forbids 0.0.2__tar.gz

forbids-0.0.2/.devcontainer/Dockerfile

@@ -0,0 +1,12 @@
+FROM mcr.microsoft.com/devcontainers/python:3
+
+RUN python -m pip install --upgrade pip \
+    && python -m pip install 'flit>=3.8.0'
+
+ENV FLIT_ROOT_INSTALL=1
+
+COPY pyproject.toml .
+RUN touch README.md \
+    && mkdir -p src/python_package \
+    && python -m flit install --only-deps --deps develop \
+    && rm -r pyproject.toml README.md src

forbids-0.0.2/.devcontainer/devcontainer.json

@@ -0,0 +1,44 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.222.0/containers/python-3-miniconda
+{
+	"name": "Python Environment",
+	"build": {
+		"dockerfile": "Dockerfile",
+		"context": ".."
+	},
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"editorconfig.editorconfig",
+				"github.vscode-pull-request-github",
+				"ms-azuretools.vscode-docker",
+				"ms-python.python",
+				"ms-python.vscode-pylance",
+				"ms-python.pylint",
+				"ms-python.isort",
+				"ms-python.flake8",
+				"ms-python.black-formatter",
+				"ms-vsliveshare.vsliveshare",
+				"ryanluker.vscode-coverage-gutters",
+				"bungcip.better-toml",
+				"GitHub.copilot"
+			],
+			"settings": {
+				"python.defaultInterpreterPath": "/usr/local/bin/python",
+				"black-formatter.path": [
+					"/usr/local/py-utils/bin/black"
+				],
+				"pylint.path": [
+					"/usr/local/py-utils/bin/pylint"
+				],
+				"flake8.path": [
+					"/usr/local/py-utils/bin/flake8"
+				],
+				"isort.path": [
+					"/usr/local/py-utils/bin/isort"
+				]
+			}
+		}
+	},
+	"onCreateCommand": "pre-commit install-hooks"
+}

forbids-0.0.2/.github/dependabot.yml

@@ -0,0 +1,22 @@
+version: 2
+updates:
+- package-ecosystem: pip
+  directory: "/"
+  schedule:
+    interval: daily
+    time: "13:00"
+  open-pull-requests-limit: 10
+  reviewers:
+  - bpinsard
+  allow:
+  - dependency-type: direct
+  - dependency-type: indirect
+  commit-message:
+    prefix: "fix: "
+- package-ecosystem: "github-actions"
+  directory: "/"
+  schedule:
+    interval: daily
+    time: "13:00"
+  commit-message:
+    prefix: "fix: "

forbids-0.0.2/.github/template-sync.yml

@@ -0,0 +1,21 @@
+files:
+  - ".gitignore"  # include
+  - ".github"
+  - ".vscode"
+  - "tests/conftest.py"
+  - ".flake8"
+  - ".pre-commit-config.yml"
+  - ".pypirc"
+  - "docs"
+  - "src/README.md"
+  - "CODE_OF_CONDUCT.md"
+  - "LICENSE"
+  - "README.md"
+  - "SECURITY.md"
+  - "SUPPORT.md"
+  - "pyproject.toml"
+
+  - "!.github/workflows/template-sync.yml"
+  - "!.github/template-sync.yml"
+  - "!src/python_project"
+  - "!tests/test_methods.py"

forbids-0.0.2/.github/workflows/CI.yml

@@ -0,0 +1,21 @@
+name: Python CI
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  release:
+    types: [created]
+  workflow_dispatch:
+
+jobs:
+  validation:
+    uses: microsoft/action-python/.github/workflows/validation.yml@0.7.3
+    with:
+      workdir: '.'
+
+  publish:
+    uses: microsoft/action-python/.github/workflows/publish.yml@0.7.3
+    secrets:
+      PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      TEST_PYPI_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD  }}

forbids-0.0.2/.github/workflows/publish.yml

@@ -0,0 +1,10 @@
+name: Python Publish Workflow
+on:
+  workflow_call:
+
+jobs:
+  publish:
+    uses: microsoft/action-python/.github/workflows/publish.yml@0.7.3
+    secrets:
+      PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      TEST_PYPI_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD  }}

