelCount": { "type": "number" }, "VELChannelCount": { "type": "number" }, "LATENCYChannelCount": { "type": "number" }, - "MissingValues": { "type": "string" }, - "RotationOrder": { - "type": "string", - "enum": ["XYZ", "XZY", "YXZ", "YZX", "ZXY", "ZYX"] - }, - "RotationRule": { - "type": "string", - "enum": ["left-hand", "right-hand"] - }, - "SpatialAxes": { "type": "string" } + "MissingValues": { "type": "string" } }, "required": ["TaskName", "SamplingFrequency"], "additionalProperties": false diff --git a/bids-validator/validators/tsv/tsv.js b/bids-validator/validators/tsv/tsv.js index f4ca95b75..62b9f43fa 100644 --- a/bids-validator/validators/tsv/tsv.js +++ b/bids-validator/validators/tsv/tsv.js @@ -557,7 +557,7 @@ const TSV = (file, contents, fileList, callback) => { } */ - // check partcipants.tsv for age 89+ + // check participants.tsv for age 89+ if (file.name === 'participants.tsv') { checkAge89(rows, file, issues) } diff --git a/bids-validator/versioneer.py b/bids-validator/versioneer.py deleted file mode 100644 index 223db1d9c..000000000 --- a/bids-validator/versioneer.py +++ /dev/null @@ -1,2194 +0,0 @@ - -# Version: 0.26 - -"""The Versioneer - like a rocketeer, but for versions. - -The Versioneer -============== - -* like a rocketeer, but for versions! -* https://github.com/python-versioneer/python-versioneer -* Brian Warner -* License: Public Domain (Unlicense) -* Compatible with: Python 3.7, 3.8, 3.9, 3.10 and pypy3 -* [![Latest Version][pypi-image]][pypi-url] -* [![Build Status][travis-image]][travis-url] - -This is a tool for managing a recorded version number in setuptools-based -python projects. The goal is to remove the tedious and error-prone "update -the embedded version string" step from your release process. Making a new -release should be as easy as recording a new tag in your version-control -system, and maybe making new tarballs. - - -## Quick Install - -Versioneer provides two installation modes. The "classic" vendored mode installs -a copy of versioneer into your repository. The experimental build-time dependency mode -is intended to allow you to skip this step and simplify the process of upgrading. - -### Vendored mode - -* `pip install versioneer` to somewhere in your $PATH -* add a `[tool.versioneer]` section to your `pyproject.toml or a - `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md)) -* run `versioneer install --vendor` in your source tree, commit the results -* verify version information with `python setup.py version` - -### Build-time dependency mode - -* `pip install versioneer` to somewhere in your $PATH -* add a `[tool.versioneer]` section to your `pyproject.toml or a - `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md)) -* add `versioneer` to the `requires` key of the `build-system` table in - `pyproject.toml`: - ```toml - [build-system] - requires = ["setuptools", "versioneer"] - build-backend = "setuptools.build_meta" - ``` -* run `versioneer install --no-vendor` in your source tree, commit the results -* verify version information with `python setup.py version` - -## Version Identifiers - -Source trees come from a variety of places: - -* a version-control system checkout (mostly used by developers) -* a nightly tarball, produced by build automation -* a snapshot tarball, produced by a web-based VCS browser, like github's - "tarball from tag" feature -* a release tarball, produced by "setup.py sdist", distributed through PyPI - -Within each source tree, the version identifier (either a string or a number, -this tool is format-agnostic) can come from a variety of places: - -* ask the VCS tool itself, e.g. "git describe" (for checkouts), which knows - about recent "tags" and an absolute revision-id -* the name of the directory into which the tarball was unpacked -* an expanded VCS keyword ($Id$, etc) -* a `_version.py` created by some earlier build step - -For released software, the version identifier is closely related to a VCS -tag. Some projects use tag names that include more than just the version -string (e.g. "myproject-1.2" instead of just "1.2"), in which case the tool -needs to strip the tag prefix to extract the version identifier. For -unreleased software (between tags), the version identifier should provide -enough information to help developers recreate the same tree, while also -giving them an idea of roughly how old the tree is (after version 1.2, before -version 1.3). Many VCS systems can report a description that captures this, -for example `git describe --tags --dirty --always` reports things like -"0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the -0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has -uncommitted changes). - -The version identifier is used for multiple purposes: - -* to allow the module to self-identify its version: `myproject.