2025-09-08T12:32:44,912 Created temporary directory: /tmp/pip-build-tracker-8kab71wy 2025-09-08T12:32:44,912 Initialized build tracking at /tmp/pip-build-tracker-8kab71wy 2025-09-08T12:32:44,912 Created build tracker: /tmp/pip-build-tracker-8kab71wy 2025-09-08T12:32:44,913 Entered build tracker: /tmp/pip-build-tracker-8kab71wy 2025-09-08T12:32:44,913 Created temporary directory: /tmp/pip-wheel-d4dqryj8 2025-09-08T12:32:44,916 Created temporary directory: /tmp/pip-ephem-wheel-cache-ml1_emy6 2025-09-08T12:32:44,970 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T12:32:44,973 2 location(s) to search for versions of isambard: 2025-09-08T12:32:44,973 * https://pypi.org/simple/isambard/ 2025-09-08T12:32:44,973 * https://www.piwheels.org/simple/isambard/ 2025-09-08T12:32:44,973 Fetching project page and analyzing links: https://pypi.org/simple/isambard/ 2025-09-08T12:32:44,973 Getting page https://pypi.org/simple/isambard/ 2025-09-08T12:32:44,974 Found index url https://pypi.org/simple/ 2025-09-08T12:32:45,179 Fetched page https://pypi.org/simple/isambard/ as application/vnd.pypi.simple.v1+json 2025-09-08T12:32:45,181 Found link https://files.pythonhosted.org/packages/ca/6d/9456a011721c3376fc03e77d5ea89f563dfac30660be8b2517ad1ba2c44a/ISAMBARD-2.0.1.tar.gz (from https://pypi.org/simple/isambard/), version: 2.0.1 2025-09-08T12:32:45,181 Found link https://files.pythonhosted.org/packages/9c/ba/636028b8e309e217e171016e34b2a9f5f0b37f3be916d02ad55f97cf4991/ISAMBARD-2.2.0.tar.gz (from https://pypi.org/simple/isambard/), version: 2.2.0 2025-09-08T12:32:45,182 Found link https://files.pythonhosted.org/packages/6d/5d/36e0369e6e7bdb1061074aff44dab96caf1e1809a289f41156a0a34bce49/ISAMBARD-2.3.1.tar.gz (from https://pypi.org/simple/isambard/), version: 2.3.1 2025-09-08T12:32:45,183 Fetching project page and analyzing links: https://www.piwheels.org/simple/isambard/ 2025-09-08T12:32:45,183 Getting page https://www.piwheels.org/simple/isambard/ 2025-09-08T12:32:45,185 Found index url https://www.piwheels.org/simple/ 2025-09-08T12:32:45,288 Fetched page https://www.piwheels.org/simple/isambard/ as text/html 2025-09-08T12:32:45,295 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp35-cp35m-linux_armv6l.whl#sha256=5456ca91d4e8a25515a72ce369c3dc3bd75771154926907a13ee229c5c775c90 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,295 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp35-cp35m-linux_armv7l.whl#sha256=5456ca91d4e8a25515a72ce369c3dc3bd75771154926907a13ee229c5c775c90 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,295 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp37-cp37m-linux_armv6l.whl#sha256=efae9efaebdc3a20e5d63f7004a92e689f3e6e5836be027bc95d82dfc3a96931 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,295 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp37-cp37m-linux_armv7l.whl#sha256=efae9efaebdc3a20e5d63f7004a92e689f3e6e5836be027bc95d82dfc3a96931 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,295 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp311-cp311-linux_armv6l.whl#sha256=0c3ad4f0c4a0b8169c1ea441c243457c4de16bbc36eaaa2aa170c0965e87c84e (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,295 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp311-cp311-linux_armv7l.whl#sha256=0c3ad4f0c4a0b8169c1ea441c243457c4de16bbc36eaaa2aa170c0965e87c84e (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,296 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp39-cp39-linux_armv6l.whl#sha256=697398715022626b617288089a4d8f169aba9b6a2741bb64a57baf0008f4a682 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,296 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp39-cp39-linux_armv7l.whl#sha256=697398715022626b617288089a4d8f169aba9b6a2741bb64a57baf0008f4a682 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,296 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp39-cp39-linux_armv6l.whl#sha256=0010224aeec40539f9f2ef43ef893a7b0735d1b3f4e95dc31708219c0337dc30 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,296 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp39-cp39-linux_armv7l.whl#sha256=0010224aeec40539f9f2ef43ef893a7b0735d1b3f4e95dc31708219c0337dc30 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,296 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp34-cp34m-linux_armv6l.whl#sha256=97c289f5089392b53f0c6d552d6d48650a1fb4dfc834cfc8b472a8a01c98dc89 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,296 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp34-cp34m-linux_armv7l.whl#sha256=97c289f5089392b53f0c6d552d6d48650a1fb4dfc834cfc8b472a8a01c98dc89 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,296 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp35-cp35m-linux_armv7l.whl#sha256=3fd2a12daa3a717fd4fcba1f02c00189966f88fdecfd4fe27a826bbc5e2e9e0d (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,297 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp35-cp35m-linux_armv6l.whl#sha256=3fd2a12daa3a717fd4fcba1f02c00189966f88fdecfd4fe27a826bbc5e2e9e0d (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,297 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp37-cp37m-linux_armv7l.whl#sha256=1ed4e4469c6a429a8d7983454afa221ed4de77c4f796928fe85b8ca9493ce9b7 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,297 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp37-cp37m-linux_armv6l.whl#sha256=1ed4e4469c6a429a8d7983454afa221ed4de77c4f796928fe85b8ca9493ce9b7 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,297 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp311-cp311-linux_armv6l.whl#sha256=da0939c6735170d08c9e5c63a3d82bb9003d2457ae53546e18eca4b785976758 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,297 