click: implement option subclass (see #808) (#809)

* click: implement option subclass (see #808)

* Fix rebase conflicted import

* cli: add explicit tests

Note: BlobDetector is not being printed due to the new decorator.

* click: add workaround for explicit help

* click: properly dispatch to deepest subcommand

* ws: unwrap doc to ~100

* Minor test adjustments

* click: move all to `starfish.util.click`

* click: handle parse_results bottom-out

* Update help text test for origin/master

* Simplify help tests

examples/format_osmfish.py

@@ -4,13 +4,13 @@
 import re
 from typing import Mapping, Tuple, Union
 
-import click
 import numpy as np
 from slicedimage import ImageFormat
 
 import starfish.util.try_import
 from starfish.experiment.builder import FetchedTile, TileFetcher, write_experiment_json
 from starfish.types import Coordinates, Features, Indices, Number
+from starfish.util import click
 
 
 # We use this to cache images across tiles.  In the case of the osmFISH data set, volumes are saved

examples/get_imc_data.py

@@ -2,13 +2,13 @@
 import os
 from typing import List, Mapping, Tuple, Union
 
-import click
 import numpy as np
 from skimage.io import imread
 from slicedimage import ImageFormat
 
 from starfish.experiment.builder import FetchedTile, TileFetcher, write_experiment_json
 from starfish.types import Coordinates, Features, Indices, Number
+from starfish.util import click
 
 
 class ImagingMassCytometryTile(FetchedTile):

sptx_format/cli.py

@@ -1,6 +1,5 @@
-import click
-
 from sptx_format import validate_sptx
+from starfish.util import click
 
 
 @click.command()

sptx_format/validate_sptx.py

@@ -3,11 +3,11 @@
 import sys
 from typing import Dict
 
-import click
 from pkg_resources import resource_filename
 from slicedimage.io import resolve_path_or_url
 
 from starfish.config import StarfishConfig
+from starfish.util import click
 from .util import SpaceTxValidator
 
 

starfish/experiment/builder/cli.py

@@ -1,9 +1,9 @@
 import json
 
-import click
 from slicedimage import ImageFormat
 
 from starfish.types import Indices
+from starfish.util import click
 from . import AUX_IMAGE_NAMES, write_experiment_json
 
 

starfish/image/_filter/__init__.py

@@ -1,9 +1,8 @@
 from typing import Type
 
-import click
-
 from starfish.imagestack.imagestack import ImageStack
 from starfish.pipeline import AlgorithmBase, import_all_submodules, PipelineComponent
+from starfish.util import click
 from . import _base
 import_all_submodules(__file__, __package__)
 

starfish/image/_filter/bandpass.py

@@ -1,12 +1,12 @@
 from functools import partial
 from typing import Optional
 
-import click
 import numpy as np
 from trackpy import bandpass
 
 from starfish.imagestack.imagestack import ImageStack
 from starfish.types import Number
+from starfish.util import click
 from ._base import FilterAlgorithmBase
 from .util import determine_axes_to_group_by, preserve_float_range
 

starfish/image/_filter/clip.py

@@ -1,10 +1,10 @@
 from functools import partial
 from typing import Optional
 
-import click
 import numpy as np
 
 from starfish.imagestack.imagestack import ImageStack
+from starfish.util import click
 from ._base import FilterAlgorithmBase
 from .util import determine_axes_to_group_by
 

starfish/image/_filter/gaussian_high_pass.py

@@ -1,13 +1,13 @@
 from functools import partial
 from typing import Callable, Optional, Tuple, Union
 
-import click
 import numpy as np
 import xarray as xr
 
 from starfish.image._filter.gaussian_low_pass import GaussianLowPass
 from starfish.imagestack.imagestack import ImageStack
 from starfish.types import Number
+from starfish.util import click
 from ._base import FilterAlgorithmBase
 from .util import (
     determine_axes_to_group_by,

starfish/image/_filter/gaussian_low_pass.py

@@ -1,12 +1,12 @@
 from functools import partial
 from typing import Callable, Optional, Tuple, Union
 
-import click
 import numpy as np
 from skimage.filters import gaussian
 
 from starfish.imagestack.imagestack import ImageStack
 from starfish.types import Number
+from starfish.util import click
 from ._base import FilterAlgorithmBase
 from .util import (
     determine_axes_to_group_by,

starfish/image/_filter/laplace.py

@@ -2,7 +2,6 @@
 from functools import partial
 from typing import Callable, Optional, Tuple, Union
 