__version__` -* to choose a name and prefix for a 'setup.py sdist' tarball - -## Theory of Operation - -Versioneer works by adding a special `_version.py` file into your source -tree, where your `__init__.py` can import it. This `_version.py` knows how to -dynamically ask the VCS tool for version information at import time. - -`_version.py` also contains `$Revision$` markers, and the installation -process marks `_version.py` to have this marker rewritten with a tag name -during the `git archive` command. As a result, generated tarballs will -contain enough information to get the proper version. - -To allow `setup.py` to compute a version too, a `versioneer.py` is added to -the top level of your source tree, next to `setup.py` and the `setup.cfg` -that configures it. This overrides several distutils/setuptools commands to -compute the version when invoked, and changes `setup.py build` and `setup.py -sdist` to replace `_version.py` with a small static file that contains just -the generated version data. - -## Installation - -See [INSTALL.md](./INSTALL.md) for detailed installation instructions. - -## Version-String Flavors - -Code which uses Versioneer can learn about its version string at runtime by -importing `_version` from your main `__init__.py` file and running the -`get_versions()` function. From the "outside" (e.g. in `setup.py`), you can -import the top-level `versioneer.py` and run `get_versions()`. - -Both functions return a dictionary with different flavors of version -information: - -* `['version']`: A condensed version string, rendered using the selected - style. This is the most commonly used value for the project's version - string. The default "pep440" style yields strings like `0.11`, - `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section - below for alternative styles. - -* `['full-revisionid']`: detailed revision identifier. For Git, this is the - full SHA1 commit id, e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac". - -* `['date']`: Date and time of the latest `HEAD` commit. For Git, it is the - commit date in ISO 8601 format. This will be None if the date is not - available. - -* `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that - this is only accurate if run in a VCS checkout, otherwise it is likely to - be False or None - -* `['error']`: if the version string could not be computed, this will be set - to a string describing the problem, otherwise it will be None. It may be - useful to throw an exception in setup.py if this is set, to avoid e.g. - creating tarballs with a version string of "unknown". - -Some variants are more useful than others. Including `full-revisionid` in a -bug report should allow developers to reconstruct the exact code being tested -(or indicate the presence of local changes that should be shared with the -developers). `version` is suitable for display in an "about" box or a CLI -`--version` output: it can be easily compared against release notes and lists -of bugs fixed in various releases. - -The installer adds the following text to your `__init__.py` to place a basic -version in `YOURPROJECT.__version__`: - - from ._version import get_versions - __version__ = get_versions()['version'] - del get_versions - -## Styles - -The setup.cfg `style=` configuration controls how the VCS information is -rendered into a version string. - -The default style, "pep440", produces a PEP440-compliant string, equal to the -un-prefixed tag name for actual releases, and containing an additional "local -version" section with more detail for in-between builds. For Git, this is -TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags ---dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the -tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and -that this commit is two revisions ("+2") beyond the "0.11" tag. For released -software (exactly equal to a known tag), the identifier will only contain the -stripped tag, e.g. "0.11". - -Other styles are available. See [details.md](details.md) in the Versioneer -source tree for descriptions. - -## Debugging - -Versioneer tries to avoid fatal errors: if something goes wrong, it will tend -to return a version of "0+unknown". To investigate the problem, run `setup.py -version`, which will run the version-lookup code in a verbose mode, and will -display the full contents of `get_versions()` (including the `error` string, -which may help identify what went wrong). - -## Known Limitations - -Some situations are known to cause problems for Versioneer. This details the -most significant ones. More can be found on Github -[issues page](https://github.com/python-versioneer/python-versioneer/issues). - -### Subprojects - -Versioneer has limited support for source trees in which `setup.py` is not in -the root directory (e.g. `setup.py` and `.git/` are *not* siblings). The are -two common reasons why `setup.py` might not be in the root: - -* Source trees which contain multiple subprojects, such as - [Buildbot](https://github.com/buildbot/buildbot), which contains both - "master" and "slave" subprojects, each with their own `setup.py`, - `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI - distributions (and upload multiple independently-installable tarballs). -* Source trees whose main purpose is to contain a C library, but which also - provide bindings to Python (and perhaps other languages) in subdirectories. - -Versioneer will look for `.git` in parent directories, and most operations -should get the right version string. However `pip` and `setuptools` have bugs -and implementation details which frequently cause `pip install .