pydra-compose-bidsapp 0.1.1__tar.gz

pydra_compose_bidsapp-0.1.1/.coveragerc

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+[run]
+branch = True
+omit =
+    */_version.py

pydra_compose_bidsapp-0.1.1/.flake8

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+
+[flake8]
+doctests = True
+exclude =
+    **/__init__.py
+    *build/
+    docs/sphinxext/
+    docs/tools/
+    docs/conf.py
+    docs/source/conf.py
+max-line-length = 88
+select = C,E,F,W,B,B950
+extend-ignore = E203,E501,E129,W503
+per-file-ignores =
+    __init__.py:F401,F403

pydra_compose_bidsapp-0.1.1/.github/workflows/ci-cd.yaml

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+#This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+# For deployment, it will be necessary to create a PyPI API token and store it as a secret
+# https://docs.github.com/en/actions/reference/encrypted-secrets
+
+name: CI/CD
+
+on:
+  push:
+    branches: [ main, develop ]
+    tags: [ '*' ]
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11', '3.12', '3.13']
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install build dependencies
+      run: |
+        python -m pip install --upgrade pip
+    - name: Install task package
+      run: |
+        pip install ".[test]"
+        python -c "import pydra.compose.bidsapp as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+    - name: Test with pytest
+      run: |
+        pytest -sv --doctest-modules pydra/compose/bidsapp \
+            --cov pydra.compose.bidsapp --cov-report xml
+    - uses: codecov/codecov-action@v3
+      if: ${{ always() }}
+
+
+  deploy:
+    needs: [test]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.9]
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+        fetch-depth: 0
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install build tools
+      run: python -m pip install build twine
+    - name: Build source and wheel distributions
+      run: python -m build
+    - name: Check distributions
+      run: twine check dist/*
+    - uses: actions/upload-artifact@v4
+      with:
+        name: distributions
+        path: dist/
+    # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets.
+    # Secrets are not accessible in the if: condition [0], so set an output variable [1]
+    # [0] https://github.community/t/16928
+    # [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter
+    - name: Check for PyPI token on tag
+      id: deployable
+      if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+      env:
+        PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}"
+      run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
+    - name: Upload to PyPI
+      if: steps.deployable.outputs.DEPLOY
+      uses: pypa/gh-action-pypi-publish@37f50c210e3d2f9450da2cd423303d6a14a6e29f  # v1.5.1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

pydra_compose_bidsapp-0.1.1/.gitignore

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+# 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/
+
+# Pycharm
+.idea
+
+# Vim
+.*.sw[op]
+
+# VS Code
+.vscode
+
+# Mac garbarge
+.DS_store
+
+# Generated files
+/pydra/compose/bidsapp/_version.py

pydra_compose_bidsapp-0.1.1/.pre-commit-config.yaml

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+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 22.12.0
+    hooks:
+    -   id: black

pydra_compose_bidsapp-0.1.1/LICENSE

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+   Copyright 2021 Nipype developers
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

pydra_compose_bidsapp-0.1.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: pydra-compose-bidsapp
+Version: 0.1.1
+Summary: Pydra compose package for wrapping BIDS Apps in Pydra tasks
+Author-email: "Thomas G. Close" <tom.g.close@gmail.com>
+Maintainer-email: "Thomas G. Close" <tom.g.close@gmail.com>
+License:    Copyright 2021 Nipype developers
+        
+           Licensed under the Apache License, Version 2.0 (the "License");
+           you may not use this file except in compliance with the License.
+           You may obtain a copy of the License at
+        
+               http://www.apache.org/licenses/LICENSE-2.0
+        
+           Unless required by applicable law or agreed to in writing, software
+           distributed under the License is distributed on an "AS IS" BASIS,
+           WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+           See the License for the specific language governing permissions and
+           limitations under the License.
+License-File: LICENSE
+Keywords: pydra
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.11
+Requires-Dist: docker>=7.0.0
+Requires-Dist: frametree-bids
+Requires-Dist: pydra>=1.0a
+Provides-Extra: dev
+Requires-Dist: black; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Provides-Extra: doc
+Requires-Dist: packaging; extra == 'doc'
+Requires-Dist: sphinx-rtd-theme; extra == 'doc'
+Requires-Dist: sphinx>=2.1.2; extra == 'doc'
+Requires-Dist: sphinxcontrib-apidoc~=0.3.0; extra == 'doc'
+Requires-Dist: sphinxcontrib-napoleon; extra == 'doc'
+Requires-Dist: sphinxcontrib-versioning; extra == 'doc'
+Provides-Extra: test
+Requires-Dist: codecov; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Requires-Dist: pytest-env; extra == 'test'
+Requires-Dist: pytest-rerunfailures; extra == 'test'
+Requires-Dist: pytest-xdist; extra == 'test'
+Requires-Dist: pytest>=4.4.0; extra == 'test'
+Description-Content-Type: text/markdown
+
+# Pydra-compose-bidsapp plugin
+
+Pydra-compose-bidsapp is a plugin package for the [Pydra dataflow engine](https://nipype.github.io/pydra),
+which adds the feature to wrap up [BIDS Apps](https://bids-apps.neuroimaging.io/) into
+Pydra task classes that take input files, stores them in a BIDS dataset created on the
+fly, runs the BIDS App on them, then extracts the files into the tasks outputs. It can
+be useful when running BIDS app on non-BIDS structured data (e.g. XNAT or LORIS repositories).
+
+## For developers
+
+Install repo in developer mode from the source directory. It is also useful to
+install pre-commit to take care of styling via [black](https://black.readthedocs.io/):
+
+```bash
+python3 -m pip install -e '.[dev]'
+pre-commit install
+```

