RAxML-NG and Pythia in same conda environment causes unresolvable numpy dependency conflict #22
Description
System information
$ python --version
Python 3.10.19
$ uname -a
Darwin evans-Apple-MacBook-Pro 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:33:00 PDT 2023; root:xnu-10002.41.9~7/RELEASE_ARM64_T6031 arm64
Description
When installing RAxML-NG on the bioconda conda channel, numpy<2 is enforced:
$ conda install -c bioconda raxml-ng
Retrieving notices: done
Channels:
- bioconda
- defaults
- conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): done
Solving environment: / warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
done
## Package Plan ##
environment location: /Users/evan/miniconda3/envs/2025-phylogenetic-analysis-of-msa-pairformer
added / updated specs:
- raxml-ng
The following packages will be downloaded:
package | build
---------------------------|-----------------
blas-2.137 | openblas 17 KB conda-forge
blas-devel-3.9.0 |37_hbf4f893_openblas 17 KB conda-forge
liblapacke-3.9.0 |37_h94b3770_openblas 17 KB conda-forge
numpy-1.26.4 | py310hf6dca73_0 12 KB
numpy-base-1.26.4 | py310hd8f4981_0 6.7 MB
openblas-0.3.30 |openmp_h30af337_4 5.4 MB conda-forge
raxml-ng-1.2.2 | hb53313b_2 785 KB bioconda
------------------------------------------------------------
Total: 13.0 MB
The following NEW packages will be INSTALLED:
blas conda-forge/osx-64::blas-2.137-openblas
blas-devel conda-forge/osx-64::blas-devel-3.9.0-37_hbf4f893_openblas
liblapacke conda-forge/osx-64::liblapacke-3.9.0-37_h94b3770_openblas
mpi pkgs/main/osx-64::mpi-1.0-openmpi
numpy-base pkgs/main/osx-64::numpy-base-1.26.4-py310hd8f4981_0
openblas conda-forge/osx-64::openblas-0.3.30-openmp_h30af337_4
openmpi conda-forge/osx-64::openmpi-4.1.6-h7406208_101
raxml-ng bioconda/osx-64::raxml-ng-1.2.2-hb53313b_2
zlib conda-forge/osx-64::zlib-1.3.1-hd23fc13_2
The following packages will be REMOVED:
pythiaphylopredictor-2.0.0-pypi_0
The following packages will be UPDATED:
libopenblas 0.3.30-openmp_h6006d49_2 --> 0.3.30-openmp_h6006d49_4
The following packages will be SUPERSEDED by a higher-priority channel:
numpy pypi/pypi::numpy-2.2.6-pypi_0 --> pkgs/main/osx-64::numpy-1.26.4-py310hf6dca73_0
Proceed ([y]/n)? y
But pythia enforces numpy>2, which leads to an unresolvable dependency conflict.
$ conda install pythiaphylopredictor -c conda-forge -c nodefaults
Channels:
- conda-forge
- nodefaults
- defaults
- bioconda
Platform: osx-64
Collecting package metadata (repodata.json): done
Solving environment: / warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
failed
LibMambaUnsatisfiableError: Encountered problems while solving:
- nothing provides _python_rc needed by python-3.14.0rc2-h780d05a_0_cp314t
Could not solve for environment specs
The following packages are incompatible
├─ numpy 1.26** is installable with the potential options
│ ├─ numpy [1.26.0|1.26.2|...|2.3.2] would require
│ │ └─ python >=3.11,<3.12.0a0 , which can be installed;
│ ├─ numpy [1.26.0|1.26.2|...|2.3.2] would require
│ │ └─ python [>=3.12,<3.13.0a0 |>=3.12.0rc3,<3.13.0a0 ], which can be installed;
│ ├─ numpy [1.26.0|1.26.2|...|2.0.2] would require
│ │ └─ python >=3.9,<3.10.0a0 , which can be installed;
│ └─ numpy [1.26.0|1.26.2|1.26.3|1.26.4], which can be installed;
├─ pin-1 is not installable because it requires
│ └─ python 3.10.* , which conflicts with any installable versions previously reported;
└─ pythiaphylopredictor is installable and it requires
└─ numpy >=2.0 with the potential options
├─ numpy [2.0.0|2.0.1|...|2.4.1] conflicts with any installable versions previously reported;
├─ numpy [1.26.0|1.26.2|...|2.3.2], which can be installed (as previously explained);
├─ numpy [1.26.0|1.26.2|...|2.3.2], which can be installed (as previously explained);
├─ numpy [1.26.0|1.26.2|...|2.0.2], which can be installed (as previously explained);
├─ numpy [2.1.0|2.1.1|...|2.3.2] would require
│ └─ python [>=3.13,<3.14.0a0 |>=3.13.0rc1,<3.14.0a0 |>=3.13.0rc3,<3.14.0a0 ], which can be installed;
└─ numpy 2.3.2 would require
└─ python >=3.14.0rc2,<3.15.0a0 with the potential options
├─ python [3.14.0|3.14.1|3.14.2], which can be installed;
└─ python [3.14.0rc2|3.14.0rc3] would require
└─ _python_rc, which does not exist (perhaps a missing channel).
The problem
Pythia places a lower bound pin on numpy:
dependencies = [
"pandas",
"biopython",
"lightgbm>=4.4",
"numpy>=2.0",
"shap>=0.41",
"matplotlib",
"loguru"
]
Is this really a required pin? It's at odds with its own dependency (raxml-ng), which requires numpy<2. I would recommend releasing or at least lowering this pin to include 1.26.4.