` from a -subproject directory to fail to find a correct version string (so it usually -defaults to `0+unknown`). - -`pip install --editable .` should work correctly. `setup.py install` might -work too. - -Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in -some later version. - -[Bug #38](https://github.com/python-versioneer/python-versioneer/issues/38) is tracking -this issue. The discussion in -[PR #61](https://github.com/python-versioneer/python-versioneer/pull/61) describes the -issue from the Versioneer side in more detail. -[pip PR#3176](https://github.com/pypa/pip/pull/3176) and -[pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve -pip to let Versioneer work correctly. - -Versioneer-0.16 and earlier only looked for a `.git` directory next to the -`setup.cfg`, so subprojects were completely unsupported with those releases. - -### Editable installs with setuptools <= 18.5 - -`setup.py develop` and `pip install --editable .` allow you to install a -project into a virtualenv once, then continue editing the source code (and -test) without re-installing after every change. - -"Entry-point scripts" (`setup(entry_points={"console_scripts": ..})`) are a -convenient way to specify executable scripts that should be installed along -with the python package. - -These both work as expected when using modern setuptools. When using -setuptools-18.5 or earlier, however, certain operations will cause -`pkg_resources.DistributionNotFound` errors when running the entrypoint -script, which must be resolved by re-installing the package. This happens -when the install happens with one version, then the egg_info data is -regenerated while a different version is checked out. Many setup.py commands -cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into -a different virtualenv), so this can be surprising. - -[Bug #83](https://github.com/python-versioneer/python-versioneer/issues/83) describes -this one, but upgrading to a newer version of setuptools should probably -resolve it. - - -## Updating Versioneer - -To upgrade your project to a new release of Versioneer, do the following: - -* install the new Versioneer (`pip install -U versioneer` or equivalent) -* edit `setup.cfg` and `pyproject.toml`, if necessary, - to include any new configuration settings indicated by the release notes. - See [UPGRADING](./UPGRADING.md) for details. -* re-run `versioneer install --[no-]vendor` in your source tree, to replace - `SRC/_version.py` -* commit any changed files - -## Future Directions - -This tool is designed to make it easily extended to other version-control -systems: all VCS-specific components are in separate directories like -src/git/ . The top-level `versioneer.py` script is assembled from these -components by running make-versioneer.py . In the future, make-versioneer.py -will take a VCS name as an argument, and will construct a version of -`versioneer.py` that is specific to the given VCS. It might also take the -configuration arguments that are currently provided manually during -installation by editing setup.py . Alternatively, it might go the other -direction and include code from all supported VCS systems, reducing the -number of intermediate scripts. - -## Similar projects - -* [setuptools_scm](https://github.com/pypa/setuptools_scm/) - a non-vendored build-time - dependency -* [minver](https://github.com/jbweston/miniver) - a lightweight reimplementation of - versioneer -* [versioningit](https://github.com/jwodder/versioningit) - a PEP 518-based setuptools - plugin - -## License - -To make Versioneer easier to embed, all its code is dedicated to the public -domain. The `_version.py` that it creates is also in the public domain. -Specifically, both are released under the Creative Commons "Public Domain -Dedication" license (CC0-1.0), as described in -https://creativecommons.org/publicdomain/zero/1.0/ . - -[pypi-image]: https://img.shields.io/pypi/v/versioneer.svg -[pypi-url]: https://pypi.python.org/pypi/versioneer/ -[travis-image]: -https://img.shields.io/travis/com/python-versioneer/python-versioneer.svg -[travis-url]: https://travis-ci.com/github/python-versioneer/python-versioneer - -""" -# pylint:disable=invalid-name,import-outside-toplevel,missing-function-docstring -# pylint:disable=missing-class-docstring,too-many-branches,too-many-statements -# pylint:disable=raise-missing-from,too-many-lines,too-many-locals,import-error -# pylint:disable=too-few-public-methods,redefined-outer-name,consider-using-with -# pylint:disable=attribute-defined-outside-init,too-many-arguments - -import configparser -import errno -import json -import os -import re -import subprocess -import sys -from pathlib import Path -from typing import Callable, Dict -import functools -try: - import tomli - have_tomli = True -except ImportError: - have_tomli = False - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_root(): - """Get the project root directory. - - We require that all commands are run from the project root, i.e. the - directory that contains setup.py, setup.cfg, and versioneer.py . - """ - root = os.path.realpath(os.path.abspath(os.getcwd())) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - # allow 