-import click
 import numpy as np
 from scipy.ndimage import gaussian_laplace
 
@@ -14,6 +13,7 @@
 )
 from starfish.imagestack.imagestack import ImageStack
 from starfish.types import Number
+from starfish.util import click
 
 
 class Laplace(FilterAlgorithmBase):

starfish/image/_filter/max_proj.py

@@ -1,9 +1,8 @@
 from typing import Optional
 
-import click
-
 from starfish.imagestack.imagestack import ImageStack
 from starfish.types import Indices
+from starfish.util import click
 from ._base import FilterAlgorithmBase
 
 

starfish/image/_filter/mean_high_pass.py

@@ -1,12 +1,12 @@
 from functools import partial
 from typing import Callable, Optional, Tuple, Union
 
-import click
 import numpy as np
 from scipy.ndimage.filters import uniform_filter
 
 from starfish.imagestack.imagestack import ImageStack
 from starfish.types import Number
+from starfish.util import click
 from ._base import FilterAlgorithmBase
 from .util import (
     determine_axes_to_group_by, preserve_float_range, validate_and_broadcast_kernel_size

starfish/image/_filter/richardson_lucy_deconvolution.py

@@ -1,12 +1,12 @@
 from functools import partial
 from typing import Optional
 
-import click
 import numpy as np
 from scipy.signal import convolve, fftconvolve
 
 from starfish.imagestack.imagestack import ImageStack
 from starfish.types import Indices, Number
+from starfish.util import click
 from ._base import FilterAlgorithmBase
 from .util import gaussian_kernel, preserve_float_range
 

starfish/image/_filter/scale_by_percentile.py

@@ -1,10 +1,10 @@
 from functools import partial
 from typing import Optional
 
-import click
 import numpy as np
 
 from starfish.imagestack.imagestack import ImageStack
+from starfish.util import click
 from ._base import FilterAlgorithmBase
 from .util import determine_axes_to_group_by, preserve_float_range
 

starfish/image/_filter/white_tophat.py

@@ -1,10 +1,10 @@
 from typing import Optional
 
-import click
 import numpy as np
 from skimage.morphology import ball, disk, white_tophat
 
 from starfish.imagestack.imagestack import ImageStack
+from starfish.util import click
 from ._base import FilterAlgorithmBase
 from .util import determine_axes_to_group_by
 

starfish/image/_filter/zero_by_channel_magnitude.py

@@ -1,13 +1,13 @@
 from copy import deepcopy
 from typing import Optional
 
-import click
 import numpy as np
 from tqdm import tqdm
 
 from starfish.config import StarfishConfig
 from starfish.imagestack.imagestack import ImageStack
 from starfish.types import Indices
+from starfish.util import click
 from ._base import FilterAlgorithmBase
 
 

starfish/image/_registration/__init__.py

@@ -1,9 +1,8 @@
 from typing import Type
 
-import click
-
 from starfish.imagestack.imagestack import ImageStack
 from starfish.pipeline import AlgorithmBase, import_all_submodules, PipelineComponent
+from starfish.util import click
 from . import _base
 import_all_submodules(__file__, __package__)
 

starfish/image/_registration/fourier_shift.py

@@ -1,14 +1,14 @@
 from copy import deepcopy
 from typing import Optional, Tuple, Union
 
-import click
 import numpy as np
 from scipy.ndimage import fourier_shift
 from skimage.feature import register_translation
 
 from starfish.image._filter.util import preserve_float_range
 from starfish.imagestack.imagestack import ImageStack
 from starfish.types import Indices
+from starfish.util import click
 from ._base import RegistrationAlgorithmBase
 
 

starfish/image/_segmentation/__init__.py

@@ -1,10 +1,10 @@
 from typing import Type
 
-import click
 from skimage.io import imsave
 
 from starfish.imagestack.imagestack import ImageStack
 from starfish.pipeline import AlgorithmBase, import_all_submodules, PipelineComponent
+from starfish.util import click
 from . import _base
 import_all_submodules(__file__, __package__)
 

starfish/image/_segmentation/watershed.py

@@ -1,6 +1,5 @@
 from typing import Optional, Tuple
 
-import click
 import numpy as np
 import scipy.ndimage.measurements as spm
 from scipy.ndimage import distance_transform_edt
@@ -11,6 +10,7 @@
 from starfish.image._filter.util import bin_open, bin_thresh
 from starfish.imagestack.imagestack import ImageStack
 from starfish.types import Indices, Number
+from starfish.util import click
 from ._base import SegmentationAlgorithmBase
 
