uwmisl poretitioner issues

uwmisl / poretitioner

https://misl.cs.washington.edu

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Run formatting precommit hooks on all files.

#59 thequicksort closed 4 years ago
0
Cache pytorch

#58 thequicksort opened 4 years ago
1
#12 Logging logic

#57 thequicksort closed 4 years ago
0
[Not ready for merging] Add logging module. Get verbosity and debug mode from command line.

#56 thequicksort closed 4 years ago
0
Use ONT style for reading/writing fast5 data

#55 kdoroschak opened 4 years ago
0
#53 Install pre-commit during bootstrap

#54 thequicksort closed 4 years ago
0
[Bug] Pre-commit needs to be installed during bootstrap

#53 thequicksort closed 4 years ago
0
#45 Make application version readable at run-time

#52 thequicksort closed 4 years ago
0
Build and upload artifacts on release.

#51 thequicksort closed 4 years ago
0
Prevent uploading artifacts on master builds

#50 thequicksort closed 4 years ago
0
Refactor module names

#49 kdoroschak closed 4 years ago
0
Investigate: why are warnings being suppressed in classify.py?

#48 kdoroschak closed 3 years ago
0
Write unittests for raw_signal_utils

#47 kdoroschak closed 3 years ago
0
Deprecate or refactor alternate quantification method

#46 kdoroschak closed 3 years ago
1
Access the poretitioner version # from within segment.py

#45 kdoroschak closed 4 years ago
0
Document calibration curves

#44 kdoroschak closed 3 years ago
1
Separate filtering & classifying

#43 kdoroschak closed 3 years ago
1
Implement new filter method based on fast5

#42 kdoroschak closed 3 years ago
0
Support CPU and GPU for pytorch

#41 kdoroschak opened 4 years ago
0
Implement capture fast5 I/O in quantifier

#40 kdoroschak closed 3 years ago
0
Implement capture fast5 I/O in classifier

#39 kdoroschak closed 3 years ago
0
Implement sklearn suggestions for model maintainability

#38 kdoroschak opened 4 years ago
0
Ditch YAMLAssistant (or improve)

#37 kdoroschak opened 4 years ago
0
Functionality improvements

#36 kdoroschak closed 4 years ago
1
Add more unit tests for writing to fast5

#35 kdoroschak opened 4 years ago
0
Function naming conventions

#34 kdoroschak opened 4 years ago
0
Running poretitioner from command line

#33 kdoroschak opened 4 years ago
0
Generate segmentation test data

#32 kdoroschak closed 4 years ago
0
Write to fast5 instead of intermediate pkl files & npy raw data files

#31 kdoroschak closed 4 years ago
0
Reduce segmenter memory usage - low hanging fruit

#30 kdoroschak closed 4 years ago
0
Update README with install/uninstall instructions

#29 thequicksort closed 4 years ago
0
[Fixes #26] Create uninstall script

#28 thequicksort closed 4 years ago
0
Document & validate allowed configuration parameters for segmenter

#27 kdoroschak opened 4 years ago
1
nix installation went missing [solved]

#26 kdoroschak closed 4 years ago
2
Import pytorch and torchvision

#25 thequicksort closed 4 years ago
0
Decouple channel judgment from visualization

#24 kdoroschak closed 4 years ago
2
Deprecate use of read-based fast5 files in raw_signal_utils

#23 kdoroschak closed 4 years ago
0
open_pore --> open_channel

#22 kdoroschak closed 4 years ago
1
Reduce RF trained model size

#21 kdoroschak opened 4 years ago
0
Create specification for storing results in fast5 files

#20 kdoroschak opened 4 years ago
6
Reduce dependency on file name structure

#19 kdoroschak closed 3 years ago
0
[v1.0] Minimize image size

#18 thequicksort opened 4 years ago
0
Create new function get_voltage in raw_signal_utils

#17 kdoroschak closed 4 years ago
0
quantify.py: collect sets of valid files output by get_related_files

#16 kdoroschak closed 4 years ago
1
quantify.py: calc_time_until_capture_blockages

#15 kdoroschak closed 4 years ago
0
Build a docker image in the pipeline

#14 thequicksort closed 4 years ago
1
Debug pytest discovery

#13 kdoroschak closed 4 years ago
0
Logger best practices?

#12 kdoroschak closed 4 years ago
1
Define inputs to calc_time_until_capture

#11 kdoroschak closed 4 years ago
0
Refactor peptide_quantifier_utils

#10 kdoroschak closed 3 years ago
1

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