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/g9xhjlx8aa88km8nz2dy299l081w1kf7-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/x1cn2sda2973syixniwbrrxwd1mrlbjc-biorefs-cli-0.1.0
checking for references to /build/ in /nix/store/x1cn2sda2973syixniwbrrxwd1mrlbjc-biorefs-cli-0.1.0...
patching script interpreter paths in /nix/store/x1cn2sda2973syixniwbrrxwd1mrlbjc-biorefs-cli-0.1.0
stripping (with command strip and flags -S -p) in  /nix/store/x1cn2sda2973syixniwbrrxwd1mrlbjc-biorefs-cli-0.1.0/lib /nix/store/x1cn2sda2973syixniwbrrxwd1mrlbjc-biorefs-cli-0.1.0/bin
shrinking RPATHs of ELF executables and libraries in /nix/store/w9v9hka3c941makjmfd8wfxny6g1vr87-biorefs-cli-0.1.0-dist
checking for references to /build/ in /nix/store/w9v9hka3c941makjmfd8wfxny6g1vr87-biorefs-cli-0.1.0-dist...
patching script interpreter paths in /nix/store/w9v9hka3c941makjmfd8wfxny6g1vr87-biorefs-cli-0.1.0-dist
Rewriting #!/nix/store/gxzhl7aaiid7zp3y47jqqiq7zg5mqpwp-python3-3.14.6/bin/python3.14 to #!/nix/store/gxzhl7aaiid7zp3y47jqqiq7zg5mqpwp-python3-3.14.6
wrapping `/nix/store/x1cn2sda2973syixniwbrrxwd1mrlbjc-biorefs-cli-0.1.0/bin/biorefs-cli'...
Executing pythonRemoveTestsDir
Finished executing pythonRemoveTestsDir
Running phase: installCheckPhase
47 files already formatted
RUF100 [*] Unused `noqa` directive (non-enabled: `S314`)
   --> biorefs_cli/commands/paper.py:443:37
    |
441 |     if not xml_text.strip():
442 |         return []
443 |     root = ET.fromstring(xml_text)  # noqa: S314 - NCBI/PubMed XML; no defusedxml dependency.
    |                                     ^^^^^^^^^^^^
444 |     return [
445 |         parse_pubmed_article(article, include)
    |
help: Remove unused `noqa` directive
    |
442 |         return []
    -     root = ET.fromstring(xml_text)  # noqa: S314 - NCBI/PubMed XML; no defusedxml dependency.
443 +     root = ET.fromstring(xml_text)
444 |     return [
    |

RUF100 [*] Unused `noqa` directive (non-enabled: `S314`)
   --> biorefs_cli/commands/paper.py:623:37
    |
621 |     if not xml_text.strip():
622 |         return unavailable("pmc:empty-response")
623 |     root = ET.fromstring(xml_text)  # noqa: S314 - NCBI/PMC XML; no defusedxml dependency.
    |                                     ^^^^^^^^^^^^
624 |     article = root if strip_ns(root.tag) == "article" else first(root, "article")
625 |     if article is None:
    |
help: Remove unused `noqa` directive
    |
622 |         return unavailable("pmc:empty-response")
    -     root = ET.fromstring(xml_text)  # noqa: S314 - NCBI/PMC XML; no defusedxml dependency.
623 +     root = ET.fromstring(xml_text)
624 |     article = root if strip_ns(root.tag) == "article" else first(root, "article")
    |

RUF100 [*] Unused `noqa` directive (non-enabled: `S602`)
   --> biorefs_cli/config.py:103:38
    |
101 | def run_secret_command(command: str, *, timeout_seconds: int) -> str:
102 |     try:
103 |         completed = subprocess.run(  # noqa: S602 - config intentionally stores shell commands.
    |                                      ^^^^^^^^^^^^
104 |             command,
105 |             shell=True,
    |
help: Remove unused `noqa` directive
    |
102 |     try:
    -         completed = subprocess.run(  # noqa: S602 - config intentionally stores shell commands.
