Pytest revamp #743

CBroz1 · 2023-12-29T23:08:02Z

Description

Completely revises pytests to favor use of minirec as a data source. Avoids direct assertion of values read from data, instead favoring a cross-ref of data in tables with data in the raw file.

If coverage assessment is limited to common, lfp and utils subpackages, this PR increases coverage from 26% to 67%

Adjustments to package proper motivated by testing needs or linting suggestions
- .github/workflow/test-conda.yaml: add download of data from box
- ./pyproject.toml: Add docker package as tests dependency. Add config options for running tests
- common/common_device.py: use new test_mode boolean to determine if user should be prompted for confirmation. Centralize prompt logic to prompt_insert function to be used across all device tables.
- common_dio.py, common_filter.py, and common_interval.py: Add boolean flag for returning plots from functions. This permits tests to check then contents of plots. Do people use these plots or can they be deprecated?
- common_position: @edeno - did you make a release of the updated position_tools? Rather than set requirements to pull from git, I run a try/except import that falls back on get_centriod and log a warning.
- common_session: rewrap comment to 80c, permit *args, **kwargs for helper functions. This permits tests to pass safemode=False to avoid prompts.
- data_import/__init__.py add note regarding the naming collision across module and func insert_session. This caused some errors in testing I was able to overcome, but should be changed in the future.
- insert_sessions.py: warnings->logger to make printouts show as spyglass-specific
- decoding_merge.py: add noqa to pass pre-commit linter check
- settings.py: add test_mode to prevent prompts
- dj_merge_tables.py: typo on edge case
- dj_mixin.py: add refresh cache secondary check.
Increase coverage of common and lfp pipelines as first pass
- tests/readme: Developer notes
- tests/datajoint/etc -> container.py: remove kackery dependency as a wrapper on subprocess in favor of docker package designed for container management
- tests/*/conftest.py: home of fixtures shared across tests
- tests/{pipeline}/: reorganize to mirror package organization.
- test_interval: parameterize tests to run same funcs on expected input/output
- various: add pytest.mark.skip on items we don't expect to cover

Checklist:

This PR should be accompanied by a release: no
(If release) I have updated the CITATION.cff
I have updated the CHANGELOG.md
I have added/edited docs/notebooks to reflect the changes

src/spyglass/common/common_position.py

src/spyglass/common/common_session.py

src/spyglass/common/common_device.py

pyproject.toml

src/spyglass/common/common_session.py

tests/conftest.py

tests/data_import/test_insert_sessions.py

tests/old_tests.py

tests/utils/test_nwb_helper_fn.py

…to tests

- Add `return_fig` param to plotting helper functions to permit tests - `common_filter` - `common_interval` - Add coverage for ~1/2 of `common` - `common_behav` - `common_device` - `common_ephys` - `common_filter` - `common_interval` - with helper funcs tested seperately - `common_lab` - `common_nwbfile` - partial

…to tests

edeno

Just one minor change. I did make an updated position_tools release.

