Installation through conda seems to yield outdated code

[GGasch]

Hello K2SOHIGH,

I truly love your software, it's an amazing piece of tech. Yet when I have installed it through conda, I had 2 bugs. When I compare the codes between the one on github and the one I have installed, I have spotted 2 differences.

In pcalf/pcalf/workflow/annotate/rule/pcalf.sml line 86, the GitHub code is :

region,start,stop,strand,partial,pseudo,src = parse_ncbi_header(ccya.description)

While on my installation it is :

region,start,stop,strand,partial,pseudo = parse_ncbi_header(ccya.description)

Which returns an error.

As well in the function download_genbank_report within pcalf/pcalf/workflow/datasets/scripts/get_ncbi_reports.py "#accession" was written "# accession" in my instalation, wich also returns an error.

Besides there seem to be slightly different layout between each codes.

All the best

[K2SOHIGH]

Hello,

Yes i saw this error weeks ago but didn't take the time to fix it. Did the pip install work fine ? I will try to update the conda repository tomorrow.

Max

[GGasch]

Haven't tried to install it through pip yet, for I would like pcalf to be in a conda env, and I am not sure if I can install a package in a conda env with pip.

But I have corrected the code manually and so far data-set-workflow and annotate are working smoothly.

However there seems to be an issue with pcalf-report : in render.py line 384

features_df["e-value"] = features_df.apply(lambda x : '{:0.2e}'.format(x["e-value"]),axis=1)

is giving an error:

ValueError: Unknown format code 'e' for object of type 'str'

Might be due to the deprecated code. I am trying to find a work around.

[GGasch]

I am moderaltly confident that I did a bad thing, but I have installed pcalf with pip3 in a conda environment.

I tried to run pcalf-dataset-workflow and i receive this error :

File "/home/guest-biom/miniconda3/bin/pcalf-datasets-workflow", line 129, in main() File "/home/guest-biom/miniconda3/bin/pcalf-datasets-workflow", line 111, in main datasets_module_path = resources.files(datasets) AttributeError: module 'importlib.resources' has no attribute 'files'

[GGasch]

Final update, removing line 384 in render.py allows a smooth run.

[K2SOHIGH]

I am moderaltly confident that I did a bad thing, but I have installed pcalf with pip3 in a conda environment.

I tried to run pcalf-dataset-workflow and i receive this error :

File "/home/guest-biom/miniconda3/bin/pcalf-datasets-workflow", line 129, in main() File "/home/guest-biom/miniconda3/bin/pcalf-datasets-workflow", line 111, in main datasets_module_path = resources.files(datasets) AttributeError: module 'importlib.resources' has no attribute 'files'

How did you create your conda environment ? check that you use the right pip command : which pip3 Is the path of pip3 under your conda environment ? If not try with which pip.

If neither pip3 nor pip are under your conda environment, considere installing it using conda conda install pip.

[GGasch]

How did you create your conda environment ? check that you use the right pip command : which pip3 Is the path of pip3 under your conda environment ? If not try with which pip. Like an absolute madman under the influence of several substances, 3 of which being illegals:

conda create -n myenv conda activate myenv pip3 install pcalf

If neither pip3 nor pip are under your conda environment, considere installing it using conda conda install pip.

The path of pip3 is /home/user/miniconda3/bin/pip3

[K2SOHIGH]

Do you have some news regarding this issue ?

If you have made some update, can you make a pull request please ?

[GGasch]

I haven't tried to re install pcalf with conda. Did you update the conda package ?

The problem with pip was probably linked to the fact that I don't have an importlib package up to date on my computer (see the other issue). I will try to fix that, and come back to it.

[K2SOHIGH]

related to #10.

Nop, i don't update the conda package yet, sorry.

[GGasch]

Side note : can I merge the modification I made on devgg with main ? Or do you want to assess them first (there are a few fixes in them)

[GGasch]

Do you want me to take care of updating conda channel ?

[K2SOHIGH]

Yes please. I will delete the recipe for now.