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"Standard" directories, testing and Travis #15

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"Standard" directories, testing and Travis #15

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amarburg
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@amarburg amarburg commented Sep 4, 2018

I took one step towards the "standard" directory structure, including unit testing and Travis integration (issue #4). It requires a big shuffling of all of the code, so it is somewhat disruptive.

To run the tests, you must manually download Y1801_EK60-D20180211-T164025.raw into the test/data/ directory (see comment on issue #5 (comment))

For simple testing, run "pytest" from the top level.

@leewujung
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So we've been working on the same thing 😂 more to learn about managing issues!
I'll push up mine and merge with yours. Probably need to mess around with merge.

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amarburg commented Sep 4, 2018

Great! I'll check out the new version tonight.

@amarburg amarburg closed this Sep 7, 2018
leewujung added a commit that referenced this pull request Dec 22, 2022
@leewujung @b-reyes
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Test merge split beam angle (#15)
ad48768 
* create general structure of add_splitbeam_angle function

* create simrad.py and start working on a check of the waveform and encode modes

* rearange and improve logic for checking the encode and waveform modes

* finish documenting functions in simrad and finalizing their outputs, incorporate new waveform/encode mode check into calibrate_ek and consolidate api

* allow for 2 beam groups for waveform_mode=BB and add check_waveform_encode_mode to compute_Sv and compute_TS

* move core split-beam angle functions to split_beam_angle.py, finish implementation of _get_splitbeam_angle_power_CW, _add_splitbeam_angle_to_ds, add an empty test suite for echodata.simrad, and start working on test_add_splitbeam_angle

* make check_waveform_encode_mode return only the echodata group name corresponding to the encode mode

* change test_add_splitbeam_angle so that it takes a list of echoview mat paths, construct a function that creates a numpy array from mat paths, and select echodata beam_group data in add_splitbeam_angle based on ds channel dims

* add pulse_compression input to add_splitbeam_angle, implement (CW, complex) and (BB, complex, no pulse compression) options, and create tests for them

* modify test_add_splitbeam_angle pytest parameters to account for data location, finish docstring for add_splitbeam_angle, drop beam wherever necessary

* add comment at the top of test_consolidate.py specifying where the split-beam angle tests data exists

* creat apply_mask function without implementing it

* create general structure implementation of apply_mask

* create first simple test for apply_mask with mock Dataset creation

* create apply_mask paramter test for when mask is a list of DataArrays

* change the function name validate_source_ds to validate_source_ds_da and allow it to handle a DataArray input, modify existing tests for validate_source_ds

* create routines that check the input of apply_mask and form the inputs for the core method in apply_mask

* allow get_mock_source_ds_apply_mask to produced delayed variables and add associated test in test_apply_mask

* add code and parameters to test_apply_mask to test for a mask that is provided as a path

* add tests for different fill_value types and accout for type(fill_value)=DataArray conflict with xr.where

* correct docstring in _check_mode_input_without_data

Co-authored-by: Wu-Jung Lee <[email protected]>

* raise ValueError instead of RuntimeError in _check_mode_input_without_data

* remove TODO in _check_mode_input_with_data_EK60

* improve grammar in error output in _check_mode_input_with_data_EK80

Co-authored-by: Wu-Jung Lee <[email protected]>

* remove check for EK80-like sensors in _check_mode_input_with_data_EK80 as it is not necessary

* improve docstring function description for add_splitbeam_angle

Co-authored-by: Wu-Jung Lee <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* remove States in pulse_compression docstring description

Co-authored-by: Wu-Jung Lee <[email protected]>

* improve logic associated with split-beam angle function calls in add_splitbeam_angle

Co-authored-by: Wu-Jung Lee <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* remove remnant else statement caused by GH commit in add_splitbeam_angle

* rename _check_mode_input_without_data to _check_input_args_combination

* add reminder to add a test for _check_input_args_combination

* change _check_mode_input_with_data_EK60/EK80 to _retrieve_correct_beam_group_EK60/EK80

* rename check_waveform_encode_mode to retrieve_correct_beam_group

* finish constructing test_check_input_args_combination

* remove reference to MVBS for ds input in add_splitbeam_angle function

Co-authored-by: Wu-Jung Lee <[email protected]>

* rename ds to source_Sv in add_splitbeam_angle

* allow source_Sv to be a Dataset, str, or pathlib.Path

* add return_dataset argument to add_splitb_ang and modify _add_splitbeam_angle_to_ds so that it will write the data to a zarr or netcdf, if necessary

* remove auto chunking when opening a Dataset since netcdf files have issues with this and free resources linked to ds in _add_splitbeam_angle_to_ds as netcdf also has an issue if the file remains open

* modify test_add_splitbeam_angle to allow writing ds_Sv to a file and add associated test parameters

* raise not implemented error if source_Sv corresponds to MVBS

* implement split-beam angle calculation for waveform_mode=BB, encode_mode=complex, and pulse_compression=False, and add corresponding test

* Improve documentation by clarifying statements

Co-authored-by: Wu-Jung Lee <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* remove whitespace caused by GH commit

* replace RuntimeError with ValueError

* replace chunks=auto with chunks={}

* add default value to apply_mask input var_name and modify documentation accordingly

* Fix meta_source_filenames bug and enable (meta)source_filenames appending of path and list (#908)

* Expand prov.source_files_vars to support path sequences that mix a str/path and another sequence

* For EK80, ES70, ES80, EA640, conversion was inserting an unnecessary, empty meta_source_filenames variable

* Add more comprehensive and readable prov source-files type hints; rename _source_files

* Fix prov type hint bug with Py 3.8

* Add unit test for prov _sanitize_source_files; plus small fixes to np.ndarray type references in prov

* fix validate_source_ds to validate_source_ds_da

* improve Notes section in docstring for add_splitbeam_angle

Co-authored-by: Wu-Jung Lee <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* clarify when the split-beam angle data potentially exist

Co-authored-by: Wu-Jung Lee <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix long lines

* Add clarification in NotImplemented error statement

Co-authored-by: Wu-Jung Lee <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* split up line in NotImplemented error statement

* rename function compute_split_beam_beamtype1 to _e2f

* put radian to degree conversion on one line

Co-authored-by: Wu-Jung Lee <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* change sin to arcsin

Co-authored-by: Wu-Jung Lee <[email protected]>

* remove unnecessary statement

Co-authored-by: Wu-Jung Lee <[email protected]>

* replace RuntimeError with ValueError

* change theta_fc --> theta and phi_fc --> phi

* allow splitbeam calculation for power and CW options when beam_type is not equal to zero

* replace core functions in _get_splitbeam_angle_complex_CW with get_splitbeam and then remove them

* shorten function names, minor docstring tweaks

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* add TODO to test

* fix bug in logic for at least 1 channel being split-beam

Co-authored-by: b-reyes <[email protected]>
Co-authored-by: b-reyes <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Emilio Mayorga <[email protected]>
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@amarburg @leewujung