python version too high?

[splaisan]

Hi,

I have trouble installing dependencies (homopolish now)
It failed with the builtin install but also trying to install the tool with mamba.

It seems that my current python (set automatically by conda) is too high.
Can you please indicate which highest version of python has been validated with all the yaml install configs?

I tried set/unset conda strict priority but it does not improve

Also, mamba seems required but is not installed with conda-main.yaml. I prefer not to installmamba system-wide as it causes many problems with many other packages, having it within the ont-assembly-snake itself seems a more secure solution.

best
S

$ mamba install homopolish

Looking for: ['homopolish']

conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache
r/linux-64                                                  Using cache
r/noarch                                                    Using cache
anaconda/linux-64                                           Using cache
anaconda/noarch                                             Using cache
pkgs/main/linux-64                                            No change
pkgs/main/noarch                                              No change
pkgs/r/noarch                                                 No change
pkgs/r/linux-64                                               No change

Pinned packages:
  - python 3.12.*


warning  libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
Could not solve for environment specs
The following packages are incompatible
└─ homopolish is installable with the potential options
   ├─ homopolish [0.0.1|0.4.1] would require
   │  └─ scikit-learn 0.21.3.*  with the potential options
   │     ├─ scikit-learn 0.21.3 would require
   │     │  └─ python >=3.6,<3.7.0a0  with the potential options
   │     │     ├─ python [2.7.15|3.6.7|3.7.1] would require
   │     │     │  └─ openssl >=1.1.1,<1.1.2.0a0 , which does not exist (perhaps a missing channel);
   │     │     └─ python [3.6.0|3.6.1|...|3.6.9], which can be installed;
   │     └─ scikit-learn 0.21.3 would require
   │        └─ python >=3.7,<3.8.0a0  with the potential options
   │           ├─ python [2.7.15|3.6.7|3.7.1], which cannot be installed (as previously explained);
   │           └─ python [3.7.0|3.7.1|...|3.7.9], which can be installed;
   ├─ homopolish [0.0.2|0.2.1|0.3.3] would require
   │  └─ pyarrow 0.17.1.*  with the potential options
   │     ├─ pyarrow 0.17.1 would require
   │     │  └─ python >=3.6,<3.7.0a0  with the potential options
   │     │     ├─ python [2.7.15|3.6.7|3.7.1], which cannot be installed (as previously explained);
   │     │     └─ python [3.6.0|3.6.1|...|3.6.9], which can be installed;
   │     ├─ pyarrow 0.17.1 would require
   │     │  └─ python >=3.7,<3.8.0a0  with the potential options
   │     │     ├─ python [2.7.15|3.6.7|3.7.1], which cannot be installed (as previously explained);
   │     │     └─ python [3.7.0|3.7.1|...|3.7.9], which can be installed;
   │     ├─ pyarrow 0.17.1 would require
   │     │  └─ python >=3.8,<3.9.0a0 , which can be installed;
   │     └─ pyarrow 0.17.1 would require
   │        └─ python >=3.9,<3.10.0a0 , which can be installed;
   └─ homopolish 0.4.1 would require
      └─ pysam >=0.15.3  with the potential options
         ├─ pysam [0.15.3|0.15.4|...|0.20.0] would require
         │  └─ python >=2.7,<2.8.0a0  with the potential options
         │     ├─ python [2.7.12|2.7.13|...|2.7.18], which can be installed;
         │     └─ python [2.7.15|3.6.7|3.7.1], which cannot be installed (as previously explained);
         ├─ pysam [0.15.3|0.15.4|...|0.21.0] would require
         │  └─ python >=3.6,<3.7.0a0  with the potential options
         │     ├─ python [2.7.15|3.6.7|3.7.1], which cannot be installed (as previously explained);
         │     └─ python [3.6.0|3.6.1|...|3.6.9], which can be installed;
         ├─ pysam [0.15.3|0.15.4|...|0.21.0] would require
         │  └─ python >=3.7,<3.8.0a0  with the potential options
         │     ├─ python [2.7.15|3.6.7|3.7.1], which cannot be installed (as previously explained);
         │     └─ python [3.7.0|3.7.1|...|3.7.9], which can be installed;
         ├─ pysam [0.16.0.1|0.17.0|...|0.22.0] would require
         │  └─ python >=3.8,<3.9.0a0 , which can be installed;
         ├─ pysam [0.16.0.1|0.17.0|...|0.22.0] would require
         │  └─ python >=3.9,<3.10.0a0 , which can be installed;
         └─ pysam [0.19.1|0.20.0|0.21.0|0.22.0] would require
            └─ python >=3.10,<3.11.0a0 , which can be installed.

[pmenzel]

Hi,
I just tried to install homopolish into a new conda environment:

conda create -n homopolish
conda activate homopolish
mamba install homopolish

It went throught, but gave this error when starting the program:

ImportError: cannot import name 'cached_property' from 'functools'

The Python version was 3.7.12, so I did:

mamba install 'python>=3.8'

which raised the Python version to 3.8.15.

Next, I got this error when running homopolish:

ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject

and I did:

mamba install 'numpy==1.20.0'   

which eventually solved the issue and I could start homopolish.

I updated the file env/conda-homopolish.yaml to include the right versions numbers