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Optimalisations, unit testing, travis (#60)
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| language: bash | ||
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| os: | ||
| - windows | ||
| - linux | ||
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| # jobs: | ||
| # include: | ||
| # - os: linux | ||
| # python: 3.8.1 | ||
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| branches: | ||
| only: | ||
| - master | ||
| - dev | ||
| - "/^pull.$" | ||
| - "/^hotfix-.+$/" | ||
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| before_install: | ||
| - . scripts/travis/before_install_nix_win.sh | ||
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| install: | ||
| # Install miniconda | ||
| - . scripts/travis/install_nix_win.sh | ||
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| - source $MINICONDA_PATH/etc/profile.d/conda.sh; | ||
| - hash -r | ||
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| # Setting up conda env and install deps | ||
| - conda env create -q -n minian -f environment.yml | ||
| - conda activate minian | ||
| - conda list | ||
| - conda install -c conda-forge -y jupyterlab | ||
| - jupyter labextension install @pyviz/jupyterlab_pyviz | ||
| - conda env export | ||
| - conda install -y pytest-cov | ||
| - conda install -c anaconda -y black | ||
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| script: | ||
| # The test/check scripts go here | ||
| - travis_fold start "Black-check code quality" | ||
| - black --check minian | ||
| - travis_fold end "Black-check code quality" | ||
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| - travis_fold start "pytest" | ||
| - pytest -v --color=yes --cov=minian --pyargs minian | ||
| - travis_fold end "pytest" | ||
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| # - travis_fold start "Jupyter notebook pipeline" | ||
| # - papermill pipeline.ipynb pipeline_output.ipynb | ||
| # - travis_fold end "Jupyter notebook pipeline" | ||
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| after_success: | ||
| - echo conda install codecov | ||
| - echo codecov |
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| # Minian | ||
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| ## Running unit tests | ||
| Minian uses pytest for unit testing. | ||
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| To run the unit tests run the following command from the root of the Minian project: | ||
| ``` | ||
| pytest --pyargs minian | ||
| ``` |
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| import pytest | ||
| import numpy as np | ||
| import holoviews as hv | ||
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| from ..utilities import load_videos | ||
| from ..preprocessing import denoise | ||
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| dpath = "./demo_movies" | ||
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| param_load_videos = { | ||
| 'pattern': 'msCam[0-9]+\.avi$', | ||
| 'dtype': np.uint8, | ||
| 'downsample': dict(frame=2,height=1,width=1), | ||
| 'downsample_strategy': 'subset' | ||
| } | ||
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| param_denoise = { | ||
| 'method': 'median', | ||
| 'ksize': 7 | ||
| } | ||
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| @pytest.fixture | ||
| def varr(): | ||
| return load_videos(dpath, **param_load_videos) | ||
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| def test_can_load_videos(varr): | ||
| assert varr.shape[0] == 1000 # frames | ||
| assert varr.shape[1] == 480 # height | ||
| assert varr.shape[2] == 752 # width | ||
| return varr | ||
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| def test_can_init_holoviews(): | ||
| hv.notebook_extension('bokeh') | ||
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| def test_subset_part_video(varr): | ||
| subset = dict(frame=slice(0,None)) | ||
| varr_ref = varr.sel(subset) | ||
| assert varr_ref.all() == varr.all() | ||
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| def test_denoise(varr): | ||
| varr_ref = denoise(varr, **param_denoise) | ||
| assert varr_ref.all() != varr.all() # when both are equal the denoise didn't do anything --> fail |
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