this derivation will be built:
  /nix/store/9wdzclwj1c8jwy74v4y2y7aynrjqfjsl-biorefs-cli-0.1.0.drv
these 6 paths will be fetched (16.4 MiB download, 68.4 MiB unpacked):
  /nix/store/ap5y17n5m4gkrgh1h9dbb8k45d63an6k-pytest-check-hook
  /nix/store/jagynfd4bqgzrn0nksv9bg1gg6rj0a67-python3.14-editables-0.6
  /nix/store/71mand2cdicbgmrjysll4ab7d9pdx3y6-python3.14-hatchling-1.31.0
  /nix/store/n490d9yqbc4mv5gq79gr04wvbk9mqik0-python3.14-mypy-2.1.0
  /nix/store/zx9c4rmbf463w2nc4xxynaxcqihl58yi-python3.14-ruff-0.16.1
  /nix/store/jswbbiy047y4ymvsh12a6izl4qa7f6jr-python3.14-trove-classifiers-2026.6.1.19
building '/nix/store/9wdzclwj1c8jwy74v4y2y7aynrjqfjsl-biorefs-cli-0.1.0.drv'
biorefs-cli-0.1.0> Sourcing python-remove-tests-dir-hook
biorefs-cli-0.1.0> Sourcing python-catch-conflicts-hook.sh
biorefs-cli-0.1.0> Sourcing python-remove-bin-bytecode-hook.sh
biorefs-cli-0.1.0> Sourcing pypa-build-hook
biorefs-cli-0.1.0> Using pypaBuildPhase
biorefs-cli-0.1.0> Sourcing python-runtime-deps-check-hook
biorefs-cli-0.1.0> Using pythonRuntimeDepsCheckHook
biorefs-cli-0.1.0> Sourcing pypa-install-hook
biorefs-cli-0.1.0> Using pypaInstallPhase
biorefs-cli-0.1.0> Sourcing python-imports-check-hook.sh
biorefs-cli-0.1.0> Using pythonImportsCheckPhase
biorefs-cli-0.1.0> Sourcing python-namespaces-hook
biorefs-cli-0.1.0> Sourcing python-catch-conflicts-hook.sh
biorefs-cli-0.1.0> Sourcing pytest-check-hook
biorefs-cli-0.1.0> Running phase: unpackPhase
biorefs-cli-0.1.0> unpacking source archive /nix/store/g9xhjlx8aa88km8nz2dy299l081w1kf7-biorefs-cli
biorefs-cli-0.1.0> source root is biorefs-cli
biorefs-cli-0.1.0> setting SOURCE_DATE_EPOCH to timestamp 315619200 of file "biorefs-cli/tests/test_uniprot.py"
biorefs-cli-0.1.0> Running phase: patchPhase
biorefs-cli-0.1.0> Running phase: updateAutotoolsGnuConfigScriptsPhase
biorefs-cli-0.1.0> Running phase: configurePhase
biorefs-cli-0.1.0> no configure script, doing nothing
biorefs-cli-0.1.0> Running phase: buildPhase
biorefs-cli-0.1.0> Executing pypaBuildPhase
biorefs-cli-0.1.0> Creating a wheel...
biorefs-cli-0.1.0> pypa build flags: --no-isolation --outdir dist/ --wheel
biorefs-cli-0.1.0> * Getting build dependencies for wheel...
biorefs-cli-0.1.0> * Building wheel...
biorefs-cli-0.1.0> Successfully built biorefs_cli-0.1.0-py3-none-any.whl
biorefs-cli-0.1.0> Finished creating a wheel...
biorefs-cli-0.1.0> Finished executing pypaBuildPhase
biorefs-cli-0.1.0> Running phase: pythonRuntimeDepsCheckHook
biorefs-cli-0.1.0> Executing pythonRuntimeDepsCheck
biorefs-cli-0.1.0> Checking runtime dependencies for biorefs_cli-0.1.0-py3-none-any.whl
biorefs-cli-0.1.0> Finished executing pythonRuntimeDepsCheck
biorefs-cli-0.1.0> Running phase: installPhase
biorefs-cli-0.1.0> Executing pypaInstallPhase
biorefs-cli-0.1.0> Successfully installed biorefs_cli-0.1.0-py3-none-any.whl
biorefs-cli-0.1.0> Finished executing pypaInstallPhase
biorefs-cli-0.1.0> Running phase: pythonOutputDistPhase
biorefs-cli-0.1.0> Executing pythonOutputDistPhase
biorefs-cli-0.1.0> Finished executing pythonOutputDistPhase
biorefs-cli-0.1.0> Running phase: fixupPhase
biorefs-cli-0.1.0> shrinking RPATHs of ELF executables and libraries in /nix/store/x1cn2sda2973syixniwbrrxwd1mrlbjc-biorefs-cli-0.1.0
biorefs-cli-0.1.0> checking for references to /build/ in /nix/store/x1cn2sda2973syixniwbrrxwd1mrlbjc-biorefs-cli-0.1.0...
