nixbot

builds
sign in

biorefs-cli-0.1.0 default.checks.x86_64-linux.package-biorefs-cli · build #40 · raw

1Sourcing python-remove-tests-dir-hook2Sourcing python-catch-conflicts-hook.sh3Sourcing python-remove-bin-bytecode-hook.sh4Sourcing pypa-build-hook5Using pypaBuildPhase6Sourcing python-runtime-deps-check-hook7Using pythonRuntimeDepsCheckHook8Sourcing pypa-install-hook9Using pypaInstallPhase10Sourcing python-imports-check-hook.sh11Using pythonImportsCheckPhase12Sourcing python-namespaces-hook13Sourcing python-catch-conflicts-hook.sh14Sourcing pytest-check-hook
unpackPhase
15unpacking source archive /nix/store/g9xhjlx8aa88km8nz2dy299l081w1kf7-biorefs-cli16source root is biorefs-cli17setting SOURCE_DATE_EPOCH to timestamp 315619200 of file "biorefs-cli/tests/test_uniprot.py"
configurePhase
18no configure script, doing nothing
buildPhase
19Executing pypaBuildPhase20Creating a wheel...21pypa build flags: --no-isolation --outdir dist/ --wheel22* Getting build dependencies for wheel...23* Building wheel...24Successfully built biorefs_cli-0.1.0-py3-none-any.whl25Finished creating a wheel...26Finished executing pypaBuildPhase
pythonRuntimeDepsCheckHook
27Executing pythonRuntimeDepsCheck28Checking runtime dependencies for biorefs_cli-0.1.0-py3-none-any.whl29Finished executing pythonRuntimeDepsCheck
installPhase
30Executing pypaInstallPhase31Successfully installed biorefs_cli-0.1.0-py3-none-any.whl32Finished executing pypaInstallPhase
pythonOutputDistPhase
33Executing pythonOutputDistPhase34Finished executing pythonOutputDistPhase
fixupPhase
35shrinking RPATHs of ELF executables and libraries in /nix/store/x1cn2sda2973syixniwbrrxwd1mrlbjc-biorefs-cli-0.1.036checking for references to /build/ in /nix/store/x1cn2sda2973syixniwbrrxwd1mrlbjc-biorefs-cli-0.1.0...37patching script interpreter paths in /nix/store/x1cn2sda2973syixniwbrrxwd1mrlbjc-biorefs-cli-0.1.038stripping (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/bin39shrinking RPATHs of ELF executables and libraries in /nix/store/w9v9hka3c941makjmfd8wfxny6g1vr87-biorefs-cli-0.1.0-dist40checking for references to /build/ in /nix/store/w9v9hka3c941makjmfd8wfxny6g1vr87-biorefs-cli-0.1.0-dist...41patching script interpreter paths in /nix/store/w9v9hka3c941makjmfd8wfxny6g1vr87-biorefs-cli-0.1.0-dist42Rewriting #!/nix/store/gxzhl7aaiid7zp3y47jqqiq7zg5mqpwp-python3-3.14.6/bin/python3.14 to #!/nix/store/gxzhl7aaiid7zp3y47jqqiq7zg5mqpwp-python3-3.14.643wrapping `/nix/store/x1cn2sda2973syixniwbrrxwd1mrlbjc-biorefs-cli-0.1.0/bin/biorefs-cli'...44Executing pythonRemoveTestsDir45Finished executing pythonRemoveTestsDir
installCheckPhase
4647 files already formatted47RUF100 [*] Unused `noqa` directive (non-enabled: `S314`)48 --> biorefs_cli/commands/paper.py:443:3749 |50441 | if not xml_text.strip():51442 | return []52443 | root = ET.fromstring(xml_text) # noqa: S314 - NCBI/PubMed XML; no defusedxml dependency.53 | ^^^^^^^^^^^^54444 | return [55445 | parse_pubmed_article(article, include)56 |57help: Remove unused `noqa` directive58 |59442 | return []60 - root = ET.fromstring(xml_text) # noqa: S314 - NCBI/PubMed XML; no defusedxml dependency.61443 + root = ET.fromstring(xml_text)62444 | return [63 |6465RUF100 [*] Unused `noqa` directive (non-enabled: `S314`)66 --> biorefs_cli/commands/paper.py:623:3767 |68621 | if not xml_text.strip():69622 | return unavailable("pmc:empty-response")70623 | root = ET.fromstring(xml_text) # noqa: S314 - NCBI/PMC XML; no defusedxml dependency.71 | ^^^^^^^^^^^^72624 | article = root if strip_ns(root.tag) == "article" else first(root, "article")73625 | if article is None:74 |75help: Remove unused `noqa` directive76 |77622 | return unavailable("pmc:empty-response")78 - root = ET.fromstring(xml_text) # noqa: S314 - NCBI/PMC XML; no defusedxml dependency.79623 + root = ET.fromstring(xml_text)80624 | article = root if strip_ns(root.tag) == "article" else first(root, "article")81 |8283RUF100 [*] Unused `noqa` directive (non-enabled: `S602`)84 --> biorefs_cli/config.py:103:3885 |86101 | def run_secret_command(command: str, *, timeout_seconds: int) -> str:87102 | try:88103 | completed = subprocess.run( # noqa: S602 - config intentionally stores shell commands.89 | ^^^^^^^^^^^^90104 | command,91105 | shell=True,92 |93help: Remove unused `noqa` directive94 |95102 | try:96 - completed = subprocess.run( # noqa: S602 - config intentionally stores shell commands.97103 + completed = subprocess.run(98104 | command,99 |100101I001 [*] Import block is un-sorted or un-formatted102 --> tests/test_assay.py:3:1103 |104 1 | # Copyright (c) 2026 Seungwon Lee105 2 | # SPDX-License-Identifier: MIT106 3 | / from __future__ import annotations107 4 | |108 5 | | from typing import TYPE_CHECKING, cast109 6 | |110 7 | | import pytest111 8 | | from biorefs_cli.commands.assay import (112 9 | | PubChemAssayClient,11310 | | handle_http_error,11411 | | parse_assay_description,11512 | | parse_concise_activity,11613 | | parse_include,11714 | | )11815 | | from biorefs_cli.errors import RateLimitError11916 | | from biorefs_cli.http import HttpClient, JsonObject, JsonValue12017 | | from biorefs_cli.main import main121 | |_________________________________^12218 |12319 | if TYPE_CHECKING:124 |125help: Organize imports126 |1277 | import pytest1288 +1299 | from biorefs_cli.commands.assay import (130 |131132I001 [*] Import block is un-sorted or un-formatted133 --> tests/test_compound.py:3:1134 |135 1 | # Copyright (c) 2026 Seungwon Lee136 2 | # SPDX-License-Identifier: MIT137 3 | / from __future__ import annotations138 4 | |139 5 | | from typing import TYPE_CHECKING140 6 | |141 7 | | import pytest142 8 | | from biorefs_cli.commands import compound143 9 | | from biorefs_cli.errors import CLIError14410 | | from biorefs_cli.main import build_parser145 | |_________________________________________^14611 |14712 | if TYPE_CHECKING:148 |149help: Organize imports150 |1517 | import pytest1528 +1539 | from biorefs_cli.commands import compound154 |155156I001 [*] Import block is un-sorted or un-formatted157 --> tests/test_core_helpers.py:3:1158 |159 1 | # Copyright (c) 2026 Seungwon Lee160 2 | # SPDX-License-Identifier: MIT161 3 | / from __future__ import annotations162 4 | |163 5 | | import json164 6 | | import stat165 7 | | from typing import TYPE_CHECKING166 8 | |167 9 | | import pytest16810 | | from biorefs_cli.config import (16911 | | Config,17012 | | check_configured_secrets,17113 | | config_to_public_dict,17214 | | load_config,17315 | | merge_config,17416 | | run_secret_command,17517 | | write_config,17618 | | )17719 | | from biorefs_cli.errors import (17820 | | ConfigError,17921 | | CredentialCheckError,18022 | | HTTPError,18123 | | RateLimitError,18224 | | )18325 | | from biorefs_cli.http import HttpClient, HttpResponse, RetryPolicy18426 | | from biorefs_cli.output import escape_cell, markdown_heading, markdown_table, print_json18527 | | from biorefs_cli.rate_limit import RateLimitPolicy186 | |__________________________________________________^18728 |18829 | if TYPE_CHECKING:189 |190help: Organize imports191 |1929 | import pytest19310 +19411 | from biorefs_cli.config import (195 |196197I001 [*] Import block is un-sorted or un-formatted198 --> tests/test_gene.py:3:1199 |200 1 | # Copyright (c) 2026 Seungwon Lee201 2 | # SPDX-License-Identifier: MIT202 3 | / from __future__ import annotations203 4 | |204 5 | | import json205 6 | | from typing import cast206 7 | | from urllib.parse import parse_qs, urlparse207 8 | |208 9 | | import pytest20910 | | from biorefs_cli.commands import gene21011 | | from biorefs_cli.config import Config21112 | | from biorefs_cli.errors import CLIError, RateLimitError21213 | | from biorefs_cli.http import HttpClient, HttpResponse, JsonObject, RetryPolicy21314 | | from biorefs_cli.main import build_parser, main21415 | | from biorefs_cli.ncbi_client import NCBIClient21516 | | from biorefs_cli.rate_limit import RateLimiter216 | |______________________________________________^21717 |21818 | GENE_SUMMARY: JsonObject = {219 |220help: Organize imports221 |2229 | import pytest22310 +22411 | from biorefs_cli.commands import gene225 |226227I001 [*] Import block is un-sorted or un-formatted228 --> tests/test_http_post.py:3:1229 |2301 | # Copyright (c) 2026 Seungwon Lee2312 | # SPDX-License-Identifier: MIT2323 | / from __future__ import annotations2334 | |2345 | | import json2356 | |2367 | | import pytest2378 | | from biorefs_cli.errors import HTTPError2389 | | from biorefs_cli.http import HttpClient, HttpResponse, RetryPolicy239 | |__________________________________________________________________^240help: Organize imports241 |2427 | import pytest2438 +2449 | from biorefs_cli.errors import HTTPError245 |246247I001 [*] Import block is un-sorted or un-formatted248 --> tests/test_ncbi_command.py:3:1249 |250 1 | # Copyright (c) 2026 Seungwon Lee251 2 | # SPDX-License-Identifier: MIT252 3 | / from __future__ import annotations253 4 | |254 5 | | import json255 6 | | import shlex256 7 | | import sys257 8 | | import urllib.parse258 9 | | from typing import TYPE_CHECKING25910 | |26011 | | import pytest26112 | | from biorefs_cli.commands import ncbi26213 | | from biorefs_cli.config import Config26314 | | from biorefs_cli.http import HttpClient, HttpResponse, RetryPolicy26415 | | from biorefs_cli.main import build_parser, main26516 | | from biorefs_cli.ncbi_client import NCBIClient26617 | | from biorefs_cli.rate_limit import RateLimiter, RateLimitPolicy267 | |_______________________________________________________________^26818 |26919 | if TYPE_CHECKING:270 |271help: Organize imports272 |27311 | import pytest27412 +27513 | from biorefs_cli.commands import ncbi276 |277278I001 [*] Import block is un-sorted or un-formatted279 --> tests/test_ncbi_extra.py:3:1280 |281 1 | # Copyright (c) 2026 Seungwon Lee282 2 | # SPDX-License-Identifier: MIT283 3 | / from __future__ import annotations284 4 | |285 5 | | import argparse286 6 | | from typing import TYPE_CHECKING, cast287 7 | |288 8 | | import pytest289 9 | | from biorefs_cli.commands import ncbi29010 | | from biorefs_cli.errors import CLIError291 | |_______________________________________^29211 |29312 | if TYPE_CHECKING:294 |295help: Organize imports296 |2978 | import pytest2989 +29910 | from biorefs_cli.commands import ncbi300 |301302I001 [*] Import block is un-sorted or un-formatted303 --> tests/test_nucleotide.py:5:1304 |305 3 | """Nucleotide command tests."""306 4 |307 5 | / from __future__ import annotations308 6 | |309 7 | | import json310 8 | | from typing import cast311 9 | | from urllib.parse import parse_qs, urlparse31210 | |31311 | | import pytest31412 | | from biorefs_cli.commands import nucleotide31513 | | from biorefs_cli.config import Config31614 | | from biorefs_cli.errors import CLIError, RateLimitError31715 | | from biorefs_cli.http import HttpClient, HttpResponse, JsonObject31816 | | from biorefs_cli.main import build_parser, main31917 | | from biorefs_cli.ncbi_client import NCBIClient320 | |______________________________________________^321help: Organize imports322 |32311 | import pytest32412 +32513 | from biorefs_cli.commands import nucleotide326 |327328I001 [*] Import block is un-sorted or un-formatted329 --> tests/test_openalex.py:3:1330 |331 1 | # Copyright (c) 2026 Seungwon Lee332 2 | # SPDX-License-Identifier: MIT333 3 | / from __future__ import annotations334 4 | |335 5 | | import argparse336 6 | | from typing import TYPE_CHECKING, cast337 7 | |338 8 | | import pytest339 9 | | from biorefs_cli.commands import openalex34010 | | from biorefs_cli.config import Config34111 | | from biorefs_cli.http import HttpClient342 | |_______________________________________^34312 |34413 | if TYPE_CHECKING:345 |346help: Organize imports347 |3488 | import pytest3499 +35010 | from biorefs_cli.commands import openalex351 |352353I001 [*] Import block is un-sorted or un-formatted354 --> tests/test_paper.py:11:1355 |356 9 | from collections.abc import Sequence35710 |35811 | / import pytest35912 | | from