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp311-cp311-linux_armv7l.whl#sha256=da0939c6735170d08c9e5c63a3d82bb9003d2457ae53546e18eca4b785976758 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,297 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp35-cp35m-linux_armv6l.whl#sha256=e0fc68b3f5047b9165d5153bc4dc316bab81664ff21671571b7513628b90b5a1 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,297 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp35-cp35m-linux_armv7l.whl#sha256=e0fc68b3f5047b9165d5153bc4dc316bab81664ff21671571b7513628b90b5a1 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,298 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp34-cp34m-linux_armv7l.whl#sha256=887549f381be5e2479ffed07b8c2eb4f307e592beccbe3290feba06d0c3790f9 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,298 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp34-cp34m-linux_armv6l.whl#sha256=887549f381be5e2479ffed07b8c2eb4f307e592beccbe3290feba06d0c3790f9 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,298 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp37-cp37m-linux_armv7l.whl#sha256=bd0f20e61ccc5234636764d226a0798035a8fbf626bcac75c0b0ecca150f5006 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,298 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp37-cp37m-linux_armv6l.whl#sha256=bd0f20e61ccc5234636764d226a0798035a8fbf626bcac75c0b0ecca150f5006 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,298 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp311-cp311-linux_armv6l.whl#sha256=4cf86ff1923fd823d90a7bd0993af4a2a172829212bf9de92f255ee304f38307 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,298 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp311-cp311-linux_armv7l.whl#sha256=4cf86ff1923fd823d90a7bd0993af4a2a172829212bf9de92f255ee304f38307 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,298 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp39-cp39-linux_armv6l.whl#sha256=45f89745fb452c115ce88125bc0668253c3f3b887d7ece84108e217dd6760ec8 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,299 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp39-cp39-linux_armv7l.whl#sha256=45f89745fb452c115ce88125bc0668253c3f3b887d7ece84108e217dd6760ec8 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T12:32:45,299 Skipping link: not a file: https://www.piwheels.org/simple/isambard/ 2025-09-08T12:32:45,299 Skipping link: not a file: https://pypi.org/simple/isambard/ 2025-09-08T12:32:45,322 Given no hashes to check 1 links for project 'isambard': discarding no candidates 2025-09-08T12:32:45,323 Collecting isambard==2.0.1 2025-09-08T12:32:45,324 Created temporary directory: /tmp/pip-unpack-h3sanq2m 2025-09-08T12:32:45,472 Downloading ISAMBARD-2.0.1.tar.gz (337 kB) 2025-09-08T12:32:45,585 Added isambard==2.0.1 from https://files.pythonhosted.org/packages/ca/6d/9456a011721c3376fc03e77d5ea89f563dfac30660be8b2517ad1ba2c44a/ISAMBARD-2.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-8kab71wy' 2025-09-08T12:32:45,586 Running setup.py (path:/tmp/pip-wheel-d4dqryj8/isambard_f6f9d5b24d194de79013cf9b8077fc06/setup.py) egg_info for package isambard 2025-09-08T12:32:45,586 Created temporary directory: /tmp/pip-pip-egg-info-hm_s61yd 2025-09-08T12:32:45,586 Preparing metadata (setup.py): started 2025-09-08T12:32:45,587 Running command python setup.py egg_info 2025-09-08T12:32:47,993 Compiling src/isambard/specifications/ta_polypeptide.pyx because it changed. 2025-09-08T12:32:47,993 [1/1] Cythonizing src/isambard/specifications/ta_polypeptide.pyx 2025-09-08T12:32:48,384 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T12:32:48,384 !! 2025-09-08T12:32:48,384 ******************************************************************************** 2025-09-08T12:32:48,384 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T12:32:48,385 License :: OSI Approved :: MIT License 2025-09-08T12:32:48,385 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T12:32:48,385 ******************************************************************************** 2025-09-08T12:32:48,385 !! 2025-09-08T12:32:48,385 self._finalize_license_expression() 2025-09-08T12:32:48,460 running egg_info 2025-09-08T12:32:48,536 creating /tmp/pip-pip-egg-info-hm_s61yd/ISAMBARD.egg-info 2025-09-08T12:32:48,536 writing /tmp/pip-pip-egg-info-hm_s61yd/ISAMBARD.egg-info/PKG-INFO 2025-09-08T12:32:48,537 writing dependency_links to /tmp/pip-pip-egg-info-hm_s61yd/ISAMBARD.egg-info/dependency_links.txt 2025-09-08T12:32:48,538 writing requirements to /tmp/pip-pip-egg-info-hm_s61yd/ISAMBARD.egg-info/requires.txt 2025-09-08T12:32:48,538 writing top-level names to /tmp/pip-pip-egg-info-hm_s61yd/ISAMBARD.egg-info/top_level.txt 2025-09-08T12:32:48,539 writing manifest file '/tmp/pip-pip-egg-info-hm_s61yd/ISAMBARD.egg-info/SOURCES.txt' 2025-09-08T12:32:48,841 reading manifest file '/tmp/pip-pip-egg-info-hm_s61yd/ISAMBARD.egg-info/SOURCES.txt' 2025-09-08T12:32:48,842 reading manifest template 'MANIFEST.in' 2025-09-08T12:32:48,847 adding license file 'LICENSE.txt' 2025-09-08T12:32:48,850 writing manifest file '/tmp/pip-pip-egg-info-hm_s61yd/ISAMBARD.egg-info/SOURCES.txt' 2025-09-08T12:32:49,120 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T12:32:49,125 Source in /tmp/pip-wheel-d4dqryj8/isambard_f6f9d5b24d194de79013cf9b8077fc06 has version 2.0.1, which satisfies requirement isambard==2.0.1 from https://files.pythonhosted.org/packages/ca/6d/9456a011721c3376fc03e77d5ea89f563dfac30660be8b2517ad1ba2c44a/ISAMBARD-2.0.1.tar.gz 2025-09-08T12:32:49,125 Removed isambard==2.0.1 from https://files.pythonhosted.org/packages/ca/6d/9456a011721c3376fc03e77d5ea89f563dfac30660be8b2517ad1ba2c44a/ISAMBARD-2.