biorefs-cli-0.1.0> patching script interpreter paths in /nix/store/x1cn2sda2973syixniwbrrxwd1mrlbjc-biorefs-cli-0.1.0
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
biorefs-cli-0.1.0> shrinking RPATHs of ELF executables and libraries in /nix/store/w9v9hka3c941makjmfd8wfxny6g1vr87-biorefs-cli-0.1.0-dist
biorefs-cli-0.1.0> checking for references to /build/ in /nix/store/w9v9hka3c941makjmfd8wfxny6g1vr87-biorefs-cli-0.1.0-dist...
biorefs-cli-0.1.0> patching script interpreter paths in /nix/store/w9v9hka3c941makjmfd8wfxny6g1vr87-biorefs-cli-0.1.0-dist
biorefs-cli-0.1.0> Rewriting #!/nix/store/gxzhl7aaiid7zp3y47jqqiq7zg5mqpwp-python3-3.14.6/bin/python3.14 to #!/nix/store/gxzhl7aaiid7zp3y47jqqiq7zg5mqpwp-python3-3.14.6
biorefs-cli-0.1.0> wrapping `/nix/store/x1cn2sda2973syixniwbrrxwd1mrlbjc-biorefs-cli-0.1.0/bin/biorefs-cli'...
biorefs-cli-0.1.0> Executing pythonRemoveTestsDir
biorefs-cli-0.1.0> Finished executing pythonRemoveTestsDir
biorefs-cli-0.1.0> Running phase: installCheckPhase
biorefs-cli-0.1.0> 47 files already formatted
biorefs-cli-0.1.0> RUF100 [*] Unused `noqa` directive (non-enabled: `S314`)
biorefs-cli-0.1.0>    --> biorefs_cli/commands/paper.py:443:37
biorefs-cli-0.1.0>     |
biorefs-cli-0.1.0> 441 |     if not xml_text.strip():
biorefs-cli-0.1.0> 442 |         return []
biorefs-cli-0.1.0> 443 |     root = ET.fromstring(xml_text)  # noqa: S314 - NCBI/PubMed XML; no defusedxml dependency.
biorefs-cli-0.1.0>     |                                     ^^^^^^^^^^^^
biorefs-cli-0.1.0> 444 |     return [
biorefs-cli-0.1.0> 445 |         parse_pubmed_article(article, include)
biorefs-cli-0.1.0>     |
biorefs-cli-0.1.0> help: Remove unused `noqa` directive
biorefs-cli-0.1.0>     |
biorefs-cli-0.1.0> 442 |         return []
biorefs-cli-0.1.0>     -     root = ET.fromstring(xml_text)  # noqa: S314 - NCBI/PubMed XML; no defusedxml dependency.
biorefs-cli-0.1.0> 443 +     root = ET.fromstring(xml_text)
biorefs-cli-0.1.0> 444 |     return [
biorefs-cli-0.1.0>     |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> RUF100 [*] Unused `noqa` directive (non-enabled: `S314`)
biorefs-cli-0.1.0>    --> biorefs_cli/commands/paper.py:623:37
biorefs-cli-0.1.0>     |
biorefs-cli-0.1.0> 621 |     if not xml_text.strip():
biorefs-cli-0.1.0> 622 |         return unavailable("pmc:empty-response")
biorefs-cli-0.1.0> 623 |     root = ET.fromstring(xml_text)  # noqa: S314 - NCBI/PMC XML; no defusedxml dependency.
biorefs-cli-0.1.0>     |                                     ^^^^^^^^^^^^
biorefs-cli-0.1.0> 624 |     article = root if strip_ns(root.tag) == "article" else first(root, "article")
biorefs-cli-0.1.0> 625 |     if article is None:
biorefs-cli-0.1.0>     |
biorefs-cli-0.1.0> help: Remove unused `noqa` directive
biorefs-cli-0.1.0>     |
biorefs-cli-0.1.0> 622 |         return unavailable("pmc:empty-response")
biorefs-cli-0.1.0>     -     root = ET.fromstring(xml_text)  # noqa: S314 - NCBI/PMC XML; no defusedxml dependency.
biorefs-cli-0.1.0> 623 +     root = ET.fromstring(xml_text)
biorefs-cli-0.1.0> 624 |     article = root if strip_ns(root.tag) == "article" else first(root, "article")
biorefs-cli-0.1.0>     |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> RUF100 [*] Unused `noqa` directive (non-enabled: `S602`)
biorefs-cli-0.1.0>    --> biorefs_cli/config.py:103:38
biorefs-cli-0.1.0>     |
biorefs-cli-0.1.0> 101 | def run_secret_command(command: str, *, timeout_seconds: int) -> str:
biorefs-cli-0.1.0> 102 |     try:
biorefs-cli-0.1.0> 103 |         completed = subprocess.run(  # noqa: S602 - config intentionally stores shell commands.
