python311Packages.ngs-tools, python312Packages.ngs-tools: init at 1.8.5 #344240
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natsukium
requested changes
Sep 25, 2024
| homepage = "https://github.com/Lioscro/ngs-tools"; | ||
| description = "Reusable tools for working with next-generation sequencing (NGS) data"; | ||
| license = lib.licenses.mit; | ||
| maintainers = with lib.maintainers; [ youhaveme9 ]; |
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Hey @natsukium
Already created a PR regarding this
#343954
| buildPythonPackage rec { | ||
| pname = "ngs-tools"; | ||
| version = "1.8.5"; | ||
| format = "setuptools"; |
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Suggested change
| format = "setuptools"; | |
| pyproject = true; |
Please add pyproject = true; and build-system = [ setuptools ]; to avoid the legacy setuptools build.
Note that the pyproject format falls back to using setuptools, so you can use pyproject = true even if the package only has a setup.py. When set to false, you can use the existing hooks or provide your own logic to build the package. This can be useful for packages that don't support the pyproject format. When unset, the legacy setuptools hooks are used for backwards compatibility.
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| src = fetchPypi { | ||
| inherit pname version; | ||
| sha256 = "OA4jahAcWxrDwPzbzJCKIQF5tu8qk/vqn06w7C7cHeA="; |
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Suggested change
| sha256 = "OA4jahAcWxrDwPzbzJCKIQF5tu8qk/vqn06w7C7cHeA="; | |
| hash = "sha256-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA="; |
Please use SRI hash instead.
| sha256 = "OA4jahAcWxrDwPzbzJCKIQF5tu8qk/vqn06w7C7cHeA="; | ||
| }; | ||
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| propagatedBuildInputs = [ |
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Suggested change
| propagatedBuildInputs = [ | |
| dependencies = [ |
| typing-extensions | ||
| ]; | ||
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| nativeBuildInputs = [ setuptools-scm ]; |
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setuptools-scm should go to build-system.
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| nativeBuildInputs = [ setuptools-scm ]; | ||
| pythonImportsCheck = [ "ngs_tools" ]; | ||
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Could you enable tests with pytestCheckHook or similar?
Make sure the tests are enabled using for example pytestCheckHook and, in the case of libraries, are passing for all interpreters. If certain tests fail they can be disabled individually. Try to avoid disabling the tests altogether. In any case, when you disable tests, leave a comment explaining why.
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Enabled test using pytestCheckHook
But getting import errors
==================================== ERRORS ====================================
______________________ ERROR collecting tests/test_bam.py ______________________
ImportError while importing test module '/private/tmp/nix-build-python3.12-ngs-tools-1.8.5.drv-0/ngs-tools-1.8.5/tests/test_bam.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/nix/store/9pj4rzx5pbynkkxq1srzwjhywmcfxws3-python3-3.12.5/lib/python3.12/importlib/__init__.py:90: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_bam.py:7: in <module>
from tests.mixins import TestMixin, tqdm_mock
E ModuleNotFoundError: No module named 'tests'
____________________ ERROR collecting tests/test_binary.py _____________________
ImportError while importing test module '/private/tmp/nix-build-python3.12-ngs-tools-1.8.5.drv-0/ngs-tools-1.8.5/tests/test_binary.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/nix/store/9pj4rzx5pbynkkxq1srzwjhywmcfxws3-python3-3.12.5/lib/python3.12/importlib/__init__.py:90: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_binary.py:6: in <module>
from . import mixins
E ImportError: attempted relative import with no known parent package
___________________ ERROR collecting tests/test_chemistry.py ___________________
ImportError while importing test module '/private/tmp/nix-build-python3.12-ngs-tools-1.8.5.drv-0/ngs-tools-1.8.5/tests/test_chemistry.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/nix/store/9pj4rzx5pbynkkxq1srzwjhywmcfxws3-python3-3.12.5/lib/python3.12/importlib/__init__.py:90: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_chemistry.py:4: in <module>
from tests.mixins import TestMixin
E ModuleNotFoundError: No module named 'tests'
_____________________ ERROR collecting tests/test_fasta.py _____________________
ImportError while importing test module '/private/tmp/nix-build-python3.12-ngs-tools-1.8.5.drv-0/ngs-tools-1.8.5/tests/test_fasta.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/nix/store/9pj4rzx5pbynkkxq1srzwjhywmcfxws3-python3-3.12.5/lib/python3.12/importlib/__init__.py:90: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_fasta.py:6: in <module>
