Sourcing python-remove-tests-dir-hook
Sourcing python-catch-conflicts-hook.sh
Sourcing python-remove-bin-bytecode-hook.sh
Sourcing pypa-build-hook
Using pypaBuildPhase
Sourcing python-runtime-deps-check-hook
Using pythonRuntimeDepsCheckHook
Sourcing pypa-install-hook
Using pypaInstallPhase
Sourcing python-imports-check-hook.sh
Using pythonImportsCheckPhase
Sourcing python-namespaces-hook
Sourcing python-catch-conflicts-hook.sh
Running phase: unpackPhase
unpacking source archive /nix/store/2gng8b8lig79qppb1fkisqnlg691ky1c-source
source root is source
setting SOURCE_DATE_EPOCH to timestamp 315619200 of file "source/test/__init__.py"
Running phase: patchPhase
Running phase: updateAutotoolsGnuConfigScriptsPhase
Running phase: configurePhase
no configure script, doing nothing
Running phase: buildPhase
Executing pypaBuildPhase
Creating a wheel...
pypa build flags: --no-isolation --outdir dist/ --wheel
* Getting build dependencies for wheel...
* Building wheel...
Successfully built evcouplings-0.3.0-py2.py3-none-any.whl
Finished creating a wheel...
Finished executing pypaBuildPhase
Running phase: pythonRuntimeDepsCheckHook
Executing pythonRuntimeDepsCheck
Checking runtime dependencies for evcouplings-0.3.0-py2.py3-none-any.whl
Finished executing pythonRuntimeDepsCheck
Running phase: installPhase
Executing pypaInstallPhase
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/align/alignment.py:400: SyntaxWarning: invalid escape sequence '\d'
  m = re.search("(.+)/(\d+)-(\d+)", header)
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/align/alignment.py:400: SyntaxWarning: invalid escape sequence '\d'
  m = re.search("(.+)/(\d+)-(\d+)", header)
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/align/ids.py:14: SyntaxWarning: invalid escape sequence '\w'
  "^Uni\w+\_(\w+).*/",
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/align/ids.py:17: SyntaxWarning: invalid escape sequence '\w'
  "^\w+\|(\w+)\|\w+\/",
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/align/ids.py:20: SyntaxWarning: invalid escape sequence '\w'
  "^(\w+).*/.*$",
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/align/ids.py:23: SyntaxWarning: invalid escape sequence '\w'
  "^\w+\|\w+\|(\w+)",
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/align/ids.py:14: SyntaxWarning: invalid escape sequence '\w'
  "^Uni\w+\_(\w+).*/",
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/align/ids.py:17: SyntaxWarning: invalid escape sequence '\w'
  "^\w+\|(\w+)\|\w+\/",
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/align/ids.py:20: SyntaxWarning: invalid escape sequence '\w'
  "^(\w+).*/.*$",
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/align/ids.py:23: SyntaxWarning: invalid escape sequence '\w'
  "^\w+\|\w+\|(\w+)",
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/align/protocol.py:423: SyntaxWarning: invalid escape sequence '\s'
  regex = re.compile("\s({})=".format(
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/align/protocol.py:423: SyntaxWarning: invalid escape sequence '\s'
  regex = re.compile("\s({})=".format(
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/compare/pdb.py:225: SyntaxWarning: invalid escape sequence '\*'
  numbering. End index or range is \*inclusive*\
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/compare/pdb.py:225: SyntaxWarning: invalid escape sequence '\*'
  numbering. End index or range is \*inclusive*\
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/couplings/tools.py:51: SyntaxWarning: invalid escape sequence '\d'
  "focus": re.compile("Found focus (.+) as sequence (\d+)"),
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/couplings/tools.py:52: SyntaxWarning: invalid escape sequence '\d'
  "seqs": re.compile("(\d+) valid sequences out of (\d+)"),
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/couplings/tools.py:53: SyntaxWarning: invalid escape sequence '\d'
  "sites": re.compile("(\d+) sites out of (\d+)"),
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/couplings/tools.py:54: SyntaxWarning: invalid escape sequence '\d'
  "region": re.compile("Region starts at (\d+)"),
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/couplings/tools.py:56: SyntaxWarning: invalid escape sequence '\d'
  "samples": re.compile("Effective number of samples(.*): (\d+\.\d+)"),
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/couplings/tools.py:60: SyntaxWarning: invalid escape sequence '\d'
  re_iter = re.compile("(\d+){}".format(
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/couplings/tools.py:61: SyntaxWarning: invalid escape sequence '\s'
  "".join(["\s+(\d+\.\d+)"] * 6)
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/couplings/tools.py:51: SyntaxWarning: invalid escape sequence '\d'
  "focus": re.compile("Found focus (.+) as sequence (\d+)"),
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/couplings/tools.py:52: SyntaxWarning: invalid escape sequence '\d'
  "seqs": re.compile("(\d+) valid sequences out of (\d+)"),
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/couplings/tools.py:53: SyntaxWarning: invalid escape sequence '\d'