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-8kab71wy' 2025-09-08T12:32:49,129 Created temporary directory: /tmp/pip-unpack-gtpo9zlb 2025-09-08T12:32:49,130 Created temporary directory: /tmp/pip-unpack-j834fke1 2025-09-08T12:32:49,130 Building wheels for collected packages: isambard 2025-09-08T12:32:49,131 Created temporary directory: /tmp/pip-wheel-akew_c6x 2025-09-08T12:32:49,131 DEPRECATION: Building 'isambard' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'isambard'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T12:32:49,132 Building wheel for isambard (setup.py): started 2025-09-08T12:32:49,133 Destination directory: /tmp/pip-wheel-akew_c6x 2025-09-08T12:32:49,133 Running command python setup.py bdist_wheel 2025-09-08T12:32:50,787 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T12:32:50,787 !! 2025-09-08T12:32:50,787 ******************************************************************************** 2025-09-08T12:32:50,787 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T12:32:50,788 License :: OSI Approved :: MIT License 2025-09-08T12:32:50,788 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T12:32:50,788 ******************************************************************************** 2025-09-08T12:32:50,788 !! 2025-09-08T12:32:50,788 self._finalize_license_expression() 2025-09-08T12:32:50,788 running bdist_wheel 2025-09-08T12:32:51,145 running build 2025-09-08T12:32:51,146 running build_py 2025-09-08T12:32:51,222 creating build/lib.linux-armv7l-cpython-313/isambard 2025-09-08T12:32:51,223 copying src/isambard/__init__.py -> build/lib.linux-armv7l-cpython-313/isambard 2025-09-08T12:32:51,223 creating build/lib.linux-armv7l-cpython-313/isambard/optimisation 2025-09-08T12:32:51,224 copying src/isambard/optimisation/base_evo_opt.py -> build/lib.linux-armv7l-cpython-313/isambard/optimisation 2025-09-08T12:32:51,224 copying src/isambard/optimisation/mmc_optimizer.py -> build/lib.linux-armv7l-cpython-313/isambard/optimisation 2025-09-08T12:32:51,225 copying src/isambard/optimisation/__init__.py -> build/lib.linux-armv7l-cpython-313/isambard/optimisation 2025-09-08T12:32:51,225 copying src/isambard/optimisation/evo_optimizers.py -> build/lib.linux-armv7l-cpython-313/isambard/optimisation 2025-09-08T12:32:51,226 creating build/lib.linux-armv7l-cpython-313/isambard/modelling 2025-09-08T12:32:51,227 copying src/isambard/modelling/non_canonical.py -> build/lib.linux-armv7l-cpython-313/isambard/modelling 2025-09-08T12:32:51,227 copying src/isambard/modelling/scwrl.py -> build/lib.linux-armv7l-cpython-313/isambard/modelling 2025-09-08T12:32:51,228 copying src/isambard/modelling/__init__.py -> build/lib.linux-armv7l-cpython-313/isambard/modelling 2025-09-08T12:32:51,228 creating build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T12:32:51,229 copying src/isambard/specifications/coiledcoil.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T12:32:51,229 copying src/isambard/specifications/helix.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T12:32:51,230 copying src/isambard/specifications/nucleic_acid_duplex.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T12:32:51,230 copying src/isambard/specifications/nucleic_acid_strand.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T12:32:51,231 copying src/isambard/specifications/__init__.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T12:32:51,231 copying src/isambard/specifications/solenoid.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T12:32:51,232 creating build/lib.linux-armv7l-cpython-313/isambard/evaluation 2025-09-08T12:32:51,232 copying src/isambard/evaluation/hydrophobic_fitness.py -> build/lib.linux-armv7l-cpython-313/isambard/evaluation 2025-09-08T12:32:51,233 copying src/isambard/evaluation/contact_order.py -> build/lib.linux-armv7l-cpython-313/isambard/evaluation 2025-09-08T12:32:51,233 copying src/isambard/evaluation/__init__.py -> build/lib.linux-armv7l-cpython-313/isambard/evaluation 2025-09-08T12:32:51,234 running egg_info 2025-09-08T12:32:51,308 writing src/ISAMBARD.egg-info/PKG-INFO 2025-09-08T12:32:51,309 writing dependency_links to src/ISAMBARD.egg-info/dependency_links.txt 2025-09-08T12:32:51,310 writing requirements to src/ISAMBARD.egg-info/requires.txt 2025-09-08T12:32:51,310 writing top-level names to src/ISAMBARD.egg-info/top_level.txt 2025-09-08T12:32:51,386 reading manifest file 'src/ISAMBARD.egg-info/SOURCES.txt' 2025-09-08T12:32:51,389 reading manifest template 'MANIFEST.in' 2025-09-08T12:32:51,394 adding license file 'LICENSE.txt' 2025-09-08T12:32:51,398 writing manifest file 'src/ISAMBARD.egg-info/SOURCES.txt' 2025-09-08T12:32:51,399 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.__pycache__' is absent from the `packages` configuration. 2025-09-08T12:32:51,399 !! 2025-09-08T12:32:51,400 ******************************************************************************** 2025-09-08T12:32:51,400 ############################ 2025-09-08T12:32:51,400 # Package would be ignored # 2025-09-08T12:32:51,400 ############################ 2025-09-08T12:32:51,400 Python recognizes 'isambard.__pycache__' as an importable package[^1], 2025-09-08T12:32:51,400 but it is absent from setuptools' `packages` configuration. 2025-09-08T12:32:51,400 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T12:32:51,400 package, please make sure that 'isambard.__pycache__' is explicitly added 2025-09-08T12:32:51,400 to the `packages` configuration field. 2025-09-08T12:32:51,401 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T12:32:51,401 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T12:32:51,401 instead of `find_packages(...)`/`find:`). 2025-09-08T12:32:51,401 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T12:32:51,401 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T12:32:51,401 If you don't want 'isambard.__pycache__' to be distributed and are 2025-09-08T12:32:51,401 already explicitly excluding 'isambard.