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‎.github/workflows/ci-tests.yml‎

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name: Continous integration tests
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on:
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push:
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branches: [ main ]
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pull_request:
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branches: [ main ]
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workflow_dispatch:
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env:
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singularity_version: 3.6.4
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jobs:
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tox:
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name: CI tests via Tox
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runs-on: ubuntu-20.04
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strategy:
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matrix:
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py-ver-major: [3]
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py-ver-minor: [6, 7, 8, 9]
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step: [lint, unit, mypy]
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env:
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py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }}
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TOXENV: ${{ format('py{0}{1}-{2}', matrix.py-ver-major, matrix.py-ver-minor, matrix.step) }}
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: Set up Singularity
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if: ${{ matrix.step == 'unit' || matrix.step == 'mypy' }}
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uses: eWaterCycle/setup-singularity@v6
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with:
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singularity-version: ${{ env.singularity_version }}
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- name: Give the test runner user a name to make provenance happy.
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if: ${{ matrix.step == 'unit' || matrix.step == 'mypy' }}
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run: sudo usermod -c 'CI Runner' $(whoami)
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: ${{ env.py-semver }}
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- name: Cache for pip
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uses: actions/cache@v2
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ matrix.step }}-${{ hashFiles('requirements.txt', 'tox.ini') }}
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- name: Upgrade setuptools and install tox
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run: |
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pip install -U pip setuptools wheel
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pip install tox tox-gh-actions
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- name: MyPy cache
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if: ${{ matrix.step == 'mypy' }}
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uses: actions/cache@v2
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with:
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path: .mypy_cache/${{ env.py-semver }}
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key: mypy-${{ env.py-semver }}
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- name: Test with tox
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run: tox
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- name: Upload coverage to Codecov
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if: ${{ matrix.step == 'unit' }}
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uses: codecov/codecov-action@v1
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with:
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fail_ci_if_error: true
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tox-style:
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name: CI linters via Tox
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runs-on: ubuntu-20.04
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strategy:
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matrix:
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step: [lint-readme, pydocstyle]
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env:
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py-semver: 3.9
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TOXENV: ${{ format('py39-{0}', matrix.step) }}
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: ${{ env.py-semver }}
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- name: Cache for pip
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uses: actions/cache@v2
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ matrix.step }}-${{ hashFiles('requirements.txt') }}
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- name: Upgrade setuptools and install tox
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run: |
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pip install -U pip setuptools wheel
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pip install tox tox-gh-actions
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- if: ${{ matrix.step == 'pydocstyle' && github.event_name == 'pull_request'}}
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name: Create local branch for diff-quality for PRs
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run: git branch ${{github.base_ref}} origin/${{github.base_ref}}
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- name: Test with tox
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run: tox
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release_test:
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name: cwl-utils release test
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runs-on: ubuntu-20.04
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steps:
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- uses: actions/checkout@v2
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- name: Set up Singularity
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uses: eWaterCycle/setup-singularity@v6
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with:
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singularity-version: ${{ env.singularity_version }}
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: 3.9
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- name: Give the test runner user a name to make provenance happy.
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run: sudo usermod -c 'CI Runner' $(whoami)
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- name: Cache for pip
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uses: actions/cache@v2
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-release-${{ hashFiles('requirements.txt', 'test-requirements.txt') }}
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- name: Install packages
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run: |
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pip install -U pip setuptools wheel
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pip install virtualenv
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- name: Release test
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env:
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RELEASE_SKIP: head
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run: ./release-test.sh
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- name: Publish package
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}
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packages_dir: testenv3_3/dist

‎.travis.singularity_key.txt‎

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‎.travis.yml‎

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‎Makefile‎

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@@ -69,6 +69,10 @@ dist: dist/${MODULE}-$(VERSION).tar.gz
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dist/${MODULE}-$(VERSION).tar.gz: $(SOURCES)
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./setup.py sdist bdist_wheel
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## docs : make the docs
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docs: FORCE
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cd docs && $(MAKE) html
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## clean : clean up all temporary / machine-generated files
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clean: FORCE
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rm -f ${MODILE}/*.pyc tests/*.pyc
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ln -s $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))') \
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typeshed/ruamel/ ; \
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fi # if minimally required ruamel.yaml version is 0.15.99 or greater, than the above can be removed
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MYPYPATH=$$MYPYPATH:typeshed/ mypy --disallow-untyped-calls \
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--warn-redundant-casts \
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$^
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mypyc: ${PYSOURCES}
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MYPYPATH=typeshed/ CWLTOOL_USE_MYPYC=1 pip install --verbose -e . && pytest --basetemp ./tmp
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MYPYPATH=$$MYPYPATH:typeshed mypy $^
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release-test: FORCE
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git diff-index --quiet HEAD -- || ( echo You have uncommited changes, please commit them and try again; false )

‎README.md‎

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@@ -105,4 +105,5 @@ To regenerate install the `schema_salad` package and run:
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### Release
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To release CWLUtils, bump the version in `cwl_utils/__meta__.py`, and tag that
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commit with the new version. TravisCI should release that tag.
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commit with the new version. The [gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish)
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should release that tag.

‎cwl_utils/cwl_expression_refactor.py‎

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@@ -139,7 +139,7 @@ def run(args: argparse.Namespace) -> int:
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output_filehandle.write(
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"#!/usr/bin/env cwl-runner\n"
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) # TODO: teach the codegen to do this?
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yaml.round_trip_dump(result_json, output_filehandle)
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yaml.main.round_trip_dump(result_json, output_filehandle)
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return 0
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‎cwl_utils/cwl_v1_0_expression_refactor.py‎

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raise WorkflowException(
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"param {} not found in {}\n or\n {}.".format(
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sourcename,
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yaml.round_trip_dump(cwl.save(process)),
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yaml.round_trip_dump(cwl.save(parent)),
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yaml.main.round_trip_dump(cwl.save(process)),
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yaml.main.round_trip_dump(cwl.save(parent)),
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)
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)
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‎cwl_utils/cwl_v1_1_expression_refactor.py‎

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raise WorkflowException(
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"param {} not found in {}\n or\n {}.".format(
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sourcename,
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yaml.round_trip_dump(cwl.save(process)),
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yaml.round_trip_dump(cwl.save(parent)),
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yaml.main.round_trip_dump(cwl.save(process)),
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yaml.main.round_trip_dump(cwl.save(parent)),
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)
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)
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‎cwl_utils/cwl_v1_2_expression_refactor.py‎

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raise WorkflowException(
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"param {} not found in {}\n or\n {}.".format(
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sourcename,
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yaml.round_trip_dump(cwl.save(process)),
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yaml.round_trip_dump(cwl.save(parent)),
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yaml.main.round_trip_dump(cwl.save(process)),
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yaml.main.round_trip_dump(cwl.save(parent)),
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)
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)
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‎cwl_utils/graph_split.py‎

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import argparse
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import json
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import os
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from typing import Any, IO, MutableMapping, Set, Text, Union, cast
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from typing import IO, Any, MutableMapping, Set, Text, Union, cast
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from cwlformat.formatter import stringify_dict
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from ruamel import yaml
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field["name"] = field["name"].split("/")[2]
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rewrite_types(field, entry_file, True)
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with open(entry_file[1:], "a", encoding="utf-8") as entry_handle:
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yaml.dump([entry], entry_handle, Dumper=yaml.RoundTripDumper)
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yaml.main.dump(
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[entry], entry_handle, Dumper=yaml.dumper.RoundTripDumper
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)
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entry["$import"] = entry_file[1:]
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del entry["name"]
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del entry["type"]

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