'python path/to/setup.py COMMAND' - root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0]))) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - err = ("Versioneer was unable to run the project root directory. " - "Versioneer requires setup.py to be executed from " - "its immediate directory (like 'python setup.py COMMAND'), " - "or in a way that lets it use sys.argv[0] to find the root " - "(like 'python path/to/setup.py COMMAND').") - raise VersioneerBadRootError(err) - try: - # Certain runtime workflows (setup.py install/develop in a setuptools - # tree) execute all dependencies in a single python process, so - # "versioneer" may be imported multiple times, and python's shared - # module-import table will cache the first one. So we can't use - # os.path.dirname(__file__), as that will find whichever - # versioneer.py was first imported, even in later projects. - my_path = os.path.realpath(os.path.abspath(__file__)) - me_dir = os.path.normcase(os.path.splitext(my_path)[0]) - vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0]) - if me_dir != vsr_dir and "VERSIONEER_PEP518" not in globals(): - print("Warning: build in %s is using versioneer.py from %s" - % (os.path.dirname(my_path), versioneer_py)) - except NameError: - pass - return root - - -def get_config_from_root(root): - """Read the project setup.cfg file to determine Versioneer config.""" - # This might raise OSError (if setup.cfg is missing), or - # configparser.NoSectionError (if it lacks a [versioneer] section), or - # configparser.NoOptionError (if it lacks "VCS="). See the docstring at - # the top of versioneer.py for instructions on writing your setup.cfg . - root = Path(root) - pyproject_toml = root / "pyproject.toml" - setup_cfg = root / "setup.cfg" - section = None - if pyproject_toml.exists() and have_tomli: - try: - with open(pyproject_toml, 'rb') as fobj: - pp = tomli.load(fobj) - section = pp['tool']['versioneer'] - except (tomli.TOMLDecodeError, KeyError): - pass - if not section: - parser = configparser.ConfigParser() - with open(setup_cfg) as cfg_file: - parser.read_file(cfg_file) - parser.get("versioneer", "VCS") # raise error if missing - - section = parser["versioneer"] - - cfg = VersioneerConfig() - cfg.VCS = section['VCS'] - cfg.style = section.get("style", "") - cfg.versionfile_source = section.get("versionfile_source") - cfg.versionfile_build = section.get("versionfile_build") - cfg.tag_prefix = section.get("tag_prefix") - if cfg.tag_prefix in ("''", '""', None): - cfg.tag_prefix = "" - cfg.parentdir_prefix = section.get("parentdir_prefix") - cfg.verbose = section.get("verbose") - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -# these dictionaries contain VCS-specific tools -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs, method): # decorator - """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - HANDLERS.setdefault(vcs, {})[method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen([command] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None), **popen_kwargs) - break - except OSError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, process.returncode - return stdout, process.returncode - - -LONG_VERSION_PY['git'] = r''' -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. -# Generated by versioneer-0.26 -# https://github.com/python-versioneer/python-versioneer - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys -from typing import Callable, Dict -import functools - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s" - git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s" - git_date = "%(DOLLAR)sFormat:%%ci%(DOLLAR)s" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "%(STYLE)s" - cfg.tag_prefix = "%(TAG_PREFIX)s" - cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s" - cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs, method): # decorator - """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen([command] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None), **popen_kwargs) - break - except OSError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %%s" %% dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %%s" %% (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %%s (error)" %% dispcmd) - print("stdout was %%s" %% stdout) - return None, process.returncode - return stdout, process.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %%s but none started with prefix %%s" %% - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %%d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r'\d', r)} - if verbose: - print("discarding '%%s', no digits" %% ",".join(refs - tags)) - if verbose: - print("likely tags: %%s" %% ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r'\d', r): - continue - if verbose: - print("picking %%s" %% r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %%s not under git control" %% root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner(GITS, [ - "describe", "--tags", "--dirty", "--always", "--long", - "--match", f"{tag_prefix}[[:digit:]]*" - ], cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], - cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%%s'" - %% describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%%s' doesn't