Support Python 3.11 on conda?
Closed this issue · 3 comments
schorlton commented
Not sure where this issue is arising, but it seems like the pyfastx on conda is not compatible with Python 3.11. I'm under the understanding that it should be?
docker run --rm -it mambaorg/micromamba bash -c "micromamba install pyfastx -c conda-forge -c bioconda -c defaults"
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bioconda/linux-64 4.6MB @ 3.7MB/s 1.3s
pkgs/main/linux-64 5.5MB @ 4.3MB/s 1.3s
pkgs/main/noarch 821.1kB @ 550.5kB/s 0.2s
bioconda/noarch 4.2MB @ 2.5MB/s 1.7s
pkgs/r/noarch 1.3MB @ 712.2kB/s 0.6s
pkgs/r/linux-64 1.4MB @ 766.0kB/s 0.4s
conda-forge/noarch 11.8MB @ 3.6MB/s 3.3s
conda-forge/linux-64 30.7MB @ 3.5MB/s 8.9s
Transaction
Prefix: /opt/conda
Updating specs:
- pyfastx
Package Version Build Channel Size
─────────────────────────────────────────────────────────────────────────────────────
Install:
─────────────────────────────────────────────────────────────────────────────────────
+ _libgcc_mutex 0.1 conda_forge conda-forge/linux-64 3kB
+ _openmp_mutex 4.5 2_gnu conda-forge/linux-64 24kB
+ bzip2 1.0.8 h7f98852_4 conda-forge/linux-64 496kB
+ ca-certificates 2022.12.7 ha878542_0 conda-forge/linux-64 146kB
+ ld_impl_linux-64 2.40 h41732ed_0 conda-forge/linux-64 705kB
+ libffi 3.4.2 h7f98852_5 conda-forge/linux-64 58kB
+ libgcc-ng 12.2.0 h65d4601_19 conda-forge/linux-64 954kB
+ libgomp 12.2.0 h65d4601_19 conda-forge/linux-64 466kB
+ libnsl 2.0.0 h7f98852_0 conda-forge/linux-64 31kB
+ libsqlite 3.40.0 h753d276_0 conda-forge/linux-64 810kB
+ libuuid 2.38.1 h0b41bf4_0 conda-forge/linux-64 34kB
+ libzlib 1.2.13 h166bdaf_4 conda-forge/linux-64 66kB
+ ncurses 6.3 h27087fc_1 conda-forge/linux-64 1MB
+ openssl 3.1.0 h0b41bf4_0 conda-forge/linux-64 3MB
+ pip 23.0.1 pyhd8ed1ab_0 conda-forge/noarch 1MB
+ pyfastx 1.0.1 py310h8472f5a_0 bioconda/linux-64 80kB
+ python 3.10.10 he550d4f_0_cpython conda-forge/linux-64 26MB
+ python_abi 3.10 3_cp310 conda-forge/linux-64 6kB
+ readline 8.2 h8228510_1 conda-forge/linux-64 281kB
+ setuptools 67.6.1 pyhd8ed1ab_0 conda-forge/noarch 580kB
+ tk 8.6.12 h27826a3_0 conda-forge/linux-64 3MB
+ tzdata 2023c h71feb2d_0 conda-forge/noarch 118kB
+ wheel 0.40.0 pyhd8ed1ab_0 conda-forge/noarch 56kB
+ xz 5.2.6 h166bdaf_0 conda-forge/linux-64 418kB
+ zlib 1.2.13 h166bdaf_4 conda-forge/linux-64 94kB
Summary:
Install: 25 packages
Total download: 40MB
─────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n]
Trying with specifying Python 3.11:
docker run --rm -it mambaorg/micromamba bash -c "micromamba install pyfastx python=3.11 -c conda-forge -c bioconda -c defaults"
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/ / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
/ /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
/ .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
/_/
bioconda/noarch 4.2MB @ 3.8MB/s 1.1s
bioconda/linux-64 4.6MB @ 3.8MB/s 1.2s
pkgs/main/linux-64 5.5MB @ 4.4MB/s 1.3s
pkgs/main/noarch 821.1kB @ 564.9kB/s 0.2s
