2026-03-31T09:51:13,477 Created temporary directory: /tmp/pip-ephem-wheel-cache-_ulsjwhe
2026-03-31T09:51:13,479 Created temporary directory: /tmp/pip-build-tracker-1hc20m2c
2026-03-31T09:51:13,479 Initialized build tracking at /tmp/pip-build-tracker-1hc20m2c
2026-03-31T09:51:13,480 Created build tracker: /tmp/pip-build-tracker-1hc20m2c
2026-03-31T09:51:13,480 Entered build tracker: /tmp/pip-build-tracker-1hc20m2c
2026-03-31T09:51:13,481 Created temporary directory: /tmp/pip-wheel-81jqyg2m
2026-03-31T09:51:13,484 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2026-03-31T09:51:13,487 Created temporary directory: /tmp/pip-ephem-wheel-cache-6wi4pfv3
2026-03-31T09:51:13,508 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-03-31T09:51:13,512 2 location(s) to search for versions of pyinfernal:
2026-03-31T09:51:13,512 * https://pypi.org/simple/pyinfernal/
2026-03-31T09:51:13,512 * https://www.piwheels.org/simple/pyinfernal/
2026-03-31T09:51:13,513 Fetching project page and analyzing links: https://pypi.org/simple/pyinfernal/
2026-03-31T09:51:13,514 Getting page https://pypi.org/simple/pyinfernal/
2026-03-31T09:51:13,515 Found index url https://pypi.org/simple
2026-03-31T09:51:13,739 Fetched page https://pypi.org/simple/pyinfernal/ as application/vnd.pypi.simple.v1+json
2026-03-31T09:51:13,744   Found link https://files.pythonhosted.org/packages/31/a0/6bf7427ebc462adbc514bb08156bec2aaaafe0fbf0451963395ee90396f8/pyinfernal-0.1.0.dev1.tar.gz (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7), version: 0.1.0.dev1
2026-03-31T09:51:13,745   Found link https://files.pythonhosted.org/packages/0e/3d/a84bbd14073b5c86e0aa953db9d52b695c7174d18bc999d97936bb6185ef/pyinfernal-0.1.0a2.tar.gz (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7), version: 0.1.0a2
2026-03-31T09:51:13,746   Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/bf/5f/584cc0ab37ac0b5a84b6d23eb33a4231d689094942cb20f6374ddb7cb201/pyinfernal-0.1.0-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,746   Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/8c/36/9fd1b69e75631ae2d458c7ab785274b57d85962d069c845188fffb125a2b/pyinfernal-0.1.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,747   Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/71/d9/f7c239ee6ace98b14231128c170ac27dc23b10aa0e5610b7c12e402ec848/pyinfernal-0.1.0-cp312-abi3-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,748   Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/5f/a6/928048d02cd4454ef342a39abf87aae3c8bd85766cae2645a2062538ac63/pyinfernal-0.1.0-cp314-cp314t-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,749   Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/c3/e6/ea37886a2a2f02d0749170ea19bc381997b37fdd7b57839719aaeb8e7458/pyinfernal-0.1.0-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,749   Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/51/ae/26ef3e48dfdcc1e25efbbc140e25006c0ae5a9a6772c7132d895e1a400dc/pyinfernal-0.1.0-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,750   Found link https://files.pythonhosted.org/packages/8f/76/7f5d68284fdf09776b12ce0a892f55e1204ae576b72f46bba17dd0a7adc1/pyinfernal-0.1.0.tar.gz (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7), version: 0.1.0