pydra_compose_bidsapp-0.1.1/README.md

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+# Pydra-compose-bidsapp plugin
+
+Pydra-compose-bidsapp is a plugin package for the [Pydra dataflow engine](https://nipype.github.io/pydra),
+which adds the feature to wrap up [BIDS Apps](https://bids-apps.neuroimaging.io/) into
+Pydra task classes that take input files, stores them in a BIDS dataset created on the
+fly, runs the BIDS App on them, then extracts the files into the tasks outputs. It can
+be useful when running BIDS app on non-BIDS structured data (e.g. XNAT or LORIS repositories).
+
+## For developers
+
+Install repo in developer mode from the source directory. It is also useful to
+install pre-commit to take care of styling via [black](https://black.readthedocs.io/):
+
+```bash
+python3 -m pip install -e '.[dev]'
+pre-commit install
+```

pydra_compose_bidsapp-0.1.1/codecov.yml

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+coverage:
+  range: "50...100"
+  ignore:          # files and folders that will be removed during processing
+    - "**/tests"
+    - "**/_version.py"
+  status:
+    project:
+      default:
+        threshold: 1
+    patch:
+      default:
+        target: 80

pydra_compose_bidsapp-0.1.1/conftest.py

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+import os
+import pytest
+import requests
+from warnings import warn
+import typing as ty
+from tempfile import mkdtemp
+from pathlib import Path
+import docker
+from fileformats.medimage import NiftiGzX
+
+PKG_DIR = Path(__file__).parent
+
+
+@pytest.fixture(scope="session")
+def build_cache_dir() -> Path:
+    # build_cache_dir = Path.home() / '.frametree-test-build-cache'
+    # if build_cache_dir.exists():
+    #     shutil.rmtree(build_cache_dir)
+    # build_cache_dir.mkdir()
+    return Path(mkdtemp())
+    # return build_cache_dir
+
+
+@pytest.fixture
+def work_dir() -> Path:  # type: ignore[misc]
+    # work_dir = Path.home() / '.frametree-tests'
+    # work_dir.mkdir(exist_ok=True)
+    # return work_dir
+    work_dir = mkdtemp()
+    yield Path(work_dir)
+    # shutil.rmtree(work_dir)
+
+
+@pytest.fixture(scope="session")
+def pkg_dir() -> Path:
+    return PKG_DIR
+
+
+@pytest.fixture(scope="session")
+def nifti_sample_dir(pkg_dir):
+    return pkg_dir / "test-data" / "nifti"
+
+
+# FIXME: should be converted to python script to be Windows compatible
+@pytest.fixture(scope="session")
+def mock_bids_app_script():
+    file_tests = ""
+    for inpt_path, datatype in [
+        ("anat/T1w", NiftiGzX),
+        ("anat/T2w", NiftiGzX),
+        ("dwi/dwi", NiftiGzX),
+    ]:
+        subdir, suffix = inpt_path.split("/")
+        fpath = (
+            f"$BIDS_DATASET/sub-${{SUBJ_ID}}/{subdir}/"
+            f"sub-${{SUBJ_ID}}_{suffix}{datatype.ext}"
+        )
+        file_tests += f"""
+        if [ ! -f {fpath} ]; then
+            echo "Did not find {suffix} file at {fpath}"
+            exit 1;
+        fi
+        """
+
+    return f"""#!/bin/sh
+BIDS_DATASET=$1
+OUTPUTS_DIR=$2
+SUBJ_ID=$5
+{file_tests}
+# Write mock output files to 'derivatives' Directory
+mkdir -p $OUTPUTS_DIR
+echo 'file1' > $OUTPUTS_DIR/sub-${{SUBJ_ID}}_file1.txt
+echo 'file2' > $OUTPUTS_DIR/sub-${{SUBJ_ID}}_file2.txt
+"""
+
+
+# For debugging in IDE's don't catch raised exceptions and let the IDE
+# break at it
+if os.getenv("_PYTEST_RAISE", "0") != "0":
+
+    @pytest.hookimpl(tryfirst=True)
+    def pytest_exception_interact(call: pytest.CallInfo[ty.Any]) -> None:
+        if call.excinfo is not None:
+            raise call.excinfo.value
+
+    @pytest.hookimpl(tryfirst=True)
+    def pytest_internalerror(excinfo: pytest.ExceptionInfo[BaseException]) -> None:
+        raise excinfo.value
+
+    CATCH_CLI_EXCEPTIONS = False
+else:
+    CATCH_CLI_EXCEPTIONS = True
+
+
+@pytest.fixture(scope="session")
+def bids_validator_app_image(
+    bids_validator_app_script, bids_validator_docker, build_cache_dir
+):
+    return build_app_image(
+        BIDS_VALIDATOR_APP_IMAGE,
+        bids_validator_app_script,
+        build_cache_dir,