start with prefix '%%s'" - print(fmt %% (full_tag, tag_prefix)) - pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'" - %% (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces): - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver): - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces): - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%%d.dev%%d" %% (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%%d" %% (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%%d" %% pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%%s'" %% style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for _ in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} -''' - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r'\d', r)} - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r'\d', r): - continue - if verbose: - print("picking %s" % r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner(GITS, [ - "describe", "--tags", "--dirty", "--always", "--long", - "--match", f"{tag_prefix}[[:digit:]]*" - ], cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], - cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%s'" - % describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = ("tag '%s' doesn't start with prefix '%s'" - % (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def do_vcs_install(versionfile_source, ipy): - """Git-specific installation logic for Versioneer. - - For Git, this means creating/changing .gitattributes to mark _version.py - for export-subst keyword substitution. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - files = [versionfile_source] - if ipy: - files.append(ipy) - if "VERSIONEER_PEP518" not in globals(): - try: - my_path = __file__ - if my_path.endswith(".pyc") or my_path.endswith(".pyo"): - my_path = os.path.splitext(my_path)[0] + ".py" - versioneer_file = os.path.relpath(my_path) - except NameError: - versioneer_file = "versioneer.py" - files.append(versioneer_file) - present = False - try: - with open(".gitattributes", "r") as fobj: - for line in fobj: - if line.strip().startswith(versionfile_source): - if "export-subst" in line.strip().split()[1:]: - present = True - break - except OSError: - pass - if not present: - with open(".gitattributes", "a+") as fobj: - fobj.write(f"{versionfile_source} export-subst\n") - files.append(".gitattributes") - run_command(GITS, ["add", "--"] + files) - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %s but none started with prefix %s" % - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -SHORT_VERSION_PY = """ -# This file was generated by 'versioneer.py' (0.26) from -# revision-control system data, or from the parent directory name of an -# unpacked source archive. Distribution tarballs contain a pre-generated copy -# of this file. - -import json - -version_json = ''' -%s -''' # END VERSION_JSON - - -def get_versions(): - return json.loads(version_json) -""" - - -def versions_from_file(filename): - """Try to determine the version from _version.py if present.""" - try: - with open(filename) as f: - contents = f.read() - except OSError: - raise NotThisMethod("unable to read _version.py") - mo = re.search(r"version_json = '''\n(.*)''' # END VERSION_JSON", - contents, re.M | re.S) - if not mo: - mo = re.search(r"version_json = '''\r\n(.*)''' # END VERSION_JSON", - contents, re.M | re.S) - if not mo: - raise NotThisMethod("no version_json in _version.py") - return json.loads(mo.group(1)) - - -def write_to_version_file(filename, versions): - """Write the given version number to the given _version.py file.""" - os.unlink(filename) - contents = json.dumps(versions, sort_keys=True, - indent=1, separators=(",", ": ")) - with open(filename, "w") as f: - f.write(SHORT_VERSION_PY % contents) - - print("set %s to '%s'" % (filename, versions["version"])) - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces): - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver): - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces): - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%d" % (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -class VersioneerBadRootError(Exception): - """The project root directory is unknown or missing key files.""" - - -def get_versions(verbose=False): - """Get the project version from whatever source is available. - - Returns dict with two keys: 'version' and 'full'. - """ - if "versioneer" in sys.modules: - # see the discussion in cmdclass.py:get_cmdclass() - del sys.modules["versioneer"] - - root = get_root() - cfg = get_config_from_root(root) - - assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg" - handlers = HANDLERS.get(cfg.VCS) - assert handlers, "unrecognized VCS '%s'" % cfg.VCS - verbose = verbose or cfg.verbose - assert cfg.versionfile_source is not None, \ - "please set versioneer.versionfile_source" - assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix" - - versionfile_abs = os.path.join(root, cfg.versionfile_source) - - # extract version from first of: _version.py, VCS command (e.g. 