pkgs/r/noarch 1.3MB @ 870.7kB/s 0.4s
pkgs/r/linux-64 1.4MB @ 846.5kB/s 0.5s
conda-forge/noarch 11.8MB @ 3.9MB/s 3.1s
conda-forge/linux-64 30.7MB @ 3.7MB/s 8.5s
error libmamba Could not solve for environment specs
The following packages are incompatible
├─ pyfastx is installable with the potential options
│ ├─ pyfastx [0.6.4|0.6.5|0.6.6|0.6.7] would require
│ │ └─ python >=3.6,<3.7.0a0 with the potential options
│ │ ├─ python [3.6.0|3.6.1|...|3.6.9], which can be installed;
│ │ ├─ python 3.6.3 would require
│ │ │ └─ zlib 1.2.8 , which can be installed;
│ │ └─ python [3.6.3|3.6.4|3.6.5] would require
│ │ └─ zlib 1.2.11 , which can be installed;
│ ├─ pyfastx [0.6.10|0.6.11|...|0.8.4] would require
│ │ ├─ python >=3.6,<3.7.0a0 with the potential options
│ │ │ ├─ python [3.6.0|3.6.1|...|3.6.9], which can be installed;
│ │ │ ├─ python 3.6.3, which can be installed (as previously explained);
│ │ │ └─ python [3.6.3|3.6.4|3.6.5], which can be installed (as previously explained);
│ │ └─ python_abi 3.6.* *_cp36m, which can be installed;
│ ├─ pyfastx [0.6.10|0.6.11|...|1.0.1] would require
│ │ ├─ python >=3.7,<3.8.0a0 , which can be installed;
│ │ └─ python_abi 3.7.* *_cp37m, which can be installed;
│ ├─ pyfastx [0.6.16|0.7.0|...|1.0.1] would require
│ │ ├─ python >=3.8,<3.9.0a0 , which can be installed;
│ │ └─ python_abi 3.8.* *_cp38, which can be installed;
│ ├─ pyfastx [0.6.4|0.6.5|0.6.6|0.6.7] would require
│ │ └─ python >=3.7,<3.8.0a0 , which can be installed;
│ ├─ pyfastx [0.8.2|0.8.3|0.8.4|0.9.1|1.0.1] would require
│ │ ├─ python >=3.9,<3.10.0a0 , which can be installed;
│ │ └─ python_abi 3.9.* *_cp39, which can be installed;
│ ├─ pyfastx [0.8.4|0.9.1|1.0.1] would require
│ │ ├─ python >=3.10,<3.11.0a0 , which can be installed;
│ │ └─ python_abi 3.10.* *_cp310, which can be installed;
│ └─ pyfastx [0.9.1|1.0.1] would require
│ ├─ libzlib >=1.2.13,<1.3.0a0 , which requires
│ │ └─ zlib 1.2.13 *_4, which conflicts with any installable versions previously reported;
│ ├─ python >=3.6,<3.7.0a0 with the potential options
│ │ ├─ python [3.6.0|3.6.1|...|3.6.9], which can be installed;
│ │ ├─ python 3.6.3, which can be installed (as previously explained);
│ │ └─ python [3.6.3|3.6.4|3.6.5], which can be installed (as previously explained);
│ └─ python_abi 3.6.* *_cp36m, which can be installed;
└─ python 3.11** is uninstallable because there are no viable options
├─ python [3.11.0|3.11.2] conflicts with any installable versions previously reported;
└─ python [3.11.0|3.11.1|3.11.2] would require
└─ python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported.
critical libmamba Could not solve for environment specsThanks for your help!
lmdu commented
I am sorry. I have not used conda. Currently, I could not fix it.
shenker commented
It's a bioconda-wide issue, see bioconda/bioconda-recipes#37805 and bioconda/bioconda-utils#878.
schorlton commented
Thanks for pointing that out. I'll close this issue and wait for bioconda, which will hopefully be soon given that Python 3.12 was released today.