2026-03-31T09:51:13,751   Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/4c/08/1aebd1f421db524eb57f41222680c58db3ffbdd8a64fff25ab6f6af2ad12/pyinfernal-0.1.1-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,752   Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/7c/06/7ee14b6709e29f53b68981a77fb378687bf2a656426b4d73df40c6726b76/pyinfernal-0.1.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,752   Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/d2/2e/d586930cf9f394068531b1eb5169b36ab07aaaec8267fefb8036d2baca80/pyinfernal-0.1.1-cp312-abi3-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,753   Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/b6/72/d8b7ba1337842f6259ba3dfc3e62658bcdf3b5933dd781f0dff3a6f45b76/pyinfernal-0.1.1-cp314-cp314t-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,753   Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/2a/bd/1b072bcc4afd4c13c1c3cbcbd5c0b60c348c0d03be2cfbdffb3060105717/pyinfernal-0.1.1-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,754   Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/ff/60/e2e449d6127f973b67bbe4f4503ba82dc88be6e61981d4c03be7c79eba96/pyinfernal-0.1.1-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,755   Found link https://files.pythonhosted.org/packages/7a/88/b6801fe0db4ef72bfd4d4613be61450f57550069e6f29f373847edf58dd2/pyinfernal-0.1.1.tar.gz (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7), version: 0.1.1
2026-03-31T09:51:13,756 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyinfernal/
2026-03-31T09:51:13,757 Getting page https://www.piwheels.org/simple/pyinfernal/
2026-03-31T09:51:13,758 Found index url https://www.piwheels.org/simple
2026-03-31T09:51:13,931 Fetched page https://www.piwheels.org/simple/pyinfernal/ as text/html
2026-03-31T09:51:13,934   Skipping link: No binaries permitted for pyinfernal: https://archive1.piwheels.org/simple/pyinfernal/pyinfernal-0.1.0-cp39-cp39-linux_armv6l.whl#sha256=27eef861c760191c31285d7e9117dcea8236b7fea78a9f028361f60f9e63b0b0 (from https://www.piwheels.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,935   Skipping link: No binaries permitted for pyinfernal: https://archive1.piwheels.org/simple/pyinfernal/pyinfernal-0.1.0-cp39-cp39-linux_armv7l.whl#sha256=27eef861c760191c31285d7e9117dcea8236b7fea78a9f028361f60f9e63b0b0 (from https://www.piwheels.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,936   Skipping link: No binaries permitted for pyinfernal: https://archive1.piwheels.org/simple/pyinfernal/pyinfernal-0.1.0.dev1-cp313-cp313-linux_armv6l.whl#sha256=e8f82d698afea0aac958c17ff07114022aa9ae0af8047d941c03f5532198d7bf (from https://www.piwheels.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,936   Skipping link: No binaries permitted for pyinfernal: https://archive1.piwheels.org/simple/pyinfernal/pyinfernal-0.1.0.dev1-cp313-cp313-linux_armv7l.whl#sha256=e8f82d698afea0aac958c17ff07114022aa9ae0af8047d941c03f5532198d7bf (from https://www.piwheels.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,937   Skipping link: No binaries permitted for pyinfernal: https://archive1.piwheels.org/simple/pyinfernal/pyinfernal-0.1.0.dev1-cp39-cp39-linux_armv6l.whl#sha256=1f14857dce1388dfcb08daec8f93171772e4bf60fb08d64547915376a62c3861 (from https://www.piwheels.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,938   Skipping link: No binaries permitted for pyinfernal: https://archive1.piwheels.org/simple/pyinfernal/pyinfernal-0.1.0.dev1-cp39-cp39-linux_armv7l.whl#sha256=1f14857dce1388dfcb08daec8f93171772e4bf60fb08d64547915376a62c3861 (from https://www.piwheels.org/simple/pyinfernal/) (requires-python:>=3.7)
