spacetx / slicedimage

MIT License
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Re-add () to contextmanager call in _tile.py #54

Closed joshmoore closed 6 years ago

joshmoore commented 6 years ago

see: gh-40

I think this is leading to the failure from https://github.com/joshmoore/build-starfish/issues/1#issuecomment-416537231

Traceback (most recent call last):
  File "/home/starfish/.conda/envs/env/bin/starfish", line 11, in <module>
    sys.exit(starfish())
  File "/home/starfish/.conda/envs/env/lib/python3.7/site-packages/starfish/starfish.py", line 80, in starfish
    args.starfish_command(args, len(argv) != 0)
  File "/home/starfish/.conda/envs/env/lib/python3.7/site-packages/starfish/experiment/builder/cli.py", line 72, in run
    for aux_image_name in AUX_IMAGE_NAMES
  File "/home/starfish/.conda/envs/env/lib/python3.7/site-packages/starfish/experiment/builder/__init__.py", line 170, in write_experiment_json
    tile_writer=tile_writer,
  File "/home/starfish/.conda/envs/env/lib/python3.7/site-packages/slicedimage/io.py", line 117, in write_to_path
    partition, path, pretty, *args, **kwargs)
  File "/home/starfish/.conda/envs/env/lib/python3.7/site-packages/slicedimage/io.py", line 235, in generate_partition_document
    tile_writer=tile_writer
  File "/home/starfish/.conda/envs/env/lib/python3.7/site-packages/slicedimage/io.py", line 117, in write_to_path
    partition, path, pretty, *args, **kwargs)
  File "/home/starfish/.conda/envs/env/lib/python3.7/site-packages/slicedimage/io.py", line 261, in generate_partition_document
    tile_format = tile_writer(tile, writer_fh)
  File "/home/starfish/.conda/envs/env/lib/python3.7/site-packages/starfish/experiment/builder/__init__.py", line 38, in tile_writer
    tile.copy(fh)
  File "/home/starfish/.conda/envs/env/lib/python3.7/site-packages/slicedimage/_tile.py", line 75, in copy
    with self._source_fh_contextmanager as src_fh:
AttributeError: __enter__
codecov-io commented 6 years ago

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@e51d62e). Click here to learn what that means. The diff coverage is 0%.

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@@           Coverage Diff            @@
##             master     #54   +/-   ##
========================================
  Coverage          ?   80.9%           
========================================
  Files             ?      18           
  Lines             ?     529           
  Branches          ?       0           
========================================
  Hits              ?     428           
  Misses            ?     101           
  Partials          ?       0
Impacted Files Coverage Δ
slicedimage/_tile.py 80.39% <0%> (ø)

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joshmoore commented 6 years ago

Closing in favor of https://github.com/spacetx/starfish/pull/490