RFC: Fix Unit Tests #108

simmsa · 2023-11-17T23:41:12Z

Status

Request for Comment
- This pull request is open for comments and feedback. Please review the changes and provide any necessary input.

Summary of Changes

Continuation of ebbflood branch
Fix GitHub actions/workflow
- Linux, macOS, and Windows Units are performing nominally
Fix/update failing unit tests where possible
- 100% (151 / 151) of test cases are passing
Improve code style
Update toolbox to version 0.4.1

Detail of Changes

This PR

Actions/Workflow

Separate Unix (MacOS & Linux) and Windows unit tests into separate workflow files
Use Anaconda to install Python and required packages
Pass Anaconda version of python to MATLAB
Add version matrix of MATLAB and Python
- Python: 3.8 - 3.11
- MATLAB: R2021b to R2023b
- Exclude Python/MATLAB combinations that are not supported
  - 15 different combinations on each operating system
- Exclude combinations that are error out when calling Python from MATLAB
  - Windows MATLAB > 2022a
  - MacOS MATLAB latest
Add caching/artifact for hindcast data calls
- This API is rate limited and the tests make successive requests causes intermittent failures in test_WPTO_point_multiloc and test_WPTO_point_multiparm.
- Adds a cache_population job that runs a test with caching enable before the main job
  - Caches api call results in mhkit_webread_cache
  - main job reads in mhkit_webread_cache and uses the cache

Tests

151/151 of known good unit tests are passing
Addresses issue 1st Time user error log #77

Fixed Tests

This PR fixes or adds the following tests:

Loads_TestExtreme
- test_mler_coefficients (b40f427)
QC_Test:
- test_check_corrupt (83dbc31)
- test_check_delta (83dbc31)
- test_check_increment (83dbc31)
- test_check_missing (83dbc31)
- test_check_timestamp (83dbc31)
River_TestDevice
- test_circular (42c9a58)
  - This MHKiT-Python commit changes the value of this calculation, and this fix updates the assertion.
River_TestResource
- test_exceedance_probability (cd0271d)
  - Setup Q as a struct with Discharge and time keys
Tidal_TestIO:
- test_request_noaa_data (e2613e4)
Tidal_TestResource:
- test_plot_phase_exceedance (30ead68)
Wave_TestResourceMetrics:
- test_metrics_HsP (40cd75e)
- test_metrics_AH (40cd75e)
- test_metrics_CDIP1 (40cd75e)
- test_plot_elevation_timeseries (1b973e4)
- test_energy_flux_deep (40cd75e)
Wave_TestResourceSpectrum
- test_surface_elevation_seed (a0cb0ef)
- test_surface_elevation_phasing (e2f6080)
- test_surface_elevation_moments (b0d93bb)

Added Tests

Python_Import
- Add test to verify Python import mhkit performs nominally
- Add test to verify Python import pandas performs nominally
- Add test to verify Python import h5py performs nominally
- Add test to verify operation of MHKiT Python per Test MHKiT-Python installation
Python_IO
- Add Tests to verify MATLAB -> Python -> MATLAB serialization for different types
  - This is a WIP/Proof of Concept
  - Finishing this is out of scope for this PR. Future work could/should include expanding these tests

Warnings

Fix warnings caused by importing python libraries that have functions with the same name as MATLAB functions (be70376)
- Remove every call of py.importlib.import_module('numpy');
  - This imports all numpy functions into the global namespace and matplotlib gives the following warning for every function
    - [Warning: The name '<numpy function>' is already in use as a method name. This will become an error in a future release.]

Deprecated Tests

The following tests are not compatible with the latest versions of MHKiT-Python:

Note: Known failing tests use assertFail to force them to pass.

Wave_TestResourceMetrics:
- test_environmental_contour
  - Not compatible with latest version of MHKiT Python
- test_plot_environmental_contour
  - Not compatible with latest version of MHKiT Python
- test_plot_environmental_contour_multiyear
  - Not compatible with latest version of MHKiT Python

Code Coverage

Add built in MATLAB code coverage (1f5f93a)
- Addreses issue Run a Code Compatibility Report #67 and issue Code Coverage Report #86
- Does not run automatically

Style

Fix common spelling errors
Trims whitespace in all files
Convert files with dos line endings to unix line endings

Documentation

Update README and other documentation to reflect changes from the ebbflood branch and this PR
- Add MATLAB/Python compatibility to README
- Update Testing Badges
  - Add Linux and macOS Unit Test Badge
  - Add Windows Unit Test Badge