__pycache__' via 2025-09-08T12:32:51,401 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T12:32:51,402 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T12:32:51,402 combination with a more fine grained `package-data` configuration. 2025-09-08T12:32:51,402 You can read more about "package data files" on setuptools documentation page: 2025-09-08T12:32:51,402 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T12:32:51,402 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T12:32:51,402 even if it does not contain any `.py` files. 2025-09-08T12:32:51,402 On the other hand, currently there is no concept of package data 2025-09-08T12:32:51,403 directory, all directories are treated like packages. 2025-09-08T12:32:51,403 ******************************************************************************** 2025-09-08T12:32:51,403 !! 2025-09-08T12:32:51,403 check.warn(importable) 2025-09-08T12:32:51,403 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.evaluation.__pycache__' is absent from the `packages` configuration. 2025-09-08T12:32:51,403 !! 2025-09-08T12:32:51,403 ******************************************************************************** 2025-09-08T12:32:51,403 ############################ 2025-09-08T12:32:51,403 # Package would be ignored # 2025-09-08T12:32:51,404 ############################ 2025-09-08T12:32:51,404 Python recognizes 'isambard.evaluation.__pycache__' as an importable package[^1], 2025-09-08T12:32:51,404 but it is absent from setuptools' `packages` configuration. 2025-09-08T12:32:51,404 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T12:32:51,404 package, please make sure that 'isambard.evaluation.__pycache__' is explicitly added 2025-09-08T12:32:51,404 to the `packages` configuration field. 2025-09-08T12:32:51,404 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T12:32:51,404 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T12:32:51,404 instead of `find_packages(...)`/`find:`). 2025-09-08T12:32:51,405 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T12:32:51,405 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T12:32:51,405 If you don't want 'isambard.evaluation.__pycache__' to be distributed and are 2025-09-08T12:32:51,405 already explicitly excluding 'isambard.evaluation.__pycache__' via 2025-09-08T12:32:51,405 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T12:32:51,405 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T12:32:51,405 combination with a more fine grained `package-data` configuration. 2025-09-08T12:32:51,406 You can read more about "package data files" on setuptools documentation page: 2025-09-08T12:32:51,406 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T12:32:51,406 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T12:32:51,406 even if it does not contain any `.py` files. 2025-09-08T12:32:51,406 On the other hand, currently there is no concept of package data 2025-09-08T12:32:51,406 directory, all directories are treated like packages. 2025-09-08T12:32:51,406 ******************************************************************************** 2025-09-08T12:32:51,407 !! 2025-09-08T12:32:51,407 check.warn(importable) 2025-09-08T12:32:51,407 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.modelling.__pycache__' is absent from the `packages` configuration. 2025-09-08T12:32:51,407 !! 2025-09-08T12:32:51,407 ******************************************************************************** 2025-09-08T12:32:51,407 ############################ 2025-09-08T12:32:51,407 # Package would be ignored # 2025-09-08T12:32:51,407 ############################ 2025-09-08T12:32:51,407 Python recognizes 'isambard.modelling.__pycache__' as an importable package[^1], 2025-09-08T12:32:51,408 but it is absent from setuptools' `packages` configuration. 2025-09-08T12:32:51,408 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T12:32:51,408 package, please make sure that 'isambard.modelling.__pycache__' is explicitly added 2025-09-08T12:32:51,408 to the `packages` configuration field. 2025-09-08T12:32:51,408 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T12:32:51,408 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T12:32:51,408 instead of `find_packages(...)`/`find:`). 2025-09-08T12:32:51,408 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T12:32:51,409 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T12:32:51,409 If you don't want 'isambard.modelling.__pycache__' to be distributed and are 2025-09-08T12:32:51,409 already explicitly excluding 'isambard.modelling.__pycache__' via 2025-09-08T12:32:51,409 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T12:32:51,409 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T12:32:51,409 combination with a more fine grained `package-data` configuration. 2025-09-08T12:32:51,409 You can read more about "package data files" on setuptools documentation page: 2025-09-08T12:32:51,410 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T12:32:51,410 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T12:32:51,410 even if it does not contain any `.py` files. 2025-09-08T12:32:51,410 On the other hand, currently there is no concept of package data 2025-09-08T12:32:51,410 directory, all directories are treated like packages. 2025-09-08T12:32:51,410 ******************************************************************************** 2025-09-08T12:32:51,410 !! 2025-09-08T12:32:51,410 check.warn(importable) 2025-09-08T12:32:51,411 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.modelling.reference_ampals' is absent from the `packages` configuration. 2025-09-08T12:32:51,411 !! 