  "sites": re.compile("(\d+) sites out of (\d+)"),
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/couplings/tools.py:54: SyntaxWarning: invalid escape sequence '\d'
  "region": re.compile("Region starts at (\d+)"),
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/couplings/tools.py:56: SyntaxWarning: invalid escape sequence '\d'
  "samples": re.compile("Effective number of samples(.*): (\d+\.\d+)"),
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/couplings/tools.py:60: SyntaxWarning: invalid escape sequence '\d'
  re_iter = re.compile("(\d+){}".format(
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/couplings/tools.py:61: SyntaxWarning: invalid escape sequence '\s'
  "".join(["\s+(\d+\.\d+)"] * 6)
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/fold/tools.py:335: SyntaxWarning: invalid escape sequence '\s'
  "vs. (.+?)\s+Pairs=\s*(\d+), RMSD=\s*(\d+\.\d+), "
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/fold/tools.py:336: SyntaxWarning: invalid escape sequence '\s'
  "MaxSub=\s*(\d+\.\d+), TM=\s*(\d+\.\d+), MSI=\s*(\d+\.\d+)"
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/fold/tools.py:437: SyntaxWarning: invalid escape sequence '\s'
  m = re.compile("INFO\s*:\s*(\d+)\s*:\s*(\d+)\s+(.+)")
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/fold/tools.py:335: SyntaxWarning: invalid escape sequence '\s'
  "vs. (.+?)\s+Pairs=\s*(\d+), RMSD=\s*(\d+\.\d+), "
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/fold/tools.py:336: SyntaxWarning: invalid escape sequence '\s'
  "MaxSub=\s*(\d+\.\d+), TM=\s*(\d+\.\d+), MSI=\s*(\d+\.\d+)"
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/fold/tools.py:437: SyntaxWarning: invalid escape sequence '\s'
  m = re.compile("INFO\s*:\s*(\d+)\s*:\s*(\d+)\s+(.+)")
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/utils/app.py:109: SyntaxWarning: invalid escape sequence '\d'
  m = re.search("(\d+)-(\d+)", region)
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/utils/app.py:109: SyntaxWarning: invalid escape sequence '\d'
  m = re.search("(\d+)-(\d+)", region)
Successfully installed evcouplings-0.3.0-py2.py3-none-any.whl
Finished executing pypaInstallPhase
Running phase: pythonOutputDistPhase
Executing pythonOutputDistPhase
Finished executing pythonOutputDistPhase
Running phase: fixupPhase
shrinking RPATHs of ELF executables and libraries in /nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1
checking for references to /build/ in /nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1...
patching script interpreter paths in /nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1
stripping (with command strip and flags -S -p) in  /nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib /nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/bin
shrinking RPATHs of ELF executables and libraries in /nix/store/4c7b4aip4gp860cmg0csc7z4v3y9w1rd-python3.13-evcouplings-0.2.1-dist
checking for references to /build/ in /nix/store/4c7b4aip4gp860cmg0csc7z4v3y9w1rd-python3.13-evcouplings-0.2.1-dist...
patching script interpreter paths in /nix/store/4c7b4aip4gp860cmg0csc7z4v3y9w1rd-python3.13-evcouplings-0.2.1-dist
Rewriting #!/nix/store/l9k0anq0z7zz81zcwy035jfwap9ga6rl-python3-3.13.13/bin/python3.13 to #!/nix/store/l9k0anq0z7zz81zcwy035jfwap9ga6rl-python3-3.13.13
wrapping `/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/bin/evcouplings'...
Rewriting #!/nix/store/l9k0anq0z7zz81zcwy035jfwap9ga6rl-python3-3.13.13/bin/python3.13 to #!/nix/store/l9k0anq0z7zz81zcwy035jfwap9ga6rl-python3-3.13.13
wrapping `/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/bin/evcouplings_dbupdate'...
Rewriting #!/nix/store/l9k0anq0z7zz81zcwy035jfwap9ga6rl-python3-3.13.13/bin/python3.13 to #!/nix/store/l9k0anq0z7zz81zcwy035jfwap9ga6rl-python3-3.13.13
wrapping `/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/bin/evcouplings_runcfg'...
Rewriting #!/nix/store/l9k0anq0z7zz81zcwy035jfwap9ga6rl-python3-3.13.13/bin/python3.13 to #!/nix/store/l9k0anq0z7zz81zcwy035jfwap9ga6rl-python3-3.13.13
wrapping `/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/bin/evcouplings_summarize'...
Executing pythonRemoveTestsDir
Finished executing pythonRemoveTestsDir
Running phase: installCheckPhase
no Makefile or custom installCheckPhase, doing nothing
Running phase: pythonCatchConflictsPhase
Running phase: pythonRemoveBinBytecodePhase
Running phase: pythonImportsCheckPhase
Executing pythonImportsCheckPhase
Check whether the following modules can be imported: evcouplings evcouplings.align evcouplings.couplings evcouplings.mutate evcouplings.utils.config
/nix/store/9x5fdc7mgdxxsfghbn0halamaia5nllp-python3.13-evcouplings-0.2.1/lib/python3.13/site-packages/evcouplings/couplings/pairs.py:21: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import resource_filename
mkdir -p failed for path /homeless-shelter/.config/matplotlib: [Errno 13] Permission denied: '/homeless-shelter'
Matplotlib created a temporary cache directory at /build/matplotlib-byodmkfd because there was an issue with the default path (/homeless-shelter/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.