from . import mixins
E ImportError: attempted relative import with no known parent package
_____________________ ERROR collecting tests/test_fastq.py _____________________
ImportError while importing test module '/private/tmp/nix-build-python3.12-ngs-tools-1.8.5.drv-0/ngs-tools-1.8.5/tests/test_fastq.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/nix/store/9pj4rzx5pbynkkxq1srzwjhywmcfxws3-python3-3.12.5/lib/python3.12/importlib/__init__.py:90: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_fastq.py:8: in <module>
from . import mixins
E ImportError: attempted relative import with no known parent package
______________________ ERROR collecting tests/test_gtf.py ______________________
ImportError while importing test module '/private/tmp/nix-build-python3.12-ngs-tools-1.8.5.drv-0/ngs-tools-1.8.5/tests/test_gtf.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/nix/store/9pj4rzx5pbynkkxq1srzwjhywmcfxws3-python3-3.12.5/lib/python3.12/importlib/__init__.py:90: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_gtf.py:6: in <module>
from . import mixins
E ImportError: attempted relative import with no known parent package
___________________ ERROR collecting tests/test_sequence.py ____________________
ImportError while importing test module '/private/tmp/nix-build-python3.12-ngs-tools-1.8.5.drv-0/ngs-tools-1.8.5/tests/test_sequence.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/nix/store/9pj4rzx5pbynkkxq1srzwjhywmcfxws3-python3-3.12.5/lib/python3.12/importlib/__init__.py:90: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_sequence.py:8: in <module>
from . import mixins
E ImportError: attempted relative import with no known parent package
_____________________ ERROR collecting tests/test_utils.py _____________________
ImportError while importing test module '/private/tmp/nix-build-python3.12-ngs-tools-1.8.5.drv-0/ngs-tools-1.8.5/tests/test_utils.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/nix/store/9pj4rzx5pbynkkxq1srzwjhywmcfxws3-python3-3.12.5/lib/python3.12/importlib/__init__.py:90: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_utils.py:11: in <module>
from . import mixins
E ImportError: attempted relative import with no known parent package
=========================== short test summary info ============================
ERROR tests/test_bam.py
ERROR tests/test_binary.py
ERROR tests/test_chemistry.py
ERROR tests/test_fasta.py
ERROR tests/test_fastq.py
ERROR tests/test_gtf.py
ERROR tests/test_sequence.py
ERROR tests/test_utils.py
!!!!!!!!!!!!!!!!!!! Interrupted: 8 errors during collection !!!!!!!!!!!!!!!!!!!!
============================== 8 errors in 0.63s ===============================
error: builder for '/nix/store/ly95bm3jqb625s9qqczr8zc58qdwpvqi-python3.12-ngs-tools-1.8.5.drv' failed with exit code 2;
last 25 log lines:
> /nix/store/9pj4rzx5pbynkkxq1srzwjhywmcfxws3-python3-3.12.5/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> tests/test_sequence.py:8: in <module>
> from . import mixins
> E ImportError: attempted relative import with no known parent package
> _____________________ ERROR collecting tests/test_utils.py _____________________
> ImportError while importing test module '/private/tmp/nix-build-python3.12-ngs-tools-1.8.5.drv-0/ngs-tools-1.8.5/tests/test_utils.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /nix/store/9pj4rzx5pbynkkxq1srzwjhywmcfxws3-python3-3.12.5/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> tests/test_utils.py:11: in <module>
> from . import mixins
> E ImportError: attempted relative import with no known parent package
> =========================== short test summary info ============================
> ERROR tests/test_bam.py
> ERROR tests/test_binary.py
> ERROR tests/test_chemistry.py
> ERROR tests/test_fasta.py
> ERROR tests/test_fastq.py
> ERROR tests/test_gtf.py
> ERROR tests/test_sequence.py
> ERROR tests/test_utils.py
> !!!!!!!!!!!!!!!!!!! Interrupted: 8 errors during collection !!!!!!!!!!!!!!!!!!!!
> ============================== 8 errors in 0.63s ===============================
For full logs, run 'nix-store -l /nix/store/ly95bm3jqb625s9qqczr8zc58qdwpvqi-python3.12-ngs-tools-1.8.5.drv'.
While running pytest in the ngs-tools, passes all the test
I tried using pytest manually
nativeCheckInputs = [ pytest ];
postInstall = ''
pytest
'';But still getting the same error
Can you please tell me what am I missing here?
FliegendeWurst
added
the
2.status: needs-changes
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Description of changes
Reusable tools for working with next-generation sequencing (NGS) data
Things done
nix.conf? (See Nix manual)sandbox = relaxedsandbox = truenix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage./result/bin/)Add a 👍 reaction to pull requests you find important.