First commit

.bumpversion.cfg

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+[bumpversion]
+current_version = 1.0.0
+commit = True
+tag = True
+tag_name = {new_version}
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:src/d2b_dcm2niix.py]
+search = __version__ = "{current_version}"
+replace = __version__ = "{new_version}"

.flake8

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+[flake8]
+min_python_version = 3.8.1

.github/workflows/lint.yaml

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+name: Code Style
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    name: "Lint Code Base"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install poetry==1.1.8
+          BLACK_VERSION=$(poetry show black | grep version | rev | cut -d " "  -f 1 | rev)
+          FLAKE8_VERSION=$(poetry show flake8 | grep version | rev | cut -d " "  -f 1 | rev)
+          pip install "black==${BLACK_VERSION}" "flake8==${FLAKE8_VERSION}"
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          flake8 . --count --max-complexity=10 --max-line-length=88 --statistics
+      - name: Check with black
+        run: |
+          black . --check --diff
+      - name: Run GitHub super-linter
+        uses: docker://github/super-linter:v3
+        env:
+          VALIDATE_ALL_CODEBASE: true
+          VALIDATE_YAML: true
+          VALIDATE_JSON: true
+          VALIDATE_MD: true
+          VALIDATE_BASH: true
+          VALIDATE_DOCKER: true
+          VALIDATE_GO: true
+          VALIDATE_ENV: true

.github/workflows/publish.yaml

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+name: Publish to PyPI
+
+on:
+  release:
+    types:
+      - created
+
+jobs:
+  wheels:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.x
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install poetry==1.1.8
+      - name: Build and Publish
+        run: |
+          poetry config pypi-token.pypi "$PYPI_TOKEN"
+          poetry publish --build
+        env:
+          PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}

.github/workflows/type-check.yaml

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+name: Type Check
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    name: "Type Check Code Base"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: "Set up Python 3.8"
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: "Install Dependencies"
+        run: |
+          python -m pip install --upgrade pip
+          pip install poetry
+          poetry config virtualenvs.create false
+          poetry install --no-interaction --no-dev
+      - name: "Set up Node.js"
+        uses: actions/setup-node@v1
+        with:
+          node-version: "12.x"
+      - name: "Install Pyright"
+        run: |
+          npm install -g pyright
+      - name: "Type Check with Pyright"
+        run: |
+          pyright src

.gitignore

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+tmp*
+
+
+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
+
+### Python ###
+# 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/
+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/
+cover/
+
+# 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
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# End of https://www.toptal.com/developers/gitignore/api/python

.pre-commit-config.yaml

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+default_language_version:
+  python: python3.8
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-json
+      - id: check-toml
+      - id: check-vcs-permalinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: name-tests-test
+      - id: requirements-txt-fixer
+  - repo: https://github.com/psf/black
+    rev: 21.5b2
+    hooks:
+      - id: black
+  - repo: https://github.com/PyCQA/flake8
+    rev: 3.9.2
+    hooks:
+      - id: flake8
+        additional_dependencies: ["flake8-typing-imports==1.10.1"]
+        args:
+          - "--max-complexity=10"
+          - "--max-line-length=88"
+  - repo: https://github.com/asottile/reorder_python_imports
+    rev: v2.5.0
+    hooks:
+      - id: reorder-python-imports
+        args: [--py3-plus]
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.19.0
+    hooks:
+      - id: pyupgrade
+        args: [--py36-plus]
+  - repo: https://github.com/asottile/add-trailing-comma
+    rev: v2.1.0
+    hooks:
+      - id: add-trailing-comma
+        args: [--py36-plus]
+  - repo: https://github.com/asottile/setup-cfg-fmt
+    rev: v1.17.0
+    hooks:
+      - id: setup-cfg-fmt
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.8.0
+    hooks:
+      - id: python-check-blanket-noqa
+      - id: python-use-type-annotations
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v0.812
+  #   hooks:
+  #     - id: mypy

README.md

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+# d2b-dcm2niix
+
+Dcm2niix plugin for the d2b package
+
+[![PyPI Version](https://img.shields.io/pypi/v/d2b-dcm2niix.svg)](https://pypi.org/project/d2b-dcm2niix/)
+
+## Installation
+
+```bash
+pip install d2b-dcm2niix
+```
+
+## Usage
+
+After installation the `d2b run` command should have additional `dcm2niix`-specific flags:
+
+```text
+$ d2b run --help
+usage: d2b run [-h] -c CONFIG_FILE -p PARTICIPANT -o OUT_DIR [-s SESSION] [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [--no-dcm2niix | --dcm2niix | --force-dcm2niix] in_dir [in_dir ...]
+
+Organize data in the BIDS format
+
+positional arguments:
+  in_dir                Directory(ies) containing files to organize
+
+required arguments:
+  -c CONFIG_FILE, --config CONFIG_FILE
+                        JSON configuration file (see example/config.json)
+  -p PARTICIPANT, --participant PARTICIPANT
+                        Participant ID
+  -o OUT_DIR, --out-dir OUT_DIR
+                        Output BIDS directory
+  --no-dcm2niix         Don't run dcm2niix on the input directories. (This is the default)
+  --dcm2niix            Run dcm2niix on each of the input directories before organization code executes. dcm2niix execution will be skipped for directories for which converted results from a previous run are found.
+  --force-dcm2niix      Run dcm2niix on each of the input directories before organization code executes. Previous dcm2niix results will be overwritten
+
+optional arguments:
+  -s SESSION, --session SESSION
+                        Session ID
+  -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
+                        Set logging level
+```
+
+Specifically, the following new (mutually exclusive) options are available:
+
+- `--no-dcm2niix`: This is the default behaviour (i.e. the behaviour of the `d2b run` command if none of the dcm2niix flags are set)
+
+- `--dcm2niix`: This will try to run `dcm2niix` on (copies of) each of the input directories prior to proceeding with BIDS-ification. **NOTE:** If any NIfTI files are found from a previous `d2b run --dcm2niix ...` run, then dcm2niix will not be invoked on that (copy of that) specific input directory.
+
+- `--force-dcm2niix`: This will run `dcm2niix` on (copies of) each of the input directories _always_, regardless of files from previous `d2b run` runs.
+
+Also, there should be a new subcommand `d2b dcm2niix` available:
+
+```text
+$ d2b dcm2niix --help
+usage: d2b dcm2niix [-h] in_dir [in_dir ...] out_dir
+
+Run dcm2niix with the options used by d2b
+
+positional arguments:
+  in_dir      DICOM directory(ies)
+  out_dir     Output BIDS directory
+
+optional arguments:
+  -h, --help  show this help message and exit
+```
+
+This command is the equivalent of `dcm2bids`'s `dcm2bids_helper` command. In particular it's serves as a way to run dcm2niix in the exact same way that `d2b run --[force-]dcm2niix` would run the command (i.e. potentially useful to see what the resulting sidecars/filenames would look like).