biorefs_cli.commands.paper import (36013 | | PaperClient,36114 | | PaperInputError,36215 | | cmd_convert,36316 | | one_identifier,36417 | | parse_jats_xml,36518 | | parse_pubmed_xml,36619 | | )36720 | | from biorefs_cli.errors import RateLimitError36821 | | from biorefs_cli.main import main369 | |_________________________________^37022 |37123 | PUBMED_XML = """372 |373help: Organize imports374 |37511 | import pytest37612 +37713 | from biorefs_cli.commands.paper import (378 |379380I001 [*] Import block is un-sorted or un-formatted381 --> tests/test_paper_extra.py:3:1382 |383 1 | # Copyright (c) 2026 Seungwon Lee384 2 | # SPDX-License-Identifier: MIT385 3 | / from __future__ import annotations386 4 | |387 5 | | import argparse388 6 | | from typing import Any, cast389 7 | |390 8 | | import pytest391 9 | | from biorefs_cli.commands.paper import (39210 | | PaperClient,39311 | | PaperInputError,39412 | | bibtex,39513 | | cmd_cite,39614 | | cmd_fulltext,39715 | | cmd_related,39816 | | crossref_year,39917 | | europepmc_unavailable,40018 | | fetch_record,40119 | | format_citation,40220 | | normalize_crossref_work,40321 | | normalize_doi,40422 | | normalize_idconv,40523 | | normalize_identifier,40624 | | normalize_pmcid,40725 | | normalize_pmid,40826 | | parse_include,40927 | | parse_jats_xml,41028 | | parse_sections,41129 | | print_convert,41230 | | print_fetch,41331 | | print_fulltext,41432 | | print_related,41533 | | print_search,41634 | | ris,41735 | | source_urls,41836 | | strict_validate,41937 | | unavailable,42038 | | )42139 | | from biorefs_cli.errors import HTTPError422 | |________________________________________^42340 |42441 | MINIMAL_PUBMED_XML = """425 |426help: Organize imports427 |4288 | import pytest4299 +43010 | from biorefs_cli.commands.paper import (431 |432433I001 [*] Import block is un-sorted or un-formatted434 --> tests/test_protein.py:3:1435 |436 1 | # Copyright (c) 2026 Seungwon Lee437 2 | # SPDX-License-Identifier: MIT438 3 | / from __future__ import annotations439 4 | |440 5 | | import json441 6 | | from typing import cast442 7 | | from urllib.parse import parse_qs, urlencode, urlparse443 8 | |444 9 | | import pytest44510 | | from biorefs_cli.commands.protein import (44611 | | ProteinService,44712 | | build_search_term,44813 | | normalize_accession,44914 | | parse_protein_summaries,45015 | | )45116 | | from biorefs_cli.errors import CLIError, RateLimitError45217 | | from biorefs_cli.http import HttpResponse, JsonObject45318 | | from biorefs_cli.main import main454 | |_________________________________^455help: Organize imports456 |4579 | import pytest45810 +45911 | from biorefs_cli.commands.protein import (460 |461462I001 [*] Import block is un-sorted or un-formatted463 --> tests/test_render_helpers.py:3:1464 |465 1 | # Copyright (c) 2026 Seungwon Lee466 2 | # SPDX-License-Identifier: MIT467 3 | / from __future__ import annotations468 4 | |469 5 | | import argparse470 6 | | from typing import TYPE_CHECKING, cast471 7 | |472 8 | | import pytest473 9 | | from biorefs_cli.commands import assay, compound, gene, nucleotide, openalex, protein47410 | | from biorefs_cli.errors import CLIError, HTTPError, RateLimitError475 | |__________________________________________________________________^47611 |47712 | if TYPE_CHECKING:478 |479help: Organize imports480 |4818 | import pytest4829 +48310 | from biorefs_cli.commands import assay, compound, gene, nucleotide, openalex, protein484 |485486I001 [*] Import block is un-sorted or un-formatted487 --> tests/test_scaffold.py:3:1488 |4891 | # Copyright (c) 2026 Seungwon Lee4902 | # SPDX-License-Identifier: MIT4913 | / from __future__ import annotations4924 | |4935 | | import pytest4946 | | from biorefs_cli.main import build_parser, main495 | |_______________________________________________^4967 |4978 | TOP_LEVEL_COMMANDS = (498 |499help: Organize imports500 |5015 | import pytest5026 +5037 | from biorefs_cli.main import build_parser, main504 |505506I001 [*] Import block is un-sorted or un-formatted507 --> tests/test_structure_fetch.py:3:1508 |509 1 | # Copyright (c) 2026 Seungwon Lee510 2 | # SPDX-License-Identifier: MIT511 3 | / from __future__ import annotations512 4 | |513 5 | | import json514 6 | | from pathlib import Path515 7 | |516 8 | | import pytest517 9 | | from biorefs_cli.commands.structure import (51810 | | AlphaFoldFile,51911 | | FetchClient,52012 | | FetchResult,52113 | | FetchService,52214 | | first_prediction,52315 | | write_structure,52416 | | )52517 | | from biorefs_cli.config import Config52618 | | from biorefs_cli.errors import CLIError, HTTPError52719 | | from biorefs_cli.http import HttpClient, HttpResponse52820 | | from biorefs_cli.main import main529 | |_________________________________^530help: Organize imports531 |5328 | import pytest5339 +53410 | from biorefs_cli.commands.structure import (535 |536537I001 [*] Import block is un-sorted or un-formatted538 --> tests/test_structure_info.py:3:1539 |540 1 | # Copyright (c) 2026 Seungwon Lee541 2 | # SPDX-License-Identifier: MIT542 3 | / from __future__ import annotations543 4 | |544 5 | | from typing import TYPE_CHECKING, cast545 6 | |546 7 | | import pytest547 8 | | from biorefs_cli.commands.structure import (548 9 | | InfoService,54910 | | build_info_result,55011 | | parse_entry,55112 | | )55213 | | from biorefs_cli.main import main553 | |_________________________________^55414 |55515 | if TYPE_CHECKING:556 |557help: Organize imports558 |5597 | import pytest5608 +5619 | from biorefs_cli.commands.structure import (562 |563564I001 [*] Import block is un-sorted or un-formatted565 --> tests/test_structure_render.py:3:1566 |567 1 | # Copyright (c) 2026 Seungwon Lee568 2 | # SPDX-License-Identifier: MIT569 3 | / from __future__ import annotations570 4 | |571 5 | | import pytest572 6 | | from biorefs_cli.commands.structure import (573 7 | | parse_include,574 8 | | print_info_table,575 9 | | print_search_table,57610 | | validate_organism,57711 | | )57812 | | from biorefs_cli.errors import CLIError579 | |_______________________________________^580help: Organize imports581 |5825 | import pytest5836 +5847 | from biorefs_cli.commands.structure import (585 |586587I001 [*] Import block is un-sorted or un-formatted588 --> tests/test_structure_search.py:3:1589 |590 1 | # Copyright (c) 2026 Seungwon Lee591 2 | # SPDX-License-Identifier: MIT592 3 | / from __future__ import annotations593 4 | |594 5 | | import argparse595 6 | | from typing import TYPE_CHECKING, cast596 7 | |597 8 | | import pytest598 9 | | from biorefs_cli.commands.structure import (59910 | | SearchQuery,60011 | | SearchService,60112 | | build_query_from_args,60213 | | build_search_payload,60314 | | clean_sequence,60415 | | normalize_pdb_id,60516 | | normalize_uniprot_accession,60617 | | parse_hits,60718 | | )60819 | | from biorefs_cli.errors import CLIError, HTTPError60920 | | from biorefs_cli.main import main61021 | | from biorefs_cli.rcsb_graphql import EntryMeta611 | |______________________________________________^61222 |61323 | if TYPE_CHECKING:614 |615help: Organize imports616 |6178 | import pytest6189 +61910 | from biorefs_cli.commands.structure import (620 |621622I001 [*] Import block is un-sorted or un-formatted623 --> tests/test_uniprot.py:3:1624 |625 1 | # Copyright (c) 2026 Seungwon Lee626 2 | # SPDX-License-Identifier: MIT627 3 | / from __future__ import annotations628 4 | |629 5 | | import json630 6 | | from typing import TYPE_CHECKING, cast631 7 | |632 8 | | import pytest633 9 | | from biorefs_cli.commands.uniprot import (63410 | | UniProtService,63511 | | build_search_query,63612 | | normalize_accession,63713 | | parse_entry,63814 | | )63915 | | from biorefs_cli.errors import CLIError, RateLimitError64016 | | from biorefs_cli.main import main641 | |_________________________________^64217 |64318 | if TYPE_CHECKING:644 |645help: Organize imports646 |6478 | import pytest6489 +64910 | from biorefs_cli.commands.uniprot import (650 |651652Found 22 errors.653[*] 22 fixable with the `--fix` option.