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
Sourcing pytest-check-hook
Running phase: unpackPhase
unpacking source archive /nix/store/q4jxmbgh2m4sz5wx34196v8cpmy9x7vl-biorefs-cli
source root is biorefs-cli
setting SOURCE_DATE_EPOCH to timestamp 315619200 of file "biorefs-cli/tests/test_uniprot.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 biorefs_cli-0.1.0-py3-none-any.whl
Finished creating a wheel...
Finished executing pypaBuildPhase
Running phase: pythonRuntimeDepsCheckHook
Executing pythonRuntimeDepsCheck
Checking runtime dependencies for biorefs_cli-0.1.0-py3-none-any.whl
Finished executing pythonRuntimeDepsCheck
Running phase: installPhase
Executing pypaInstallPhase
Successfully installed biorefs_cli-0.1.0-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/ih0aividi8qldpyq86kl092ai6r626v7-biorefs-cli-0.1.0
checking for references to /build/ in /nix/store/ih0aividi8qldpyq86kl092ai6r626v7-biorefs-cli-0.1.0...
patching script interpreter paths in /nix/store/ih0aividi8qldpyq86kl092ai6r626v7-biorefs-cli-0.1.0
stripping (with command strip and flags -S -p) in  /nix/store/ih0aividi8qldpyq86kl092ai6r626v7-biorefs-cli-0.1.0/lib /nix/store/ih0aividi8qldpyq86kl092ai6r626v7-biorefs-cli-0.1.0/bin
shrinking RPATHs of ELF executables and libraries in /nix/store/rxzvgx1z3lam8z44pn9d0szrgdbxi02f-biorefs-cli-0.1.0-dist
checking for references to /build/ in /nix/store/rxzvgx1z3lam8z44pn9d0szrgdbxi02f-biorefs-cli-0.1.0-dist...
patching script interpreter paths in /nix/store/rxzvgx1z3lam8z44pn9d0szrgdbxi02f-biorefs-cli-0.1.0-dist
Rewriting #!/nix/store/rgnappqqc5vbq60gza5fflyk84sylwl6-python3-3.14.6/bin/python3.14 to #!/nix/store/rgnappqqc5vbq60gza5fflyk84sylwl6-python3-3.14.6
wrapping `/nix/store/ih0aividi8qldpyq86kl092ai6r626v7-biorefs-cli-0.1.0/bin/biorefs-cli'...
Executing pythonRemoveTestsDir
Finished executing pythonRemoveTestsDir
Running phase: installCheckPhase
47 files already formatted
All checks passed!
Success: no issues found in 47 source files
============================= test session starts ==============================
platform linux -- Python 3.14.6, pytest-9.1.1, pluggy-1.6.0
rootdir: /build/biorefs-cli
configfile: pyproject.toml
collected 185 items                                                            

tests/test_api_specs.py ..                                               [  1%]
tests/test_assay.py .........                                            [  5%]
tests/test_compound.py .......                                           [  9%]
tests/test_core_helpers.py .......                                       [ 13%]
tests/test_gene.py ..........                                            [ 18%]
tests/test_http_post.py ........                                         [ 23%]
tests/test_ncbi_command.py ..........                                    [ 28%]
tests/test_ncbi_extra.py ...                                             [ 30%]
tests/test_nucleotide.py ..........                                      [ 35%]
tests/test_openalex.py .........                                         [ 40%]
tests/test_paper.py ......                                               [ 43%]
tests/test_paper_extra.py ........                                       [ 48%]
tests/test_protein.py .............                                      [ 55%]
tests/test_rate_limit.py .........                                       [ 60%]
tests/test_rcsb_graphql.py ....                                          [ 62%]
tests/test_render_helpers.py ......                                      [ 65%]
tests/test_scaffold.py .....                                             [ 68%]
tests/test_setup.py .......                                              [ 71%]
tests/test_structure_fetch.py ...........                                [ 77%]
tests/test_structure_info.py .....                                       [ 80%]
tests/test_structure_render.py .......                                   [ 84%]
tests/test_structure_search.py ............                              [ 90%]
tests/test_uniprot.py .................                                  [100%]

============================= 185 passed in 1.46s ==============================
Running phase: pythonCatchConflictsPhase
Running phase: pythonRemoveBinBytecodePhase
Running phase: pythonImportsCheckPhase
Executing pythonImportsCheckPhase
Running phase: pytestcachePhase
Running phase: pytestRemoveBytecodePhase