 

starfish/spots/_decoder/__init__.py

@@ -1,10 +1,9 @@
 from typing import Type
 
-import click
-
 from starfish.codebook.codebook import Codebook
 from starfish.intensity_table.intensity_table import IntensityTable
 from starfish.pipeline import AlgorithmBase, import_all_submodules, PipelineComponent
+from starfish.util import click
 from . import _base
 
 import_all_submodules(__file__, __package__)

starfish/spots/_decoder/per_round_max_channel_decoder.py

@@ -1,7 +1,6 @@
-import click
-
 from starfish.codebook.codebook import Codebook
 from starfish.intensity_table.intensity_table import IntensityTable
+from starfish.util import click
 from ._base import DecoderAlgorithmBase
 
 

starfish/spots/_detector/__init__.py

@@ -1,11 +1,10 @@
 from typing import Type
 
-import click
-
 from starfish.codebook.codebook import Codebook
 from starfish.imagestack.imagestack import ImageStack
 from starfish.pipeline import AlgorithmBase, import_all_submodules, PipelineComponent
 from starfish.types import Indices
+from starfish.util import click
 from . import _base
 
 import_all_submodules(__file__, __package__)

starfish/spots/_detector/blob.py

@@ -1,6 +1,5 @@
 from typing import Optional, Union
 
-import click
 import numpy as np
 import pandas as pd
 import xarray as xr
@@ -9,6 +8,7 @@
 from starfish.imagestack.imagestack import ImageStack
 from starfish.intensity_table.intensity_table import IntensityTable
 from starfish.types import Features, Indices, Number, SpotAttributes
+from starfish.util import click
 from ._base import SpotFinderAlgorithmBase
 from .detect import detect_spots, measure_spot_intensity
 

starfish/spots/_detector/local_max_peak_finder.py

@@ -1,6 +1,5 @@
 from typing import List, Optional, Tuple, Union
 
-import click
 import numpy as np
 import pandas as pd
 import xarray as xr
@@ -14,6 +13,7 @@
 from starfish.imagestack.imagestack import ImageStack
 from starfish.intensity_table.intensity_table import IntensityTable
 from starfish.types import Features, Indices, Number, SpotAttributes
+from starfish.util import click
 from ._base import SpotFinderAlgorithmBase
 from .detect import detect_spots
 

starfish/spots/_detector/pixel_spot_detector.py

@@ -1,11 +1,11 @@
 from typing import Tuple
 
-import click
 import numpy as np
 
 from starfish.codebook.codebook import Codebook
 from starfish.imagestack.imagestack import ImageStack
 from starfish.intensity_table.intensity_table import IntensityTable
+from starfish.util import click
 from ._base import SpotFinderAlgorithmBase
 from .combine_adjacent_features import CombineAdjacentFeatures, ConnectedComponentDecodingResult
 

starfish/spots/_detector/trackpy_local_max_peak_finder.py

@@ -1,14 +1,14 @@
 import warnings
 from typing import Optional, Tuple, Union
 
-import click
 import numpy as np
 import xarray as xr
 from trackpy import locate
 
 from starfish.imagestack.imagestack import ImageStack
 from starfish.intensity_table.intensity_table import IntensityTable
 from starfish.types import SpotAttributes
+from starfish.util import click
 from ._base import SpotFinderAlgorithmBase
 from .detect import detect_spots
 

starfish/spots/_target_assignment/__init__.py

@@ -1,11 +1,11 @@
 import os
 from typing import Type
 
-import click
 from skimage.io import imread
 
 from starfish.intensity_table.intensity_table import IntensityTable
 from starfish.pipeline import AlgorithmBase, PipelineComponent
+from starfish.util import click
 from . import label
 from ._base import TargetAssignmentAlgorithm
 

starfish/spots/_target_assignment/label.py

@@ -1,8 +1,8 @@
-import click
 import numpy as np
 
 from starfish.intensity_table.intensity_table import IntensityTable
 from starfish.types import Features, Indices
+from starfish.util import click
 from ._base import TargetAssignmentAlgorithm