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/qrjfb9k71g87b1ipx3iwb051yjq5b7dp-biorefs-cli-0.1.0
checking for references to /build/ in /nix/store/qrjfb9k71g87b1ipx3iwb051yjq5b7dp-biorefs-cli-0.1.0...
patching script interpreter paths in /nix/store/qrjfb9k71g87b1ipx3iwb051yjq5b7dp-biorefs-cli-0.1.0
stripping (with command strip and flags -S -p) in  /nix/store/qrjfb9k71g87b1ipx3iwb051yjq5b7dp-biorefs-cli-0.1.0/lib /nix/store/qrjfb9k71g87b1ipx3iwb051yjq5b7dp-biorefs-cli-0.1.0/bin
shrinking RPATHs of ELF executables and libraries in /nix/store/d1qs99nvraiix2phmknf025hfv0lgms9-biorefs-cli-0.1.0-dist
checking for references to /build/ in /nix/store/d1qs99nvraiix2phmknf025hfv0lgms9-biorefs-cli-0.1.0-dist...
patching script interpreter paths in /nix/store/d1qs99nvraiix2phmknf025hfv0lgms9-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/qrjfb9k71g87b1ipx3iwb051yjq5b7dp-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:441:37
    |
439 |     if not xml_text.strip():
440 |         return []
441 |     root = ET.fromstring(xml_text)  # noqa: S314 - NCBI/PubMed XML; no defusedxml dependency.
    |                                     ^^^^^^^^^^^^
442 |     return [
443 |         parse_pubmed_article(article, include)
    |
help: Remove unused `noqa` directive
    |
440 |         return []
    -     root = ET.fromstring(xml_text)  # noqa: S314 - NCBI/PubMed XML; no defusedxml dependency.
441 +     root = ET.fromstring(xml_text)
442 |     return [
    |

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

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

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

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_compound.py:1:1
   |
 1 | / from __future__ import annotations
 2 | |
 3 | | from typing import TYPE_CHECKING
 4 | |
 5 | | import pytest
 6 | | from biorefs_cli.commands import compound
 7 | | from biorefs_cli.errors import CLIError
 8 | | from biorefs_cli.main import build_parser
   | |_________________________________________^
 9 |
10 |   if TYPE_CHECKING:
   |
help: Organize imports
  |
5 | import pytest
6 +
7 | from biorefs_cli.commands import compound
  |

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

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

I001 [*] Import block is un-sorted or un-formatted
 --> tests/test_http_post.py:1:1
  |
1 | / from __future__ import annotations
2 | |
3 | | import json
4 | |
5 | | import pytest
6 | | from biorefs_cli.errors import HTTPError
7 | | from biorefs_cli.http import HttpClient, HttpResponse, RetryPolicy
  | |__________________________________________________________________^
help: Organize imports
  |
5 | import pytest
6 +
7 | from biorefs_cli.errors import HTTPError
  |

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

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_ncbi_extra.py:1:1
   |
 1 | / from __future__ import annotations
 2 | |
 3 | | import argparse
 4 | | from typing import TYPE_CHECKING, cast
 5 | |
 6 | | import pytest
 7 | | from biorefs_cli.commands import ncbi
 8 | | from biorefs_cli.errors import CLIError
   | |_______________________________________^
 9 |
10 |   if TYPE_CHECKING:
   |
help: Organize imports
  |
6 | import pytest
7 +
8 | from biorefs_cli.commands import ncbi
  |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_nucleotide.py:3:1
   |
 1 |   """Nucleotide command tests."""
 2 |
 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 nucleotide
11 | | from biorefs_cli.config import Config
12 | | from biorefs_cli.errors import CLIError, RateLimitError
13 | | from biorefs_cli.http import HttpClient, HttpResponse, JsonObject
14 | | from biorefs_cli.main import build_parser, main
15 | | from biorefs_cli.ncbi_client import NCBIClient
   | |______________________________________________^
help: Organize imports
   |
9  | import pytest
10 +
11 | from biorefs_cli.commands import nucleotide
   |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_openalex.py:1:1
   |
 1 | / from __future__ import annotations
 2 | |
 3 | | import argparse
 4 | | from typing import TYPE_CHECKING, cast
 5 | |
 6 | | import pytest
 7 | | from biorefs_cli.commands import openalex
 8 | | from biorefs_cli.config import Config
 9 | | from biorefs_cli.http import HttpClient
   | |_______________________________________^
10 |
11 |   if TYPE_CHECKING:
   |
help: Organize imports
  |
6 | import pytest
7 +
8 | from biorefs_cli.commands import openalex
  |

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_paper.py:9:1
   |
 7 |       from collections.abc import Sequence
 8 |
 9 | / import pytest
10 | | from biorefs_cli.commands.paper import (
11 | |     PaperClient,
12 | |     PaperInputError,
13 | |     cmd_convert,
14 | |     one_identifier,
15 | |     parse_jats_xml,
16 | |     parse_pubmed_xml,
17 | | )
18 | | from biorefs_cli.errors import RateLimitError
19 | | from biorefs_cli.main import main
   | |_________________________________^
20 |
21 |   PUBMED_XML = """
   |
help: Organize imports
   |
9  | import pytest
10 +
11 | from biorefs_cli.commands.paper import (
   |

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

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

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

I001 [*] Import block is un-sorted or un-formatted
 --> tests/test_scaffold.py:1:1
  |
1 | / from __future__ import annotations
2 | |
3 | | import pytest
4 | | from biorefs_cli.main import build_parser, main
  | |_______________________________________________^
5 |
6 |   TOP_LEVEL_COMMANDS = (
  |
help: Organize imports
  |
3 | import pytest
4 +
5 | from biorefs_cli.main import build_parser, main
  |

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

I001 [*] Import block is un-sorted or un-formatted
  --> tests/test_structure_info.py:1:1
   |
 1 | / from __future__ import annotations
 2 | |
 3 | | from typing import TYPE_CHECKING, cast
 4 | |
 5 | | import pytest
 6 | | from biorefs_cli.commands.structure import (
 7 | |     InfoService,
 8 | |     build_info_result,
 9 | |     parse_entry,
10 | | )
11 | | from biorefs_cli.main import main
   | |_________________________________^
12 |
13 |   if TYPE_CHECKING:
   |
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_render.py:1:1
   |
 1 | / from __future__ import annotations
 2 | |
 3 | | import pytest
 4 | | from biorefs_cli.commands.structure import (
 5 | |     parse_include,
 6 | |     print_info_table,
 7 | |     print_search_table,
 8 | |     validate_organism,
 9 | | )
10 | | from biorefs_cli.errors import CLIError
   | |_______________________________________^
help: Organize imports
  |
3 | import pytest
4 +
5 | from biorefs_cli.commands.structure import (
  |

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

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

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