Description of the problem

Try running the following:

mamba create -n very-sus "python = 3.7"

On my machine this creates a small environment with, as of writing, Python 3.7.16. So far so good.

Now let's try to install strainFlye into this environment:

conda activate very-sus
mamba install -c bioconda strainflye

This gives me a bizarre error:

...
Looking for: ['strainflye']

Encountered problems while solving.
Problem: nothing provides numpy 1.10* needed by scikit-bio-0.2.3-np110py27_0

This is confusing, because the very-sus environment doesn't contain numpy or scikit-bio. (Running conda list | grep numpy doesn't output anything; same for conda list | grep scikit or conda list | grep skbio.) So why does mamba assume we have to use such an ancient version of scikit-bio (and thus an ancient version of numpy)?

We can directly install a relatively recent version of scikit-bio without problems:

mamba install -c conda-forge "scikit-bio>=0.5.6"

On my machine this installs numpy 1.21.6 and scikit-bio 0.5.7. Again, that seems normal.

So you'd think that installing strainFlye should work now, right? But running mamba install -c bioconda strainflye at this point gives the following insane error message:

...
Looking for: ['strainflye']

Encountered problems while solving.
Problem: package strainflye-0.2.0-pyhca03a8a_0 requires python >=3.6,<3.8, but none of the providers can be installed

Now that's interesting, because we are literally using Python 3.7. To prove this, conda list | grep python gives:

brotli-python             1.0.9            py37hd23a5d3_7    conda-forge
ipython                   7.33.0           py37h89c1867_0    conda-forge
msgpack-python            1.0.3            py37h7cecad7_1    conda-forge
python                    3.7.16               h7a1cb2a_0  
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.7                     2_cp37m    conda-forge

Weird, right?

I think this is a symptom of a problem with mamba / conda -- this sort of obviously incorrect error message has been documented in a few other places (example 1, example 2, example 3).

Workaround solution

It seems like creating a conda environment with strainFlye in it (rather than installing strainFlye into an existing conda environment) works fine, though:

mamba create -n less-sus -c bioconda strainflye

This creates a working environment with strainFlye (and Python 3.7.6, and numpy 1.21.5, and scikit-bio 0.5.6) installed. Soooooo if this problem comes up again for users, they should be able to work around it by just creating a new environment. Eeesh.