Python 3.13 removes pipes

[stefanor]

https://github.com/open2c/pairtools/blob/6303de6d9e992e426285840bfd10e7d5dbbc1c84/pairtools/lib/fileio.py#L2

https://docs.python.org/3.13/whatsnew/3.13.html#whatsnew313-pep594 https://docs.python.org/3.13/whatsnew/3.13.html#summary-release-highlights

============================= test session starts ==============================
platform linux -- Python 3.13.0rc2, pytest-8.3.2, pluggy-1.5.0 -- /usr/bin/python3.13
cachedir: .pytest_cache
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build
configfile: pytest.ini
testpaths: tests
plugins: typeguard-4.3.0
collecting ... collected 17 items / 2 errors

==================================== ERRORS ====================================
___________________ ERROR collecting tests/test_headerops.py ___________________
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/tests/test_headerops.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_headerops.py:2: in <module>
    from pairtools.lib import headerops
pairtools/lib/__init__.py:1: in <module>
    from . import fileio
pairtools/lib/fileio.py:2: in <module>
    import pipes
E   ModuleNotFoundError: No module named 'pipes'
____________________ ERROR collecting tests/test_select.py _____________________
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/tests/test_select.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_select.py:6: in <module>
    from pairtools.lib import pairsam_format
pairtools/lib/__init__.py:1: in <module>
    from . import fileio
pairtools/lib/fileio.py:2: in <module>
    import pipes
E   ModuleNotFoundError: No module named 'pipes'
=========================== short test summary info ============================
ERROR tests/test_headerops.py
ERROR tests/test_select.py
!!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!!
============================== 2 errors in 0.50s ===============================

[golobor]

Arrrgghh. Many thanks for the heads-up!!

On Fri, Sep 13, 2024, 19:08 Stefano Rivera @.***> wrote:

https://github.com/open2c/pairtools/blob/6303de6d9e992e426285840bfd10e7d5dbbc1c84/pairtools/lib/fileio.py#L2

https://docs.python.org/3.13/whatsnew/3.13.html#whatsnew313-pep594 https://docs.python.org/3.13/whatsnew/3.13.html#summary-release-highlights

============================= test session starts ============================== platform linux -- Python 3.13.0rc2, pytest-8.3.2, pluggy-1.5.0 -- /usr/bin/python3.13 cachedir: .pytest_cache rootdir: /<>/.pybuild/cpython3_3.13/build configfile: pytest.ini testpaths: tests plugins: typeguard-4.3.0 collecting ... collected 17 items / 2 errors

==================================== ERRORS ==================================== _____ ERROR collecting tests/test_headerops.py ___ ImportError while importing test module '/<>/.pybuild/cpython3_3.13/build/tests/test_headerops.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: /usr/lib/python3.13/importlib/init.py:88: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_headerops.py:2: in from pairtools.lib import headerops pairtools/lib/init.py:1: in from . import fileio pairtools/lib/fileio.py:2: in import pipes E ModuleNotFoundError: No module named 'pipes' __ ERROR collecting tests/testselect.py ____ ImportError while importing test module '/<>/.pybuild/cpython3_3.13/build/tests/test_select.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: /usr/lib/python3.13/importlib/init.py:88: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_select.py:6: in from pairtools.lib import pairsam_format pairtools/lib/init.py:1: in from . import fileio pairtools/lib/fileio.py:2: in import pipes E ModuleNotFoundError: No module named 'pipes' =========================== short test summary info ============================ ERROR tests/test_headerops.py ERROR tests/test_select.py !!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!! ============================== 2 errors in 0.50s ===============================

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