chore: update github CI #1725
ci.yml
on: pull_request
Matrix: linting
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4s
Matrix: testing
Annotations
1 error and 5 warnings
linting (3.12)
The process '/usr/share/miniconda/condabin/conda' failed with exit code 1
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ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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linting (3.12)
'nodefaults' channel detected: will remove 'defaults' if added implicitly. In the future, 'nodefaults' as a way of removing 'defaults' won't be supported. Please set 'conda-remove-defaults' = 'true' to remove this warning.
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linting (3.12)
CondaKeyError: 'channels': value 'defaults' not present in config
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linting (3.12)
/usr/share/miniconda/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
action(self, namespace, argument_values, option_string)
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linting (3.12)
LibMambaUnsatisfiableError: Encountered problems while solving:
- nothing provides requested sphinx_rtd_theme ~=2.0.0
- nothing provides requested sphinx-mdinclude ~=0.6.0
- nothing provides requested sphinx ~=7.3.7
- nothing provides black >=23.1.0,<24.0 needed by snakefmt-0.8.5-pyhdfd78af_0
- nothing provides requested ruff ~=0.4.8
- nothing provides requested ruamel.yaml 0.18.6
- nothing provides requested python 3.12.*,3.12.*
- nothing provides requested pytest-subprocess ~=1.5.0
- nothing provides requested pytest-mock ~=3.14.0
- nothing provides requested pytest-cov ~=5.0.0
- nothing provides requested pytest ~=8.2.2
- nothing provides requested pyfakefs ~=5.5.0
- nothing provides requested pydantic 2.7**
- nothing provides requested pre-commit ~=3.7.1
- nothing provides requested matplotlib 3.8.4
- nothing provides requested jinja2 3.1.4
- nothing provides requested gzip ~=1.13
- nothing provides requested gxx_linux-64 ~=13.2.0
- nothing provides requested git-lfs ~=3.5.1
- nothing provides requested gcc_linux-64 ~=13.2.0
- nothing provides requested gawk ~=5.3.0
- nothing provides requested coveralls ~=4.0.1
- nothing provides requested coverage ~=7.5.3
- nothing provides requested coreutils ~=9.5
- nothing provides requested bash ~=5.2.21
- nothing provides ncurses >=6.4.20240210,<7.0a0 needed by samtools-1.20-h50ea8bc_0
- nothing provides libcurl >=8.8.0,<9.0a0 needed by htslib-1.20-h5efdd21_1
- nothing provides toposort >=1.10 needed by snakemake-minimal-7.32.0-pyhdfd78af_0
- nothing provides libcurl >=8.8.0,<9.0a0 needed by htslib-1.20-h5efdd21_1
Could not solve for environment specs
The following packages are incompatible
├─ bash ~=5.2.21 does not exist (perhaps a typo or a missing channel);
├─ bcftools 1.20 is not installable because it requires
│ └─ htslib >=1.20,<1.22.0a0 but there are no viable options
│ ├─ htslib 1.20 would require
│ │ └─ libcurl >=8.8.0,<9.0a0 , which does not exist (perhaps a missing channel);
│ ├─ htslib 1.20 would require
│ │ └─ openssl >=3.2.1,<4.0a0 , which does not exist (perhaps a missing channel);
│ └─ htslib 1.21 would require
│ └─ libgcc >=12 , which does not exist (perhaps a missing channel);
├─ coreutils ~=9.5 does not exist (perhaps a typo or a missing channel);
├─ coverage ~=7.5.3 does not exist (perhaps a typo or a missing channel);
├─ coveralls ~=4.0.1 does not exist (perhaps a typo or a missing channel);
├─ gawk ~=5.3.0 does not exist (perhaps a typo or a missing channel);
├─ gcc_linux-64 ~=13.2.0 does not exist (perhaps a typo or a missing channel);
├─ git-lfs ~=3.5.1 does not exist (perhaps a typo or a missing channel);
├─ gxx_linux-64 ~=13.2.0 does not exist (perhaps a typo or a missing channel);
├─ gzip ~=1.13 does not exist (perhaps a typo or a missing channel);
├─ htslib 1.20 , which cannot be installed (as previously explained);
├─ jinja2 3.1.4 does not exist (perhaps a typo or a missing channel);
├─ matplotlib 3.8.4 does not exist (perhaps a typo or a missing channel);
├─ pre-commit ~=3.7.1 does not exist (perhaps a typo or a missing channel);
├─ pydantic 2.7** does not exist (perhaps a typo or a missing channel);
├─ pyfakefs ~=5.5.0 does not exist (perhaps a typo or a missing channel);
├─ pytest-cov ~=5.0.0 does not exist (perhaps a typo or a missing channel);
├─ pytest-mock ~=3.14.0 does not exist (perhaps a typo or a missing channel);
├─ pytest-subprocess ~=1.5.0 does not exist (perhaps a typo or a missing channel);
├─ pytest ~=8.2.2 does not exist (perhaps a typo or a missing channel);
├─ python 3.12.*,3.12.* does not exist (perhaps a typo or a missing channel);
├─ ruamel.yaml 0.18.6 does not exist (perhaps a typo or a missing channel);
├─ ruff ~=0.4.8 does not exist (perhaps a typo or a missing channel);
├─ samtools 1.20 is not installable because there are no viable options
│ ├─ samtools 1.20 would require
│ │ └─ ncurses >=6.4.20240210,<7.0a0 , which does not exist (perhaps a missing channel);
│ └─ samtools 1.20 would require
│ └─ ncur
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