2026-03-31T09:51:13,938 Skipping link: not a file: https://www.piwheels.org/simple/pyinfernal/
2026-03-31T09:51:13,939 Skipping link: not a file: https://pypi.org/simple/pyinfernal/
2026-03-31T09:51:13,958 Given no hashes to check 1 links for project 'pyinfernal': discarding no candidates
2026-03-31T09:51:13,975 Collecting pyinfernal==0.1.1
2026-03-31T09:51:13,978   Created temporary directory: /tmp/pip-unpack-ggxyrzoc
2026-03-31T09:51:14,215   Downloading pyinfernal-0.1.1.tar.gz (4.7 MB)
2026-03-31T09:51:16,543   Added pyinfernal==0.1.1 from https://files.pythonhosted.org/packages/7a/88/b6801fe0db4ef72bfd4d4613be61450f57550069e6f29f373847edf58dd2/pyinfernal-0.1.1.tar.gz to build tracker '/tmp/pip-build-tracker-1hc20m2c'
2026-03-31T09:51:16,552   Created temporary directory: /tmp/pip-build-env-kvudig94
2026-03-31T09:51:16,556   Installing build dependencies: started
2026-03-31T09:51:16,558   Running command pip subprocess to install build dependencies
2026-03-31T09:51:17,687   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-03-31T09:51:18,123   DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2026-03-31T09:51:18,145   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-03-31T09:51:18,745   Collecting scikit-build-core>=0.11
2026-03-31T09:51:18,771     Using cached https://www.piwheels.org/simple/scikit-build-core/scikit_build_core-0.12.2-py3-none-any.whl (192 kB)
2026-03-31T09:51:20,828   Collecting cython>=3.0
2026-03-31T09:51:21,622     Using cached https://www.piwheels.org/simple/cython/cython-3.2.4-cp311-cp311-linux_armv7l.whl (11.1 MB)
2026-03-31T09:51:22,503   Collecting pyhmmer~=0.12.0
2026-03-31T09:51:22,742     Downloading https://archive1.piwheels.org/simple/pyhmmer/pyhmmer-0.12.0-cp311-cp311-linux_armv7l.whl (4.1 MB)
2026-03-31T09:51:23,213        ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.1/4.1 MB 8.8 MB/s eta 0:00:00
2026-03-31T09:51:23,503   Collecting packaging>=23.2
2026-03-31T09:51:23,520     Using cached https://www.piwheels.org/simple/packaging/packaging-26.0-py3-none-any.whl (74 kB)
2026-03-31T09:51:23,634   Collecting pathspec>=0.12.0
2026-03-31T09:51:23,650     Using cached https://www.piwheels.org/simple/pathspec/pathspec-1.0.4-py3-none-any.whl (55 kB)
2026-03-31T09:51:24,779   Collecting psutil<8.0,>=5.0
2026-03-31T09:51:24,799     WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))': /simple/psutil/psutil-6.0.0-cp311-abi3-linux_armv7l.whl
2026-03-31T09:51:24,988     Using cached https://archive1.piwheels.org/simple/psutil/psutil-6.0.0-cp311-abi3-linux_armv7l.whl (285 kB)
2026-03-31T09:51:27,731   Installing collected packages: psutil, pathspec, packaging, cython, scikit-build-core, pyhmmer
2026-03-31T09:51:32,945     Creating /tmp/pip-build-env-kvudig94/overlay/local/bin
2026-03-31T09:51:32,947     changing mode of /tmp/pip-build-env-kvudig94/overlay/local/bin/cygdb to 755
2026-03-31T09:51:32,949     changing mode of /tmp/pip-build-env-kvudig94/overlay/local/bin/cython to 755
2026-03-31T09:51:32,951     changing mode of /tmp/pip-build-env-kvudig94/overlay/local/bin/cythonize to 755
2026-03-31T09:51:34,974   Successfully installed cython-3.2.4 packaging-26.0 pathspec-1.0.4 psutil-6.0.0 pyhmmer-0.12.0 scikit-build-core-0.12.2
2026-03-31T09:51:35,395   Installing build dependencies: finished with status 'done'
2026-03-31T09:51:35,402   Getting requirements to build wheel: started
