Install instructions don't work

[dkoslicki]

On two different machines: conda create -y -n KDE python=3.8 works just fine, but then installing the --file requirements.txt I get:

$ conda activate KDE
(KDE) e5-cse-mdkdk01:KEGG_data_extraction dmk333$ conda install -y -c bioconda -c conda-forge --file requirements.txt 
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: - 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                         /  

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package certifi conflicts for:
pandas -> setuptools[version='<60.0.0'] -> certifi[version='>=2016.9.26']
requests -> urllib3[version='>=1.21.1,<1.27'] -> certifi
sourmash -> matplotlib-base -> certifi[version='>=2020.06.20']
requests -> certifi[version='>=2017.4.17']

Package numpy conflicts for:
sourmash -> matplotlib-base -> numpy[version='>=1.17|>=1.19|>=1.20.3,<2.0a0|>=1.21.6,<2.0a0|>=1.19.5,<2.0a0|>=1.21.4,<2.0a0|>=1.19.4,<2.0a0|>=1.21.5,<2.0a0|>=1.19.2,<2.0a0']
biopython -> numpy
sourmash -> numpy
pandas -> numpy[version='>=1.19.2,<2.0a0|>=1.19.4,<2.0a0|>=1.19.5,<2.0a0|>=1.20.3,<2.0a0|>=1.21.6,<2.0a0|>=1.21.5,<2.0a0|>=1.21.4,<2.0a0']
pytaxonkit -> pandas[version='>=1.0'] -> numpy[version='>=1.19.2,<2.0a0|>=1.19.4,<2.0a0|>=1.19.5,<2.0a0|>=1.20.3,<2.0a0|>=1.21.6,<2.0a0|>=1.21.5,<2.0a0|>=1.21.4,<2.0a0']

Package tzdata conflicts for:
tqdm -> python[version='>=2.7'] -> tzdata
sourmash -> python -> tzdata
requests -> python[version='>=3.7,<4.0'] -> tzdata
pytaxonkit -> python[version='>=3'] -> tzdata
pandas -> python[version='>=3.10,<3.11.0a0'] -> tzdata
biopython -> python[version='>=3.10,<3.11.0a0'] -> tzdata

Package pandas conflicts for:
pandas
pytaxonkit -> pandas[version='>=1.0']
sourmash -> bam2fasta[version='>=1.0.1'] -> pandas[version='>=0.24.1']

Package python_abi conflicts for:
requests -> certifi[version='>=2017.4.17'] -> python_abi[version='3.10.*|3.9.*|3.8.*',build='*_cp38|*_cp39|*_cp310']
pandas -> python_abi[version='3.10.*|3.8.*|3.9.*',build='*_cp38|*_cp310|*_cp39']
biopython -> python_abi[version='3.10.*|3.9.*|3.8.*',build='*_cp38|*_cp39|*_cp310']
pytaxonkit -> pandas[version='>=1.0'] -> python_abi[version='3.10.*|3.8.*|3.9.*',build='*_cp38|*_cp310|*_cp39']
sourmash -> sourmash-minimal=4.5.0 -> python_abi[version='3.10.*|3.8.*|3.9.*',build='*_cp38|*_cp310|*_cp39']

Package sqlite conflicts for:
sourmash -> python -> sqlite[version='>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|>=3.37.0,<4.0a0|>=3.37.1,<4.0a0|>=3.38.5,<4.0a0']
requests -> python[version='>=3.7,<4.0'] -> sqlite[version='>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|>=3.37.0,<4.0a0|>=3.37.1,<4.0a0|>=3.38.5,<4.0a0']
python=3.8 -> sqlite[version='>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|>=3.37.0,<4.0a0|>=3.37.1,<4.0a0']
biopython -> python[version='>=3.10,<3.11.0a0'] -> sqlite[version='>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|>=3.37.0,<4.0a0|>=3.37.1,<4.0a0|>=3.38.5,<4.0a0']
tqdm -> python[version='>=2.7'] -> sqlite[version='>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|>=3.37.0,<4.0a0|>=3.37.1,<4.0a0|>=3.38.5,<4.0a0']
pytaxonkit -> python[version='>=3'] -> sqlite[version='>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|>=3.37.0,<4.0a0|>=3.37.1,<4.0a0|>=3.38.5,<4.0a0']
pandas -> python[version='>=3.10,<3.11.0a0'] -> sqlite[version='>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|>=3.37.0,<4.0a0|>=3.37.1,<4.0a0|>=3.38.5,<4.0a0']

Package packaging conflicts for:
pytaxonkit -> pytest[version='>=5.4'] -> packaging
sourmash -> matplotlib-base -> packaging[version='>=20.0']

Package pytz conflicts for:
pandas -> pytz[version='>=2017.2|>=2020.1']
pytaxonkit -> pandas[version='>=1.0'] -> pytz[version='>=2017.2|>=2020.1']

Package setuptools conflicts for:
sourmash -> sourmash-minimal=4.5.0 -> setuptools
pytaxonkit -> pandas[version='>=1.0'] -> setuptools[version='<60.0.0']
python=3.8 -> pip -> setuptools
pandas -> setuptools[version='<60.0.0']

Package tqdm conflicts for:
tqdm
sourmash -> bam2fasta[version='>=1.0.1'] -> tqdm[version='>=4.36.1']

Package libblas conflicts for:
sourmash -> scipy -> libblas[version='>=3.9.0,<4.0a0']
biopython -> numpy -> libblas[version='>=3.9.0,<4.0a0']
pandas -> numpy[version='>=1.21.6,<2.0a0'] -> libblas[version='>=3.9.0,<4.0a0']

[dkoslicki]

The issue appears to be pytaxonkit as all the others install together just fine

[dkoslicki]

Looks like pytaxonkit might just be broken. The following doesn't even work

conda create -y -n KDE python=3.8
conda activate KDE
conda install -y -c bioconda pytaxonkit

[dkoslicki]

Nor does trying to install pytaxonkit by itself:

$ conda create -n KDE -c bioconda pytaxonkit
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: - 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                            

UnsatisfiableError: 

Oddly, no Unsatisfiable error was listed