'git - # describe'), parentdir. This is meant to work for developers using a - # source checkout, for users of a tarball created by 'setup.py sdist', - # and for users of a tarball/zipball created by 'git archive' or github's - # download-from-tag feature or the equivalent in other VCSes. - - get_keywords_f = handlers.get("get_keywords") - from_keywords_f = handlers.get("keywords") - if get_keywords_f and from_keywords_f: - try: - keywords = get_keywords_f(versionfile_abs) - ver = from_keywords_f(keywords, cfg.tag_prefix, verbose) - if verbose: - print("got version from expanded keyword %s" % ver) - return ver - except NotThisMethod: - pass - - try: - ver = versions_from_file(versionfile_abs) - if verbose: - print("got version from file %s %s" % (versionfile_abs, ver)) - return ver - except NotThisMethod: - pass - - from_vcs_f = handlers.get("pieces_from_vcs") - if from_vcs_f: - try: - pieces = from_vcs_f(cfg.tag_prefix, root, verbose) - ver = render(pieces, cfg.style) - if verbose: - print("got version from VCS %s" % ver) - return ver - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - if verbose: - print("got version from parentdir %s" % ver) - return ver - except NotThisMethod: - pass - - if verbose: - print("unable to compute version") - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, "error": "unable to compute version", - "date": None} - - -def get_version(): - """Get the short version string for this project.""" - return get_versions()["version"] - - -def get_cmdclass(cmdclass=None): - """Get the custom setuptools subclasses used by Versioneer. - - If the package uses a different cmdclass (e.g. one from numpy), it - should be provide as an argument. - """ - if "versioneer" in sys.modules: - del sys.modules["versioneer"] - # this fixes the "python setup.py develop" case (also 'install' and - # 'easy_install .'), in which subdependencies of the main project are - # built (using setup.py bdist_egg) in the same python process. Assume - # a main project A and a dependency B, which use different versions - # of Versioneer. A's setup.py imports A's Versioneer, leaving it in - # sys.modules by the time B's setup.py is executed, causing B to run - # with the wrong versioneer. Setuptools wraps the sub-dep builds in a - # sandbox that restores sys.modules to it's pre-build state, so the - # parent is protected against the child's "import versioneer". By - # removing ourselves from sys.modules here, before the child build - # happens, we protect the child from the parent's versioneer too. - # Also see https://github.com/python-versioneer/python-versioneer/issues/52 - - cmds = {} if cmdclass is None else cmdclass.copy() - - # we add "version" to setuptools - from setuptools import Command - - class cmd_version(Command): - description = "report generated version string" - user_options = [] - boolean_options = [] - - def initialize_options(self): - pass - - def finalize_options(self): - pass - - def run(self): - vers = get_versions(verbose=True) - print("Version: %s" % vers["version"]) - print(" full-revisionid: %s" % vers.get("full-revisionid")) - print(" dirty: %s" % vers.get("dirty")) - print(" date: %s" % vers.get("date")) - if vers["error"]: - print(" error: %s" % vers["error"]) - cmds["version"] = cmd_version - - # we override "build_py" in setuptools - # - # most invocation pathways end up running build_py: - # distutils/build -> build_py - # distutils/install -> distutils/build ->.. - # setuptools/bdist_wheel -> distutils/install ->.. - # setuptools/bdist_egg -> distutils/install_lib -> build_py - # setuptools/install -> bdist_egg ->.. - # setuptools/develop -> ? - # pip install: - # copies source tree to a tempdir before running egg_info/etc - # if .git isn't copied too, 'git describe' will fail - # then does setup.py bdist_wheel, or sometimes setup.py install - # setup.py egg_info -> ? - - # pip install -e . and setuptool/editable_wheel will invoke build_py - # but the build_py command is not expected to copy any files. - - # we override different "build_py" commands for both environments - if 'build_py' in cmds: - _build_py = cmds['build_py'] - else: - from setuptools.command.build_py import build_py as _build_py - - class cmd_build_py(_build_py): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_py.run(self) - if getattr(self, "editable_mode", False): - # During editable installs `.py` and data files are - # not copied to build_lib - return - # now locate _version.py in the new build/ directory and replace - # it with an updated value - if cfg.versionfile_build: - target_versionfile = os.path.join(self.build_lib, - cfg.versionfile_build) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - cmds["build_py"] = cmd_build_py - - if 'build_ext' in cmds: - _build_ext = cmds['build_ext'] - else: - from setuptools.command.build_ext import build_ext as _build_ext - - class cmd_build_ext(_build_ext): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_ext.run(self) - if self.inplace: - # build_ext --inplace will only build extensions in - # build/lib<..