Remove Cli #1444
Remove Cli #1444
Conversation
Codecov Report
@@ Coverage Diff @@
## master #1444 +/- ##
==========================================
- Coverage 89.78% 87.42% -2.36%
==========================================
Files 161 139 -22
Lines 5972 5178 -794
==========================================
- Hits 5362 4527 -835
- Misses 610 651 +41
Continue to review full report at Codecov.
|
| @@ -57,9 +57,6 @@ jobs: | |||
| - name: 3D smFISH data processing example | |||
| if: type = push and branch =~ /^(master|merge)/ | |||
| script: make install-dev 3d_smFISH.py | |||
| - name: iss_cli.sh data processing example | |||
There was a problem hiding this comment.
You can plausibly remove the Makefile rules for running .sh data processing examples.
| from starfish.core.image.Filter.reduce import Reduce | ||
|
|
||
|
|
||
| methods: Mapping[str, Type] = { |
There was a problem hiding this comment.
Can you just do a dir(Filter) to get this?
There was a problem hiding this comment.
I tried this and it doesn't quite give me what I need. ['Bandpass', 'Clip', 'ClipPercentileToZero', 'ClipValueToZero', 'DeconvolvePSF', 'ElementWiseMultiply', 'GaussianHighPass', 'GaussianLowPass', 'Laplace', 'LinearUnmixing', 'MatchHistograms', 'MaxProject', 'MeanHighPass', 'Reduce', 'WhiteTophat', 'ZeroByChannelMagnitude', '__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', '_base', 'bandpass', 'clip', 'clip_percentile_to_zero', 'clip_value_to_zero', 'element_wise_mult', 'gaussian_high_pass', 'gaussian_low_pass', 'laplace', 'linear_unmixing', 'match_histograms', 'max_proj', 'mean_high_pass', 'reduce', 'richardson_lucy_deconvolution', 'util', 'white_tophat', 'zero_by_channel_magnitude'] but I think the refactor to make another clever auto import method will work when I do that!
| @@ -75,20 +75,6 @@ origin. At this point, it's trivial to create a cell x gene matrix. | |||
|
|
|||
| tutorials/exec_feature_identification_and_annotation.rst | |||
|
|
|||
| Putting Together a Pipeline Recipe and Running it | |||
There was a problem hiding this comment.
Are we dropping the recipe runner?
There was a problem hiding this comment.
I took out all the recipe stuff :/ should leave the runner in?
|
|
||
| :: | ||
|
|
||
| $ starfish validate experiment tmp/experiment.json |
There was a problem hiding this comment.
Do we want to preserve some documentation about starfish validate?
There was a problem hiding this comment.
I still have just the validate documentation in but I took out the builder bit
There was a problem hiding this comment.
It is plausible that we want to retain the example about validating an existing experiment.
| @@ -57,9 +57,6 @@ jobs: | |||
| - name: 3D smFISH data processing example | |||
| if: type = push and branch =~ /^(master|merge)/ | |||
| script: make install-dev 3d_smFISH.py | |||
| - name: iss_cli.sh data processing example | |||
|
|
||
| :: | ||
|
|
||
| $ starfish validate experiment tmp/experiment.json |
There was a problem hiding this comment.
It is plausible that we want to retain the example about validating an existing experiment.
| from starfish.core.image.Filter.reduce import Reduce | ||
|
|
||
|
|
||
| methods: Mapping[str, Type] = { |
Co-Authored-By: Tony Tung <ttung@chanzuckerberg.com>
|
This broke the docker test. |
Remove CLI code and pipeline component class.
Rename package names so that the algorithms can be used in the same way, ex.
Changed AlgorithmBase to be the MetaClass for logging.
Everything api-wise should work the same. Everything cli-wise should be removed.
One exception was the starfish validate command. Also I kept the ascii art cause that's essential