2025-09-08T12:32:51,411 ******************************************************************************** 2025-09-08T12:32:51,411 ############################ 2025-09-08T12:32:51,411 # Package would be ignored # 2025-09-08T12:32:51,411 ############################ 2025-09-08T12:32:51,411 Python recognizes 'isambard.modelling.reference_ampals' as an importable package[^1], 2025-09-08T12:32:51,411 but it is absent from setuptools' `packages` configuration. 2025-09-08T12:32:51,411 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T12:32:51,412 package, please make sure that 'isambard.modelling.reference_ampals' is explicitly added 2025-09-08T12:32:51,412 to the `packages` configuration field. 2025-09-08T12:32:51,412 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T12:32:51,412 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T12:32:51,412 instead of `find_packages(...)`/`find:`). 2025-09-08T12:32:51,412 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T12:32:51,412 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T12:32:51,412 If you don't want 'isambard.modelling.reference_ampals' to be distributed and are 2025-09-08T12:32:51,413 already explicitly excluding 'isambard.modelling.reference_ampals' via 2025-09-08T12:32:51,413 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T12:32:51,413 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T12:32:51,413 combination with a more fine grained `package-data` configuration. 2025-09-08T12:32:51,413 You can read more about "package data files" on setuptools documentation page: 2025-09-08T12:32:51,413 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T12:32:51,413 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T12:32:51,414 even if it does not contain any `.py` files. 2025-09-08T12:32:51,414 On the other hand, currently there is no concept of package data 2025-09-08T12:32:51,414 directory, all directories are treated like packages. 2025-09-08T12:32:51,414 ******************************************************************************** 2025-09-08T12:32:51,414 !! 2025-09-08T12:32:51,414 check.warn(importable) 2025-09-08T12:32:51,414 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.modelling.reference_ampals.non_canonical_amino_acids' is absent from the `packages` configuration. 2025-09-08T12:32:51,414 !! 2025-09-08T12:32:51,414 ******************************************************************************** 2025-09-08T12:32:51,414 ############################ 2025-09-08T12:32:51,415 # Package would be ignored # 2025-09-08T12:32:51,415 ############################ 2025-09-08T12:32:51,415 Python recognizes 'isambard.modelling.reference_ampals.non_canonical_amino_acids' as an importable package[^1], 2025-09-08T12:32:51,415 but it is absent from setuptools' `packages` configuration. 2025-09-08T12:32:51,415 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T12:32:51,415 package, please make sure that 'isambard.modelling.reference_ampals.non_canonical_amino_acids' is explicitly added 2025-09-08T12:32:51,415 to the `packages` configuration field. 2025-09-08T12:32:51,415 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T12:32:51,415 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T12:32:51,416 instead of `find_packages(...)`/`find:`). 2025-09-08T12:32:51,416 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T12:32:51,416 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T12:32:51,416 If you don't want 'isambard.modelling.reference_ampals.non_canonical_amino_acids' to be distributed and are 2025-09-08T12:32:51,416 already explicitly excluding 'isambard.modelling.reference_ampals.non_canonical_amino_acids' via 2025-09-08T12:32:51,416 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T12:32:51,416 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T12:32:51,416 combination with a more fine grained `package-data` configuration. 2025-09-08T12:32:51,417 You can read more about "package data files" on setuptools documentation page: 2025-09-08T12:32:51,417 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T12:32:51,417 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T12:32:51,417 even if it does not contain any `.py` files. 2025-09-08T12:32:51,417 On the other hand, currently there is no concept of package data 2025-09-08T12:32:51,417 directory, all directories are treated like packages. 2025-09-08T12:32:51,417 ******************************************************************************** 2025-09-08T12:32:51,418 !! 2025-09-08T12:32:51,418 check.warn(importable) 2025-09-08T12:32:51,418 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.optimisation.__pycache__' is absent from the `packages` configuration. 2025-09-08T12:32:51,418 !! 2025-09-08T12:32:51,418 ******************************************************************************** 2025-09-08T12:32:51,418 ############################ 2025-09-08T12:32:51,418 # Package would be ignored # 2025-09-08T12:32:51,418 ############################ 2025-09-08T12:32:51,418 Python recognizes 'isambard.optimisation.__pycache__' as an importable package[^1], 2025-09-08T12:32:51,419 but it is absent from setuptools' `packages` configuration. 2025-09-08T12:32:51,419 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T12:32:51,419 package, please make sure that 'isambard.optimisation.__pycache__' is explicitly added 2025-09-08T12:32:51,419 to the `packages` configuration field. 2025-09-08T12:32:51,419 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T12:32:51,419 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T12:32:51,419 instead of `find_packages(...)`/`find:`). 2025-09-08T12:32:51,419 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T12:32:51,420 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T12:32:51,420 If you don't want 'isambard.optimisation.__pycache__' to be distributed and are 2025-09-08T12:32:51,420 already explicitly excluding 'isambard.optimisation.