src/spyglass/common/common_filter.py

src/spyglass/data_import/insert_sessions.py

* Docs fixes: tidy decoding docstrings, change hatch version get, add inits * Pytest revamp (#743) * WIP: Pull from old stash, resolve conflicts * Pytest WIP. Position centriod fix. Centralize device prompt logic * Add tests for all tables in * WIP: Improve coverage behav, dio * WIP: Add coverage, see details: - Add `return_fig` param to plotting helper functions to permit tests - `common_filter` - `common_interval` - Add coverage for ~1/2 of `common` - `common_behav` - `common_device` - `common_ephys` - `common_filter` - `common_interval` - with helper funcs tested seperately - `common_lab` - `common_nwbfile` - partial * WIP pytest common 2nd half, start lfp * WIP lfp tests, ahead of fetch upstream * Add lfp pipeline tests * Run pre-commit checks * Fix bug * Unpin position_tools for CI * Change download data dir * Change download data dir 2 * Fix teardown. Coverage 67% * Update changelog * logger.warn -> logger.warning * Minor decoding fixes (#769) * Add non-local detector and remove replay_trajectory_classification * Reorganize * Fix formatting and imports * Update .gitignore * Remove because of circular import * Fix name of parameter * Handle case where ther is only one interval * Fix settings * Handle single interval * from_unit_dict does not exist in 0.98.2 of spike interface * Simplify call * Update for SpikeSorting merge table and add spyglass mixin * Fix dependencies * Fix merge conflict * Update src/spyglass/decoding/v1/clusterless.py Co-authored-by: Chris Brozdowski <[email protected]> * Update src/spyglass/decoding/v1/clusterless.py Co-authored-by: Chris Brozdowski <[email protected]> * Update src/spyglass/decoding/v1/clusterless.py Co-authored-by: Chris Brozdowski <[email protected]> * Update src/spyglass/decoding/v1/clusterless.py Co-authored-by: Chris Brozdowski <[email protected]> * Apply suggestions from code review Co-authored-by: Chris Brozdowski <[email protected]> * Remove unused imports and format * Add saving of waveform features * Don't store electrodes, full waveforms, waveform mean * Fix spike times and add convenience method * Add spike location and some formatting * Remove circular import * Fix dict expansion * Initial working clusterless pipeline * Add position group * Rename classifier to decoding * Handle encoding and decoding intervals * Put old files under v0, try/except for old decoding package * Rename visualization and remove from v0 v0 visualization is redundant with visualization * Place parameters and position group in core.py * Add sorted spikes decoding * Add objects to init for convenience * Remove unused imports * Fix fetching of spike times * Insert into merge table * Update CHANGELOG.md * Function for removing decoding outputs not in DecodingOutput * Fix name * Add draft of tutorials and rearrange notebooks * Fix config loading * Add 1D decoding and some notes on estimate_parameters kwarg * Update 43_Decoding_SortedSpikes.ipynb * Remove old decoding notebook * Save initial conditions and discrete transitions * Apply suggestions from code review Co-authored-by: Chris Brozdowski <[email protected]> * Be more specific with import error * Remove unneeded comments * Remove incorrect dimension name * Project merge_id from SpikeSortingOutput for clarity * Update src/spyglass/decoding/v0/clusterless.py Co-authored-by: Chris Brozdowski <[email protected]> * Update src/spyglass/decoding/v0/clusterless.py Co-authored-by: Chris Brozdowski <[email protected]> * Update src/spyglass/decoding/v0/clusterless.py Co-authored-by: Chris Brozdowski <[email protected]> * Fix linting * Update notebooks * Ignore .pem * Add session as a primary key for Groups * Add some helper methods * Update notebooks * Update README.md * Update pyscripts * Update 42_Decoding_Clusterless.ipynb * Update CHANGELOG.md * Add fetch and insert * Simplify class conversion * Do the dictionary conversion of class for the user * Update CHANGELOG.md * Update .gitignore * Use methods in populate * Avoid fetching interval range if not needed * Generalize finding class from modules * Use args/kwargs * Simplify tuple unpacking * Make decoding kwargs nullable * Add function for get_recording and get_sorting to the spikesorting merge table * make decoding waveform features agnostic to spikesorting source * Fix spelling * Use fetch1_dataframe for position * Use self instead of class * Update src/spyglass/decoding/v1/sorted_spikes.py Co-authored-by: Samuel Bray <[email protected]> * Be more careful about populating select keys * Make more readable/remove unused imports * Save classifier * Clean up saved model paths * add function load_linear_position_info * Update src/spyglass/decoding/v1/sorted_spikes.py Co-authored-by: Samuel Bray <[email protected]> * Update 41_Extracting_Clusterless_Waveform_Features.py * Update docstring * Apply suggestions from code review Co-authored-by: Chris Brozdowski <[email protected]> * Update src/spyglass/decoding/v1/clusterless.py Co-authored-by: Chris Brozdowski <[email protected]> * Update src/spyglass/decoding/v1/clusterless.py Co-authored-by: Chris Brozdowski <[email protected]> * Fix linting * Fix syntax * Rename variable to avoid confusion * Restrict UnitWaveformFeaturesGroup and SortedSpikesGroup * Concatenate linear position and position dataframes * Static methods don't require instantiating class * Avoid merge restrict * Add version to defaults * Remove unused import * Fix classifier path * Add dry run * Remove non-default * Handle permissions and file not found * Keep position info within encoding/decoding interval * Add methods to get the spike_times, spike_indicators, firing rate * Fix docstring to match default * Implement function rather than import * Remove unused broken imports * Add decoding cleanup * Fix import * Put old vis code back * Fix import * Add draft helper functions * Limit options on input * Fix logic * Fix where the key is passed * Update notebooks * Host main visualizations in non_local_detector repo * Update notebooks/py_scripts/41_Extracting_Clusterless_Waveform_Features.py Co-authored-by: Chris Brozdowski <[email protected]> * Update src/spyglass/spikesorting/merge.py Co-authored-by: Chris Brozdowski <[email protected]> * Update src/spyglass/decoding/decoding_merge.py Co-authored-by: Chris Brozdowski <[email protected]> * Revert "Limit options on input" This reverts commit 386714c. * Use f-string for version * Add useful imports to the top level This would have to change a bit if there were multiple versions of the pipeline. * Make source class a hidden attribute * Update CHANGELOG.md --------- Co-authored-by: Chris Brozdowski <[email protected]> Co-authored-by: Sam Bray <[email protected]> * DLC notebooks 21 and 22 (#772) * add envs to bashrc; multi cam addition * 12/11/23 using TackEpoch to define interval_names * 12/11/23 remove comment * del smooth duration * jan 10 again * DLC noteboks 5 and 6 * 5 and 6 * fix ignore and 21 * Removed submodule * removed .gitignore * DLC notebooks * Docs fixes: tidy decoding docstrings, change hatch version get, add inits * Jupysync, blackify, purge old .py nbs * Docs updates for new notebooks * Update changelog * Spell fix, pre-commit --------- Co-authored-by: Eric Denovellis <[email protected]> Co-authored-by: Sam Bray <[email protected]> Co-authored-by: emreybroyles <[email protected]>

