Test stability of pepper for contributors before 1st release

[F-said]

Describe the feature to be tested
Before creating a discrete release its crucial to test the stability.

Which tests need to be made for the feature
This involves running all pytests over

• local (using conda)
• local (using dockerfile)
• hpc (using singularity)

Running regular pipeline over

• local (using conda)
• local (using dockerfile)
• hpc (using singularity)

As well as testing

• dockerfile builds
• conda environment builds
• singularity recipe builds

And no new bugs are discovered.

This should be an automated process using Github actions eventually. Will record protocol and automate using Jenkins or Actions.

[F-said]

Dockerfile test

Notes

• Test for commit 4544302
  • AKA Pre-release Szegedi
• changed "load_data:root" to "/projects/CMI/rawdata"
• changed "output_data"root" to "/projects/CMI"
• created data volume using docker README to mount PEPPER code and data
• activated conda environment w/in container

in progress, will attach screenshots

Build

✔️Succeeded. Image builds w/o error

Pytest

Tested the following modules for successful run (all packages load):

• test_filter_data.py
  ✔️Succeeded. test fails same as local
  
• test_final_reject.py
  ✔️Succeeded. test succeeds same as local
  
• test_ica_raw.py
  ✔️Succeeded. test fails same as local
  
• test_ident_badchans.py
  ✔️Succeeded. test fails same as local
  
• test_interp_data.py
  ✔️Succeeded. test succeeds same as local
  
• test_reref_data.py
  ✔️Succeeded. test fails same as local
  
• test_segment_data.py
  ✔️Succeeded. test fails same as local
  
• test_select_data.py
  ✔️Succeeded. test fails same as local
  

Run.py

Tested the following modules for a successful run (all packages load):

• run.py
  ❌Failed. No permission to write, even in /projects
  

Data

Tested the following modules for a successful run (all packages load):

• load.py

  • load_params()
    ✔️Succeeded. loads user_params
    
  • load_files()
    ✔️Succeeded. loads files from user_params
    

• write.py

  • write_template_params()
    ✔️Succeeded. returns default user_params
    
  • write_eeg_data()
    ❌Failed. No permission to write, even in /projects
    
  • read_dict_to_json()
    ❌Failed. No permission to write, even in /projects
    

Preprocess

Tested the following modules for a successful run (all packages load):

• preprocess.py
  • filter()
    ✔️Succeeded.
    
  • ident_badchans_raw()
    ✔️Succeeded.
    
  • ica_raw()
    ✔️Succeeded.
    
  • segment_data()
    ✔️Succeeded.
    
  • final_reject_epoch()
    ✔️Succeeded.
    
  • interpolate_data()
    ✔️Succeeded.
    
  • reref_raw()
    ✔️Succeeded.
    

[F-said]

Singularity Container Test

Notes

• Test for commit 4544302
  • AKA Pre-release Szegedi

Pytest

Tested the following modules for successful run (all packages load):

• test_filter_data.py
• test_final_reject.py
• test_ica_raw.py
• test_ident_badchans.py
• test_interp_data.py
• test_reref_data.py
• test_segment_data.py
• test_select_data.py

Run.py

Tested the following modules for successful run (all packages load):

• run.py

Data

Tested the following modules for successful run (all packages load):

• load.py
• write.py

Preprocess

Tested the following modules for successful run (all packages load):

• preprocess.py

[F-said]

Conda Test

Notes

• Test for commit 4544302
  • AKA Pre-release Szegedi
• Built env using anaconda navigator

Pytest

Tested the following modules for successful run (all packages load):

• test_filter_data.py
  ✔️ Builds and runs
  
• test_final_reject.py
  ✔️ Builds and runs
  
• test_ica_raw.py
  ✔️ Builds and runs
  
• test_ident_badchans.py
  ✔️Builds and runs
  
• test_interp_data.py
  ✔️Builds and runs
  
• test_reref_data.py
  ✔️Builds and runs
  
• test_segment_data.py
  ✔️Builds and runs
  
• test_select_data.py
  ✔️Builds and runs
  

Run.py

Tested the following modules for a successful run (all packages load):

• run.py
  ✔️Builds and runs
  

Data

Tested the following modules for a successful run (all packages load):

• load.py

  • load_params()
    ✔️Builds and runs
    
  • load_files()
    ✔️Builds and runs
    

• write.py
  ✔️Builds and runs

Preprocess

Tested the following modules for a successful run (all packages load):

• preprocess.py
  • filter()
    ✔️Succeeded.
    
  • ident_badchans_raw()
    ✔️Succeeded.
    
  • ica_raw()
    ✔️Succeeded.
    
  • segment_data()
    ✔️Succeeded.
    
  • final_reject_epoch()
    ✔️Succeeded.
    
  • interpolate_data()
    ✔️Succeeded.
    
  • reref_raw()
    ✔️Succeeded.
    

[F-said]

Revisit bind vs mount in closed discussion

[F-said]

Resolved docker error via #306

[F-said]

Removing singularity stability test and moving to diff issue for closure

[F-said]

Resolved singularity stability #307