`ebbflood` Branch #101

Features

Power Quality Flicker Assessment Update (Update power quality flicker assessment #105)
- Update power quality flicker assessment workflow and calculations (077f525)
Dolfyn Functionality: IO and Rotations (Dolfyn Functionality: IO and rotations #79)
- Implement Dolfyn IO functionality for classic Nortek data format (d29d5e3)
- Add support for RDI file read (d29d5e3)
- Initial development for NetCDF read and write functionality (d29d5e3)
- Speed optimizations, bug fixes, and rotations for Dolfyn (d29d5e3, 4761a23, 71b0b38)
- Addresses issue 66
CDIP Data IO and Graphics (v2) [develop] (CDIP Data IO and Graphics (v2) [develop] #83)
- Implement CDIP data collection and plotting functions (2e91690, d723b3a, 9318f4f)
Wave Updates (Wave updates #70)
- Add depth_regime, wave_length, and depth flags (6be98b5)
- Implement updates to wave-related functions and tests (6be98b5, 2e91690)
General Updates (General updates #71)
- Miscellaneous updates to spectrum, elevation, and IO paths (5d4cb8d, 8c28dcd, 722f42e)
Addressing issue Develop Magnitude and phase function #59 Magnitude and Phase Function for Matlab (Addressing issue #59 magnitude and phase function for Matlab #76)
- Implement magnitude and phase function for Matlab (c557c43, 219879e)
Addressing issue Tidal ebb and flood plots #65 Tidal Ebb and Flood Plots for Matlab (Addressing issue #65 tidal ebb and flood plots for Matlab #73)
- Implement tidal ebb and flood plots for Matlab (c7f3992, 3916302, 3c9bd51)
Move CI Unit Tests to GitHub Actions (Move CI Unit Tests to GitHub Actions #80)
- Migrate CI unit tests to GitHub Actions (114c443, deedd7e, 45e15fd)

Bug Fixes

Typo Fix in Examples (typo fix in examples #103)
- Correct typos in example files (7895020)
Revert "Addressing issue Tidal ebb and flood plots #65 tidal ebb and flood plots for Matlab (Addressing issue #65 tidal ebb and flood plots for Matlab #73)" (Revert "Addressing issue #65 tidal ebb and flood plots for Matlab" #84)
- Revert the tidal ebb and flood plot changes (39f11dc)
Revert "Revert "Addressing issue Tidal ebb and flood plots #65 tidal ebb and flood plots for Matlab (Addressing issue #65 tidal ebb and flood plots for Matlab #73)" (Revert "Addressing issue #65 tidal ebb and flood plots for Matlab" #84)" (Revert "Revert "Addressing issue #65 tidal ebb and flood plots for Matlab"" #85)
- Revert the revert of tidal ebb and flood plot changes (85f5f5d)
Revert "Run tests on my fork at the same time" (33da001)
- Revert running tests on fork simultaneously (33da001)
Fixing File Path Call in Tests (Add Windows MATLAB-Actions Runners #81)
- Correct file path calls in tests (ed0992d)
Fixing Typo (Addressing issue #59 magnitude and phase function for Matlab #76)
- Resolve typos (ffe58bb)
WPTO for Matlab (WPTO for Matlab #61)
- Address issues related to WPTO for Matlab (114c443, deedd7e, 45e15fd)

Other

Conditional Run of Hindcast Tests (Dolfyn Functionality: IO and rotations #79)
- Conditionally run hindcast tests (3697735)
Updating Package (CDIP Data IO and Graphics (v2) [develop] #83)
- Package updates and error fixes (2e91690, d723b3a, 9318f4f)
Finalize Workflow (General updates #71)
- Finalize workflow for testing and update IO paths (8c28dcd, 722f42e, 386ac97)
Updating Power Example with Whole Workflow of Flicker (Update power quality flicker assessment #105)
- Update power example with complete flicker assessment workflow (077f525)
Minor Changes (Update power quality flicker assessment #105)
- Miscellaneous minor changes in the power quality flicker assessment (077f525)

Caveats

Windows Unit Tests

Deactivation of selected Windows Unit Tests (MATLAB > 2022a) is necessary for the following reasons:

Running MATLAB tests on a GitHub Actions Windows server fails due to errors using Python in MATLAB in the GitHub actions environment.
- Running Python OutOfProcess yields Unable to launch Simple server: Unable to launch C:\Program Files\MATLAB\R2023b\interprocess\bin\win64\pycli\MATLABPyHost.exe
- pyenv(ExecutionMode='OutOfProcess') allows access to Python libraries installed by the user and is required to use mhkit within MATLAB
- Running Python InProcess yields Unable to launch Simple server: Unable to launch C:\Program Files\MATLAB\R2023b\interprocess\bin\win64\pycli\MATLABPyHost.exe

MacOS Unit Tests

Deactivation of selected MacOS Unit Tests for Python 3.11 and MATLAB latest is necessary for the following reasons:

Throws the following error on every Python call from MATLAB (macos-latest, MATLAB latest, Python 3.11)

Python Error: ImportError:
      dlopen(/usr/local/miniconda/envs/TEST/lib/python3.11/site-packages/netCDF4/_netCDF4.cpython-311-darwin.so,
      0x0002): Symbol not found: (_SSL_get0_group_name)
        Referenced from: '/usr/local/miniconda/envs/TEST/lib/libcurl.4.dylib'
        Expected in:
        '/Users/runner/hostedtoolcache/MATLAB/2023.2.999/x64/MATLAB.app/bin/maci64/libssl.3.dylib'

