Improve Testing #115

ctuguinay · 2023-07-07T00:45:49Z

Improve Testing

This PR addresses #58, #107, #85, #112, #113, #99, #53, #28, #120:

Created and used a new testing suite: New EVL, new EVR, new Zarr file
New testing suite resolved the warning that arose from Warnings that arose from PR #81 #85
Refactored tests
Added fixtures
Added hints
Added marks
Added/improved upon numpy docstrings for tests and fixtures
Added further tests for Lines and Regions2D
Added functionality and tests for EVR parser to handle missing bbox values and no regions
Removed the unused convert_points function
Fixes docstrings that appeared as errors in the readthedocs
Used Pathlib instead of OS

* add transect zarr from valentina * add transect evl and evr from subsampled transect evl and evr files

* add transect (zarr and evl) testing for lines

* remove computing since dask does this automatically in masking

* add compute data

* make sure that all values are within time range

* remove unused helper functions * remove old evr and nc file and replace with new evr and new zarr file

* sometimes M.data is computed automatically and sometimes it is not, so in the case where it is, we capture it in an exception

* add markers into pytest.ini

* rename test_lines file * check type for da_Sv * add marks * add fixtures * add numpy docstring * add hints * create test for mask errors * create test for masking empty lines object * create test checking for correct parsing values

* add more type hints for test_lines

* remove and replace redundant data_dir * add comments

* rename test_r2d to test_regions2d * add fixtures * add marks * add test for parsing * add test for to csv * add numpy docstrings * add hints

* test_convert's tests have been moved to other test files

* add marks * add type hints * add short merge test * add TODO

codecov · 2023-07-07T00:47:37Z

Codecov Report

Merging #115 (467a26a) into main (25a4518) will increase coverage by 4.42%.
The diff coverage is 89.65%.

@@            Coverage Diff             @@
##             main     #115      +/-   ##
==========================================
+ Coverage   80.21%   84.64%   +4.42%     
==========================================
  Files          13       13              
  Lines         551      534      -17     
==========================================
+ Hits          442      452      +10     
+ Misses        109       82      -27

Files Changed	Coverage Δ
echoregions/utils/api.py	`76.38% <ø> (ø)`
echoregions/utils/time.py	`82.75% <75.00%> (-2.43%)`	⬇️
echoregions/regions2d/regions2d.py	`83.72% <80.00%> (+3.20%)`	⬆️
echoregions/lines/lines.py	`91.76% <100.00%> (+3.81%)`	⬆️
echoregions/regions2d/regions2d_parser.py	`100.00% <100.00%> (+4.34%)`	⬆️
echoregions/utils/__init__.py	`100.00% <100.00%> (ø)`
echoregions/utils/io.py	`67.56% <100.00%> (+22.88%)`	⬆️

... and 1 file with indirect coverage changes

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

* create parser code to handle empty regions and return empty dataset * create test for empty region * create data for empty region

* remove old tests

* implement read_evr handle missing bbox * create test data for missing bbox * create test for missing bbox

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

* dask computing is imprecise, so we use non-exact tests for tested values

* add todo for spline and krogh * remove krogh * add other interp options

* fix docstring in convert mask functions

* remove test_r2d (merge conflict)

* add r2d conversion mask tests from deleted test_r2d.py

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

* remove convert points * fix select region docstring

* cosmetic print changes

* remove test directory comment

* refactor test and test data in response to main merge

* update within_transect tests for cleanliness

* add new within_transect test data

ctuguinay · 2023-07-25T17:45:39Z

Hey, could you guys take a look at this PR when you are free? @leewujung @valentina-s

Mostly fixing up tests and some cosmetic/documentation modifications. Nothing really changed with functionality.

valentina-s

The fixture make the data loading for the tests really smooth! The tests look good, I added a few very minor comments.

valentina-s · 2023-07-28T22:26:19Z

echoregions/tests/test_lines.py

+        end_time=end_date,
+        max_depth=800,
+        fill_between=True,
+    )


did you intend to test compare this one against some plot or plot property or just want to see if it runs?

To see if it runs!

valentina-s · 2023-07-29T21:47:44Z

echoregions/tests/test_regions2d.py

+
+    Parameters
+    ----------
+    lines_fixture : Lines


regions2d_fixture : Regions2D

Just fixed.

valentina-s · 2023-07-30T02:10:11Z

echoregions/tests/test_regions2d.py

+    # within-transect.
+    assert len(list(np.unique(M.data))) == 1
+    assert list(np.unique(M.data))[0] == 1
+


test the dimensions, and the 0 values, in case we change something in the future.

Tested the 0 index values by checking counts and tested for M's dimensions.

valentina-s · 2023-07-30T02:14:14Z

echoregions/tests/test_regions2d.py

+
+
+@pytest.mark.regions2d
+def test_select_sonar_file(regions2d_fixture: Regions2D) -> None:


maybe test the case when sonar filenames do not follow expected format. Can also add in the documentation of the select_sonar_file that is specific to SIMRAD format and write it out how it looks like.

Sounds good. Added a test and checks for valid SIMRAD and sonar_file_inputs.

* fix test EVR to file documentation * add test for dimensions and 1 values for test_within_transect * add test for selection of bad sonar files and add code for checking for invalid inputs for SIMRAD parsing * add documentation for explaining SIMRAD format.