forbids-0.0.2/.github/workflows/schedule-update-actions.yml

@@ -0,0 +1,25 @@
+name: GitHub Actions Version Updater
+
+# Controls when the action will run.
+on:
+  workflow_dispatch:
+  schedule:
+    # Automatically run on every Sunday
+    - cron:  '0 0 * * 0'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4.1.7
+        with:
+          # [Required] Access token with `workflow` scope.
+          token: ${{ secrets.PAT }}
+
+      - name: Run GitHub Actions Version Updater
+        uses: saadmk11/github-actions-version-updater@v0.8.1
+        with:
+          # [Required] Access token with `workflow` scope.
+          token: ${{ secrets.PAT }}
+          pull_request_title: "ci: Update GitHub Actions to Latest Version"

forbids-0.0.2/.github/workflows/semantic-pr-check.yml

@@ -0,0 +1,17 @@
+name: "Semantic PR Check"
+
+on:
+  pull_request_target:
+    types:
+      - opened
+      - edited
+      - synchronize
+
+jobs:
+  main:
+    name: Validate PR title
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/action-semantic-pull-request@v5.5.3
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

forbids-0.0.2/.github/workflows/sphinx.yml

@@ -0,0 +1,18 @@
+name: Deploy Sphinx documentation to Pages
+
+on:
+  push:
+    branches: [main] # branch to trigger deployment
+
+jobs:
+  pages:
+    runs-on: ubuntu-20.04
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    permissions:
+      pages: write
+      id-token: write
+    steps:
+    - id: deployment
+      uses: sphinx-notes/pages@v3

forbids-0.0.2/.github/workflows/template-sync.yml

@@ -0,0 +1,12 @@
+name: Template Sync
+on:
+  workflow_dispatch:
+jobs:
+  sync:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4.1.7 # important!
+      - uses: euphoricsystems/action-sync-template-repository@v2.5.1
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          dry-run: true

forbids-0.0.2/.gitignore

@@ -0,0 +1,132 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+
+data-multi-subject

forbids-0.0.2/.pre-commit-config.yaml

@@ -0,0 +1,60 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["-a", "from __future__ import annotations"]
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.31.0
+    hooks:
+      - id: pyupgrade
+        args: [--py37-plus]
+
+  - repo: https://github.com/hadialqattan/pycln
+    rev: v1.2.5
+    hooks:
+      - id: pycln
+        args: [--config=pyproject.toml]
+        stages: [manual]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.1.0
+    hooks:
+      - id: codespell
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.9.0
+    hooks:
+      - id: python-check-blanket-noqa
+      - id: python-check-blanket-type-ignore
+      - id: python-no-log-warn
+      - id: python-no-eval
+      - id: python-use-type-annotations
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/mgedmin/check-manifest
+    rev: "0.47"
+    hooks:
+      - id: check-manifest
+        stages: [manual]

forbids-0.0.2/.pypirc

@@ -0,0 +1,10 @@
+[distutils]
+index-servers =
+    pypi
+    testpypi
+
+[pypi]
+repository = https://upload.pypi.org/legacy/
+
+[testpypi]
+repository = https://test.pypi.org/legacy/

forbids-0.0.2/.vscode/launch.json

@@ -0,0 +1,19 @@
+{
+    "version": "0.1.0",
+    "configurations": [
+        {
+            "name": "Python: Debug Tests",
+            "type": "python",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": [
+                "debug-test"
+            ],
+            "console": "integratedTerminal",
+            "justMyCode": false,
+            "env": {
+                "PYTEST_ADDOPTS": "--no-cov -n0 --dist no"
+            }
+        }
+    ]
+}

forbids-0.0.2/.vscode/settings.json

@@ -0,0 +1,29 @@
+{
+    "editor.formatOnSave": true,
+    "editor.formatOnPaste": true,
+    "files.trimTrailingWhitespace": true,
+    "files.autoSave": "onFocusChange",
+    "git.autofetch": true,
+    "[jsonc]": {
+        "editor.defaultFormatter": "vscode.json-language-features"
+    },
+    "[python]": {
+        "editor.defaultFormatter": "ms-python.black-formatter"
+    },
+    "python.defaultInterpreterPath": "/usr/local/bin/python",
+    "python.formatting.provider": "black",
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true,
+    "pylint.args": [
+        "--rcfile=pyproject.toml"
+    ],
+    "black-formatter.args": [
+        "--config=pyproject.toml"
+    ],
+    "flake8.args": [
+        "--toml-config=pyproject.toml"
+    ],
+    "isort.args": [
+        "--settings-path=pyproject.toml"
+    ]
+}

forbids-0.0.2/CODE_OF_CONDUCT.md

@@ -0,0 +1,9 @@
+# Microsoft Open Source Code of Conduct
+
+This project has adopted the [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/).
+
+Resources:
+
+- [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/)
+- [Microsoft Code of Conduct FAQ](https://opensource.microsoft.com/codeofconduct/faq/)
+- Contact [opencode@microsoft.com](mailto:opencode@microsoft.com) with questions or concerns