biorefs-cli-0.1.0>     |                                      ^^^^^^^^^^^^
biorefs-cli-0.1.0> 104 |             command,
biorefs-cli-0.1.0> 105 |             shell=True,
biorefs-cli-0.1.0>     |
biorefs-cli-0.1.0> help: Remove unused `noqa` directive
biorefs-cli-0.1.0>     |
biorefs-cli-0.1.0> 102 |     try:
biorefs-cli-0.1.0>     -         completed = subprocess.run(  # noqa: S602 - config intentionally stores shell commands.
biorefs-cli-0.1.0> 103 +         completed = subprocess.run(
biorefs-cli-0.1.0> 104 |             command,
biorefs-cli-0.1.0>     |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_assay.py:3:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0>  2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0>  3 | / from __future__ import annotations
biorefs-cli-0.1.0>  4 | |
biorefs-cli-0.1.0>  5 | | from typing import TYPE_CHECKING, cast
biorefs-cli-0.1.0>  6 | |
biorefs-cli-0.1.0>  7 | | import pytest
biorefs-cli-0.1.0>  8 | | from biorefs_cli.commands.assay import (
biorefs-cli-0.1.0>  9 | |     PubChemAssayClient,
biorefs-cli-0.1.0> 10 | |     handle_http_error,
biorefs-cli-0.1.0> 11 | |     parse_assay_description,
biorefs-cli-0.1.0> 12 | |     parse_concise_activity,
biorefs-cli-0.1.0> 13 | |     parse_include,
biorefs-cli-0.1.0> 14 | | )
biorefs-cli-0.1.0> 15 | | from biorefs_cli.errors import RateLimitError
biorefs-cli-0.1.0> 16 | | from biorefs_cli.http import HttpClient, JsonObject, JsonValue
biorefs-cli-0.1.0> 17 | | from biorefs_cli.main import main
biorefs-cli-0.1.0>    | |_________________________________^
biorefs-cli-0.1.0> 18 |
biorefs-cli-0.1.0> 19 |   if TYPE_CHECKING:
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>   |
biorefs-cli-0.1.0> 7 | import pytest
biorefs-cli-0.1.0> 8 +
biorefs-cli-0.1.0> 9 | from biorefs_cli.commands.assay import (
biorefs-cli-0.1.0>   |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_compound.py:3:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0>  2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0>  3 | / from __future__ import annotations
biorefs-cli-0.1.0>  4 | |
biorefs-cli-0.1.0>  5 | | from typing import TYPE_CHECKING
biorefs-cli-0.1.0>  6 | |
biorefs-cli-0.1.0>  7 | | import pytest
biorefs-cli-0.1.0>  8 | | from biorefs_cli.commands import compound
biorefs-cli-0.1.0>  9 | | from biorefs_cli.errors import CLIError
biorefs-cli-0.1.0> 10 | | from biorefs_cli.main import build_parser
biorefs-cli-0.1.0>    | |_________________________________________^
biorefs-cli-0.1.0> 11 |
biorefs-cli-0.1.0> 12 |   if TYPE_CHECKING:
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>   |
biorefs-cli-0.1.0> 7 | import pytest
biorefs-cli-0.1.0> 8 +
biorefs-cli-0.1.0> 9 | from biorefs_cli.commands import compound
biorefs-cli-0.1.0>   |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_core_helpers.py:3:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0>  2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0>  3 | / from __future__ import annotations
biorefs-cli-0.1.0>  4 | |
biorefs-cli-0.1.0>  5 | | import json
biorefs-cli-0.1.0>  6 | | import stat
biorefs-cli-0.1.0>  7 | | from typing import TYPE_CHECKING
biorefs-cli-0.1.0>  8 | |
biorefs-cli-0.1.0>  9 | | import pytest
biorefs-cli-0.1.0> 10 | | from biorefs_cli.config import (
biorefs-cli-0.1.0> 11 | |     Config,
biorefs-cli-0.1.0> 12 | |     check_configured_secrets,
biorefs-cli-0.1.0> 13 | |     config_to_public_dict,
biorefs-cli-0.1.0> 14 | |     load_config,
biorefs-cli-0.1.0> 15 | |     merge_config,
biorefs-cli-0.1.0> 16 | |     run_secret_command,
biorefs-cli-0.1.0> 17 | |     write_config,
biorefs-cli-0.1.0> 18 | | )
biorefs-cli-0.1.0> 19 | | from biorefs_cli.errors import (
biorefs-cli-0.1.0> 20 | |     ConfigError,
biorefs-cli-0.1.0> 21 | |     CredentialCheckError,
biorefs-cli-0.1.0> 22 | |     HTTPError,
biorefs-cli-0.1.0> 23 | |     RateLimitError,
biorefs-cli-0.1.0> 24 | | )
biorefs-cli-0.1.0> 25 | | from biorefs_cli.http import HttpClient, HttpResponse, RetryPolicy
biorefs-cli-0.1.0> 26 | | from biorefs_cli.output import escape_cell, markdown_heading, markdown_table, print_json
biorefs-cli-0.1.0> 27 | | from biorefs_cli.rate_limit import RateLimitPolicy
biorefs-cli-0.1.0>    | |__________________________________________________^
biorefs-cli-0.1.0> 28 |
biorefs-cli-0.1.0> 29 |   if TYPE_CHECKING:
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 9  | import pytest
biorefs-cli-0.1.0> 10 +
biorefs-cli-0.1.0> 11 | from biorefs_cli.config import (