…ebb_flood

* wpto playground * format changes * upload temporary test script * wpto extract with REST API * fix directional wave spectrum bug * upload hindcast example * auto format time_index into datetime array * add tests for hindcast * remove temp file * bug fix for available buoy data vs hindcast * upload data * moving test files into hindcast folder * updating toolbox paths * updating hindcast example * Setup CI, v16.2, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.3, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.4, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.5, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.6, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.7, list installed toolboxes and addons * Setup CI, v17, uninstall all pre-installed toolboxes * Setup CI, v17.1, uninstall all pre-installed toolboxes * Setup CI, v17.2, toggle off all pre-installed toolboxes * Setup CI, v17.3, toggle off all pre-installed toolboxes * Setup CI, v17.4, toggle off all pre-installed toolboxes * Setup CI, v17.5, toggle off all pre-installed toolboxes * Setup CI, v17.6, toggle off all pre-installed toolboxes * Setup CI, v17.7, toggle off all pre-installed toolboxes * Setup CI, v17.8, toggle off all pre-installed toolboxes * Setup CI, v17.9, toggle off all pre-installed toolboxes * Setup CI, v17.10, list installed addons and toolboxes * Setup CI, v17.11, start uninstalling toolboxes * Setup CI, v17.12, start uninstalling toolboxes * Setup CI, v17.13, start uninstalling toolboxes * Setup CI, v17.14, start uninstalling toolboxes * Setup CI, v17.15, start uninstalling toolboxes * Setup CI, v17.16, start uninstalling toolboxes * Setup CI, v17.17, start uninstalling toolboxes * Setup CI, v17.18, start uninstalling toolboxes * Setup CI, v17.19, start uninstalling toolboxes * Setup CI, v17.20, start uninstalling toolboxes * Setup CI, v17.21, start uninstalling toolboxes * Setup CI, v17.22, start uninstalling toolboxes * Setup CI, v17.23, start uninstalling toolboxes * Setup CI, v17.24, start uninstalling toolboxes * Setup CI, v17.25, start uninstalling toolboxes * Setup CI, v17.26, start uninstalling toolboxes * Setup CI, v17.27, start uninstalling toolboxes * Setup CI, v17.28, start uninstalling toolboxes * Setup CI, v17.29, start uninstalling toolboxes * Setup CI, v17.30, start uninstalling toolboxes * Setup CI, v17.31, start uninstalling toolboxes * Setup CI, v17.32, start uninstalling toolboxes * Setup CI, v17.33, start uninstalling toolboxes * Setup CI, v17.34, start uninstalling toolboxes * Setup CI, v17.35, start uninstalling toolboxes * Setup CI, v18, simplify to most basic test * Setup CI, v19, install mhkit toolbox * Setup CI, v20, run a single test that uses mhkit * Setup CI, v21, run a single different test that uses mhkit * Setup CI, v21.1, run a single different test that uses mhkit * Setup CI, v21.2, run a single different test that uses mhkit * Add function to reload python in matlab after python code changes * Fix paths to python usgs and noaa functions * Update pierson_moskowitz_spectrum wrapper with additional Hs parameter * Update create_spectra with additional Hs parameter * Update tests fixing mostly broken relative file paths Co-authored-by: rpauly18 <[email protected]> Co-authored-by: Matthew Boyd <[email protected]>

