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normanrznormanrz
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Fixes for Windows (#394)
1 parent abca2f6 commit 9bf8037

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+235
-198
lines changed

‎.github/workflows/main.yml‎

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python-version: [3.7, 3.8]
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steps:
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- uses: actions/checkout@v1
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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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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architecture: 'x64'
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- name: Install dependencies
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run: |
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- name: Python tests
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run: poetry run pytest tests
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- name: Test tiff cubing
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run: tests/scripts/tiff_cubing.sh
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- name: Test tile cubing
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run: tests/scripts/tile_cubing.sh
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- name: Test simple tiff cubing
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run: tests/scripts/simple_tiff_cubing.sh
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- name: Test simple tiff cubing (no compression)
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run: tests/scripts/simple_tiff_cubing_no_compression.sh
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- name: Test metadata generation
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run: tests/scripts/meta_generation.sh
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- name: Test KNOSSOS conversion
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run: tests/scripts/knossos_conversion.sh
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- name: Decompress reference magnification data
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run: |
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mkdir -p testdata/tiff_mag_2_reference
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tar -xzvf testdata/tiff_mag_2_reference.tar.gz -C testdata/tiff_mag_2_reference
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- name: Test downsampling
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run: tests/scripts/downsampling.sh
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- name: Test upsampling
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run: tests/scripts/upsampling.sh
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- name: Test anisotropic downsampling
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run: tests/scripts/anisotropic_downsampling.sh
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- name: Test compression and verification
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run: tests/scripts/compression_and_verification.sh
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- name: Test in-place compression
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run: tests/scripts/in_place_compression.sh
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- name: Remove reference magnification data
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run: rm -r testdata/tiff_mag_2_reference/
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- name: CLI tests
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run: tests/scripts/all_tests.sh
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- name: Generate Docs
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if: matrix.python-version == '3.8'
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[[ -z $(git status -s) ]]
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- name: Publish python package
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if: startsWith(github.event.ref, 'refs/tags') && matrix.python-version == '3.7'
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if: startsWith(github.event.ref, 'refs/tags') && matrix.python-version == '3.8'
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env:
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PYPI_USERNAME: ${{ secrets.PYPI_USERNAME }}
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PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
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run: ./publish.sh
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build_win:
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# Caution! The Windows VM seems to be running out of storage rather quickly.
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runs-on: windows-latest
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strategy:
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max-parallel: 4
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matrix:
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python-version: [3.7, 3.8]
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steps:
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- uses: actions/checkout@v2
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- name: Set up 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: Install dependencies
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shell: bash
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run: |
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pip install poetry
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poetry install
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- name: Decompress test data
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shell: bash
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run: tar -xzvf testdata/WT1_wkw.tar.gz
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- name: Python tests
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shell: bash
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run: poetry run pytest tests
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- name: CLI tests
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shell: bash
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run: tests/scripts/all_tests.sh
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build_mac:
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runs-on: macos-latest
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strategy:
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max-parallel: 4
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matrix:
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python-version: [3.7, 3.8]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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pip install poetry
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poetry install
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- name: Decompress test data
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run: tar -xzvf testdata/WT1_wkw.tar.gz
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- name: Python tests
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run: poetry run pytest tests
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- name: CLI tests
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run: tests/scripts/all_tests.sh
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docker:
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needs: build
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needs: [build, build_win, build_mac]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v1
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- uses: actions/checkout@v2
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- name: Build docker image
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run: docker build -t scalableminds/webknossos-cuber:$GITHUB_SHA .
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‎Changelog.md‎

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### Changed
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### Fixed
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- Fixes support for Windows. [#394](https://github.com/scalableminds/webknossos-cuber/pull/394)
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## [0.8.12](https://github.com/scalableminds/webknossos-cuber/releases/tag/v0.8.12) - 2021-08-19
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[Commits](https://github.com/scalableminds/webknossos-cuber/compare/v0.8.11...v0.8.12)

‎tests/conftest.py‎

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import pytest
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from pathlib import Path
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from os import makedirs
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from shutil import rmtree
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from typing import Generator
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TESTOUTPUT_DIR = Path("testoutput")
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@pytest.fixture(autouse=True, scope="function")
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def run_around_tests() -> Generator:
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makedirs(TESTOUTPUT_DIR, exist_ok=True)
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yield
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rmtree(TESTOUTPUT_DIR)

‎tests/scripts/all_tests.sh‎

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BASEDIR=./tests/scripts
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sh ${BASEDIR}/tiff_cubing.sh
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sh ${BASEDIR}/simple_tiff_cubing.sh
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sh ${BASEDIR}/simple_tiff_cubing_no_compression.sh
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sh ${BASEDIR}/tile_cubing.sh
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sh ${BASEDIR}/meta_generation.sh
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sh ${BASEDIR}/knossos_conversion.sh
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mkdir -p testdata/tiff_mag_2_reference
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tar -xzvf testdata/tiff_mag_2_reference.tar.gz -C testdata/tiff_mag_2_reference
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sh ${BASEDIR}/tiff_cubing.sh
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sh ${BASEDIR}/meta_generation.sh
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sh ${BASEDIR}/downsampling.sh
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sh ${BASEDIR}/upsampling.sh
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rm -r testoutput/tiff_upsampling
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rm -r testdata/tiff_mag_2_reference
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sh ${BASEDIR}/anisotropic_downsampling.sh
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sh ${BASEDIR}/compression_and_verification.sh
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sh ${BASEDIR}/downsampling.sh
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sh ${BASEDIR}/in_memory_downsampled_cubing.sh
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rm -r testoutput/tiff_compress
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sh ${BASEDIR}/in_place_compression.sh
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sh ${BASEDIR}/simple_anisotropic_tiff_cubing.sh
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rm -r testoutput/tiff_compress2
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rm -r testoutput/tiff
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sh ${BASEDIR}/tile_cubing.sh
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rm -r testoutput/temca2
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rm -r testdata/tiff_mag_2_reference/
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sh ${BASEDIR}/simple_tiff_cubing.sh
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rm -r testoutput/tiff2
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sh ${BASEDIR}/simple_tiff_cubing_no_compression.sh
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rm -r testoutput/tiff3
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sh ${BASEDIR}/knossos_conversion.sh
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rm -r testoutput/knossos

‎tests/scripts/compression_and_verification.sh‎

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echo "Create broken copy of dataset"
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rm -rf testoutput/tiff_compress-broken
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cp -R testoutput/tiff_compress{,-broken}
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cp -R testoutput/tiff_compress testoutput/tiff_compress-broken
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rm -r testoutput/tiff_compress-broken/color/1/z0/y0/x0.wkw
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echo "Compare original dataset to broken one and expect to determine difference"

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