Updating the Python environment from 3.7 to 3.10

[meren]

This PR attempts to update the Python dependency of anvi'o to 3.10.

[meren]

When I change the Python dependency to

 dependencies:
-- python=3.7
+- python=3.10

I can't run

mamba env create -f .conda/environment.yaml

without getting this error:

Could not solve for environment specs
The following packages are incompatible
├─ fastani is installable with the potential options
│  ├─ fastani 1.33 would require
│  │  ├─ gsl >=2.7,<2.8.0a0 , which can be installed;
│  │  └─ openmp >=4.0  with the potential options
│  │     ├─ openmp 4.0.0 would require
│  │     │  └─ clangdev [4.0.0 |4.0.0|4.0.0.* ], which requires
│  │     │     └─ libxml2 2.9.*  with the potential options
│  │     │        ├─ libxml2 2.9.10 would require
│  │     │        │  └─ icu >=67.1,<68.0a0 , which can be installed;
│  │     │        ├─ libxml2 [2.9.10|2.9.9] would require
│  │     │        │  └─ icu >=64.2,<65.0a0 , which conflicts with any installable versions previously reported;
│  │     │        ├─ libxml2 [2.9.10|2.9.11|2.9.12] would require
│  │     │        │  └─ icu >=68.1,<69.0a0 , which can be installed;
│  │     │        ├─ libxml2 [2.9.12|2.9.14] would require
│  │     │        │  └─ icu [69.* |>=69.1,<70.0a0 ], which can be installed;
│  │     │        ├─ libxml2 [2.10.0|2.10.1|...|2.9.14] would require
│  │     │        │  └─ icu >=70.1,<71.0a0 , which conflicts with any installable versions previously reported;

The only way to avoid this outcome is to remove fastani dependency :/

I think this is a Mac OS associated problem.

[meren]

This is how our help menus look like in Python 3.7:

And this is how they look like in Python 3.10:

MUST BE SARUMAN.

[metehaansever]

When I change the Python dependency to

 dependencies:
-- python=3.7
+- python=3.10

I can't run

mamba env create -f .conda/environment.yaml

without getting this error:

Could not solve for environment specs
The following packages are incompatible
├─ fastani is installable with the potential options
│  ├─ fastani 1.33 would require
│  │  ├─ gsl >=2.7,<2.8.0a0 , which can be installed;
│  │  └─ openmp >=4.0  with the potential options
│  │     ├─ openmp 4.0.0 would require
│  │     │  └─ clangdev [4.0.0 |4.0.0|4.0.0.* ], which requires
│  │     │     └─ libxml2 2.9.*  with the potential options
│  │     │        ├─ libxml2 2.9.10 would require
│  │     │        │  └─ icu >=67.1,<68.0a0 , which can be installed;
│  │     │        ├─ libxml2 [2.9.10|2.9.9] would require
│  │     │        │  └─ icu >=64.2,<65.0a0 , which conflicts with any installable versions previously reported;
│  │     │        ├─ libxml2 [2.9.10|2.9.11|2.9.12] would require
│  │     │        │  └─ icu >=68.1,<69.0a0 , which can be installed;
│  │     │        ├─ libxml2 [2.9.12|2.9.14] would require
│  │     │        │  └─ icu [69.* |>=69.1,<70.0a0 ], which can be installed;
│  │     │        ├─ libxml2 [2.10.0|2.10.1|...|2.9.14] would require
│  │     │        │  └─ icu >=70.1,<71.0a0 , which conflicts with any installable versions previously reported;

The only way to avoid this outcome is to remove fastani dependency :/

I think this is a Mac OS associated problem.

Actually, this installation not totally working with Ubuntu. We realize this with Alex today.

mamba env create -f .conda/environment.yaml

[meren]

Oh, perfect. A great case of trying to solve one problem, and getting 3 more problems :)