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_gene.py:3:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0>  2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0>  3 | / from __future__ import annotations
biorefs-cli-0.1.0>  4 | |
biorefs-cli-0.1.0>  5 | | import json
biorefs-cli-0.1.0>  6 | | from typing import cast
biorefs-cli-0.1.0>  7 | | from urllib.parse import parse_qs, urlparse
biorefs-cli-0.1.0>  8 | |
biorefs-cli-0.1.0>  9 | | import pytest
biorefs-cli-0.1.0> 10 | | from biorefs_cli.commands import gene
biorefs-cli-0.1.0> 11 | | from biorefs_cli.config import Config
biorefs-cli-0.1.0> 12 | | from biorefs_cli.errors import CLIError, RateLimitError
biorefs-cli-0.1.0> 13 | | from biorefs_cli.http import HttpClient, HttpResponse, JsonObject, RetryPolicy
biorefs-cli-0.1.0> 14 | | from biorefs_cli.main import build_parser, main
biorefs-cli-0.1.0> 15 | | from biorefs_cli.ncbi_client import NCBIClient
biorefs-cli-0.1.0> 16 | | from biorefs_cli.rate_limit import RateLimiter
biorefs-cli-0.1.0>    | |______________________________________________^
biorefs-cli-0.1.0> 17 |
biorefs-cli-0.1.0> 18 |   GENE_SUMMARY: JsonObject = {
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 9  | import pytest
biorefs-cli-0.1.0> 10 +
biorefs-cli-0.1.0> 11 | from biorefs_cli.commands import gene
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>  --> tests/test_http_post.py:3:1
biorefs-cli-0.1.0>   |
biorefs-cli-0.1.0> 1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0> 2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0> 3 | / from __future__ import annotations
biorefs-cli-0.1.0> 4 | |
biorefs-cli-0.1.0> 5 | | import json
biorefs-cli-0.1.0> 6 | |
biorefs-cli-0.1.0> 7 | | import pytest
biorefs-cli-0.1.0> 8 | | from biorefs_cli.errors import HTTPError
biorefs-cli-0.1.0> 9 | | from biorefs_cli.http import HttpClient, HttpResponse, RetryPolicy
biorefs-cli-0.1.0>   | |__________________________________________________________________^
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>   |
biorefs-cli-0.1.0> 7 | import pytest
biorefs-cli-0.1.0> 8 +
biorefs-cli-0.1.0> 9 | from biorefs_cli.errors import HTTPError
biorefs-cli-0.1.0>   |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_ncbi_command.py:3:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0>  2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0>  3 | / from __future__ import annotations
biorefs-cli-0.1.0>  4 | |
biorefs-cli-0.1.0>  5 | | import json
biorefs-cli-0.1.0>  6 | | import shlex
biorefs-cli-0.1.0>  7 | | import sys
biorefs-cli-0.1.0>  8 | | import urllib.parse
biorefs-cli-0.1.0>  9 | | from typing import TYPE_CHECKING
biorefs-cli-0.1.0> 10 | |
biorefs-cli-0.1.0> 11 | | import pytest
biorefs-cli-0.1.0> 12 | | from biorefs_cli.commands import ncbi
biorefs-cli-0.1.0> 13 | | from biorefs_cli.config import Config
biorefs-cli-0.1.0> 14 | | from biorefs_cli.http import HttpClient, HttpResponse, RetryPolicy
biorefs-cli-0.1.0> 15 | | from biorefs_cli.main import build_parser, main
biorefs-cli-0.1.0> 16 | | from biorefs_cli.ncbi_client import NCBIClient
biorefs-cli-0.1.0> 17 | | from biorefs_cli.rate_limit import RateLimiter, RateLimitPolicy
biorefs-cli-0.1.0>    | |_______________________________________________________________^
biorefs-cli-0.1.0> 18 |
biorefs-cli-0.1.0> 19 |   if TYPE_CHECKING:
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 11 | import pytest
biorefs-cli-0.1.0> 12 +
biorefs-cli-0.1.0> 13 | from biorefs_cli.commands import ncbi
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_ncbi_extra.py:3:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0>  2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0>  3 | / from __future__ import annotations
biorefs-cli-0.1.0>  4 | |
biorefs-cli-0.1.0>  5 | | import argparse
biorefs-cli-0.1.0>  6 | | from typing import TYPE_CHECKING, cast
biorefs-cli-0.1.0>  7 | |
biorefs-cli-0.1.0>  8 | | import pytest
biorefs-cli-0.1.0>  9 | | from biorefs_cli.commands import ncbi
biorefs-cli-0.1.0> 10 | | from biorefs_cli.errors import CLIError
biorefs-cli-0.1.0>    | |_______________________________________^
biorefs-cli-0.1.0> 11 |
biorefs-cli-0.1.0> 12 |   if TYPE_CHECKING:
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 8  | import pytest
biorefs-cli-0.1.0> 9  +
biorefs-cli-0.1.0> 10 | from biorefs_cli.commands import ncbi
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_nucleotide.py:5:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  3 |   """Nucleotide command tests."""