forbids-0.0.2/LICENSE

@@ -0,0 +1,21 @@
+    MIT License
+
+    Copyright (c) Microsoft Corporation.
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+
+    The above copyright notice and this permission notice shall be included in all
+    copies or substantial portions of the Software.
+
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+    SOFTWARE

forbids-0.0.2/PKG-INFO

@@ -0,0 +1,56 @@
+Metadata-Version: 2.4
+Name: forbids
+Version: 0.0.2
+Summary: forBIDS - BIDS protocol compliance validation
+Author-email: Basile Pinsard <basile.pinsard@gmail.com>
+Requires-Python: >=3.11.0
+Description-Content-Type: text/markdown
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+License-File: LICENSE
+Requires-Dist: pybids
+Requires-Dist: apischema
+Requires-Dist: openapi-schema-validator
+Requires-Dist: coloredlogs
+Requires-Dist: pyspark>=3.0.0 ; extra == "spark"
+Requires-Dist: bandit[toml]==1.7.10 ; extra == "test"
+Requires-Dist: black==24.8.0 ; extra == "test"
+Requires-Dist: check-manifest==0.49 ; extra == "test"
+Requires-Dist: flake8-bugbear==24.8.19 ; extra == "test"
+Requires-Dist: flake8-docstrings ; extra == "test"
+Requires-Dist: flake8-formatter_junit_xml ; extra == "test"
+Requires-Dist: flake8 ; extra == "test"
+Requires-Dist: flake8-pyproject ; extra == "test"
+Requires-Dist: pre-commit==3.8.0 ; extra == "test"
+Requires-Dist: pylint==3.3.1 ; extra == "test"
+Requires-Dist: pylint_junit ; extra == "test"
+Requires-Dist: pytest-cov==5.0.0 ; extra == "test"
+Requires-Dist: pytest-mock<3.14.1 ; extra == "test"
+Requires-Dist: pytest-runner ; extra == "test"
+Requires-Dist: pytest==8.3.3 ; extra == "test"
+Requires-Dist: pytest-github-actions-annotate-failures ; extra == "test"
+Requires-Dist: shellcheck-py==0.10.0.1 ; extra == "test"
+Project-URL: Documentation, https://github.com/UNFMontreal/forbids
+Project-URL: Source, https://github.com/UNFMontreal/forbids
+Project-URL: Tracker, https://github.com/UNFMontreal/forbids/issues
+Provides-Extra: spark
+Provides-Extra: test
+
+# ![forBIDS logo](docs/static/forbids_logo.png) forBIDS: a protocol compliance check
+
+forBIDS aims to be a tool for BIDS that forbids deviation from a established acquisition protocol.
+
+It is meant to be ran continuously on session newly converted to BIDS, as a validation before being merged into a dataset.
+
+It aims to check that all planned sequences have been acquired (allowing optional ones), and check that a configured set of sequence parameters match expected values.
+It is designed for multi-centric/multi-vendor studies: the sequence parameters constraint can be set conditional to Manufacter/Model/Instrument/SoftwareVersion.
+
+
+## design
+
+- `forbids init <bids_path>` : create a `.forbids` folder that contains a BIDS-like structure with json schemas for each series in a BIDS dataset with a set of sessions from each scanner.
+- `forbids validate <bids_path> --participant-label <sub> [--session-label <ses>]` : validate the subject/session against the schema found in `.forbids` by validating all schema files against the subject/session BIDS files and checking for missing or extra/unwanted BIDS files.
+

forbids-0.0.2/README.md

@@ -0,0 +1,14 @@
+# ![forBIDS logo](docs/static/forbids_logo.png) forBIDS: a protocol compliance check
+
+forBIDS aims to be a tool for BIDS that forbids deviation from a established acquisition protocol.
+
+It is meant to be ran continuously on session newly converted to BIDS, as a validation before being merged into a dataset.
+
+It aims to check that all planned sequences have been acquired (allowing optional ones), and check that a configured set of sequence parameters match expected values.
+It is designed for multi-centric/multi-vendor studies: the sequence parameters constraint can be set conditional to Manufacter/Model/Instrument/SoftwareVersion.
+
+
+## design
+
+- `forbids init <bids_path>` : create a `.forbids` folder that contains a BIDS-like structure with json schemas for each series in a BIDS dataset with a set of sessions from each scanner.
+- `forbids validate <bids_path> --participant-label <sub> [--session-label <ses>]` : validate the subject/session against the schema found in `.forbids` by validating all schema files against the subject/session BIDS files and checking for missing or extra/unwanted BIDS files.

