* Move cmp legacy function out into separate utility module * Python 3 fixes for basestring, cmp(), reload(), unicode(), xrange(), etc. * #3648 Update requirements files with new bioformats versions * #3648 Bump python-bioformats version ( #3653) Without this change, it is a syntax error in Python 3 * Explicit tuple required inside a comprehension in Python 3 ( #3651) * from cellprofiler.modules import images * Revert cellprofiler/modules/loadsingleimage.py * Remove from _future_ import with_statement and from. * Remove from _future_ import absolute_import * Cleanup xxx_todo_changeme and doubled coding lines * setup.py: permit pip install on Python 3.6.3 * No absolute_imports in cellprofiler/modules/images.py * Reference default strings in preferences, where they're defined * Import wx in function where it's used, spelling correction None of the other boxsizers had another reference, so I'm hoping this is fine. * Remove undefined groupbox reference in pipeline controller * Reference cellprofiler.pipelines directly This used a C file that no longer exists: cbd1d45 * Remove windows specific check for hidden files * sr_alloc_block requires no extra arguments (expecially undefined ones) * Remove ImagePlaneDetailsMetadata which no longer existsĪlso set undefined "module" reference to None. * Travis CI: Add flake8 to find syntax errors and undefined names * Add "c" and "cmap" as options for subplot_scatter ( #3637) * eliminated separate elifs for BROWSE_FILES and BROWSE_FOLDER * working now (removed unnecessary debug information) * added on_pathlist_browse_folder calls in two more places * adding changes to add Select Folder context menu Put the class variable at the start of the class (to make issues like Added spacing around all operators I found Settings from the current version do not need any update. * Only update variable names if pipeline comes from older version Like this it can be verified that channel numbers Such that they contained the channel number they should * Adds a test to load an old pipeline from v3Ī v3 pipeline was added where images were named Reflect the fact that it is now integer values. This adapts the documentation of `Add channel` to Which required a slight adaptation of some tests. The channel_choice widget is now an cps.Integer * Adapted tests to channel_choice type change Tedious, as selecting channel idx 20 would require The previous solution was elegantĪnd supported that many channels, but was in practice Thus it would be convient to easily extract single We are dealing routinely with 30+ channel images. * Adapts the channel_choice widget to cps.Integer * Make the requirements more python-canonical * Specify at least a minimum version of numpy * #3622 Address potentially incorrect equality checkĪ number of other equality checks for object_name_variable in this file check against value rather than the actual object. * Build should succeed even if unpinned fails * Don't upgrade when installing test dependencies I think this has to do with the fact that the JVM doesn't get closed if an exception is raised in main. ^C aether (e) cellprofiler bugfix/proper-return-code-exit ~ git CellProfiler 130 īoth of these processes had to be killed externally. IOError: No such file or directory: 'foo.csv' ^C aether (e) cellprofiler bugfix/proper-return-code-exit ~ git CellProfiler 130 cellprofiler -r -c -p ~/misc/ExampleHuman/ExampleHuman.cppipe -file-list 'foo.csv'įile "/home/aether/git/CellProfiler/cellprofiler/_main_.py", line 703, in run_pipeline_headlessįile "/home/aether/git/CellProfiler/cellprofiler/pipeline.py", line 2632, in read_file_list IOError: Could not find file, asdfasdf.cppipe Raise IOError("Could not find file, " + fd_or_filename) Load_entry_point('CellProfiler', 'console_scripts', 'cellprofiler')()įile "/home/aether/git/CellProfiler/cellprofiler/_main_.py", line 162, in mainĮxit_code = run_pipeline_headless(options, args)įile "/home/aether/git/CellProfiler/cellprofiler/_main_.py", line 691, in run_pipeline_headlessįile "/home/aether/git/CellProfiler/cellprofiler/pipeline.py", line 792, in load _conv import register_converters as _register_convertersįile "/home/aether/programs/anaconda3/envs/cellprofiler/bin/cellprofiler", line 11, in In future, it will be treated as `np.float64 = np.dtype(float).type`.įrom. home/aether/programs/anaconda3/envs/cellprofiler/lib/python2.7/site-packages/h5py/_init_.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated.
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