…xceedance and plot_tidal_phase_probability

…to iss65

… ebb_flood

…to ebb_flood

* Setup CI, v16.2, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.3, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.4, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.5, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.6, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.7, list installed toolboxes and addons * Setup CI, v17, uninstall all pre-installed toolboxes * Setup CI, v17.1, uninstall all pre-installed toolboxes * Setup CI, v17.2, toggle off all pre-installed toolboxes * Setup CI, v17.3, toggle off all pre-installed toolboxes * Setup CI, v17.4, toggle off all pre-installed toolboxes * Setup CI, v17.5, toggle off all pre-installed toolboxes * Setup CI, v17.6, toggle off all pre-installed toolboxes * Setup CI, v17.7, toggle off all pre-installed toolboxes * Setup CI, v17.8, toggle off all pre-installed toolboxes * Setup CI, v17.9, toggle off all pre-installed toolboxes * Setup CI, v17.10, list installed addons and toolboxes * Setup CI, v17.11, start uninstalling toolboxes * Setup CI, v17.12, start uninstalling toolboxes * Setup CI, v17.13, start uninstalling toolboxes * Setup CI, v17.14, start uninstalling toolboxes * Setup CI, v17.15, start uninstalling toolboxes * Setup CI, v17.16, start uninstalling toolboxes * Setup CI, v17.17, start uninstalling toolboxes * Setup CI, v17.18, start uninstalling toolboxes * Setup CI, v17.19, start uninstalling toolboxes * Setup CI, v17.20, start uninstalling toolboxes * Setup CI, v17.21, start uninstalling toolboxes * Setup CI, v17.22, start uninstalling toolboxes * Setup CI, v17.23, start uninstalling toolboxes * Setup CI, v17.24, start uninstalling toolboxes * Setup CI, v17.25, start uninstalling toolboxes * Setup CI, v17.26, start uninstalling toolboxes * Setup CI, v17.27, start uninstalling toolboxes * Setup CI, v17.28, start uninstalling toolboxes * Setup CI, v17.29, start uninstalling toolboxes * Setup CI, v17.30, start uninstalling toolboxes * Setup CI, v17.31, start uninstalling toolboxes * Setup CI, v17.32, start uninstalling toolboxes * Setup CI, v17.33, start uninstalling toolboxes * Setup CI, v17.34, start uninstalling toolboxes * Setup CI, v17.35, start uninstalling toolboxes * Setup CI, v18, simplify to most basic test * Setup CI, v19, install mhkit toolbox * Setup CI, v20, run a single test that uses mhkit * Setup CI, v21, run a single different test that uses mhkit * Setup CI, v21.1, run a single different test that uses mhkit * Setup CI, v21.2, run a single different test that uses mhkit * Add function to reload python in matlab after python code changes * Fix paths to python usgs and noaa functions * Update pierson_moskowitz_spectrum wrapper with additional Hs parameter * Update create_spectra with additional Hs parameter * Update tests fixing mostly broken relative file paths * Adressing issue #65 tidal ebb and flood plots for Matlab * adding the project file * updating the function descriptions * Merge QC_Test into master (#63) * Add QC_Test.m draft * check incriment working * Update qctest file * test_check_timestep passes * test_check_delta passes * cleanup Co-authored-by: kbrode22 <[email protected]> Co-authored-by: rpauly18 <[email protected]> Co-authored-by: Bhaskar <[email protected]> * Adding tests to account for the new plot functions plot_tidal_phase_exceedance and plot_tidal_phase_probability * Bug fix io request data (#78) * Rewrite usgs data request with no python calls to fix ssl error * Rewrite noaa data request with no python calls to fix ssl error, WIP * Split noaa data calls into max day periods * Rewrite ndbc available data request with no python calls to fix ssl error * Rewrite ndbc data request with no python calls to fix ssl error, WIP * Rewrite ndbc data request with no python calls to fix ssl error, include stdmet option * Handle errors from noaa data query * Update example with noaa data query after change to options argument * Check parameter input types to request_usgs_data.m * minor edits * Add proxy instructions and remove associated deprecated code * Handle more NDBC file formats and corruptions * Filter the NDBC available data by buoy * Resolve mostly relative file path issues in associated live scripts * Add automatic retries to usgs, noaa and ndbc data queries Co-authored-by: rpauly18 <[email protected]> * Move CI Unit Tests to GitHub Actions (#80) * Speed up reading of dataframe datetimes * Add datetime_index_to_ordinal function to pandas_dataframe module to convert the datetime index of dataframes to MATLAB ordinal values * Convert all methods using cell arrays to get the datetimes index to use datetime_index_to_ordinal function * Fix test assert to check for POSIX time rather than string * Skip tests of environmental_contour function which is broken * Run CI tests with all installed from source and OutOfProcess execution mode * Rename run_tests to tests and delete main * Give the workflow a more badge friendly name and add to README * Minor changes * Delete TravisCI build * Remove unused import * Remove duplicated code Co-authored-by: Matthew Boyd <[email protected]> Co-authored-by: McVey <[email protected]> Co-authored-by: rpauly18 <[email protected]> Co-authored-by: Parangat Bhaskar <[email protected]> Co-authored-by: kbrode22 <[email protected]> Co-authored-by: Bhaskar <[email protected]> Co-authored-by: Matthew Boyd <[email protected]> Co-authored-by: Mathew Topper <[email protected]>

* Addressing issue #59 magnitude and phase function for Matlab * Adding tests for magnitude_phase function Co-authored-by: McVey <[email protected]> Co-authored-by: rpauly18 <[email protected]>

…" (#84) This reverts commit 02e3440.

…tlab (#73)" (#84)" (#85) This reverts commit 39f11dc.

