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FIX: Docker and test errors related to conda, imageio_ffmpeg, and loci.formats #380

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merged 5 commits into from
Dec 13, 2020
Merged

FIX: Docker and test errors related to conda, imageio_ffmpeg, and loci.formats #380

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f91dcea
fix: Configure conda to use local .conda directory
jthetzel Nov 28, 2020
fa38358
fix: Rename loci.formats in to in_
jthetzel Nov 28, 2020
e77ea9c
fix: Call `imageio_get_ffmpeg_exe` to determine if ffmpeg available
jthetzel Nov 28, 2020
65b20f4
fix: Try/except AttributeName logic for `loci.formats.in` mangling
jthetzel Nov 28, 2020
37bf918
fix: Move get_ffmpeg_exe call within imageio_ffmpeg import block
jthetzel Nov 28, 2020
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2 changes: 2 additions & 0 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -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 👍

RUN conda config --prepend pkgs_dirs $HOME/.conda/pkgs
RUN conda env create -f environment.yml \
&& conda clean -tipsy

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6 changes: 5 additions & 1 deletion pims/bioformats.py
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Expand Up @@ -361,7 +361,11 @@ def __init__(self, filename, meta=True, java_memory='512m',
# patch for issue with ND2 files and the Chunkmap implemented in 5.4.0
# See https://github.com/openmicroscopy/bioformats/issues/2955
# circumventing the reserved keyword 'in'
mo = getattr(loci.formats, 'in').DynamicMetadataOptions()
try:
mo = getattr(loci.formats, 'in').DynamicMetadataOptions()
except AttributeError:
# Attribute name conflict causes mangling of `in` to `in_`
mo = getattr(loci.formats, 'in_').DynamicMetadataOptions()
mo.set('nativend2.chunkmap', 'False') # Format Bool as String
self.rdr.setMetadataOptions(mo)

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4 changes: 4 additions & 0 deletions pims/imageio_reader.py
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Expand Up @@ -13,6 +13,10 @@
imageio = None
try:
import imageio_ffmpeg
try:
imageio_ffmpeg.get_ffmpeg_exe()
except RuntimeError:
imageio_ffmpeg = None
except ImportError:
imageio_ffmpeg = None

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