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626 upgrade to python 11 and extend test suite (#682)
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Lines changed: 148 additions & 101 deletions

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‎.github/actions/build-py/action.yml‎

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@@ -20,7 +20,7 @@ runs:
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run: |
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cd pycode/memilio-${{ inputs.package }}/
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/opt/python/cp38-cp38/bin/python setup.py bdist_wheel
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/opt/python/cp310-cp310/bin/python setup.py bdist_wheel
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/opt/python/cp311-cp311/bin/python setup.py bdist_wheel
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# Exclude memilio-generation, because its a pure python package, cmake is only used in the build process to retrieve data from cpp
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if [[ -f "CMakeLists.txt" ]] && [ "${{ inputs.package }}" != "generation" ]; then
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# includes native dependencies in the wheel

‎.github/actions/test-py/action.yml‎

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@@ -4,6 +4,10 @@ inputs:
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package:
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description: "Package to run the tests for."
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required: true
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version:
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description: "Python version to use for the test."
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required: false
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default: "3.8"
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coverage:
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description: "Generate coverage report from running the tests, ON or OFF, default OFF."
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required: false
@@ -38,14 +42,15 @@ runs:
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with:
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name: python-wheels-simulation
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path: pycode/wheelhouse
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- name: Set up Python 3.8
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- name: Set up Python ${{ inputs.version }}
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uses: actions/setup-python@v4
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with:
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python-version: 3.8
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python-version: ${{ inputs.version }}
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- name: Install Python Wheels
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shell: bash
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run: |
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for pkg in `ls pycode/wheelhouse/*cp38*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
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export PYTHON_VERSION_NO_DOT=$(echo "${{ inputs.version }}" | sed 's/\.//g')
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for pkg in `ls pycode/wheelhouse/*cp$PYTHON_VERSION_NO_DOT*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
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for pkg in `ls pycode/wheelhouse/*py3*.whl`; do python -m pip install $pkg; done # pure python packages are not version specific
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pip install -r pycode/memilio-${{ inputs.package }}/requirements-dev.txt
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- name: Run unit tests

‎.github/actions/test-pylint/action.yml‎

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@@ -20,7 +20,7 @@ runs:
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- name: Install Python Wheels
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shell: bash
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run: |
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for pkg in `ls pycode/wheelhouse/*cp38*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
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for pkg in `ls pycode/wheelhouse/*cp311*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
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for pkg in `ls pycode/wheelhouse/*py3*.whl`; do python -m pip install $pkg; done # pure python packages are not version specific
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pip install -r pycode/memilio-${{ inputs.package }}/requirements-dev.txt
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- name: Run pylint

‎.github/workflows/epidata_main.yml‎

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@@ -25,7 +25,7 @@ jobs:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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with:
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python-version: 3.8
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python-version: 3.11
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- uses: pre-commit/[email protected]
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build-py-epidata:
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test-py-plot:
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if: github.event.pull_request.draft == false
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needs: [build-py-plot, build-py-epidata]
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strategy:
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matrix:
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version: ["3.8", "3.11"]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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with:
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name: python-wheels-epidata
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path: pycode/wheelhouse
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- name: Set up Python 3.8
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- name: Set up Python 3.11
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uses: actions/setup-python@v4
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with:
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python-version: 3.8
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python-version: 3.11
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- name: Install Python Wheels
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run: |
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for pkg in `ls pycode/wheelhouse/*cp38*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
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for pkg in `ls pycode/wheelhouse/*cp311*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
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for pkg in `ls pycode/wheelhouse/*py3*.whl`; do python -m pip install $pkg; done # pure python packages are not version specific
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- name: Download Data
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run: |

‎.github/workflows/main.yml‎

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- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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with:
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python-version: 3.8
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python-version: 3.11
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- uses: pre-commit/[email protected]
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build-cpp-gcc_clang:
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with:
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package: generation
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test-py-generation:
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if: github.event.pull_request.draft == false
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needs: build-py-generation
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: ./.github/actions/test-py
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with:
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package: generation
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build-py-simulation:
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if: github.event.pull_request.draft == false
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runs-on: ubuntu-latest
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with:
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package: surrogatemodel
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test-py-generation:
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if: github.event.pull_request.draft == false
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strategy:
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matrix:
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version: ["3.8", "3.11"]
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needs: build-py-generation
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: ./.github/actions/test-py
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with:
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package: generation
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test-py-simulation:
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if: github.event.pull_request.draft == false
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needs: build-py-simulation
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strategy:
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matrix:
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version: ["3.8", "3.11"]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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test-py-surrogatemodel:
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if: github.event.pull_request.draft == false
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needs: [build-py-surrogatemodel, build-py-simulation]
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strategy:
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matrix:
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version: ["3.8", "3.11"]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3

‎pycode/README.rst‎

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@@ -23,4 +23,6 @@ We recommend to use a virtual python environment to avoid dependency conflicts w
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source epi_venv/bin/activate
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pip install --upgrade pip
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Refer to the `Python documentation <https://docs.python.org/3/library/venv.html>`_ for more information about virtual environments.
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Refer to the `Python documentation <https://docs.python.org/3/library/venv.html>`_ for more information about virtual environments.
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The packages are tested for Python 3.8 - 3.11.

‎pycode/memilio-epidata/README.rst‎

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Required python packages:
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- pandas<1.2.0
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- pandas>=1.2.2
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- matplotlib
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- tables
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- numpy>=1.22
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- numpy>=1.22,<1.25
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- openpyxl
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- xlrd
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- requests

‎pycode/memilio-epidata/requirements-dev.txt‎

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# dev dependencies, pyfakefs 4.2.0 is broken!
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pyfakefs==4.1.0
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# dev dependencies
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# first support of python 3.11
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pyfakefs>=4.6
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coverage>=7.0.1
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pylint<=2.11.1
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pylint_json2html<=0.3.0
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# pylint 2.16 creates problem with wrapt package version
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pylint>=2.13.0,<2.16
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pylint_json2html==0.4.0

‎pycode/memilio-epidata/setup.py‎

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'pandas>=1.2.2',
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'matplotlib',
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'tables',
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'numpy>=1.22', # smaller numpy versions cause a security issue
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# smaller numpy versions cause a security issue, 1.25 breaks testing with pyfakefs
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'numpy>=1.22,<1.25',
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'openpyxl',
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'xlrd',
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'requests',
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],
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extras_require={
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'dev': [
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# smaller pyfakefs versions use deprecated functions for matplotlib versions >=3.4
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'pyfakefs>=4.2.1',
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# first support of python 3.11
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'pyfakefs>=4.6',
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# coverage 7.0.0 can't find .whl files and breaks CI
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'coverage>=7.0.1',
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'pylint<=2.11.1',
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'pylint_json2html<=0.3.0',
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# pylint 2.16 creates problem with wrapt package version
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'pylint>=2.13.0,<2.16',
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'pylint_json2html==0.4.0',
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],
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},
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cmdclass={

‎pycode/memilio-generation/memilio/generation/scanner.py‎

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file_args.append(argument)
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file_args = file_args[1:-4]
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clang_cmd = [
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"clang", self.config.source_file,
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"clang-14", self.config.source_file,
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"-std=c++17", '-emit-ast', '-o', '-']
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clang_cmd.extend(file_args)
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