2026-03-31T09:51:35,404   Running command Getting requirements to build wheel
2026-03-31T09:51:36,022   Getting requirements to build wheel: finished with status 'done'
2026-03-31T09:51:36,025   Created temporary directory: /tmp/pip-modern-metadata-ks3m0ms9
2026-03-31T09:51:36,027   Preparing metadata (pyproject.toml): started
2026-03-31T09:51:36,028   Running command Preparing metadata (pyproject.toml)
2026-03-31T09:51:36,701   2026-03-31 09:51:36,701 - scikit_build_core - WARNING - Unknown keys in top-level of pyproject.toml: tool.mypy-pyinfernal.tests.*
2026-03-31T09:51:36,757   *** scikit-build-core 0.12.2 using CMake 3.25.1 (metadata_wheel)
2026-03-31T09:51:36,860   Preparing metadata (pyproject.toml): finished with status 'done'
2026-03-31T09:51:36,865   Source in /tmp/pip-wheel-81jqyg2m/pyinfernal_ad157415cdd845d18cc7c61c77b41b81 has version 0.1.1, which satisfies requirement pyinfernal==0.1.1 from https://files.pythonhosted.org/packages/7a/88/b6801fe0db4ef72bfd4d4613be61450f57550069e6f29f373847edf58dd2/pyinfernal-0.1.1.tar.gz
2026-03-31T09:51:36,866   Removed pyinfernal==0.1.1 from https://files.pythonhosted.org/packages/7a/88/b6801fe0db4ef72bfd4d4613be61450f57550069e6f29f373847edf58dd2/pyinfernal-0.1.1.tar.gz from build tracker '/tmp/pip-build-tracker-1hc20m2c'
2026-03-31T09:51:36,872 Created temporary directory: /tmp/pip-unpack-nffydrrm
2026-03-31T09:51:36,873 Building wheels for collected packages: pyinfernal
2026-03-31T09:51:36,878   Created temporary directory: /tmp/pip-wheel-s1vv8tqe
2026-03-31T09:51:36,878   Destination directory: /tmp/pip-wheel-s1vv8tqe
2026-03-31T09:51:36,880   Building wheel for pyinfernal (pyproject.toml): started
2026-03-31T09:51:36,882   Running command Building wheel for pyinfernal (pyproject.toml)
2026-03-31T09:51:37,537   2026-03-31 09:51:37,537 - scikit_build_core - WARNING - Unknown keys in top-level of pyproject.toml: tool.mypy-pyinfernal.tests.*
2026-03-31T09:51:37,595   *** scikit-build-core 0.12.2 using CMake 3.25.1 (wheel)
2026-03-31T09:51:37,622   *** Configuring CMake...
2026-03-31T09:51:37,853   loading initial cache file build/Release/CMakeInit.txt
2026-03-31T09:51:38,129   -- The C compiler identification is GNU 12.2.0
2026-03-31T09:51:38,183   -- Detecting C compiler ABI info
2026-03-31T09:51:38,443   -- Detecting C compiler ABI info - done
2026-03-31T09:51:38,480   -- Check for working C compiler: /usr/bin/arm-linux-gnueabihf-gcc - skipped
2026-03-31T09:51:38,482   -- Detecting C compile features
2026-03-31T09:51:38,484   -- Detecting C compile features - done
2026-03-31T09:51:38,503   -- Installing shared libraries to pyinfernal.libs
2026-03-31T09:51:38,517   -- Looking for alloca.h
2026-03-31T09:51:38,844   -- Looking for alloca.h - found
2026-03-31T09:51:39,575   -- Found Python: /usr/bin/python3 (found version "3.11.2") found components: Interpreter Development.Module
2026-03-31T09:51:39,578   -- Looking for PyInterpreterState_GetID
2026-03-31T09:51:40,094   -- Looking for PyInterpreterState_GetID - not found
2026-03-31T09:51:40,096   -- Building in latest API mode for Python: 3.11
2026-03-31T09:51:40,098   -- Linking to libinfernal
2026-03-31T09:51:40,100   -- Configuring done
2026-03-31T09:51:40,164   -- Generating done
2026-03-31T09:51:40,213   -- Build files have been written to: /tmp/pip-wheel-81jqyg2m/pyinfernal_ad157415cdd845d18cc7c61c77b41b81/build/Release
2026-03-31T09:51:40,244   *** Building project with Ninja...