forbids-0.0.2/SECURITY.md

@@ -0,0 +1,41 @@
+<!-- BEGIN MICROSOFT SECURITY.MD V0.0.5 BLOCK -->
+
+## Security
+
+Microsoft takes the security of our software products and services seriously, which includes all source code repositories managed through our GitHub organizations, which include [Microsoft](https://github.com/Microsoft), [Azure](https://github.com/Azure), [DotNet](https://github.com/dotnet), [AspNet](https://github.com/aspnet), [Xamarin](https://github.com/xamarin), and [our GitHub organizations](https://opensource.microsoft.com/).
+
+If you believe you have found a security vulnerability in any Microsoft-owned repository that meets [Microsoft's definition of a security vulnerability](https://docs.microsoft.com/en-us/previous-versions/tn-archive/cc751383(v=technet.10)), please report it to us as described below.
+
+## Reporting Security Issues
+
+**Please do not report security vulnerabilities through public GitHub issues.**
+
+Instead, please report them to the Microsoft Security Response Center (MSRC) at [https://msrc.microsoft.com/create-report](https://msrc.microsoft.com/create-report).
+
+If you prefer to submit without logging in, send email to [secure@microsoft.com](mailto:secure@microsoft.com).  If possible, encrypt your message with our PGP key; please download it from the [Microsoft Security Response Center PGP Key page](https://www.microsoft.com/en-us/msrc/pgp-key-msrc).
+
+You should receive a response within 24 hours. If for some reason you do not, please follow up via email to ensure we received your original message. Additional information can be found at [microsoft.com/msrc](https://www.microsoft.com/msrc).
+
+Please include the requested information listed below (as much as you can provide) to help us better understand the nature and scope of the possible issue:
+
+  * Type of issue (e.g. buffer overflow, SQL injection, cross-site scripting, etc.)
+  * Full paths of source file(s) related to the manifestation of the issue
+  * The location of the affected source code (tag/branch/commit or direct URL)
+  * Any special configuration required to reproduce the issue
+  * Step-by-step instructions to reproduce the issue
+  * Proof-of-concept or exploit code (if possible)
+  * Impact of the issue, including how an attacker might exploit the issue
+
+This information will help us triage your report more quickly.
+
+If you are reporting for a bug bounty, more complete reports can contribute to a higher bounty award. Please visit our [Microsoft Bug Bounty Program](https://microsoft.com/msrc/bounty) page for more details about our active programs.
+
+## Preferred Languages
+
+We prefer all communications to be in English.
+
+## Policy
+
+Microsoft follows the principle of [Coordinated Vulnerability Disclosure](https://www.microsoft.com/en-us/msrc/cvd).
+
+<!-- END MICROSOFT SECURITY.MD BLOCK -->

forbids-0.0.2/SUPPORT.md

@@ -0,0 +1,25 @@
+# TODO: The maintainer of this repo has not yet edited this file
+
+**REPO OWNER**: Do you want Customer Service & Support (CSS) support for this product/project?
+
+- **No CSS support:** Fill out this template with information about how to file issues and get help.
+- **Yes CSS support:** Fill out an intake form at [aka.ms/spot](https://aka.ms/spot). CSS will work with/help you to determine next steps. More details also available at [aka.ms/onboardsupport](https://aka.ms/onboardsupport).
+- **Not sure?** Fill out a SPOT intake as though the answer were "Yes". CSS will help you decide.
+
+*Then remove this first heading from this SUPPORT.MD file before publishing your repo.*
+
+# Support
+
+## How to file issues and get help
+
+This project uses GitHub Issues to track bugs and feature requests. Please search the existing
+issues before filing new issues to avoid duplicates.  For new issues, file your bug or
+feature request as a new Issue.
+
+For help and questions about using this project, please **REPO MAINTAINER: INSERT INSTRUCTIONS HERE
+FOR HOW TO ENGAGE REPO OWNERS OR COMMUNITY FOR HELP. COULD BE A STACK OVERFLOW TAG OR OTHER
+CHANNEL. WHERE WILL YOU HELP PEOPLE?**.
+
+## Microsoft Support Policy
+
+Support for this **PROJECT or PRODUCT** is limited to the resources listed above.

forbids-0.0.2/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)