biorefs-cli-0.1.0>  4 |
biorefs-cli-0.1.0>  5 | / from __future__ import annotations
biorefs-cli-0.1.0>  6 | |
biorefs-cli-0.1.0>  7 | | import json
biorefs-cli-0.1.0>  8 | | from typing import cast
biorefs-cli-0.1.0>  9 | | from urllib.parse import parse_qs, urlparse
biorefs-cli-0.1.0> 10 | |
biorefs-cli-0.1.0> 11 | | import pytest
biorefs-cli-0.1.0> 12 | | from biorefs_cli.commands import nucleotide
biorefs-cli-0.1.0> 13 | | from biorefs_cli.config import Config
biorefs-cli-0.1.0> 14 | | from biorefs_cli.errors import CLIError, RateLimitError
biorefs-cli-0.1.0> 15 | | from biorefs_cli.http import HttpClient, HttpResponse, JsonObject
biorefs-cli-0.1.0> 16 | | from biorefs_cli.main import build_parser, main
biorefs-cli-0.1.0> 17 | | from biorefs_cli.ncbi_client import NCBIClient
biorefs-cli-0.1.0>    | |______________________________________________^
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 11 | import pytest
biorefs-cli-0.1.0> 12 +
biorefs-cli-0.1.0> 13 | from biorefs_cli.commands import nucleotide
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_openalex.py:3:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0>  2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0>  3 | / from __future__ import annotations
biorefs-cli-0.1.0>  4 | |
biorefs-cli-0.1.0>  5 | | import argparse
biorefs-cli-0.1.0>  6 | | from typing import TYPE_CHECKING, cast
biorefs-cli-0.1.0>  7 | |
biorefs-cli-0.1.0>  8 | | import pytest
biorefs-cli-0.1.0>  9 | | from biorefs_cli.commands import openalex
biorefs-cli-0.1.0> 10 | | from biorefs_cli.config import Config
biorefs-cli-0.1.0> 11 | | from biorefs_cli.http import HttpClient
biorefs-cli-0.1.0>    | |_______________________________________^
biorefs-cli-0.1.0> 12 |
biorefs-cli-0.1.0> 13 |   if TYPE_CHECKING:
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 8  | import pytest
biorefs-cli-0.1.0> 9  +
biorefs-cli-0.1.0> 10 | from biorefs_cli.commands import openalex
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_paper.py:11:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  9 |       from collections.abc import Sequence
biorefs-cli-0.1.0> 10 |
biorefs-cli-0.1.0> 11 | / import pytest
biorefs-cli-0.1.0> 12 | | from biorefs_cli.commands.paper import (
biorefs-cli-0.1.0> 13 | |     PaperClient,
biorefs-cli-0.1.0> 14 | |     PaperInputError,
biorefs-cli-0.1.0> 15 | |     cmd_convert,
biorefs-cli-0.1.0> 16 | |     one_identifier,
biorefs-cli-0.1.0> 17 | |     parse_jats_xml,
biorefs-cli-0.1.0> 18 | |     parse_pubmed_xml,
biorefs-cli-0.1.0> 19 | | )
biorefs-cli-0.1.0> 20 | | from biorefs_cli.errors import RateLimitError
biorefs-cli-0.1.0> 21 | | from biorefs_cli.main import main
biorefs-cli-0.1.0>    | |_________________________________^
biorefs-cli-0.1.0> 22 |
biorefs-cli-0.1.0> 23 |   PUBMED_XML = """
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 11 | import pytest
biorefs-cli-0.1.0> 12 +
biorefs-cli-0.1.0> 13 | from biorefs_cli.commands.paper import (
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_paper_extra.py:3:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0>  2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0>  3 | / from __future__ import annotations
biorefs-cli-0.1.0>  4 | |
biorefs-cli-0.1.0>  5 | | import argparse
biorefs-cli-0.1.0>  6 | | from typing import Any, cast
biorefs-cli-0.1.0>  7 | |
biorefs-cli-0.1.0>  8 | | import pytest
biorefs-cli-0.1.0>  9 | | from biorefs_cli.commands.paper import (
biorefs-cli-0.1.0> 10 | |     PaperClient,
biorefs-cli-0.1.0> 11 | |     PaperInputError,
biorefs-cli-0.1.0> 12 | |     bibtex,
biorefs-cli-0.1.0> 13 | |     cmd_cite,
biorefs-cli-0.1.0> 14 | |     cmd_fulltext,
biorefs-cli-0.1.0> 15 | |     cmd_related,