2026-03-31T09:51:40,385   [1/81] Copying cm_alndata.c
2026-03-31T09:51:40,387   [2/81] Copying cm.c
2026-03-31T09:51:40,390   [3/81] Copying cm_dpalign.c
2026-03-31T09:51:40,417   [4/81] Copying cm_alidisplay.c
2026-03-31T09:51:40,434   [5/81] Copying cm_dpalign_trunc.c
2026-03-31T09:51:40,474   [6/81] Copying cm_dpsearch.c
2026-03-31T09:51:40,482   [7/81] Copying cm_dpsearch_trunc.c
2026-03-31T09:51:40,543   [8/81] Patching infernal.h
2026-03-31T09:51:40,545   [9/81] Copying cm_dpsmall.c
2026-03-31T09:51:40,557   [10/81] Copying cm_modelconfig.c
2026-03-31T09:51:40,603   [11/81] Copying cm_modelmaker.c
2026-03-31T09:51:40,606   [12/81] Copying cm_mx.c
2026-03-31T09:51:40,631   [13/81] Copying cm_parsetree.c
2026-03-31T09:51:40,655   [14/81] Copying cm_qdband.c
2026-03-31T09:51:40,700   [15/81] Patching cm_file.c
2026-03-31T09:51:40,731   [16/81] Copying cm_submodel.c
2026-03-31T09:51:40,742   [17/81] Copying cm_tophits.c
2026-03-31T09:51:40,751   [18/81] Copying cm_trunc.c
2026-03-31T09:51:40,768   [19/81] Copying cm_p7_band.c
2026-03-31T09:51:40,784   [20/81] Copying cm_p7_domaindef.c
2026-03-31T09:51:40,788   [21/81] Patching cm_pipeline.c
2026-03-31T09:51:40,822   [22/81] Copying cm_p7_modelmaker.c
2026-03-31T09:51:40,843   [23/81] Copying cp9.c
2026-03-31T09:51:40,849   [24/81] Copying cm_p7_modelconfig_trunc.c
2026-03-31T09:51:40,861   [25/81] Copying cp9_modelmaker.c
2026-03-31T09:51:40,870   [26/81] Copying cp9_mx.c
2026-03-31T09:51:40,873   [27/81] Copying cp9_dp.c
2026-03-31T09:51:40,918   [28/81] Copying cp9_trace.c
2026-03-31T09:51:40,922   [29/81] Copying alphabet.c
2026-03-31T09:51:40,947   [30/81] Copying errors.c
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2026-03-31T09:52:51,267   [78/81] Linking C shared library src/infernal/liblibinfernal.so
2026-03-31T09:53:06,079   [79/81] Cythonizing cm.pyx to cm.c
2026-03-31T09:53:06,080   warning: /tmp/pip-wheel-81jqyg2m/pyinfernal_ad157415cdd845d18cc7c61c77b41b81/src/pyinfernal/cm.pyx:629:32: Assigning to 'ESL_ALPHABET *' from 'const ESL_ALPHABET *' discards const qualifier
2026-03-31T09:53:06,081   performance hint: /tmp/pip-wheel-81jqyg2m/pyinfernal_ad157415cdd845d18cc7c61c77b41b81/src/pyinfernal/cm.pyx:700:53: Exception check after calling 'cm_file_Read' will always require the GIL to be acquired. Declare 'cm_file_Read' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2026-03-31T09:53:06,082   performance hint: /tmp/pip-wheel-81jqyg2m/pyinfernal_ad157415cdd845d18cc7c61c77b41b81/src/pyinfernal/cm.pyx:2013:78: Exception check after calling 'cm_tophits_TabularTargets3' will always require the GIL to be acquired. Declare 'cm_tophits_TabularTargets3' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2026-03-31T09:53:44,265   [80/81] Building C object src/pyinfernal/CMakeFiles/pyinfernal.cm.dir/cm.c.o
2026-03-31T09:53:44,266   /tmp/pip-wheel-81jqyg2m/pyinfernal_ad157415cdd845d18cc7c61c77b41b81/build/Release/src/pyinfernal/cm.c:4306:153: warning: ‘struct __pyx_fuse_0__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline__get_om_from_query’ declared inside parameter list will not be visible outside of this definition or declaration
2026-03-31T09:53:44,267    4306 |   P7_OPROFILE *(*__pyx_fuse_0_get_om_from_query)(struct __pyx_obj_7pyhmmer_5plan7_LongTargetsPipeline *, struct __pyx_obj_7pyhmmer_5plan7_HMM *, struct __pyx_fuse_0__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline__get_om_from_query *__pyx_optional_args);
2026-03-31T09:53:44,268         |                                                                                                                                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2026-03-31T09:53:44,269   /tmp/pip-wheel-81jqyg2m/pyinfernal_ad157415cdd845d18cc7c61c77b41b81/build/Release/src/pyinfernal/cm.c:4307:157: warning: ‘struct __pyx_fuse_1__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline__get_om_from_query’ declared inside parameter list will not be visible outside of this definition or declaration
2026-03-31T09:53:44,269    4307 |   P7_OPROFILE *(*__pyx_fuse_1_get_om_from_query)(struct __pyx_obj_7pyhmmer_5plan7_LongTargetsPipeline *, struct __pyx_obj_7pyhmmer_5plan7_Profile *, struct __pyx_fuse_1__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline__get_om_from_query *__pyx_optional_args);
