search

jamescasbon / PyVCF

A Variant Call Format reader for Python.
http://pyvcf.readthedocs.org/en/latest/index.html
Other
401 stars 200 forks source link

install fails if setuptools >= 58 #332

Open myourshaw opened 2 years ago

myourshaw commented 2 years ago

pip3 install PyVCF (version 0.6.8) will fail when setuptools version is >=58. Instead PyVCF will install version 0.4.3, which fails to run with this error: ImportError: cannot import name 'Reader' from 'parser' (/home/myourshaw/.local/lib/python3.9/lib-dynload/parser.cpython-39-x86_64-linux-gnu.so)

Python version is 3.9.7 ` pip3 install --upgrade PyVCF;

Collecting PyVCF Downloading PyVCF-0.6.8.tar.gz (34 kB) ERROR: Command errored out with exit status 1: command: /home/myourshaw/.venv/dnanexus/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nl16n6e2/pyvcf_8e753a9cb7b248d2b23cefa5ff04feb8/setup.py'"'"'; file='"'"'/tmp/pip-install-nl16n6e2/pyvcf_8e753a9cb7b248d2b23cefa5ff04feb8/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-d_w3yhiw cwd: /tmp/pip-install-nl16n6e2/pyvcf_8e753a9cb7b248d2b23cefa5ff04feb8/ Complete output (1 lines): error in PyVCF setup command: use_2to3 is invalid.

WARNING: Discarding https://files.pythonhosted.org/packages/20/b6/36bfb1760f6983788d916096193fc14c83cce512c7787c93380e09458c09/PyVCF-0.6.8.tar.gz#sha256=e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9 (from https://pypi.org/simple/pyvcf/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Downloading PyVCF-0.6.7.tar.gz (31 kB) ERROR: Command errored out with exit status 1: command: /home/myourshaw/.venv/dnanexus/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nl16n6e2/pyvcf_d5e4c3e5adf04c4d9a808ae6dbee023c/setup.py'"'"'; file='"'"'/tmp/pip-install-nl16n6e2/pyvcf_d5e4c3e5adf04c4d9a808ae6dbee023c/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-1rmgoulv cwd: /tmp/pip-install-nl16n6e2/pyvcf_d5e4c3e5adf04c4d9a808ae6dbee023c/ Complete output (1 lines): error in PyVCF setup command: use_2to3 is invalid.

WARNING: Discarding https://files.pythonhosted.org/packages/64/1b/7c393d0cd5b1de2bb025d6ef45f71a013258214ae3564ede54adbd74ad00/PyVCF-0.6.7.tar.gz#sha256=998361f824f828f689e8e1043f795403c11e561d719cc85cdd17c3679fa9b4aa (from https://pypi.org/simple/pyvcf/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Downloading PyVCF-0.6.6.tar.gz (30 kB) ERROR: Command errored out with exit status 1: command: /home/myourshaw/.venv/dnanexus/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nl16n6e2/pyvcf_56bd71449dd1463e8d4bbb431c3596b3/setup.py'"'"'; file='"'"'/tmp/pip-install-nl16n6e2/pyvcf_56bd71449dd1463e8d4bbb431c3596b3/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-1bgqn8hl cwd: /tmp/pip-install-nl16n6e2/pyvcf_56bd71449dd1463e8d4bbb431c3596b3/ Complete output (1 lines): error in PyVCF setup command: use_2to3 is invalid.

WARNING: Discarding https://files.pythonhosted.org/packages/f7/b5/0c1763caa7502b71b43ef486211230fb6bfe30568b01594859150d5b2339/PyVCF-0.6.6.tar.gz#sha256=d0517b0ebd41a4064aa4cc6545617597d84ef7772c96713c170f39b68a997186 (from https://pypi.org/simple/pyvcf/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Downloading PyVCF-0.6.5.tar.gz (30 kB) ERROR: Command errored out with exit status 1: command: /home/myourshaw/.venv/dnanexus/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nl16n6e2/pyvcf_8093a21b8da84ca2b66a98ab35277981/setup.py'"'"'; file='"'"'/tmp/pip-install-nl16n6e2/pyvcf_8093a21b8da84ca2b66a98ab35277981/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-fgevzwdl cwd: /tmp/pip-install-nl16n6e2/pyvcf_8093a21b8da84ca2b66a98ab35277981/ Complete output (1 lines): error in PyVCF setup command: use_2to3 is invalid.

WARNING: Discarding https://files.pythonhosted.org/packages/10/a7/f97d71cf4b0a22a2adc55564b3dab6bf1a90ef6592ad2db0c5b8a58c5e0a/PyVCF-0.6.5.tar.gz#sha256=458b012fe69842acd49d87913f1eb068696c01b03aea7c04d6b8e14f13872c13 (from https://pypi.org/simple/pyvcf/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Downloading PyVCF-0.6.4.tar.gz (29 kB) ERROR: Command errored out with exit status 1: command: /home/myourshaw/.venv/dnanexus/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nl16n6e2/pyvcf_29ece4726a9944eca31b0cc9eb5bb8f6/setup.py'"'"'; file='"'"'/tmp/pip-install-nl16n6e2/pyvcf_29ece4726a9944eca31b0cc9eb5bb8f6/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-_zv8aoj3 cwd: /tmp/pip-install-nl16n6e2/pyvcf_29ece4726a9944eca31b0cc9eb5bb8f6/ Complete output (1 lines): error in PyVCF setup command: use_2to3 is invalid.