103 +         completed = subprocess.run(
104 |             command,
    |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_assay.py:3:1
   |
 1 |   # Copyright (c) 2026 Seungwon Lee
 2 |   # SPDX-License-Identifier: MIT
 3 | / from __future__ import annotations
 4 | |
 5 | | from typing import TYPE_CHECKING, cast
 6 | |
 7 | | import pytest
 8 | | from biorefs_cli.commands.assay import (
 9 | |     PubChemAssayClient,
10 | |     handle_http_error,
11 | |     parse_assay_description,
12 | |     parse_concise_activity,
13 | |     parse_include,
14 | | )
15 | | from biorefs_cli.errors import RateLimitError
16 | | from biorefs_cli.http import HttpClient, JsonObject, JsonValue
17 | | from biorefs_cli.main import main
   | |_________________________________^
18 |
19 |   if TYPE_CHECKING:
   |
help: Organize imports
  |
7 | import pytest
8 +
9 | from biorefs_cli.commands.assay import (
  |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_compound.py:3:1
   |
 1 |   # Copyright (c) 2026 Seungwon Lee
 2 |   # SPDX-License-Identifier: MIT
 3 | / from __future__ import annotations
 4 | |
 5 | | from typing import TYPE_CHECKING
 6 | |
 7 | | import pytest
 8 | | from biorefs_cli.commands import compound
 9 | | from biorefs_cli.errors import CLIError
10 | | from biorefs_cli.main import build_parser
   | |_________________________________________^
11 |
12 |   if TYPE_CHECKING:
   |
help: Organize imports
  |
7 | import pytest
8 +
9 | from biorefs_cli.commands import compound
  |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_core_helpers.py:3:1
   |
 1 |   # Copyright (c) 2026 Seungwon Lee
 2 |   # SPDX-License-Identifier: MIT
 3 | / from __future__ import annotations
 4 | |
 5 | | import json
 6 | | import stat
 7 | | from typing import TYPE_CHECKING
 8 | |
 9 | | import pytest
10 | | from biorefs_cli.config import (
11 | |     Config,
12 | |     check_configured_secrets,
13 | |     config_to_public_dict,
14 | |     load_config,
15 | |     merge_config,
16 | |     run_secret_command,
17 | |     write_config,
18 | | )
19 | | from biorefs_cli.errors import (
20 | |     ConfigError,
21 | |     CredentialCheckError,
22 | |     HTTPError,
23 | |     RateLimitError,
24 | | )
25 | | from biorefs_cli.http import HttpClient, HttpResponse, RetryPolicy
26 | | from biorefs_cli.output import escape_cell, markdown_heading, markdown_table, print_json
27 | | from biorefs_cli.rate_limit import RateLimitPolicy
   | |__________________________________________________^
28 |
29 |   if TYPE_CHECKING:
   |
help: Organize imports
   |
9  | import pytest
10 +
11 | from biorefs_cli.config import (
   |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_gene.py:3:1
   |
 1 |   # Copyright (c) 2026 Seungwon Lee
 2 |   # SPDX-License-Identifier: MIT
 3 | / from __future__ import annotations
 4 | |
 5 | | import json
 6 | | from typing import cast
 7 | | from urllib.parse import parse_qs, urlparse
 8 | |
 9 | | import pytest
10 | | from biorefs_cli.commands import gene
11 | | from biorefs_cli.config import Config
12 | | from biorefs_cli.errors import CLIError, RateLimitError
13 | | from biorefs_cli.http import HttpClient, HttpResponse, JsonObject, RetryPolicy
14 | | from biorefs_cli.main import build_parser, main
15 | | from biorefs_cli.ncbi_client import NCBIClient
16 | | from biorefs_cli.rate_limit import RateLimiter
   | |______________________________________________^
17 |
18 |   GENE_SUMMARY: JsonObject = {
   |
help: Organize imports
   |
9  | import pytest
10 +
11 | from biorefs_cli.commands import gene
   |

I001 [*] Import block is un-sorted or un-formatted
 --> tests/test_http_post.py:3:1
  |
1 |   # Copyright (c) 2026 Seungwon Lee
2 |   # SPDX-License-Identifier: MIT