> dir with no _version.py to write to. - # As in place builds will already have a _version.py - # in the module dir, we do not need to write one. - return - # now locate _version.py in the new build/ directory and replace - # it with an updated value - target_versionfile = os.path.join(self.build_lib, - cfg.versionfile_build) - if not os.path.exists(target_versionfile): - print(f"Warning: {target_versionfile} does not exist, skipping " - "version update. This can happen if you are running build_ext " - "without first running build_py.") - return - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - cmds["build_ext"] = cmd_build_ext - - if "cx_Freeze" in sys.modules: # cx_freeze enabled? - from cx_Freeze.dist import build_exe as _build_exe - # nczeczulin reports that py2exe won't like the pep440-style string - # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g. - # setup(console=[{ - # "version": versioneer.get_version().split("+", 1)[0], # FILEVERSION - # "product_version": versioneer.get_version(), - # ... - - class cmd_build_exe(_build_exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _build_exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % - {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - cmds["build_exe"] = cmd_build_exe - del cmds["build_py"] - - if 'py2exe' in sys.modules: # py2exe enabled? - try: - from py2exe.setuptools_buildexe import py2exe as _py2exe - except ImportError: - from py2exe.distutils_buildexe import py2exe as _py2exe - - class cmd_py2exe(_py2exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _py2exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % - {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - cmds["py2exe"] = cmd_py2exe - - # sdist farms its file list building out to egg_info - if 'egg_info' in cmds: - _sdist = cmds['egg_info'] - else: - from setuptools.command.egg_info import egg_info as _egg_info - - class cmd_egg_info(_egg_info): - def find_sources(self): - # egg_info.find_sources builds the manifest list and writes it - # in one shot - super().find_sources() - - # Modify the filelist and normalize it - root = get_root() - cfg = get_config_from_root(root) - self.filelist.append('versioneer.py') - if cfg.versionfile_source: - # There are rare cases where versionfile_source might not be - # included by default, so we must be explicit - self.filelist.append(cfg.versionfile_source) - self.filelist.sort() - self.filelist.remove_duplicates() - - # The write method is hidden in the manifest_maker instance that - # generated the filelist and was thrown away - # We will instead replicate their final normalization (to unicode, - # and POSIX-style paths) - from setuptools import unicode_utils - normalized = [unicode_utils.filesys_decode(f).replace(os.sep, '/') - for f in self.filelist.files] - - manifest_filename = os.path.join(self.egg_info, 'SOURCES.txt') - with open(manifest_filename, 'w') as fobj: - fobj.write('\n'.join(normalized)) - - cmds['egg_info'] = cmd_egg_info - - # we override different "sdist" commands for both environments - if 'sdist' in cmds: - _sdist = cmds['sdist'] - else: - from setuptools.command.sdist import sdist as _sdist - - class cmd_sdist(_sdist): - def run(self): - versions = get_versions() - self._versioneer_generated_versions = versions - # unless we update this, the command will keep using the old - # version - self.distribution.metadata.version = versions["version"] - return _sdist.run(self) - - def make_release_tree(self, base_dir, files): - root = get_root() - cfg = get_config_from_root(root) - _sdist.make_release_tree(self, base_dir, files) - # now locate _version.py in the new base_dir directory - # (remembering that it may be a hardlink) and replace it with an - # updated value - target_versionfile = os.path.join(base_dir, cfg.versionfile_source) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, - self._versioneer_generated_versions) - cmds["sdist"] = cmd_sdist - - return cmds - - -CONFIG_ERROR = """ -setup.cfg is missing the necessary Versioneer configuration. You need -a section like: - - [versioneer] - VCS = git - style = pep440 - versionfile_source = src/myproject/_version.py - versionfile_build = myproject/_version.py - tag_prefix = - parentdir_prefix = myproject- - -You will also need to edit your setup.py to use the results: - - import versioneer - setup(version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), ...) - -Please read the docstring in ./versioneer.py for configuration instructions, -edit setup.cfg, and re-run the installer or 'python versioneer.py setup'. -""" - -SAMPLE_CONFIG = """ -# See the docstring in versioneer.py for instructions. Note that you must -# re-run 'versioneer.py setup' after changing this section, and commit the -# resulting files. - -[versioneer] -#VCS = git -#style = pep440 -#versionfile_source = -#versionfile_build = -#tag_prefix = -#parentdir_prefix = - -""" - -OLD_SNIPPET = """ -from ._version import get_versions -__version__ = get_versions()['version'] -del get_versions -""" - -INIT_PY_SNIPPET = """ -from . import {0} -__version__ = {0}.get_versions()['version'] -""" - - -def do_setup(): - """Do main VCS-independent setup function for installing Versioneer.""" - root = get_root() - try: - cfg = get_config_from_root(root) - except (OSError, configparser.NoSectionError, - configparser.NoOptionError) as e: - if isinstance(e, (OSError, configparser.NoSectionError)): - print("Adding sample versioneer config to