* Setup CI, v16.2, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.3, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.4, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.5, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.6, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.7, list installed toolboxes and addons * Setup CI, v17, uninstall all pre-installed toolboxes * Setup CI, v17.1, uninstall all pre-installed toolboxes * Setup CI, v17.2, toggle off all pre-installed toolboxes * Setup CI, v17.3, toggle off all pre-installed toolboxes * Setup CI, v17.4, toggle off all pre-installed toolboxes * Setup CI, v17.5, toggle off all pre-installed toolboxes * Setup CI, v17.6, toggle off all pre-installed toolboxes * Setup CI, v17.7, toggle off all pre-installed toolboxes * Setup CI, v17.8, toggle off all pre-installed toolboxes * Setup CI, v17.9, toggle off all pre-installed toolboxes * Setup CI, v17.10, list installed addons and toolboxes * Setup CI, v17.11, start uninstalling toolboxes * Setup CI, v17.12, start uninstalling toolboxes * Setup CI, v17.13, start uninstalling toolboxes * Setup CI, v17.14, start uninstalling toolboxes * Setup CI, v17.15, start uninstalling toolboxes * Setup CI, v17.16, start uninstalling toolboxes * Setup CI, v17.17, start uninstalling toolboxes * Setup CI, v17.18, start uninstalling toolboxes * Setup CI, v17.19, start uninstalling toolboxes * Setup CI, v17.20, start uninstalling toolboxes * Setup CI, v17.21, start uninstalling toolboxes * Setup CI, v17.22, start uninstalling toolboxes * Setup CI, v17.23, start uninstalling toolboxes * Setup CI, v17.24, start uninstalling toolboxes * Setup CI, v17.25, start uninstalling toolboxes * Setup CI, v17.26, start uninstalling toolboxes * Setup CI, v17.27, start uninstalling toolboxes * Setup CI, v17.28, start uninstalling toolboxes * Setup CI, v17.29, start uninstalling toolboxes * Setup CI, v17.30, start uninstalling toolboxes * Setup CI, v17.31, start uninstalling toolboxes * Setup CI, v17.32, start uninstalling toolboxes * Setup CI, v17.33, start uninstalling toolboxes * Setup CI, v17.34, start uninstalling toolboxes * Setup CI, v17.35, start uninstalling toolboxes * updates to spectrum and elevation functions * updating io paths * Setup CI, v18, simplify to most basic test * Setup CI, v19, install mhkit toolbox * Setup CI, v20, run a single test that uses mhkit * Setup CI, v21, run a single different test that uses mhkit * Setup CI, v21.1, run a single different test that uses mhkit * Setup CI, v21.2, run a single different test that uses mhkit * Add function to reload python in matlab after python code changes * Fix paths to python usgs and noaa functions * Update pierson_moskowitz_spectrum wrapper with additional Hs parameter * Update create_spectra with additional Hs parameter * Update tests fixing mostly broken relative file paths * Merge QC_Test into master (#63) * Add QC_Test.m draft * check incriment working * Update qctest file * test_check_timestep passes * test_check_delta passes * cleanup Co-authored-by: kbrode22 <[email protected]> Co-authored-by: rpauly18 <[email protected]> Co-authored-by: Bhaskar <[email protected]> * Bug fix io request data (#78) * Rewrite usgs data request with no python calls to fix ssl error * Rewrite noaa data request with no python calls to fix ssl error, WIP * Split noaa data calls into max day periods * Rewrite ndbc available data request with no python calls to fix ssl error * Rewrite ndbc data request with no python calls to fix ssl error, WIP * Rewrite ndbc data request with no python calls to fix ssl error, include stdmet option * Handle errors from noaa data query * Update example with noaa data query after change to options argument * Check parameter input types to request_usgs_data.m * minor edits * Add proxy instructions and remove associated deprecated code * Handle more NDBC file formats and corruptions * Filter the NDBC available data by buoy * Resolve mostly relative file path issues in associated live scripts * Add automatic retries to usgs, noaa and ndbc data queries Co-authored-by: rpauly18 <[email protected]> * Move CI Unit Tests to GitHub Actions (#80) * Speed up reading of dataframe datetimes * Add datetime_index_to_ordinal function to pandas_dataframe module to convert the datetime index of dataframes to MATLAB ordinal values * Convert all methods using cell arrays to get the datetimes index to use datetime_index_to_ordinal function * Fix test assert to check for POSIX time rather than string * Skip tests of environmental_contour function which is broken * Run CI tests with all installed from source and OutOfProcess execution mode * Rename run_tests to tests and delete main * Give the workflow a more badge friendly name and add to README * Minor changes * Delete TravisCI build * Remove unused import * Remove duplicated code * resolving test issues * Add Windows MATLAB-Actions Runners (#81) * Put all test output in a single folder and hide from git * Test windows runner using InProcess mode Also removed pinning of matplotlib. See #80 (comment) * Add develop branch to on-push and on-pull_request Co-authored-by: Matthew Boyd <[email protected]> * fixing tests * removing trouble test temporairly * restarting tests * updating python calls Co-authored-by: Matthew Boyd <[email protected]> Co-authored-by: Parangat Bhaskar <[email protected]> Co-authored-by: kbrode22 <[email protected]> Co-authored-by: Bhaskar <[email protected]> Co-authored-by: Matthew Boyd <[email protected]> Co-authored-by: Mathew Topper <[email protected]> Co-authored-by: Mathew Topper <[email protected]>