2026-03-31T09:53:44,270         |                                                                                                                                                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2026-03-31T09:53:44,270   /tmp/pip-wheel-81jqyg2m/pyinfernal_ad157415cdd845d18cc7c61c77b41b81/build/Release/src/pyinfernal/cm.c:4308:166: warning: ‘struct __pyx_fuse_2__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline__get_om_from_query’ declared inside parameter list will not be visible outside of this definition or declaration
2026-03-31T09:53:44,271    4308 |   P7_OPROFILE *(*__pyx_fuse_2_get_om_from_query)(struct __pyx_obj_7pyhmmer_5plan7_LongTargetsPipeline *, struct __pyx_obj_7pyhmmer_5plan7_OptimizedProfile *, struct __pyx_fuse_2__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline__get_om_from_query *__pyx_optional_args);
2026-03-31T09:53:44,271         |                                                                                                                                                                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2026-03-31T09:53:44,272   /tmp/pip-wheel-81jqyg2m/pyinfernal_ad157415cdd845d18cc7c61c77b41b81/build/Release/src/pyinfernal/cm.c:4315:255: warning: ‘struct __pyx_fuse_0__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline_search_msa’ declared inside parameter list will not be visible outside of this definition or declaration
2026-03-31T09:53:44,272    4315 |   struct __pyx_obj_7pyhmmer_5plan7_TopHits *(*__pyx_fuse_0search_msa)(struct __pyx_obj_7pyhmmer_5plan7_LongTargetsPipeline *, struct __pyx_obj_7pyhmmer_5easel_DigitalMSA *, struct __pyx_obj_7pyhmmer_5easel_SequenceFile *, int __pyx_skip_dispatch, struct __pyx_fuse_0__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline_search_msa *__pyx_optional_args);
2026-03-31T09:53:44,273         |                                                                                                                                                                                                                                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2026-03-31T09:53:44,274   /tmp/pip-wheel-81jqyg2m/pyinfernal_ad157415cdd845d18cc7c61c77b41b81/build/Release/src/pyinfernal/cm.c:4316:263: warning: ‘struct __pyx_fuse_1__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline_search_msa’ declared inside parameter list will not be visible outside of this definition or declaration
2026-03-31T09:53:44,274    4316 |   struct __pyx_obj_7pyhmmer_5plan7_TopHits *(*__pyx_fuse_1search_msa)(struct __pyx_obj_7pyhmmer_5plan7_LongTargetsPipeline *, struct __pyx_obj_7pyhmmer_5easel_DigitalMSA *, struct __pyx_obj_7pyhmmer_5easel_DigitalSequenceBlock *, int __pyx_skip_dispatch, struct __pyx_fuse_1__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline_search_msa *__pyx_optional_args);
2026-03-31T09:53:44,275         |                                                                                                                                                                                                                                                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2026-03-31T09:53:44,275   /tmp/pip-wheel-81jqyg2m/pyinfernal_ad157415cdd845d18cc7c61c77b41b81/build/Release/src/pyinfernal/cm.c:4317:260: warning: ‘struct __pyx_fuse_0__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline_search_seq’ declared inside parameter list will not be visible outside of this definition or declaration
2026-03-31T09:53:44,276    4317 |   struct __pyx_obj_7pyhmmer_5plan7_TopHits *(*__pyx_fuse_0search_seq)(struct __pyx_obj_7pyhmmer_5plan7_LongTargetsPipeline *, struct __pyx_obj_7pyhmmer_5easel_DigitalSequence *, struct __pyx_obj_7pyhmmer_5easel_SequenceFile *, int __pyx_skip_dispatch, struct __pyx_fuse_0__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline_search_seq *__pyx_optional_args);
2026-03-31T09:53:44,276         |                                                                                                                                                                                                                                                                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2026-03-31T09:53:44,277   /tmp/pip-wheel-81jqyg2m/pyinfernal_ad157415cdd845d18cc7c61c77b41b81/build/Release/src/pyinfernal/cm.c:4318:268: warning: ‘struct __pyx_fuse_1__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline_search_seq’ declared inside parameter list will not be visible outside of this definition or declaration