setup.cfg", - file=sys.stderr) - with open(os.path.join(root, "setup.cfg"), "a") as f: - f.write(SAMPLE_CONFIG) - print(CONFIG_ERROR, file=sys.stderr) - return 1 - - print(" creating %s" % cfg.versionfile_source) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - - ipy = os.path.join(os.path.dirname(cfg.versionfile_source), - "__init__.py") - if os.path.exists(ipy): - try: - with open(ipy, "r") as f: - old = f.read() - except OSError: - old = "" - module = os.path.splitext(os.path.basename(cfg.versionfile_source))[0] - snippet = INIT_PY_SNIPPET.format(module) - if OLD_SNIPPET in old: - print(" replacing boilerplate in %s" % ipy) - with open(ipy, "w") as f: - f.write(old.replace(OLD_SNIPPET, snippet)) - elif snippet not in old: - print(" appending to %s" % ipy) - with open(ipy, "a") as f: - f.write(snippet) - else: - print(" %s unmodified" % ipy) - else: - print(" %s doesn't exist, ok" % ipy) - ipy = None - - # Make VCS-specific changes. For git, this means creating/changing - # .gitattributes to mark _version.py for export-subst keyword - # substitution. - do_vcs_install(cfg.versionfile_source, ipy) - return 0 - - -def scan_setup_py(): - """Validate the contents of setup.py against Versioneer's expectations.""" - found = set() - setters = False - errors = 0 - with open("setup.py", "r") as f: - for line in f.readlines(): - if "import versioneer" in line: - found.add("import") - if "versioneer.get_cmdclass()" in line: - found.add("cmdclass") - if "versioneer.get_version()" in line: - found.add("get_version") - if "versioneer.VCS" in line: - setters = True - if "versioneer.versionfile_source" in line: - setters = True - if len(found) != 3: - print("") - print("Your setup.py appears to be missing some important items") - print("(but I might be wrong). Please make sure it has something") - print("roughly like the following:") - print("") - print(" import versioneer") - print(" setup( version=versioneer.get_version(),") - print(" cmdclass=versioneer.get_cmdclass(), ...)") - print("") - errors += 1 - if setters: - print("You should remove lines like 'versioneer.VCS = ' and") - print("'versioneer.versionfile_source = ' . This configuration") - print("now lives in setup.cfg, and should be removed from setup.py") - print("") - errors += 1 - return errors - - -def setup_command(): - """Set up Versioneer and exit with appropriate error code.""" - errors = do_setup() - errors += scan_setup_py() - sys.exit(1 if errors else 0) - - -if __name__ == "__main__": - cmd = sys.argv[1] - if cmd == "setup": - setup_command() diff --git a/lerna.json b/lerna.json index 9f39b86ac..7a94afb14 100644 --- a/lerna.json +++ b/lerna.json @@ -1,4 +1,4 @@ { "packages": ["bids-validator", "bids-validator-web"], - "version": "1.12.1-dev.0" + "version": "1.13.2-dev.0" } diff --git a/package-lock.json b/package-lock.json index 92a6cae41..caeedbb1a 100644 --- a/package-lock.json +++ b/package-lock.json @@ -10,42 +10,42 @@ "bids-validator-web" ], "devDependencies": { - "@babel/core": "^7.22.9", - "@babel/preset-env": "^7.22.9", + "@babel/core": "^7.22.10", + "@babel/preset-env": "^7.22.10", "codecov": "^3.8.1", - "eslint": "^8.45.0", - "eslint-config-prettier": "^8.10.0", - "eslint-plugin-prettier": "^5.0.0", + "eslint": "^8.52.0", + "eslint-config-prettier": "^9.0.0", + "eslint-plugin-prettier": "^5.0.1", "husky": "^8.0.3", - "jest": "^29.6.2", - "jest-environment-jsdom": "^29.6.2", - "jest-environment-node": "^29.6.2", - "lerna": "^7.1.1", - "prettier": "^3.0.0", + "jest": "^29.7.0", + "jest-environment-jsdom": "^29.7.0", + "jest-environment-node": "^29.7.0", + "lerna": "^7.4.1", + "prettier": "^3.0.3", "pretty-quick": "^3.1.3" } }, "bids-validator": { - "version": "1.12.1-dev.0", + "version": "1.13.2-dev.0", "license": "MIT", "dependencies": { - "@aws-sdk/client-s3": "^3.9.0", + "@aws-sdk/client-s3": "^3.417.0", "ajv": "^6.5.2", "bytes": "^3.1.2", "colors": "^1.4.0", "cross-fetch": "^4.0.0", "date-fns": "^2.30.0", "events": "^3.3.0", - "exifreader": "^4.12.1", - "hed-validator": "^3.11.0", + "exifreader": "^4.13.2", + "hed-validator": "^3.12.0", "ignore": "^5.2.4", "is-utf8": "^0.2.1", - "jest": "^29.6.2", + "jest": "^29.7.0", "jshint": "^2.13.6", - "lerna": "^7.1.1", + "lerna": "^7.4.1", "lodash": "^4.17.21", "minimatch": "3.0.5", - "next": "13.4.12", + "next": "13.5.6", "nifti-js": "^1.0.1", "p-limit": "^2.1.0", "pako": "^1.0.6", @@ -65,12 +65,12 @@ "devDependencies": { "adm-zip": "", "chai": "", - "esbuild": "^0.18.17", + "esbuild": "^0.19.5", "esbuild-plugin-globals": "^0.2.0", "esbuild-runner": "^2.2.2", - "eslint": "^8.45.0", - "eslint-config-prettier": "^8.10.0", - "eslint-plugin-prettier": "^5.0.0", + "eslint": "8.52.0", + "eslint-config-prettier": "^9.0.0", + "eslint-plugin-prettier": "^5.0.1", "husky": "^8.0.3", "lockfile": "^1.0.4", "sync-request": "6.1.0" @@ -80,22 +80,206 @@ } }, "bids-validator-web": { - "version": "1.12.1-dev.0", + "version": "1.13.2-dev.0", "license": "MIT", "dependencies": { - "@babel/runtime": "^7.16.7", - "bootstrap": "^5.3.1", - "bowser": "^2.11.0", - "eslint-config-next": "^13.4.12", - "next": "^13.4.7", + "@babel/runtime": "^7.22.10", + "bootstrap": 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