Update readme to reflect stable install

[sssangha]

Requirements file and mamba no longer translate to a stable build. Updating readme to reflect this

[dbekaert]

@sssangha Is there a reason we fall back to the past approach?
I thought mamba was getting more preferred as it resolves faster than conda?

[dbekaert]

@sssangha lets disable the test for the water mask?

[bbuzz31]

@sssangha Is there a reason we fall back to the past approach? I thought mamba was getting more preferred as it resolves faster than conda?

+1

[alexfore]

The issue here is that the README does not describe a working process to create a repeatable env in which to run this software. Specifically, the line conda install mamba does not work, presumably you also need to do something else (conda forge? I don't really know). Even after using the instructions in the modified readme I am not able to obtain the same results as Simran did while running on another machine with an env he created.

Before I can implement any testing suites I actually need to be able to replicate Simran's results on my machine with my env, as clearly what I have now fails all my tests. To do that we need a way to create envs for this software that work and give the same outputs when provided the same inputs and aria-tools software. Maybe your requirements file needs work to make this happen.

[sssangha]

@dbekaert and @bbuzz31 , I was able to confirm from Alex's suggestion that mamba works when specifying it can be found through conda-forge. I've updated the READme to be more explicit to reflect a stable installation that users can follow verbatim.

Will have to still figure out what's going wrong when using requirements vs the YML from scratch though.

[sssangha]

When the jupyter_contrib_nbextensions module was installed through pip originally, as opposed to through conda-forge, the following build installation error was raised:

(base) [ssangha@trappist ARIA-tools]$ mamba env create -f environment_ariatools_new2PRtest.yml
Retrieving notices: ...working... done
Channels:
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

Downloading and Extracting Packages:
                                                                                                                                                                                                                                
Preparing transaction: done                                                                                                                                                                                                     
Verifying transaction: failed                                                                                                                                                                                                   
                                                                                                                                                                                                                                
CondaVerificationError: The package for jsonschema-specifications located at /u/trappist-r0/ssangha/conda_installation/stable_april1_2024/pkgs/jsonschema-specifications-2023.12.1-pyhd8ed1ab_0                                 
appears to be corrupted. The path 'site-packages/jsonschema_specifications/schemas/draft201909/vocabularies/core'                                                                                                               
specified in the package manifest cannot be found.                                                                                                                                                                              
                                                                                                                                                                                                                                
CondaVerificationError: The package for jsonschema-specifications located at /u/trappist-r0/ssangha/conda_installation/stable_april1_2024/pkgs/jsonschema-specifications-2023.12.1-pyhd8ed1ab_0                                 
appears to be corrupted. The path 'site-packages/jsonschema_specifications/schemas/draft202012/vocabularies/core'                                                                                                               
specified in the package manifest cannot be found.                                                                                                                                                                              
                                                                                                                                                                                                                                
ClobberError: This transaction has incompatible packages due to a shared path.                                                                                                                                                  
  packages: conda-forge/linux-64::libkml-1.3.0-h01aab08_1018, conda-forge/linux-64::minizip-4.0.5-h0ab5242_0                                                                                                                    
  path: 'include/minizip/ioapi.h'                                                                                                                                                                                               
                                                                                                                                                                                                                                
                                                                                                                                                                                                                                
ClobberError: This transaction has incompatible packages due to a shared path.                                                                                                                                                  
  packages: conda-forge/linux-64::libkml-1.3.0-h01aab08_1018, conda-forge/linux-64::minizip-4.0.5-h0ab5242_0                                                                                                                    
  path: 'include/minizip/unzip.h'                                                                                                                                                                                               
                                                                                                                                                                                                                                
                                                                                                                                                                                                                                
ClobberError: This transaction has incompatible packages due to a shared path.                                                                                                                                                  
  packages: conda-forge/linux-64::libkml-1.3.0-h01aab08_1018, conda-forge/linux-64::minizip-4.0.5-h0ab5242_0                                                                                                                    
  path: 'include/minizip/zip.h'                                                                                                                                                                                                 
                                                                                                                                                                                                                                
                                                                                                                                                                                                                                
ClobberError: This transaction has incompatible packages due to a shared path.                                                                                                                                                  
  packages: conda-forge/linux-64::libkml-1.3.0-h01aab08_1018, conda-forge/linux-64::minizip-4.0.5-h0ab5242_0                                                                                                                    
  path: 'lib/libminizip.so'

[sssangha]

@cmarshak , agreed went ahead and adjusted the readme to reflect your suggestion. Specifically, install the package using miniforge

[alexfore]

Can you also fix this line:

setenv PATH ${PATH}:${PWD}/tools/ARIAtools

which should be

setenv PATH ${PATH}:${PWD}/tools/bin

[sssangha]

Can you also fix this line:

setenv PATH ${PATH}:${PWD}/tools/ARIAtools

which should be

setenv PATH ${PATH}:${PWD}/tools/bin

done

[alexfore]

Hi @sssangha, this looks good. However, I think we also need to add the parallel and pytest packages to the mamba install.

[sssangha]

Hi @sssangha, this looks good. However, I think we also need to add the parallel and pytest packages to the mamba install.

Sure, done. I tested the new environment with these packages included and all looks good. The golden outputs I just shared for ariaDownload were successfully accessed using this environment.