diff --git a/Dockerfile b/Dockerfile index 2b939ee..c4aeca9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -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 +RUN conda config --prepend pkgs_dirs $HOME/.conda/pkgs RUN conda env create -f environment.yml \ && conda clean -tipsy diff --git a/pims/bioformats.py b/pims/bioformats.py index 95d21dc..05553b1 100644 --- a/pims/bioformats.py +++ b/pims/bioformats.py @@ -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) diff --git a/pims/imageio_reader.py b/pims/imageio_reader.py index 4d58f0f..15bdfd8 100644 --- a/pims/imageio_reader.py +++ b/pims/imageio_reader.py @@ -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