__pycache__' via 2025-09-08T12:32:51,420 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T12:32:51,420 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T12:32:51,420 combination with a more fine grained `package-data` configuration. 2025-09-08T12:32:51,420 You can read more about "package data files" on setuptools documentation page: 2025-09-08T12:32:51,421 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T12:32:51,421 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T12:32:51,421 even if it does not contain any `.py` files. 2025-09-08T12:32:51,421 On the other hand, currently there is no concept of package data 2025-09-08T12:32:51,421 directory, all directories are treated like packages. 2025-09-08T12:32:51,421 ******************************************************************************** 2025-09-08T12:32:51,421 !! 2025-09-08T12:32:51,421 check.warn(importable) 2025-09-08T12:32:51,422 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.specifications.__pycache__' is absent from the `packages` configuration. 2025-09-08T12:32:51,422 !! 2025-09-08T12:32:51,422 ******************************************************************************** 2025-09-08T12:32:51,422 ############################ 2025-09-08T12:32:51,422 # Package would be ignored # 2025-09-08T12:32:51,422 ############################ 2025-09-08T12:32:51,422 Python recognizes 'isambard.specifications.__pycache__' as an importable package[^1], 2025-09-08T12:32:51,422 but it is absent from setuptools' `packages` configuration. 2025-09-08T12:32:51,422 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T12:32:51,423 package, please make sure that 'isambard.specifications.__pycache__' is explicitly added 2025-09-08T12:32:51,423 to the `packages` configuration field. 2025-09-08T12:32:51,423 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T12:32:51,423 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T12:32:51,423 instead of `find_packages(...)`/`find:`). 2025-09-08T12:32:51,423 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T12:32:51,423 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T12:32:51,424 If you don't want 'isambard.specifications.__pycache__' to be distributed and are 2025-09-08T12:32:51,424 already explicitly excluding 'isambard.specifications.__pycache__' via 2025-09-08T12:32:51,424 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T12:32:51,424 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T12:32:51,424 combination with a more fine grained `package-data` configuration. 2025-09-08T12:32:51,424 You can read more about "package data files" on setuptools documentation page: 2025-09-08T12:32:51,424 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T12:32:51,424 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T12:32:51,425 even if it does not contain any `.py` files. 2025-09-08T12:32:51,425 On the other hand, currently there is no concept of package data 2025-09-08T12:32:51,425 directory, all directories are treated like packages. 2025-09-08T12:32:51,425 ******************************************************************************** 2025-09-08T12:32:51,425 !! 2025-09-08T12:32:51,425 check.warn(importable) 2025-09-08T12:32:51,425 creating build/lib.linux-armv7l-cpython-313/isambard/__pycache__ 2025-09-08T12:32:51,425 copying src/isambard/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/__pycache__ 2025-09-08T12:32:51,425 creating build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__ 2025-09-08T12:32:51,425 copying src/isambard/optimisation/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__ 2025-09-08T12:32:51,425 copying src/isambard/optimisation/__pycache__/base_evo_opt.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__ 2025-09-08T12:32:51,426 copying src/isambard/optimisation/__pycache__/evo_optimizers.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__ 2025-09-08T12:32:51,426 copying src/isambard/optimisation/__pycache__/mmc_optimizer.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__ 2025-09-08T12:32:51,426 creating build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__ 2025-09-08T12:32:51,426 copying src/isambard/modelling/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__ 2025-09-08T12:32:51,426 copying src/isambard/modelling/__pycache__/non_canonical.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__ 2025-09-08T12:32:51,426 copying src/isambard/modelling/__pycache__/scwrl.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__ 2025-09-08T12:32:51,426 creating build/lib.linux-armv7l-cpython-313/isambard/modelling/reference_ampals 2025-09-08T12:32:51,426 copying src/isambard/modelling/reference_ampals/README.md -> build/lib.linux-armv7l-cpython-313/isambard/modelling/reference_ampals 2025-09-08T12:32:51,426 creating build/lib.linux-armv7l-cpython-313/isambard/modelling/reference_ampals/non_canonical_amino_acids 2025-09-08T12:32:51,426 copying src/isambard/modelling/reference_ampals/non_canonical_amino_acids/hydroxyproline_ref_1bkv_0_6.pickle -> build/lib.linux-armv7l-cpython-313/isambard/modelling/reference_ampals/non_canonical_amino_acids 2025-09-08T12:32:51,426 copying src/isambard/specifications/ta_polypeptide.c -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T12:32:51,427 copying src/isambard/specifications/ta_polypeptide.cpython-36m-x86_64-linux-gnu.so -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T12:32:51,427 copying src/isambard/specifications/ta_polypeptide.pyx -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T12:32:51,427 creating build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__ 2025-09-08T12:32:51,427 copying src/isambard/specifications/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__ 2025-09-08T12:32:51,427 copying src/isambard/specifications/__pycache__/coiledcoil.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__ 2025-09-08T12:32:51,427 copying src/isambard/specifications/__pycache__/helix.