3 | / from __future__ import annotations
4 | |
5 | | import json
6 | |
7 | | import pytest
8 | | from biorefs_cli.errors import HTTPError
9 | | from biorefs_cli.http import HttpClient, HttpResponse, RetryPolicy
  | |__________________________________________________________________^
help: Organize imports
  |
7 | import pytest
8 +
9 | from biorefs_cli.errors import HTTPError
  |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_ncbi_command.py:3:1
   |
 1 |   # Copyright (c) 2026 Seungwon Lee
 2 |   # SPDX-License-Identifier: MIT
 3 | / from __future__ import annotations
 4 | |
 5 | | import json
 6 | | import shlex
 7 | | import sys
 8 | | import urllib.parse
 9 | | from typing import TYPE_CHECKING
10 | |
11 | | import pytest
12 | | from biorefs_cli.commands import ncbi
13 | | from biorefs_cli.config import Config
14 | | from biorefs_cli.http import HttpClient, HttpResponse, RetryPolicy
15 | | from biorefs_cli.main import build_parser, main
16 | | from biorefs_cli.ncbi_client import NCBIClient
17 | | from biorefs_cli.rate_limit import RateLimiter, RateLimitPolicy
   | |_______________________________________________________________^
18 |
19 |   if TYPE_CHECKING:
   |
help: Organize imports
   |
11 | import pytest
12 +
13 | from biorefs_cli.commands import ncbi
   |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_ncbi_extra.py:3:1
   |
 1 |   # Copyright (c) 2026 Seungwon Lee
 2 |   # SPDX-License-Identifier: MIT
 3 | / from __future__ import annotations
 4 | |
 5 | | import argparse
 6 | | from typing import TYPE_CHECKING, cast
 7 | |
 8 | | import pytest
 9 | | from biorefs_cli.commands import ncbi
10 | | from biorefs_cli.errors import CLIError
   | |_______________________________________^
11 |
12 |   if TYPE_CHECKING:
   |
help: Organize imports
   |
8  | import pytest
9  +
10 | from biorefs_cli.commands import ncbi
   |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_nucleotide.py:5:1
   |
 3 |   """Nucleotide command tests."""
 4 |
 5 | / from __future__ import annotations
 6 | |
 7 | | import json
 8 | | from typing import cast
 9 | | from urllib.parse import parse_qs, urlparse
10 | |
11 | | import pytest
12 | | from biorefs_cli.commands import nucleotide
13 | | from biorefs_cli.config import Config
14 | | from biorefs_cli.errors import CLIError, RateLimitError
15 | | from biorefs_cli.http import HttpClient, HttpResponse, JsonObject
16 | | from biorefs_cli.main import build_parser, main
17 | | from biorefs_cli.ncbi_client import NCBIClient
   | |______________________________________________^
help: Organize imports
   |
11 | import pytest
12 +
13 | from biorefs_cli.commands import nucleotide
   |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_openalex.py:3:1
   |
 1 |   # Copyright (c) 2026 Seungwon Lee
 2 |   # SPDX-License-Identifier: MIT
 3 | / from __future__ import annotations
 4 | |
 5 | | import argparse
 6 | | from typing import TYPE_CHECKING, cast
 7 | |
 8 | | import pytest
 9 | | from biorefs_cli.commands import openalex
10 | | from biorefs_cli.config import Config
11 | | from biorefs_cli.http import HttpClient
   | |_______________________________________^
12 |
13 |   if TYPE_CHECKING:
   |
help: Organize imports
   |
8  | import pytest
9  +
10 | from biorefs_cli.commands import openalex
   |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_paper.py:11:1
   |
 9 |       from collections.abc import Sequence
10 |
11 | / import pytest
12 | | from biorefs_cli.commands.paper import (
13 | |     PaperClient,
14 | |     PaperInputError,
15 | |     cmd_convert,
16 | |     one_identifier,
17 | |     parse_jats_xml,
18 | |     parse_pubmed_xml,
19 | | )
20 | | from biorefs_cli.errors import RateLimitError