* adding deep flag and wave_length * adding depth_regime * updates * first few tests working * adding final tests * updating toolbox * Setup CI, v16.2, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.3, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.4, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.5, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.6, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.7, list installed toolboxes and addons * Setup CI, v17, uninstall all pre-installed toolboxes * Setup CI, v17.1, uninstall all pre-installed toolboxes * Setup CI, v17.2, toggle off all pre-installed toolboxes * Setup CI, v17.3, toggle off all pre-installed toolboxes * Setup CI, v17.4, toggle off all pre-installed toolboxes * Setup CI, v17.5, toggle off all pre-installed toolboxes * Setup CI, v17.6, toggle off all pre-installed toolboxes * Setup CI, v17.7, toggle off all pre-installed toolboxes * Setup CI, v17.8, toggle off all pre-installed toolboxes * Setup CI, v17.9, toggle off all pre-installed toolboxes * Setup CI, v17.10, list installed addons and toolboxes * Setup CI, v17.11, start uninstalling toolboxes * Setup CI, v17.12, start uninstalling toolboxes * Setup CI, v17.13, start uninstalling toolboxes * Setup CI, v17.14, start uninstalling toolboxes * Setup CI, v17.15, start uninstalling toolboxes * Setup CI, v17.16, start uninstalling toolboxes * Setup CI, v17.17, start uninstalling toolboxes * Setup CI, v17.18, start uninstalling toolboxes * Setup CI, v17.19, start uninstalling toolboxes * Setup CI, v17.20, start uninstalling toolboxes * Setup CI, v17.21, start uninstalling toolboxes * Setup CI, v17.22, start uninstalling toolboxes * Setup CI, v17.23, start uninstalling toolboxes * Setup CI, v17.24, start uninstalling toolboxes * Setup CI, v17.25, start uninstalling toolboxes * Setup CI, v17.26, start uninstalling toolboxes * Setup CI, v17.27, start uninstalling toolboxes * Setup CI, v17.28, start uninstalling toolboxes * Setup CI, v17.29, start uninstalling toolboxes * Setup CI, v17.30, start uninstalling toolboxes * Setup CI, v17.31, start uninstalling toolboxes * Setup CI, v17.32, start uninstalling toolboxes * Setup CI, v17.33, start uninstalling toolboxes * Setup CI, v17.34, start uninstalling toolboxes * Setup CI, v17.35, start uninstalling toolboxes * Setup CI, v18, simplify to most basic test * Setup CI, v19, install mhkit toolbox * Setup CI, v20, run a single test that uses mhkit * Setup CI, v21, run a single different test that uses mhkit * Setup CI, v21.1, run a single different test that uses mhkit * Setup CI, v21.2, run a single different test that uses mhkit * Add function to reload python in matlab after python code changes * Fix paths to python usgs and noaa functions * Update pierson_moskowitz_spectrum wrapper with additional Hs parameter * Update create_spectra with additional Hs parameter * Update tests fixing mostly broken relative file paths * Merge QC_Test into master (#63) * Add QC_Test.m draft * check incriment working * Update qctest file * test_check_timestep passes * test_check_delta passes * cleanup Co-authored-by: kbrode22 <[email protected]> Co-authored-by: rpauly18 <[email protected]> Co-authored-by: Bhaskar <[email protected]> * Bug fix io request data (#78) * Rewrite usgs data request with no python calls to fix ssl error * Rewrite noaa data request with no python calls to fix ssl error, WIP * Split noaa data calls into max day periods * Rewrite ndbc available data request with no python calls to fix ssl error * Rewrite ndbc data request with no python calls to fix ssl error, WIP * Rewrite ndbc data request with no python calls to fix ssl error, include stdmet option * Handle errors from noaa data query * Update example with noaa data query after change to options argument * Check parameter input types to request_usgs_data.m * minor edits * Add proxy instructions and remove associated deprecated code * Handle more NDBC file formats and corruptions * Filter the NDBC available data by buoy * Resolve mostly relative file path issues in associated live scripts * Add automatic retries to usgs, noaa and ndbc data queries Co-authored-by: rpauly18 <[email protected]> * Move CI Unit Tests to GitHub Actions (#80) * Speed up reading of dataframe datetimes * Add datetime_index_to_ordinal function to pandas_dataframe module to convert the datetime index of dataframes to MATLAB ordinal values * Convert all methods using cell arrays to get the datetimes index to use datetime_index_to_ordinal function * Fix test assert to check for POSIX time rather than string * Skip tests of environmental_contour function which is broken * Run CI tests with all installed from source and OutOfProcess execution mode * Rename run_tests to tests and delete main * Give the workflow a more badge friendly name and add to README * Minor changes * Delete TravisCI build * Remove unused import * Remove duplicated code * Add Windows MATLAB-Actions Runners (#81) * Put all test output in a single folder and hide from git * Test windows runner using InProcess mode Also removed pinning of matplotlib. See #80 (comment) * Add develop branch to on-push and on-pull_request Co-authored-by: Matthew Boyd <[email protected]> * updating test Co-authored-by: Matthew Boyd <[email protected]> Co-authored-by: Parangat Bhaskar <[email protected]> Co-authored-by: kbrode22 <[email protected]> Co-authored-by: Bhaskar <[email protected]> Co-authored-by: Matthew Boyd <[email protected]> Co-authored-by: Mathew Topper <[email protected]> Co-authored-by: Mathew Topper <[email protected]>