2026-03-31T09:53:44,277    4318 |   struct __pyx_obj_7pyhmmer_5plan7_TopHits *(*__pyx_fuse_1search_seq)(struct __pyx_obj_7pyhmmer_5plan7_LongTargetsPipeline *, struct __pyx_obj_7pyhmmer_5easel_DigitalSequence *, struct __pyx_obj_7pyhmmer_5easel_DigitalSequenceBlock *, int __pyx_skip_dispatch, struct __pyx_fuse_1__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline_search_seq *__pyx_optional_args);
2026-03-31T09:53:44,278         |                                                                                                                                                                                                                                                                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2026-03-31T09:53:44,278   /tmp/pip-wheel-81jqyg2m/pyinfernal_ad157415cdd845d18cc7c61c77b41b81/build/Release/src/pyinfernal/cm.c: In function ‘__pyx_pf_10pyinfernal_2cm_6CMFile_2__init__’:
2026-03-31T09:53:44,279   /tmp/pip-wheel-81jqyg2m/pyinfernal_ad157415cdd845d18cc7c61c77b41b81/build/Release/src/pyinfernal/cm.c:29050:24: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2026-03-31T09:53:44,280   29050 |     __pyx_v_self->_abc = __pyx_t_21;
2026-03-31T09:53:44,281         |                        ^
2026-03-31T09:53:44,427   [81/81] Linking C shared module src/pyinfernal/cm.cpython-311-arm-linux-gnueabihf.so
2026-03-31T09:53:44,434   *** Installing project into wheel...
2026-03-31T09:53:44,487   -- Install configuration: "Release"
2026-03-31T09:53:44,489   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include
2026-03-31T09:53:44,493   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal
2026-03-31T09:53:44,496   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/cm_tophits.pxd
2026-03-31T09:53:44,500   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/logsum.pxd
2026-03-31T09:53:44,504   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/cm_modelconfig.pxd
2026-03-31T09:53:44,507   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/hmmband.pxd
2026-03-31T09:53:44,510   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/__init__.pxd
2026-03-31T09:53:44,513   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/cp9.pxd
2026-03-31T09:53:44,516   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/cm_qdband.pxd
2026-03-31T09:53:44,519   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/cm_alidisplay.pxd
2026-03-31T09:53:44,522   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/cm_file.pxd
2026-03-31T09:53:44,524   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/cm.pxd
2026-03-31T09:53:44,528   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/cm_mx.pxd
2026-03-31T09:53:44,531   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/stats.pxd
2026-03-31T09:53:44,534   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/cm_pipeline.pxd
2026-03-31T09:53:44,538   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/cmsearch.pxd
2026-03-31T09:53:44,540   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/cm_p7_modelconfig.pxd
2026-03-31T09:53:44,544   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/liblibinfernal.so
2026-03-31T09:53:44,569   -- Set runtime path of "/tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/liblibinfernal.so" to "$ORIGIN/"
2026-03-31T09:53:44,634   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/config.h
2026-03-31T09:53:44,637   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal.libs/include/libinfernal/infernal.h
2026-03-31T09:53:44,645   -- Installing: /tmp/tmpw40m0pj6/wheel/platlib/pyinfernal/cm.cpython-311-arm-linux-gnueabihf.so
2026-03-31T09:53:44,657   -- Set runtime path of "/tmp/tmpw40m0pj6/wheel/platlib/pyinfernal/cm.cpython-311-arm-linux-gnueabihf.so" to "$ORIGIN/../pyinfernal.libs"
2026-03-31T09:53:44,688   *** Making wheel...
2026-03-31T09:53:45,709   *** Created pyinfernal-0.1.1-cp311-cp311-linux_armv7l.whl
2026-03-31T09:53:45,812   Building wheel for pyinfernal (pyproject.toml): finished with status 'done'
2026-03-31T09:53:45,853   Created wheel for pyinfernal: filename=pyinfernal-0.1.1-cp311-cp311-linux_armv7l.whl size=1200713 sha256=f0f8649bacb661678fb8472f9d21a5b63defddc3ceb8ba82c175cbea8f3083e6
2026-03-31T09:53:45,855   Stored in directory: /tmp/pip-ephem-wheel-cache-6wi4pfv3/wheels/2e/40/b0/fb7531f535b9b5939a705aed24dc1b4883648e891606fb498b
2026-03-31T09:53:45,876 Successfully built pyinfernal
2026-03-31T09:53:45,924 Removed build tracker: '/tmp/pip-build-tracker-1hc20m2c'