21 | | from biorefs_cli.main import main
   | |_________________________________^
22 |
23 |   PUBMED_XML = """
   |
help: Organize imports
   |
11 | import pytest
12 +
13 | from biorefs_cli.commands.paper import (
   |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_paper_extra.py:3:1
   |
 1 |   # Copyright (c) 2026 Seungwon Lee
 2 |   # SPDX-License-Identifier: MIT
 3 | / from __future__ import annotations
 4 | |
 5 | | import argparse
 6 | | from typing import Any, cast
 7 | |
 8 | | import pytest
 9 | | from biorefs_cli.commands.paper import (
10 | |     PaperClient,
11 | |     PaperInputError,
12 | |     bibtex,
13 | |     cmd_cite,
14 | |     cmd_fulltext,
15 | |     cmd_related,
16 | |     crossref_year,
17 | |     europepmc_unavailable,
18 | |     fetch_record,
19 | |     format_citation,
20 | |     normalize_crossref_work,
21 | |     normalize_doi,
22 | |     normalize_idconv,
23 | |     normalize_identifier,
24 | |     normalize_pmcid,
25 | |     normalize_pmid,
26 | |     parse_include,
27 | |     parse_jats_xml,
28 | |     parse_sections,
29 | |     print_convert,
30 | |     print_fetch,
31 | |     print_fulltext,
32 | |     print_related,
33 | |     print_search,
34 | |     ris,
35 | |     source_urls,
36 | |     strict_validate,
37 | |     unavailable,
38 | | )
39 | | from biorefs_cli.errors import HTTPError
   | |________________________________________^
40 |
41 |   MINIMAL_PUBMED_XML = """
   |
help: Organize imports
   |
8  | import pytest
9  +
10 | from biorefs_cli.commands.paper import (
   |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_protein.py:3:1
   |
 1 |   # Copyright (c) 2026 Seungwon Lee
 2 |   # SPDX-License-Identifier: MIT
 3 | / from __future__ import annotations
 4 | |
 5 | | import json
 6 | | from typing import cast
 7 | | from urllib.parse import parse_qs, urlencode, urlparse
 8 | |
 9 | | import pytest
10 | | from biorefs_cli.commands.protein import (
11 | |     ProteinService,
12 | |     build_search_term,
13 | |     normalize_accession,
14 | |     parse_protein_summaries,
15 | | )
16 | | from biorefs_cli.errors import CLIError, RateLimitError
17 | | from biorefs_cli.http import HttpResponse, JsonObject
18 | | from biorefs_cli.main import main
   | |_________________________________^
help: Organize imports
   |
9  | import pytest
10 +
11 | from biorefs_cli.commands.protein import (
   |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_render_helpers.py:3:1
   |
 1 |   # Copyright (c) 2026 Seungwon Lee
 2 |   # SPDX-License-Identifier: MIT
 3 | / from __future__ import annotations
 4 | |
 5 | | import argparse
 6 | | from typing import TYPE_CHECKING, cast
 7 | |
 8 | | import pytest
 9 | | from biorefs_cli.commands import assay, compound, gene, nucleotide, openalex, protein
10 | | from biorefs_cli.errors import CLIError, HTTPError, RateLimitError
   | |__________________________________________________________________^
11 |
12 |   if TYPE_CHECKING:
   |
help: Organize imports
   |
8  | import pytest
9  +
10 | from biorefs_cli.commands import assay, compound, gene, nucleotide, openalex, protein
   |

I001 [*] Import block is un-sorted or un-formatted
 --> tests/test_scaffold.py:3:1
  |
1 |   # Copyright (c) 2026 Seungwon Lee
2 |   # SPDX-License-Identifier: MIT
3 | / from __future__ import annotations
4 | |
5 | | import pytest
6 | | from biorefs_cli.main import build_parser, main
  | |_______________________________________________^
7 |
8 |   TOP_LEVEL_COMMANDS = (
  |
help: Organize imports
  |
5 | import pytest
6 +
7 | from biorefs_cli.main import build_parser, main
  |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_structure_fetch.py:3:1
   |
 1 |   # Copyright (c) 2026 Seungwon Lee
 2 |   # SPDX-License-Identifier: MIT