WARNING: Discarding https://files.pythonhosted.org/packages/30/db/fd30981c363499c9b51687b7d06e891937c3136073b5771b2e30c0453aae/PyVCF-0.6.4.tar.gz#sha256=10aef49ed2a4de7a64d51d92dd30441d350b24619f328d879cbd86611031b18a (from https://pypi.org/simple/pyvcf/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Downloading PyVCF-0.6.3.tar.gz (27 kB) ERROR: Command errored out with exit status 1: command: /home/myourshaw/.venv/dnanexus/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nl16n6e2/pyvcf_784cb7c529e64bf2b1b675cc63f94301/setup.py'"'"'; file='"'"'/tmp/pip-install-nl16n6e2/pyvcf_784cb7c529e64bf2b1b675cc63f94301/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-w_wig34k cwd: /tmp/pip-install-nl16n6e2/pyvcf_784cb7c529e64bf2b1b675cc63f94301/ Complete output (1 lines): error in PyVCF setup command: use_2to3 is invalid.

WARNING: Discarding https://files.pythonhosted.org/packages/38/3a/a3b7a9b36cd2d8aedbe1335887c50441b942cb3e990def4b327f1ee21147/PyVCF-0.6.3.tar.gz#sha256=44b6f753472b2f9b2c5e3f08959d1f6532076fcf83223f3797256ac7b8ede60d (from https://pypi.org/simple/pyvcf/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Downloading PyVCF-0.6.2.tar.gz (26 kB) ERROR: Command errored out with exit status 1: command: /home/myourshaw/.venv/dnanexus/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nl16n6e2/pyvcf_a3d3fb04fa3d411d8a5d56cd1b549b19/setup.py'"'"'; file='"'"'/tmp/pip-install-nl16n6e2/pyvcf_a3d3fb04fa3d411d8a5d56cd1b549b19/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-a46cmorm cwd: /tmp/pip-install-nl16n6e2/pyvcf_a3d3fb04fa3d411d8a5d56cd1b549b19/ Complete output (1 lines): error in PyVCF setup command: use_2to3 is invalid.

WARNING: Discarding https://files.pythonhosted.org/packages/73/4b/2bbb1ee971de3d6b516ba4dc152027488fe6f15fc396620881750a9b51d0/PyVCF-0.6.2.tar.gz#sha256=aebd8dc67ea92d307976ae73ed0add8d9e1b6c7e09343decfa960e0e597f28b1 (from https://pypi.org/simple/pyvcf/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Downloading PyVCF-0.6.1.tar.gz (26 kB) ERROR: Command errored out with exit status 1: command: /home/myourshaw/.venv/dnanexus/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nl16n6e2/pyvcf_17bed027b0914176be707cd31d1fc385/setup.py'"'"'; file='"'"'/tmp/pip-install-nl16n6e2/pyvcf_17bed027b0914176be707cd31d1fc385/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-bmf9e3i8 cwd: /tmp/pip-install-nl16n6e2/pyvcf_17bed027b0914176be707cd31d1fc385/ Complete output (1 lines): error in PyVCF setup command: use_2to3 is invalid.

WARNING: Discarding https://files.pythonhosted.org/packages/6f/49/e46405959069b27ee605f7646e7ec7d5c220e981a11fa8a76f28bb5dee17/PyVCF-0.6.1.tar.gz#sha256=41e0369cc7852011f4fb277e2b5282439715d6edde2ee9cdde0e1262e78b2389 (from https://pypi.org/simple/pyvcf/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Downloading PyVCF-0.6.0.tar.gz (27 kB) ERROR: Command errored out with exit status 1: command: /home/myourshaw/.venv/dnanexus/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nl16n6e2/pyvcf_180b617c9d7f4fde9d97a7ef7aba3510/setup.py'"'"'; file='"'"'/tmp/pip-install-nl16n6e2/pyvcf_180b617c9d7f4fde9d97a7ef7aba3510/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-d0xo61ur cwd: /tmp/pip-install-nl16n6e2/pyvcf_180b617c9d7f4fde9d97a7ef7aba3510/ Complete output (1 lines): error in PyVCF setup command: use_2to3 is invalid.

WARNING: Discarding https://files.pythonhosted.org/packages/4e/ae/b43f6a7dca99957ebee1d0944213a6a1490595e04aa4ad95fb25c69dbcd9/PyVCF-0.6.0.tar.gz#sha256=d9ec3bbedb64fa35c2648a9c41fdefaedd3912ff597a436e073d27aeccf5de7c (from https://pypi.org/simple/pyvcf/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Downloading PyVCF-0.5.0.tar.gz (23 kB) ERROR: Command errored out with exit status 1: command: /home/myourshaw/.venv/dnanexus/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nl16n6e2/pyvcf_d4708667383a4805837b729c0e754e46/setup.py'"'"'; file='"'"'/tmp/pip-install-nl16n6e2/pyvcf_d4708667383a4805837b729c0e754e46/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-gq7makn7 cwd: /tmp/pip-install-nl16n6e2/pyvcf_d4708667383a4805837b729c0e754e46/ Complete output (1 lines): error in PyVCF setup command: use_2to3 is invalid.