* Setup CI, v16.2, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.3, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.4, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.5, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.6, try to fix HDF5 issue, try fix outlined in Troubleshooting * Setup CI, v16.7, list installed toolboxes and addons * Setup CI, v17, uninstall all pre-installed toolboxes * Setup CI, v17.1, uninstall all pre-installed toolboxes * Setup CI, v17.2, toggle off all pre-installed toolboxes * Setup CI, v17.3, toggle off all pre-installed toolboxes * Setup CI, v17.4, toggle off all pre-installed toolboxes * Setup CI, v17.5, toggle off all pre-installed toolboxes * Setup CI, v17.6, toggle off all pre-installed toolboxes * Setup CI, v17.7, toggle off all pre-installed toolboxes * Setup CI, v17.8, toggle off all pre-installed toolboxes * Setup CI, v17.9, toggle off all pre-installed toolboxes * Setup CI, v17.10, list installed addons and toolboxes * Setup CI, v17.11, start uninstalling toolboxes * Setup CI, v17.12, start uninstalling toolboxes * Setup CI, v17.13, start uninstalling toolboxes * Setup CI, v17.14, start uninstalling toolboxes * Setup CI, v17.15, start uninstalling toolboxes * Setup CI, v17.16, start uninstalling toolboxes * Setup CI, v17.17, start uninstalling toolboxes * Setup CI, v17.18, start uninstalling toolboxes * Setup CI, v17.19, start uninstalling toolboxes * Setup CI, v17.20, start uninstalling toolboxes * Setup CI, v17.21, start uninstalling toolboxes * Setup CI, v17.22, start uninstalling toolboxes * Setup CI, v17.23, start uninstalling toolboxes * Setup CI, v17.24, start uninstalling toolboxes * Setup CI, v17.25, start uninstalling toolboxes * Setup CI, v17.26, start uninstalling toolboxes * Setup CI, v17.27, start uninstalling toolboxes * Setup CI, v17.28, start uninstalling toolboxes * Setup CI, v17.29, start uninstalling toolboxes * Setup CI, v17.30, start uninstalling toolboxes * Setup CI, v17.31, start uninstalling toolboxes * Setup CI, v17.32, start uninstalling toolboxes * Setup CI, v17.33, start uninstalling toolboxes * Setup CI, v17.34, start uninstalling toolboxes * Setup CI, v17.35, start uninstalling toolboxes * Setup CI, v18, simplify to most basic test * Setup CI, v19, install mhkit toolbox * Setup CI, v20, run a single test that uses mhkit * Setup CI, v21, run a single different test that uses mhkit * Setup CI, v21.1, run a single different test that uses mhkit * Setup CI, v21.2, run a single different test that uses mhkit * Add function to reload python in matlab after python code changes * Fix paths to python usgs and noaa functions * Update pierson_moskowitz_spectrum wrapper with additional Hs parameter * Update create_spectra with additional Hs parameter * Update tests fixing mostly broken relative file paths * Merge QC_Test into master (#63) * Add QC_Test.m draft * check incriment working * Update qctest file * test_check_timestep passes * test_check_delta passes * cleanup Co-authored-by: kbrode22 <[email protected]> Co-authored-by: rpauly18 <[email protected]> Co-authored-by: Bhaskar <[email protected]> * Bug fix io request data (#78) * Rewrite usgs data request with no python calls to fix ssl error * Rewrite noaa data request with no python calls to fix ssl error, WIP * Split noaa data calls into max day periods * Rewrite ndbc available data request with no python calls to fix ssl error * Rewrite ndbc data request with no python calls to fix ssl error, WIP * Rewrite ndbc data request with no python calls to fix ssl error, include stdmet option * Handle errors from noaa data query * Update example with noaa data query after change to options argument * Check parameter input types to request_usgs_data.m * minor edits * Add proxy instructions and remove associated deprecated code * Handle more NDBC file formats and corruptions * Filter the NDBC available data by buoy * Resolve mostly relative file path issues in associated live scripts * Add automatic retries to usgs, noaa and ndbc data queries Co-authored-by: rpauly18 <[email protected]> * Move CI Unit Tests to GitHub Actions (#80) * Speed up reading of dataframe datetimes * Add datetime_index_to_ordinal function to pandas_dataframe module to convert the datetime index of dataframes to MATLAB ordinal values * Convert all methods using cell arrays to get the datetimes index to use datetime_index_to_ordinal function * Fix test assert to check for POSIX time rather than string * Skip tests of environmental_contour function which is broken * Run CI tests with all installed from source and OutOfProcess execution mode * Rename run_tests to tests and delete main * Give the workflow a more badge friendly name and add to README * Minor changes * Delete TravisCI build * Remove unused import * Remove duplicated code * Initial commit, WIP * More progress, WIP * Make first complete working version of cdip data collector * Refactor datum_categories function * Rename categories to groups * Alphabetize local functions * Fix a couple issues * Finish adding data tests, minus plot tests * Add autoretry * Refactor autoretry * Add compendium plot and associated tests * Add box plot function, not needing statistical toolbox * Customize boxplot function to look more like Python plot * Refactor compendium plot * Add boxplot and associated test * Handle when no times are given * Make plots not open in new window when in live script * Add example live script for CDIP * Make boxplot look more like Python plot * Make compendium plot look more like Python plot * Change plot time parameters from POSIX to datetime * Remove optional nc object parameter * Fix docstring * updating matlab toolbox * Warn on non-existant parameters * Fix spelling errors * Replace a try-catch block * Add low-level netcdf cdip functions for older matlab versions * Reduce query size of USGS instantaneous data test to avoid query limit * Remove USGS instantaneous data test to stop failed CI runs * Remove Python 3.7 CI jobs as it is no longer supported by hosted runners * Remove boxplot legend dependency on data file Co-authored-by: Parangat Bhaskar <[email protected]> Co-authored-by: kbrode22 <[email protected]> Co-authored-by: rpauly18 <[email protected]> Co-authored-by: Bhaskar <[email protected]> Co-authored-by: Mathew Topper <[email protected]>

Previous wording had grammatical errors. This keeps consistency between projects

rpauly18 · 2023-12-20T19:47:44Z

I'll be adding comments as I go through the review -

Please open an issue on the MHKiT-Matlab repo (if you have not already) for the depreciated tests so we can assign someone to address the incompatibility
for the code coverage report, you say it does not run automatically - how do you trigger it?

simmsa · 2023-12-21T21:19:59Z

@rpauly18,

I created Issue Refactor or deprecate Wave_TestResourceMetrics tests that call environmental_contour #109 to detail and track the current failing tests.
6b744e7 adds a "Development Notes" section to the README which includes details on generating code coverage reports.

rpauly18

Looks great. Thanks for your hard work on this!

rpauly18 · 2023-12-27T20:44:37Z

@simmsa feel free to merge this if you are 100% done with any additional changes.

simmsa · 2024-01-08T16:44:26Z

@rpauly18 Thank you for the review and the merge!