CBroz1 added 2 commits December 22, 2023 11:43

WIP: Pull from old stash, resolve conflicts

8800f99

Pytest WIP. Position centriod fix. Centralize device prompt logic

03be7d4

CBroz1 commented Dec 29, 2023

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src/spyglass/common/common_position.py Outdated Show resolved Hide resolved

CBroz1 commented Dec 29, 2023

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CBroz1 added 5 commits January 5, 2024 17:43

Add tests for all tables in

0c3d000

Merge branch 'master' of https://github.com/LorenFrankLab/spyglass in…

8e15822

…to tests

WIP: Improve coverage behav, dio

7ff01ad

WIP pytest common 2nd half, start lfp

468ae2d

CBroz1 mentioned this pull request Jan 12, 2024

Print session/exp summary, fix lfp target sample fetch #762

Merged

4 tasks

CBroz1 added 9 commits January 12, 2024 14:34

WIP lfp tests, ahead of fetch upstream

61d8325

Merge branch 'master' of https://github.com/LorenFrankLab/spyglass in…

23fdeef

…to tests

Add lfp pipeline tests

4fad2e1

Run pre-commit checks

6fdb0cc

Fix bug

5d0b15f

Unpin position_tools for CI

ef3d85e

Change download data dir

770e53e

Change download data dir 2

e8c1911

Fix teardown. Coverage 67%

dce1530

edeno mentioned this pull request Jan 18, 2024

Minor decoding fixes #769

Merged

4 tasks

Update changelog

344ca0b

CBroz1 marked this pull request as ready for review January 18, 2024 16:54

CBroz1 requested a review from edeno January 18, 2024 16:55

edeno requested changes Jan 19, 2024

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src/spyglass/common/common_filter.py Show resolved Hide resolved

src/spyglass/data_import/insert_sessions.py Outdated Show resolved Hide resolved

logger.warn -> logger.warning

587e231

edeno approved these changes Jan 19, 2024

View reviewed changes

edeno merged commit 0089d5e into LorenFrankLab:master Jan 19, 2024
7 checks passed

CBroz1 deleted the tests branch February 9, 2024 15:39

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Pytest revamp #743

Pytest revamp #743

CBroz1 commented Dec 29, 2023 •

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Pytest revamp #743

Pytest revamp #743

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