FIX: Docker and test errors related to conda, imageio_ffmpeg, and loci.formats #380
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`conda create` creates the $HOME/.conda directory but does not prepend it conda config. Closes soft-matter#377
Attribute name automatically mangled due to conflict. soft-matter#373 (comment)
Importing `imageio_ffmpeg` succeeds even if ffmpeg executable is not available. This additional check is required when checking if ffmpeg related tests should be skipped. Closes soft-matter#379.
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| @@ -15,6 +15,8 @@ USER pims | |||
| # Set up the initial conda environment | |||
| COPY --chown=pims:pims environment.yml /src/environment.yml | |||
| WORKDIR /src | |||
| RUN conda config --prepend envs_dirs $HOME/.conda/envs | |||
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Thanks for these, @jthetzel Build is working for me again locally 👍
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@nkeim @GenevieveBuckley Any thoughts on how to improve this pull request? I believe future PRs are blocked until these build errors are addressed. |
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@jthetzel Thanks for this PR!! Those issues did not look particularly easy to track down. Sorry I've (we've) been away for awhile. It looks good to merge and I'm going ahead with it. |
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Atrribute name conflict mangling causes
loci.formats.into be renamedloci.formats.in_. Added try/except logic to usein_ifinfails withAttributeError.pims.imageio_readertests for the presence of ffmpeg executable by catchingImportErrorwhen importingimageio_ffmpeg. However, import ofimageio_ffmpegsucceeds even when ffmpeg executable is not present. Added a call toimageio_ffmpeg.get_ffmpeg_exeto check if ffmpeg executable is present.conda createcreates the$HOME/.condadirectory but does not prepend it to conda config. This might be an upstream bug in miniconda, but easily worked around by explicitly prepending localenv_dirsandpkg_dirsin Dockerfile (see anaconda/docker-images#151 (comment) ).Closes #377 and #379 .