biorefs-cli-0.1.0> 16 | |     crossref_year,
biorefs-cli-0.1.0> 17 | |     europepmc_unavailable,
biorefs-cli-0.1.0> 18 | |     fetch_record,
biorefs-cli-0.1.0> 19 | |     format_citation,
biorefs-cli-0.1.0> 20 | |     normalize_crossref_work,
biorefs-cli-0.1.0> 21 | |     normalize_doi,
biorefs-cli-0.1.0> 22 | |     normalize_idconv,
biorefs-cli-0.1.0> 23 | |     normalize_identifier,
biorefs-cli-0.1.0> 24 | |     normalize_pmcid,
biorefs-cli-0.1.0> 25 | |     normalize_pmid,
biorefs-cli-0.1.0> 26 | |     parse_include,
biorefs-cli-0.1.0> 27 | |     parse_jats_xml,
biorefs-cli-0.1.0> 28 | |     parse_sections,
biorefs-cli-0.1.0> 29 | |     print_convert,
biorefs-cli-0.1.0> 30 | |     print_fetch,
biorefs-cli-0.1.0> 31 | |     print_fulltext,
biorefs-cli-0.1.0> 32 | |     print_related,
biorefs-cli-0.1.0> 33 | |     print_search,
biorefs-cli-0.1.0> 34 | |     ris,
biorefs-cli-0.1.0> 35 | |     source_urls,
biorefs-cli-0.1.0> 36 | |     strict_validate,
biorefs-cli-0.1.0> 37 | |     unavailable,
biorefs-cli-0.1.0> 38 | | )
biorefs-cli-0.1.0> 39 | | from biorefs_cli.errors import HTTPError
biorefs-cli-0.1.0>    | |________________________________________^
biorefs-cli-0.1.0> 40 |
biorefs-cli-0.1.0> 41 |   MINIMAL_PUBMED_XML = """
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 8  | import pytest
biorefs-cli-0.1.0> 9  +
biorefs-cli-0.1.0> 10 | from biorefs_cli.commands.paper import (
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_protein.py:3:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0>  2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0>  3 | / from __future__ import annotations
biorefs-cli-0.1.0>  4 | |
biorefs-cli-0.1.0>  5 | | import json
biorefs-cli-0.1.0>  6 | | from typing import cast
biorefs-cli-0.1.0>  7 | | from urllib.parse import parse_qs, urlencode, urlparse
biorefs-cli-0.1.0>  8 | |
biorefs-cli-0.1.0>  9 | | import pytest
biorefs-cli-0.1.0> 10 | | from biorefs_cli.commands.protein import (
biorefs-cli-0.1.0> 11 | |     ProteinService,
biorefs-cli-0.1.0> 12 | |     build_search_term,
biorefs-cli-0.1.0> 13 | |     normalize_accession,
biorefs-cli-0.1.0> 14 | |     parse_protein_summaries,
biorefs-cli-0.1.0> 15 | | )
biorefs-cli-0.1.0> 16 | | from biorefs_cli.errors import CLIError, RateLimitError
biorefs-cli-0.1.0> 17 | | from biorefs_cli.http import HttpResponse, JsonObject
biorefs-cli-0.1.0> 18 | | from biorefs_cli.main import main
biorefs-cli-0.1.0>    | |_________________________________^
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 9  | import pytest
biorefs-cli-0.1.0> 10 +
biorefs-cli-0.1.0> 11 | from biorefs_cli.commands.protein import (
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_render_helpers.py:3:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0>  2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0>  3 | / from __future__ import annotations
biorefs-cli-0.1.0>  4 | |
biorefs-cli-0.1.0>  5 | | import argparse
biorefs-cli-0.1.0>  6 | | from typing import TYPE_CHECKING, cast
biorefs-cli-0.1.0>  7 | |
biorefs-cli-0.1.0>  8 | | import pytest
biorefs-cli-0.1.0>  9 | | from biorefs_cli.commands import assay, compound, gene, nucleotide, openalex, protein
biorefs-cli-0.1.0> 10 | | from biorefs_cli.errors import CLIError, HTTPError, RateLimitError
biorefs-cli-0.1.0>    | |__________________________________________________________________^
biorefs-cli-0.1.0> 11 |
biorefs-cli-0.1.0> 12 |   if TYPE_CHECKING:
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 8  | import pytest
biorefs-cli-0.1.0> 9  +
biorefs-cli-0.1.0> 10 | from biorefs_cli.commands import assay, compound, gene, nucleotide, openalex, protein
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>  --> tests/test_scaffold.py:3:1