+        base_image=bids_validator_docker,
+    )
+
+
+def build_app_image(tag_name, script, build_cache_dir, base_image):
+    dc = docker.from_env()
+
+    # Create executable that runs validator then produces some mock output
+    # files
+    build_dir = build_cache_dir / tag_name.replace(":", "__i__")
+    build_dir.mkdir()
+    launch_sh = build_dir / "launch.sh"
+    with open(launch_sh, "w") as f:
+        f.write(script)
+
+    # Build mock BIDS app image
+    with open(build_dir / "Dockerfile", "w") as f:
+        f.write(
+            f"""FROM {base_image}
+ADD ./launch.sh /launch.sh
+RUN chmod +x /launch.sh
+ENTRYPOINT ["/launch.sh"]"""
+        )
+
+    dc.images.build(path=str(build_dir), tag=tag_name)
+
+    return tag_name
+
+
+@pytest.fixture(scope="session")
+def bids_command_spec(mock_bids_app_executable):
+    inputs = {
+        "T1w": {
+            "configuration": {
+                "path": "anat/T1w",
+            },
+            "datatype": "medimage:NiftiGzX",
+            "help": "T1-weighted image",
+        },
+        "T2w": {
+            "configuration": {
+                "path": "anat/T2w",
+            },
+            "datatype": "medimage:NiftiGzX",
+            "help": "T2-weighted image",
+        },
+        "DWI": {
+            "configuration": {
+                "path": "dwi/dwi",
+            },
+            "datatype": "medimage:NiftiGzXBvec",
+            "help": "DWI-weighted image",
+        },
+    }
+
+    outputs = {
+        "file1": {
+            "configuration": {
+                "path": "file1",
+            },
+            "datatype": "common:Text",
+            "help": "an output file",
+        },
+        "file2": {
+            "configuration": {
+                "path": "file2",
+            },
+            "datatype": "common:Text",
+            "help": "another output file",
+        },
+    }
+
+    return {
+        "task": "frametree.bids.tasks:bids_app",
+        "inputs": inputs,
+        "outputs": outputs,
+        "row_frequency": "session",
+        "configuration": {
+            "inputs": inputs,
+            "outputs": outputs,
+            "executable": str(mock_bids_app_executable),
+        },
+    }
+
+
+@pytest.fixture(scope="session")
+def bids_validator_docker():
+    dc = docker.from_env()
+    try:
+        dc.images.pull(BIDS_VALIDATOR_DOCKER)
+    except requests.exceptions.HTTPError:
+        warn("No internet connection, so couldn't download latest BIDS validator")
+    return BIDS_VALIDATOR_DOCKER
+
+
+@pytest.fixture(scope="session")
+def bids_validator_app_script():
+    return f"""#!/bin/sh
+# Echo inputs to get rid of any quotes
+BIDS_DATASET=$(echo $1)
+OUTPUTS_DIR=$(echo $2)
+SUBJ_ID=$5
+# Run BIDS validator to check whether BIDS dataset is created properly
+output=$(/usr/local/bin/bids-validator "$BIDS_DATASET")
+if [[ "$output" != *"{SUCCESS_STR}"* ]]; then
+    echo "BIDS validation was not successful, exiting:\n "
+    echo $output
+    exit 1;
+fi
+# Write mock output files to 'derivatives' Directory
+mkdir -p $OUTPUTS_DIR
+echo 'file1' > $OUTPUTS_DIR/sub-${{SUBJ_ID}}_file1.txt
+echo 'file2' > $OUTPUTS_DIR/sub-${{SUBJ_ID}}_file2.txt
+"""
+
+
+BIDS_VALIDATOR_DOCKER = "bids/validator:latest"
+SUCCESS_STR = "This dataset appears to be BIDS compatible"
+BIDS_VALIDATOR_APP_IMAGE = "pydra-compose-bidsapp-validator"

pydra_compose_bidsapp-0.1.1/docs/Makefile

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+# 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)

pydra_compose_bidsapp-0.1.1/docs/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "pydra-compose-bidsapp"
+copyright = "2020, Xihe Xie"
+author = "Xihe Xie"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = []
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "alabaster"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]

pydra_compose_bidsapp-0.1.1/docs/index.rst

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+Welcome to pydra-compose-bidsapp's documentation!
+==================================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`