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__ 2025-09-08T12:32:51,427 copying src/isambard/specifications/__pycache__/nucleic_acid_duplex.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__ 2025-09-08T12:32:51,427 copying src/isambard/specifications/__pycache__/nucleic_acid_strand.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__ 2025-09-08T12:32:51,427 copying src/isambard/specifications/__pycache__/solenoid.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__ 2025-09-08T12:32:51,427 creating build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__ 2025-09-08T12:32:51,427 copying src/isambard/evaluation/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__ 2025-09-08T12:32:51,428 copying src/isambard/evaluation/__pycache__/contact_order.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__ 2025-09-08T12:32:51,428 copying src/isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__ 2025-09-08T12:32:51,428 running build_ext 2025-09-08T12:32:51,434 building 'isambard.specifications.ta_polypeptide' extension 2025-09-08T12:32:51,435 creating build/temp.linux-armv7l-cpython-313/src/isambard/specifications 2025-09-08T12:32:51,435 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/python3.13 -c src/isambard/specifications/ta_polypeptide.c -o build/temp.linux-armv7l-cpython-313/src/isambard/specifications/ta_polypeptide.o 2025-09-08T12:33:08,739 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/src/isambard/specifications/ta_polypeptide.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/isambard/specifications/ta_polypeptide.cpython-313-arm-linux-gnueabihf.so 2025-09-08T12:33:08,941 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-08T12:33:08,941 !! 2025-09-08T12:33:08,942 ******************************************************************************** 2025-09-08T12:33:08,942 Please avoid running ``setup.py`` directly. 2025-09-08T12:33:08,942 Instead, use pypa/build, pypa/installer or other 2025-09-08T12:33:08,942 standards-based tools. 2025-09-08T12:33:08,942 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T12:33:08,942 or your builds will no longer be supported. 2025-09-08T12:33:08,942 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-08T12:33:08,943 ******************************************************************************** 2025-09-08T12:33:08,943 !! 2025-09-08T12:33:08,943 self.initialize_options() 2025-09-08T12:33:09,014 installing to build/bdist.linux-armv7l/wheel 2025-09-08T12:33:09,014 running install 2025-09-08T12:33:09,036 running install_lib 2025-09-08T12:33:09,109 creating build/bdist.linux-armv7l/wheel 2025-09-08T12:33:09,110 creating build/bdist.linux-armv7l/wheel/isambard 2025-09-08T12:33:09,110 creating build/bdist.linux-armv7l/wheel/isambard/__pycache__ 2025-09-08T12:33:09,111 copying build/lib.linux-armv7l-cpython-313/isambard/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/__pycache__ 2025-09-08T12:33:09,111 creating build/bdist.linux-armv7l/wheel/isambard/evaluation 2025-09-08T12:33:09,111 creating build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__ 2025-09-08T12:33:09,112 copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/evaluation/__pycache__ 2025-09-08T12:33:09,112 copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__/contact_order.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/evaluation/__pycache__ 2025-09-08T12:33:09,113 copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/evaluation/__pycache__ 2025-09-08T12:33:09,113 copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__init__.py -> build/bdist.linux-armv7l/wheel/./isambard/evaluation 2025-09-08T12:33:09,113 copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/contact_order.py -> build/bdist.linux-armv7l/wheel/./isambard/evaluation 2025-09-08T12:33:09,114 copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/hydrophobic_fitness.py -> build/bdist.linux-armv7l/wheel/./isambard/evaluation 2025-09-08T12:33:09,114 creating build/bdist.linux-armv7l/wheel/isambard/specifications 2025-09-08T12:33:09,115 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/ta_polypeptide.cpython-313-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T12:33:09,118 creating build/bdist.linux-armv7l/wheel/isambard/specifications/__pycache__ 2025-09-08T12:33:09,118 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__/solenoid.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/specifications/__pycache__ 2025-09-08T12:33:09,119 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__/nucleic_acid_strand.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/specifications/__pycache__ 2025-09-08T12:33:09,119 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__/nucleic_acid_duplex.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/specifications/__pycache__ 2025-09-08T12:33:09,119 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__/helix.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/specifications/__pycache__ 2025-09-08T12:33:09,120 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__/coiledcoil.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/specifications/__pycache__ 2025-09-08T12:33:09,120 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/specifications/__pycache__ 2025-09-08T12:33:09,121 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/ta_polypeptide.pyx -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T12:33:09,121 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/ta_polypeptide.cpython-36m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T12:33:09,124 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/ta_polypeptide.c -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T12:33:09,127 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/solenoid.