 3 | / from __future__ import annotations
 4 | |
 5 | | import json
 6 | | from pathlib import Path
 7 | |
 8 | | import pytest
 9 | | from biorefs_cli.commands.structure import (
10 | |     AlphaFoldFile,
11 | |     FetchClient,
12 | |     FetchResult,
13 | |     FetchService,
14 | |     first_prediction,
15 | |     write_structure,
16 | | )
17 | | from biorefs_cli.config import Config
18 | | from biorefs_cli.errors import CLIError, HTTPError
19 | | from biorefs_cli.http import HttpClient, HttpResponse
20 | | from biorefs_cli.main import main
   | |_________________________________^
help: Organize imports
   |
8  | import pytest
9  +
10 | from biorefs_cli.commands.structure import (
   |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_structure_info.py:3:1
   |
 1 |   # Copyright (c) 2026 Seungwon Lee
 2 |   # SPDX-License-Identifier: MIT
 3 | / from __future__ import annotations
 4 | |
 5 | | from typing import TYPE_CHECKING, cast
 6 | |
 7 | | import pytest
 8 | | from biorefs_cli.commands.structure import (
 9 | |     InfoService,
10 | |     build_info_result,
11 | |     parse_entry,
12 | | )
13 | | from biorefs_cli.main import main
   | |_________________________________^
14 |
15 |   if TYPE_CHECKING:
   |
help: Organize imports
  |
7 | import pytest
8 +
9 | from biorefs_cli.commands.structure import (
  |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_structure_render.py:3:1
   |
 1 |   # Copyright (c) 2026 Seungwon Lee
 2 |   # SPDX-License-Identifier: MIT
 3 | / from __future__ import annotations
 4 | |
 5 | | import pytest
 6 | | from biorefs_cli.commands.structure import (
 7 | |     parse_include,
 8 | |     print_info_table,
 9 | |     print_search_table,
10 | |     validate_organism,
11 | | )
12 | | from biorefs_cli.errors import CLIError
   | |_______________________________________^
help: Organize imports
  |
5 | import pytest
6 +
7 | from biorefs_cli.commands.structure import (
  |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_structure_search.py:3:1
   |
 1 |   # Copyright (c) 2026 Seungwon Lee
 2 |   # SPDX-License-Identifier: MIT
 3 | / from __future__ import annotations
 4 | |
 5 | | import argparse
 6 | | from typing import TYPE_CHECKING, cast
 7 | |
 8 | | import pytest
 9 | | from biorefs_cli.commands.structure import (
10 | |     SearchQuery,
11 | |     SearchService,
12 | |     build_query_from_args,
13 | |     build_search_payload,
14 | |     clean_sequence,
15 | |     normalize_pdb_id,
16 | |     normalize_uniprot_accession,
17 | |     parse_hits,
18 | | )
19 | | from biorefs_cli.errors import CLIError, HTTPError
20 | | from biorefs_cli.main import main
21 | | from biorefs_cli.rcsb_graphql import EntryMeta
   | |______________________________________________^
22 |
23 |   if TYPE_CHECKING:
   |
help: Organize imports
   |
8  | import pytest
9  +
10 | from biorefs_cli.commands.structure import (
   |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_uniprot.py:3:1
   |
 1 |   # Copyright (c) 2026 Seungwon Lee
 2 |   # SPDX-License-Identifier: MIT
 3 | / from __future__ import annotations
 4 | |
 5 | | import json
 6 | | from typing import TYPE_CHECKING, cast
 7 | |
 8 | | import pytest
 9 | | from biorefs_cli.commands.uniprot import (
10 | |     UniProtService,
11 | |     build_search_query,
12 | |     normalize_accession,
13 | |     parse_entry,
14 | | )
15 | | from biorefs_cli.errors import CLIError, RateLimitError
16 | | from biorefs_cli.main import main
   | |_________________________________^
17 |
18 |   if TYPE_CHECKING:
   |
help: Organize imports
   |
8  | import pytest
9  +
10 | from biorefs_cli.commands.uniprot import (
   |

Found 22 errors.
[*] 22 fixable with the `--fix` option.