* change raw_fname from str to list

ctuguinay · 2023-07-31T17:57:48Z

Hey @valentina-s, just addressed your comments in the most recent pushes!

valentina-s · 2023-08-01T03:43:50Z

echoregions/tests/test_regions2d.py

    # This entire .zarr file should be covered by the single start and end transect period
    # found in the EVR file, so the only values listed should be 1, implying everything is
    # within-transect.
    assert len(list(np.unique(M.data))) == 1
    assert list(np.unique(M.data))[0] == 1

+    # Test number of 1 values
+    assert np.unique(M.data, return_counts=True)[1][0] == 6648355


I was thinking to test the actual shape, in case in future we transpose something.

* use isinstance instead of type for region_ids checking

* check for M.shape instead of M.sizes

ctuguinay added 15 commits July 5, 2023 17:43

add transect zarr, evl, evr files

86b829f

* add transect zarr from valentina * add transect evl and evr from subsampled transect evl and evr files

add transect testing for lines

ef60f56

* add transect (zarr and evl) testing for lines

remove compute

df673d5

* remove computing since dask does this automatically in masking

lines testing

bd0ff61

* add compute data

make time indexing stricter

4cd5538

* make sure that all values are within time range

initial revamp of test_r2d

ac809ba

* remove unused helper functions * remove old evr and nc file and replace with new evr and new zarr file

add attribute error

0980bf7

* sometimes M.data is computed automatically and sometimes it is not, so in the case where it is, we capture it in an exception

add markers into pytest.ini

8632294

* add markers into pytest.ini

revamp test_lines

19823ac

* rename test_lines file * check type for da_Sv * add marks * add fixtures * add numpy docstring * add hints * create test for mask errors * create test for masking empty lines object * create test checking for correct parsing values

add more type hints test_lines

6f0ecfa

* add more type hints for test_lines

remove data_dir

e0498ac

* remove and replace redundant data_dir * add comments

revamp regions2d

5c55df4

* rename test_r2d to test_regions2d * add fixtures * add marks * add test for parsing * add test for to csv * add numpy docstrings * add hints

remove test_convert

7aac1d2

* test_convert's tests have been moved to other test files

update test_utils

71bda87

* add marks * add type hints * add short merge test * add TODO

Merge branch 'main' into improve_testing

57fa1f6

ctuguinay added enhancement tests labels Jul 7, 2023

ctuguinay added this to the Refactor echoregions (first release) milestone Jul 7, 2023

ctuguinay self-assigned this Jul 7, 2023

This was linked to issues Jul 7, 2023

Revamp testing suite with new converted file from echopype 0.7.1 #58

Closed

Warnings that arose from PR #81 #85

Closed

Regions2d Replace Nan Depth Bug #98

Closed

Increase Test Coverage #107

Closed

ctuguinay removed a link to an issue Jul 7, 2023

Regions2d Replace Nan Depth Bug #98

Closed

1 task

ctuguinay and others added 4 commits July 7, 2023 09:58

ensure evr parser can handle zero regions

72fafe7

* create parser code to handle empty regions and return empty dataset * create test for empty region * create data for empty region

remove old tests

96a0520

* remove old tests

handle evr missing bbox

ea95516

* implement read_evr handle missing bbox * create test data for missing bbox * create test for missing bbox

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

75846f5

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

ctuguinay linked an issue Jul 7, 2023 that may be closed by this pull request

Ensure read_evr handle .evr files with zero regions #112

Closed

ctuguinay and others added 14 commits July 10, 2023 14:01

make less precise test_lines

e6d5d46

* dask computing is imprecise, so we use non-exact tests for tested values

update line mask interp methods

f8b4988

* add todo for spline and krogh * remove krogh * add other interp options

Merge branch 'main' into improve_testing

9f8a39d

fix docstring

b81a8b1

* fix docstring in convert mask functions

remove test_r2d

1158761

* remove test_r2d (merge conflict)

add r2d conversion mask tests

2dd07ff

* add r2d conversion mask tests from deleted test_r2d.py

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

a144ad3

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

remove convert points

bfe3359

* remove convert points * fix select region docstring

Merge branch 'main' into improve_testing

3a32181

cosmetic print changes

45ecdc5

* cosmetic print changes

remove test directory comment

e20a448

* remove test directory comment

refactor based on main merge

7c08af4

* refactor test and test data in response to main merge

update within_transect tests

7d4ddde

* update within_transect tests for cleanliness

add new within_transect test data

19337f4

* add new within_transect test data

ctuguinay marked this pull request as ready for review July 25, 2023 17:44

ctuguinay requested review from valentina-s and leewujung July 25, 2023 17:44

valentina-s approved these changes Jul 30, 2023

View reviewed changes

ctuguinay added 2 commits July 31, 2023 10:41

fix SIMRAD utils test

45dce17

* change raw_fname from str to list

This was linked to issues Jul 31, 2023

Use pathlib instead of os #28

Closed

Synchronize point conversion steps in masking functionality #53

Closed

Remove / Use Convert Points Function #99

Closed

valentina-s reviewed Aug 1, 2023

View reviewed changes

ctuguinay added 2 commits August 2, 2023 13:06

use isinstance instead of type

d037d16

* use isinstance instead of type for region_ids checking

check for M shape

467a26a

* check for M.shape instead of M.sizes

ctuguinay linked an issue Aug 2, 2023 that may be closed by this pull request

Fix type checkings to isinstance #120

Closed

ctuguinay merged commit 36d7eaf into OSOceanAcoustics:main Aug 2, 2023
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Improve Testing #115

Improve Testing #115

ctuguinay commented Jul 7, 2023 •

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ctuguinay commented Jul 31, 2023

valentina-s Aug 1, 2023



		@pytest.mark.regions2d
		def test_select_sonar_file(regions2d_fixture: Regions2D) -> None:

Improve Testing #115

Improve Testing #115

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