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Merge pull request #416 from mpsonntag/deptests
Add dependent library release test scripts
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‎.github/workflows/run-tests.yml‎

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branches:
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- master
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jobs:
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tests:
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linux_tests:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest, macos-latest, windows-latest]
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python-version: [3.6, 3.7, 3.8, 3.9]
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os: [ubuntu-latest]
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python-version: ["3.8", "3.9", "3.10"]
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steps:
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- uses: actions/checkout@v2
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- name: Setup Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Install dependencies
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run: |
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python setup.py install
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pip install -r requirements-test.txt
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- name: Run tests
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run: pytest
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# The default Linux Ubuntu 22+ does not support Python < 3.8 any longer
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# To keep testing Python < 3.8, use Ubuntu 20
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linux_legacy_tests:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-20.04]
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python-version: ["3.6", "3.7"]
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steps:
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- uses: actions/checkout@v2
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- name: Setup Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Install dependencies
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run: |
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python setup.py install
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pip install -r requirements-test.txt
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- name: Run tests
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run: pytest
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mac_tests:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [macos-latest]
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# github actions currently resolves the pyyaml pip install package
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# for python 3.9 not to the required macos package, but to the
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# default pyyaml 6.0.tar package, which is a linux distribution
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# and fails on install. MacOS Python version 3.9 build will stay
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# disabled until this is resolved.
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#python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
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python-version: ["3.6", "3.7", "3.8", "3.10"]
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steps:
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- uses: actions/checkout@v2
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- name: Setup Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Install dependencies
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run: |
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python setup.py install
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pip install -r requirements-test.txt
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- name: Run tests
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run: pytest
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# The current rdflib dependency causes random issues on some of
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# the github actions windows builds; since the appveyor builds
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# are passing without any issue, keep most gh actions windows
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# builds deactivated until the rdflib dependency has been
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# been updated.
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win_tests:
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continue-on-error: true
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [windows-latest]
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python-version: ["3.10"]
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steps:
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- uses: actions/checkout@v2
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- name: Setup Python ${{ matrix.python-version }}
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runs-on: [ubuntu-latest]
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steps:
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- uses: actions/checkout@v2
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- name: Setup Python 3.8
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- name: Setup Python 3.10
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uses: actions/setup-python@v2
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with:
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python-version: "3.8"
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python-version: "3.10"
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Install dependencies
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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run: coveralls --service=github
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run-codecov:
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runs-on: [ubuntu-latest]
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steps:
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- uses: actions/checkout@v2
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- name: Setup Python 3.10
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uses: actions/setup-python@v2
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with:
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python-version: "3.10"
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- name: Install dependencies
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run: |
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python setup.py install
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pip install -r requirements-test.txt
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pip install pytest pytest-cov
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- name: Create coverage
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run: |
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pytest --cov=./ --cov-report=xml
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- uses: codecov/codecov-action@v1
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with:
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name: Submit Codecov coverage
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files: ./coverage.xml
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verbose: true # optional (default = false)

‎appveyor.yml‎

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APPVEYOR_BUILD_WORKER_IMAGE: Visual Studio 2019
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PYVER: 3
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BITS: 32
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- PYTHON: "C:\\Python310"
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APPVEYOR_BUILD_WORKER_IMAGE: Visual Studio 2019
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PYVER: 3
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BITS: 32
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- PYTHON: "C:\\Python36-x64"
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PYVER: 3
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BITS: 64
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APPVEYOR_BUILD_WORKER_IMAGE: Visual Studio 2019
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PYVER: 3
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BITS: 64
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- PYTHON: "C:\\Python310-x64"
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APPVEYOR_BUILD_WORKER_IMAGE: Visual Studio 2019
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PYVER: 3
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BITS: 64
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init:
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- "ECHO %PYTHON% %vcvars% (%bits%)"

‎odml/info.json‎

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"VERSION": "1.5.2",
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"FORMAT_VERSION": "1.1",
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"AUTHOR": "Hagen Fritsch, Jan Grewe, Christian Kellner, Achilleas Koutsou, Michael Sonntag, Lyuba Zehl",
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"COPYRIGHT": "(c) 2011-2021, German Neuroinformatics Node",
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"COPYRIGHT": "(c) 2011-2023, German Neuroinformatics Node",
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"CONTACT": "[email protected]",
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"HOMEPAGE": "https://github.com/G-Node/python-odml",
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"CLASSIFIERS": [

‎scripts/README.md‎

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## python-odml convenience scripts
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This folder contains convenience scripts for build and deployment tests and should not be part of any release. Check the README files in the specific folders for details.
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The `release_tests` folder contains scripts and resources to test the odML library and all its dependent libraries like odmltools, odmlui, odmlconverter and nix-odml-converter from a local odML installation, from Test-PyPI and PyPI packages.
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The local version tests the installation via `pip install .` and `python setup.py install`. The Test-PyPI and PyPI package tests use conda environments to test the installation with all Python versions >= 3.5.

