ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
bokeh 3.3.2 requires PyYAML>=3.10, which is not installed.
dask 2023.12.0 requires pyyaml>=5.3.1, which is not installed.
distributed 2023.12.0 requires psutil>=5.7.2, which is not installed.
distributed 2023.12.0 requires pyyaml>=5.3.1, which is not installed.
distributed 2023.12.0 requires urllib3>=1.24.3, which is not installed.
ipykernel 6.25.2 requires psutil, which is not installed.
jupyter-console 6.6.3 requires pygments, which is not installed.
jupyterlab-server 2.24.0 requires babel>=2.10, which is not installed.
nbconvert 7.8.0 requires markupsafe>=2.0, which is not installed.
nbconvert 7.8.0 requires pygments>=2.4.1, which is not instal
You are using conda, not just pip. Also, you are installing from an environment .yml file, which (I think) doesn’t do the usual dependency verification (it just assumes the YAML file has the right packages listed). In other words you told it “install just exactly these packages” and then it’s telling you that those packages have a conflict.
In some cases, this pip error can happen even when there is no actual problem, and that could be what’s going on here, so you could try just going on to do whatever it is you want to do and see if you get any errors.
The other possibility is that the herro-env.yml file itself has some kind of inconsistency or incompatibility with your system that results in some dependencies being unavailable. Just at a glance, it looks a bit odd, since it is specifying things like pandas and h5py as pip dependencies although they are certainly available from conda-forge.
I would suggest raising an issue on the bug tracker of this HERRO project.
Do you allow me to link to your answer? I am sorry I don’t know your background what I do is bioinformtics, well using computers to study genome sequences, they are long string of 4 characters.
But we have a hole in our training we have very little computer science (it’s chamging slowly) but it’s true some subfields in biology have little use of computers. Anyway, I thought I had to ask you and I owed you a little explanation. Thanks and I am sorry if you knew that, again I don’t know your background.