WARNING: Discarding https://files.pythonhosted.org/packages/db/4c/b2c4f3f1eba4913dc531e0b5d27a1219f3edd767007f1a02f753207e1647/PyVCF-0.5.0.tar.gz#sha256=51cc9ffea4f1e9ae2095d41abd371afe4581b4c7203094f7647e7a2a071e50c9 (from https://pypi.org/simple/pyvcf/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Downloading PyVCF-0.4.6.tar.gz (19 kB) ERROR: Command errored out with exit status 1: command: /home/myourshaw/.venv/dnanexus/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nl16n6e2/pyvcf_dbca7ea0a9d64b5388858d37f892526a/setup.py'"'"'; file='"'"'/tmp/pip-install-nl16n6e2/pyvcf_dbca7ea0a9d64b5388858d37f892526a/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-6rgxcqx6 cwd: /tmp/pip-install-nl16n6e2/pyvcf_dbca7ea0a9d64b5388858d37f892526a/ Complete output (1 lines): error in PyVCF setup command: use_2to3 is invalid.

WARNING: Discarding https://files.pythonhosted.org/packages/ca/25/bfe4a71b1f65d0bcd3e7353c26a35fce513bd8c0f5e1dfce9d42d2f37c27/PyVCF-0.4.6.tar.gz#sha256=6e41ba239b2644664bf4c64a2638ca4870afb144ff5891a1fd37ad2adad79e40 (from https://pypi.org/simple/pyvcf/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Downloading PyVCF-0.4.5.tar.gz (19 kB) ERROR: Command errored out with exit status 1: command: /home/myourshaw/.venv/dnanexus/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nl16n6e2/pyvcf_d2e138b2cb9042b78f728691c5a10899/setup.py'"'"'; file='"'"'/tmp/pip-install-nl16n6e2/pyvcf_d2e138b2cb9042b78f728691c5a10899/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-5d5pey31 cwd: /tmp/pip-install-nl16n6e2/pyvcf_d2e138b2cb9042b78f728691c5a10899/ Complete output (1 lines): error in PyVCF setup command: use_2to3 is invalid.

WARNING: Discarding https://files.pythonhosted.org/packages/8f/c4/e1c71b3e00d2c2a5149933558e088e3a42a27b94620f47f5b2cb861642a8/PyVCF-0.4.5.tar.gz#sha256=4c7367d3a55d7ba8c404241b12cbdf011b5fa7a95034a1c779489523292a2d47 (from https://pypi.org/simple/pyvcf/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Downloading PyVCF-0.4.4.tar.gz (19 kB) ERROR: Command errored out with exit status 1: command: /home/myourshaw/.venv/dnanexus/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nl16n6e2/pyvcf_6cb5c5e7564741f39a6194069b28de6d/setup.py'"'"'; file='"'"'/tmp/pip-install-nl16n6e2/pyvcf_6cb5c5e7564741f39a6194069b28de6d/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-voul_7t5 cwd: /tmp/pip-install-nl16n6e2/pyvcf_6cb5c5e7564741f39a6194069b28de6d/ Complete output (1 lines): error in PyVCF setup command: use_2to3 is invalid.

WARNING: Discarding https://files.pythonhosted.org/packages/e3/38/e1b52283c76ef5ef2fc4a5e005bfd308ff14be5483f09b2e5268bd06ae9d/PyVCF-0.4.4.tar.gz#sha256=4576d8a46958fc51a0c100ee0c8aa768e6d8a7fb84706a97a1fbdebd97f49e70 (from https://pypi.org/simple/pyvcf/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Downloading PyVCF-0.4.3.tar.gz (17 kB) Building wheels for collected packages: PyVCF Building wheel for PyVCF (setup.py) ... done Created wheel for PyVCF: filename=PyVCF-0.4.3-py3-none-any.whl size=16158 sha256=cfa327118633b62205e0d7e957d360c04caa64f9716e25bc3ec6d1e6055a6a97 Stored in directory: /home/myourshaw/.cache/pip/wheels/f9/3f/f2/4da50c1e0c57afb2b17589433e794cc9a3b688164a69e3b395 Successfully built PyVCF Installing collected packages: PyVCF Successfully installed PyVCF-0.4.3 `

ChrisMoth commented 2 years ago

In looking at some of the code, I sense it is Python2 still:

File "/home/mothcw/Downloads/PyVCF-master/vcf/parser.py", line 644, in Writer counts = dict((v,k) for k,v in field_counts.iteritems()) AttributeError: 'dict' object has no attribute 'iteritems'

I hope the maintainers might move the entire thing to Python3 and call it Version 0.7.0