biorefs-cli-0.1.0>   |
biorefs-cli-0.1.0> 1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0> 2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0> 3 | / from __future__ import annotations
biorefs-cli-0.1.0> 4 | |
biorefs-cli-0.1.0> 5 | | import pytest
biorefs-cli-0.1.0> 6 | | from biorefs_cli.main import build_parser, main
biorefs-cli-0.1.0>   | |_______________________________________________^
biorefs-cli-0.1.0> 7 |
biorefs-cli-0.1.0> 8 |   TOP_LEVEL_COMMANDS = (
biorefs-cli-0.1.0>   |
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>   |
biorefs-cli-0.1.0> 5 | import pytest
biorefs-cli-0.1.0> 6 +
biorefs-cli-0.1.0> 7 | from biorefs_cli.main import build_parser, main
biorefs-cli-0.1.0>   |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_structure_fetch.py:3:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0>  2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0>  3 | / from __future__ import annotations
biorefs-cli-0.1.0>  4 | |
biorefs-cli-0.1.0>  5 | | import json
biorefs-cli-0.1.0>  6 | | from pathlib import Path
biorefs-cli-0.1.0>  7 | |
biorefs-cli-0.1.0>  8 | | import pytest
biorefs-cli-0.1.0>  9 | | from biorefs_cli.commands.structure import (
biorefs-cli-0.1.0> 10 | |     AlphaFoldFile,
biorefs-cli-0.1.0> 11 | |     FetchClient,
biorefs-cli-0.1.0> 12 | |     FetchResult,
biorefs-cli-0.1.0> 13 | |     FetchService,
biorefs-cli-0.1.0> 14 | |     first_prediction,
biorefs-cli-0.1.0> 15 | |     write_structure,
biorefs-cli-0.1.0> 16 | | )
biorefs-cli-0.1.0> 17 | | from biorefs_cli.config import Config
biorefs-cli-0.1.0> 18 | | from biorefs_cli.errors import CLIError, HTTPError
biorefs-cli-0.1.0> 19 | | from biorefs_cli.http import HttpClient, HttpResponse
biorefs-cli-0.1.0> 20 | | from biorefs_cli.main import main
biorefs-cli-0.1.0>    | |_________________________________^
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 8  | import pytest
biorefs-cli-0.1.0> 9  +
biorefs-cli-0.1.0> 10 | from biorefs_cli.commands.structure import (
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_structure_info.py:3:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0>  2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0>  3 | / from __future__ import annotations
biorefs-cli-0.1.0>  4 | |
biorefs-cli-0.1.0>  5 | | from typing import TYPE_CHECKING, cast
biorefs-cli-0.1.0>  6 | |
biorefs-cli-0.1.0>  7 | | import pytest
biorefs-cli-0.1.0>  8 | | from biorefs_cli.commands.structure import (
biorefs-cli-0.1.0>  9 | |     InfoService,
biorefs-cli-0.1.0> 10 | |     build_info_result,
biorefs-cli-0.1.0> 11 | |     parse_entry,
biorefs-cli-0.1.0> 12 | | )
biorefs-cli-0.1.0> 13 | | from biorefs_cli.main import main
biorefs-cli-0.1.0>    | |_________________________________^
biorefs-cli-0.1.0> 14 |
biorefs-cli-0.1.0> 15 |   if TYPE_CHECKING:
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>   |
biorefs-cli-0.1.0> 7 | import pytest
biorefs-cli-0.1.0> 8 +
biorefs-cli-0.1.0> 9 | from biorefs_cli.commands.structure import (
biorefs-cli-0.1.0>   |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_structure_render.py:3:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0>  2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0>  3 | / from __future__ import annotations
biorefs-cli-0.1.0>  4 | |
biorefs-cli-0.1.0>  5 | | import pytest
biorefs-cli-0.1.0>  6 | | from biorefs_cli.commands.structure import (
biorefs-cli-0.1.0>  7 | |     parse_include,
biorefs-cli-0.1.0>  8 | |     print_info_table,
biorefs-cli-0.1.0>  9 | |     print_search_table,
biorefs-cli-0.1.0> 10 | |     validate_organism,
biorefs-cli-0.1.0> 11 | | )
biorefs-cli-0.1.0> 12 | | from biorefs_cli.errors import CLIError