‎scripts/release_tests/README.md‎

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# odml and odml dependent libraries installation tests
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Used to document the minimal automated tests for `python-odml` and `odmltools` and not fully automated tests of `odml-ui` installations with a special focus on the execution of command line scripts and gui with different local installation methods.
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## Automated odml and dependent library tests
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The tests include
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- basic odml import and file loading and saving
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- `odml` command line script execution using realistic example files
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- odmlview
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- odmltordf
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- odmlconversion
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- `odmltools` command line script execution
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- odmlimportdatacite
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- basic odml-ui installation
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### Local installation tests
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To test the various local installations of odml, execute `run_test_matrix.sh` with option 'A'. odml will be installed into fresh conda environments using `pip install .` and `python setup.py install` and all Python versions >= 3.5.
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### odml PyPI TEST installation tests
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To test the installation of the odml package from the PyPI TEST repository, execute `run_test_matrix.sh` with option 'B'. odml will be installed into fresh conda environments using `pip install odml` and all Python versions >= 3.5.
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The package `odml-ui` will be installed as well and all installable odml command line scripts will be tested after the odml installation.
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### odmltools PyPI server installation tests
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When executing `run_test_matrix.sh` with option 'C', the odml dependent package `odmltools` will be pip installed into fresh conda environments for all Python versions >= 3.6 from the PyPI TEST repository and appropriate conversion tests will be run using the installed command line tool.
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### nixodmlconverter PyPI TEST installation tests
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When executing `run_test_matrix.sh` with option 'D' the odml dependent package `nixodmlconverter` will be pip installed into fresh conda environments for all Python versions >= 3.6 from the PyPI TEST repository and appropriate conversion tests will be run using the installed command line tool.
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### odml PyPI LIVE installation tests
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To test the installation of the odml package from PyPI proper, execute `run_test_matrix.sh` with option 'E'. odml will be installed into fresh conda environments using `pip install odml` and all Python versions >= 3.5.
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The package `odml-ui` will be installed as well and all installable odml command line scripts will be tested after the odml installation.
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## Manual odml-ui tests
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To set up conda environments and run local or PyPI TEST installations run the script `run_test_matrix.sh` with option `B` from the current directory.
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Once set up, the conda environments can be used to manually test `odml-ui` as well.
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Activate python installation environment
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CONDA_ENV_SETUP=pyinst
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CONDA_ENV_PIP=pipinst
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ROOT_DIR=$(pwd)
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cd $ROOT_DIR/resources/test_load
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conda activate ${CONDA_ENV_SETUP}
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odmlui
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Run the following most tests:
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- open `test_load\load_v1.odml.xml`
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- check fail message
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- import `test_load\load_v1.odml.xml`
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- save as `pyi_conv.xml`
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- save as `pyi_conv.yaml`
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- save as `pyi_conv.json`
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- open `pyi_conv.xml`
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- open `pyi_conv.yaml`
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- open `pyi_conv.json`
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- check importing a terminology using the document wizard
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Exit and switch to pip environment
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conda deactivate
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conda activate ${CONDA_ENV_PIP}
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odmlui
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Run manual tests again
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Test odmltables plugin
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pip install odmltables
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pip install odmltables[gui]
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odmlui
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Run the following minimal tests
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- open `pyi_conv.xml`
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- use odmltables `convert` button, save as csv file
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- use odmltables `filter` button
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Exit, move back to the root and cleanup
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cd $ROOT_DIR
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conda deactivate
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rm $ROOT_DIR/resources/test_load/load_v1.odml_converted.xml
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rm $ROOT_DIR/resources/test_load/pyi_conv.json
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rm $ROOT_DIR/resources/test_load/pyi_conv.xml
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rm $ROOT_DIR/resources/test_load/pyi_conv.yaml

‎scripts/release_tests/resources/scripts/odml_basics.py‎

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import sys
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import unittest
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try:
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# Test possible imports of all parsers without importing the full odML package
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from odml.tools import ODMLReader, ODMLWriter, RDFReader, RDFWriter
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from odml.tools.converters import FormatConverter, VersionConverter
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from odml.tools import XMLReader, XMLWriter, DictReader, DictWriter
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import odml
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except Exception as exc:
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print("-- Failed on an import: %s" % exc)
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sys.exit(-1)
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class TestODMLBasics(unittest.TestCase):
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def test_load(self):
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print("-- Load odml xml file")
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xdoc = odml.load('./load.odml.xml')
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print(xdoc.pprint())
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print("-- Load odml json file")
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jdoc = odml.load('./load.odml.json', 'JSON')
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self.assertEqual(xdoc, jdoc)
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print("-- Load odml yaml file")
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ydoc = odml.load('./load.odml.yaml', 'YAML')
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self.assertEqual(xdoc, ydoc)
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print("-- Document loading tests success")
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def test_version_load(self):
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print("-- Test invalid version exception xml file load")
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with self.assertRaises(odml.tools.parser_utils.InvalidVersionException):
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_ = odml.load('./load_v1.odml.xml')
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print("-- Invalid version loading test success")
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def test_tools_init(self):
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_ = ODMLReader()
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_ = ODMLWriter()
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_ = RDFReader()
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_ = RDFWriter([odml.Document()])
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_ = FormatConverter()
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_ = VersionConverter("/I/do/not/exist.txt")
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_ = XMLReader()
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_ = XMLWriter(odml.Document())
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_ = DictReader()
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_ = DictWriter()
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if __name__ == "__main__":
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try:
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svi = sys.version_info
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print("-- Using Python '%s.%s.%s'" % (svi.major, svi.minor, svi.micro))
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print("-- Testing odml Version: '%s'" % odml.VERSION)
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unittest.main()
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except Exception as exc:
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print("-- Failed on a test: %s" % exc)
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sys.exit(-1)

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