Alex-McVey and others added 30 commits December 29, 2021 13:44

Adressing issue #65 tidal ebb and flood plots for Matlab

841d152

adding the project file

49b2f07

updating the function descriptions

b9cba86

Merge branch 'master' of github.com:MHKiT-Software/MHKiT-MATLAB into …

640a376

…ebb_flood

Adding tests to account for the new plot functions plot_tidal_phase_e…

85e3eea

…xceedance and plot_tidal_phase_probability

Merge branch 'iss65' of https://github.com/Alex-McVey/MHKiT-MATLAB in…

1934740

…to iss65

Merge branch 'develop' of github.com:MHKiT-Software/MHKiT-MATLAB into…

f63c0bc

… ebb_flood

resolving merge conflict

369d0cf

Merge branch 'iss65' of https://github.com/Alex-McVey/MHKiT-MATLAB in…

60c44d5

…to ebb_flood

Addressing issue #59 magnitude and phase function for Matlab (#76)

219879e

* Addressing issue #59 magnitude and phase function for Matlab * Adding tests for magnitude_phase function Co-authored-by: McVey <[email protected]> Co-authored-by: rpauly18 <[email protected]>

Revert "Addressing issue #65 tidal ebb and flood plots for Matlab (#73)…

39f11dc

…" (#84) This reverts commit 02e3440.

Revert "Revert "Addressing issue #65 tidal ebb and flood plots for Ma…

4b75a55

…tlab (#73)" (#84)" (#85) This reverts commit 39f11dc.

updating package

9318f4f

resolve conflicts

63cb281

fixing error

d723b3a

fixing errors take 2

2e91690

Add MHKit-Python test conditional on test failure

228b583

Merge branch 'master' into develop

ac394e0

include tests for R2020b

4114469

add workflow dispatch for testing

7463c04

fix typo

a8593e4

workflow_dispatch

704ca54

add push?

8a905e2

update variable name

386ac97

update on latest input

722f42e

simmsa added 9 commits December 8, 2023 11:05

Docs: Duplicate project information from MHKiT-Python

462e0a4

Previous wording had grammatical errors. This keeps consistency between projects

Docs: Capitalize headers

9bb1ac8

Docs: Clarify software compatibility section

9dc82f1

Tests: Remove old test report

cd168ff

Coverage: Add latest test report

a41af13

Ignore: hindcast download cache

0af0b2d

dolfyn: fix typo in AnaIn1 definition

b8aa8c3

MATLAB: Generate toolbox for version 0.4.1

1777254

Docs: Streamline installation wording

6005607

simmsa changed the title ~~WIP: Fix Unit Tests~~ RFC: Fix Unit Tests Dec 11, 2023

simmsa marked this pull request as ready for review December 11, 2023 14:12

simmsa added 7 commits December 14, 2023 14:59

Docs: Add section on Unit Testing

2344cd3

Docs: Add legend to MATLAB/Python compatibility table

576b406

Docs: Add notes about GitHub action failures

21251bc

Docs: Add footnote detailing Action errors

fd09f7d

Docs: Clarify unit test documentation

e6054dc

Docs: Make legend easier to read

3e478fa

Docs: Remove redundant unit test disclaimer

dada13d

simmsa requested a review from rpauly18 December 15, 2023 14:59

Docs: Add "Development Notes" section

6b744e7

rpauly18 approved these changes Dec 27, 2023

View reviewed changes

rpauly18 merged commit 21453d1 into MHKiT-Software:master Jan 8, 2024
28 checks passed

This was referenced Jan 31, 2024

Code Coverage Report #86

Closed

DOLfYN Functionality #66

Open

1st Time user error log #77

Closed

Tidal ebb and flood plots #65

Open

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

RFC: Fix Unit Tests #108

RFC: Fix Unit Tests #108

simmsa commented Nov 17, 2023 •

edited

Loading

rpauly18 commented Dec 20, 2023

simmsa commented Dec 21, 2023 •

edited

Loading

rpauly18 left a comment

rpauly18 commented Dec 27, 2023

simmsa commented Jan 8, 2024

RFC: Fix Unit Tests #108

RFC: Fix Unit Tests #108

Conversation

simmsa commented Nov 17, 2023 • edited Loading

Status

Summary of Changes

Detail of Changes

This PR

Actions/Workflow

Tests

Fixed Tests

Added Tests

Warnings

Deprecated Tests

Code Coverage

Style

Documentation

ebbflood Branch #101

Features

Bug Fixes

Other

Caveats

Windows Unit Tests

MacOS Unit Tests

rpauly18 commented Dec 20, 2023

simmsa commented Dec 21, 2023 • edited Loading

rpauly18 left a comment

Choose a reason for hiding this comment

rpauly18 commented Dec 27, 2023

simmsa commented Jan 8, 2024

simmsa commented Nov 17, 2023 •

edited

Loading

`ebbflood` Branch #101

simmsa commented Dec 21, 2023 •

edited

Loading