biorefs-cli-0.1.0>    | |_______________________________________^
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>   |
biorefs-cli-0.1.0> 5 | import pytest
biorefs-cli-0.1.0> 6 +
biorefs-cli-0.1.0> 7 | from biorefs_cli.commands.structure import (
biorefs-cli-0.1.0>   |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_structure_search.py:3:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0>  2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0>  3 | / from __future__ import annotations
biorefs-cli-0.1.0>  4 | |
biorefs-cli-0.1.0>  5 | | import argparse
biorefs-cli-0.1.0>  6 | | from typing import TYPE_CHECKING, cast
biorefs-cli-0.1.0>  7 | |
biorefs-cli-0.1.0>  8 | | import pytest
biorefs-cli-0.1.0>  9 | | from biorefs_cli.commands.structure import (
biorefs-cli-0.1.0> 10 | |     SearchQuery,
biorefs-cli-0.1.0> 11 | |     SearchService,
biorefs-cli-0.1.0> 12 | |     build_query_from_args,
biorefs-cli-0.1.0> 13 | |     build_search_payload,
biorefs-cli-0.1.0> 14 | |     clean_sequence,
biorefs-cli-0.1.0> 15 | |     normalize_pdb_id,
biorefs-cli-0.1.0> 16 | |     normalize_uniprot_accession,
biorefs-cli-0.1.0> 17 | |     parse_hits,
biorefs-cli-0.1.0> 18 | | )
biorefs-cli-0.1.0> 19 | | from biorefs_cli.errors import CLIError, HTTPError
biorefs-cli-0.1.0> 20 | | from biorefs_cli.main import main
biorefs-cli-0.1.0> 21 | | from biorefs_cli.rcsb_graphql import EntryMeta
biorefs-cli-0.1.0>    | |______________________________________________^
biorefs-cli-0.1.0> 22 |
biorefs-cli-0.1.0> 23 |   if TYPE_CHECKING:
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 8  | import pytest
biorefs-cli-0.1.0> 9  +
biorefs-cli-0.1.0> 10 | from biorefs_cli.commands.structure import (
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> I001 [*] Import block is un-sorted or un-formatted
biorefs-cli-0.1.0>   --> tests/test_uniprot.py:3:1
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0>  1 |   # Copyright (c) 2026 Seungwon Lee
biorefs-cli-0.1.0>  2 |   # SPDX-License-Identifier: MIT
biorefs-cli-0.1.0>  3 | / from __future__ import annotations
biorefs-cli-0.1.0>  4 | |
biorefs-cli-0.1.0>  5 | | import json
biorefs-cli-0.1.0>  6 | | from typing import TYPE_CHECKING, cast
biorefs-cli-0.1.0>  7 | |
biorefs-cli-0.1.0>  8 | | import pytest
biorefs-cli-0.1.0>  9 | | from biorefs_cli.commands.uniprot import (
biorefs-cli-0.1.0> 10 | |     UniProtService,
biorefs-cli-0.1.0> 11 | |     build_search_query,
biorefs-cli-0.1.0> 12 | |     normalize_accession,
biorefs-cli-0.1.0> 13 | |     parse_entry,
biorefs-cli-0.1.0> 14 | | )
biorefs-cli-0.1.0> 15 | | from biorefs_cli.errors import CLIError, RateLimitError
biorefs-cli-0.1.0> 16 | | from biorefs_cli.main import main
biorefs-cli-0.1.0>    | |_________________________________^
biorefs-cli-0.1.0> 17 |
biorefs-cli-0.1.0> 18 |   if TYPE_CHECKING:
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> help: Organize imports
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 8  | import pytest
biorefs-cli-0.1.0> 9  +
biorefs-cli-0.1.0> 10 | from biorefs_cli.commands.uniprot import (
biorefs-cli-0.1.0>    |
biorefs-cli-0.1.0> 
biorefs-cli-0.1.0> Found 22 errors.
biorefs-cli-0.1.0> [*] 22 fixable with the `--fix` option.
error: Cannot build '/nix/store/9wdzclwj1c8jwy74v4y2y7aynrjqfjsl-biorefs-cli-0.1.0.drv'.
       Reason: builder failed with exit code 1.
       Output paths:
         /nix/store/w9v9hka3c941makjmfd8wfxny6g1vr87-biorefs-cli-0.1.0-dist
         /nix/store/x1cn2sda2973syixniwbrrxwd1mrlbjc-biorefs-cli-0.1.0
       Last 25 log lines:
       >  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.
       For full logs, run:
         nix log /nix/store/9wdzclwj1c8jwy74v4y2y7aynrjqfjsl-biorefs-cli-0.1.0.drv