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T12:33:09,127 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/__init__.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T12:33:09,127 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/nucleic_acid_strand.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T12:33:09,128 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/nucleic_acid_duplex.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T12:33:09,128 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/helix.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T12:33:09,129 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/coiledcoil.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T12:33:09,129 creating build/bdist.linux-armv7l/wheel/isambard/modelling 2025-09-08T12:33:09,130 creating build/bdist.linux-armv7l/wheel/isambard/modelling/reference_ampals 2025-09-08T12:33:09,130 creating build/bdist.linux-armv7l/wheel/isambard/modelling/reference_ampals/non_canonical_amino_acids 2025-09-08T12:33:09,130 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/reference_ampals/non_canonical_amino_acids/hydroxyproline_ref_1bkv_0_6.pickle -> build/bdist.linux-armv7l/wheel/./isambard/modelling/reference_ampals/non_canonical_amino_acids 2025-09-08T12:33:09,131 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/reference_ampals/README.md -> build/bdist.linux-armv7l/wheel/./isambard/modelling/reference_ampals 2025-09-08T12:33:09,131 creating build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__ 2025-09-08T12:33:09,132 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/scwrl.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__ 2025-09-08T12:33:09,132 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/non_canonical.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__ 2025-09-08T12:33:09,132 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__ 2025-09-08T12:33:09,133 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__init__.py -> build/bdist.linux-armv7l/wheel/./isambard/modelling 2025-09-08T12:33:09,133 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/scwrl.py -> build/bdist.linux-armv7l/wheel/./isambard/modelling 2025-09-08T12:33:09,133 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/non_canonical.py -> build/bdist.linux-armv7l/wheel/./isambard/modelling 2025-09-08T12:33:09,134 creating build/bdist.linux-armv7l/wheel/isambard/optimisation 2025-09-08T12:33:09,134 creating build/bdist.linux-armv7l/wheel/isambard/optimisation/__pycache__ 2025-09-08T12:33:09,135 copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__/mmc_optimizer.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/optimisation/__pycache__ 2025-09-08T12:33:09,135 copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__/evo_optimizers.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/optimisation/__pycache__ 2025-09-08T12:33:09,136 copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__/base_evo_opt.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/optimisation/__pycache__ 2025-09-08T12:33:09,136 copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/optimisation/__pycache__ 2025-09-08T12:33:09,136 copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/evo_optimizers.py -> build/bdist.linux-armv7l/wheel/./isambard/optimisation 2025-09-08T12:33:09,137 copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/__init__.py -> build/bdist.linux-armv7l/wheel/./isambard/optimisation 2025-09-08T12:33:09,137 copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/mmc_optimizer.py -> build/bdist.linux-armv7l/wheel/./isambard/optimisation 2025-09-08T12:33:09,137 copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/base_evo_opt.py -> build/bdist.linux-armv7l/wheel/./isambard/optimisation 2025-09-08T12:33:09,138 copying build/lib.linux-armv7l-cpython-313/isambard/__init__.py -> build/bdist.linux-armv7l/wheel/./isambard 2025-09-08T12:33:09,138 running install_egg_info 2025-09-08T12:33:09,213 Copying src/ISAMBARD.egg-info to build/bdist.linux-armv7l/wheel/./ISAMBARD-2.0.1-py3.13.egg-info 2025-09-08T12:33:09,215 running install_scripts 2025-09-08T12:33:09,264 creating build/bdist.linux-armv7l/wheel/isambard-2.0.1.dist-info/WHEEL 2025-09-08T12:33:09,265 creating '/tmp/pip-wheel-akew_c6x/isambard-2.0.1-cp313-cp313-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-09-08T12:33:09,266 adding 'isambard/__init__.py' 2025-09-08T12:33:09,267 adding 'isambard/__pycache__/__init__.cpython-36.pyc' 2025-09-08T12:33:09,268 adding 'isambard/evaluation/__init__.py' 2025-09-08T12:33:09,268 adding 'isambard/evaluation/contact_order.py' 2025-09-08T12:33:09,270 adding 'isambard/evaluation/hydrophobic_fitness.py' 2025-09-08T12:33:09,270 adding 'isambard/evaluation/__pycache__/__init__.cpython-36.pyc' 2025-09-08T12:33:09,271 adding 'isambard/evaluation/__pycache__/contact_order.cpython-36.pyc' 2025-09-08T12:33:09,272 adding 'isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-36.pyc' 2025-09-08T12:33:09,273 adding 'isambard/modelling/__init__.py' 2025-09-08T12:33:09,273 adding 'isambard/modelling/non_canonical.py' 2025-09-08T12:33:09,274 adding 'isambard/modelling/scwrl.py' 2025-09-08T12:33:09,275 adding 'isambard/modelling/__pycache__/__init__.cpython-36.pyc' 2025-09-08T12:33:09,276 adding 'isambard/modelling/__pycache__/non_canonical.cpython-36.pyc' 2025-09-08T12:33:09,277 adding 'isambard/modelling/__pycache__/scwrl.cpython-36.pyc' 2025-09-08T12:33:09,278 adding 'isambard/modelling/reference_ampals/README.md' 2025-09-08T12:33:09,279 adding 'isambard/modelling/reference_ampals/non_canonical_amino_acids/hydroxyproline_ref_1bkv_0_6.pickle' 2025-09-08T12:33:09,279 adding 'isambard/optimisation/__init__.py' 2025-09-08T12:33:09,281 adding 'isambard/optimisation/base_evo_opt.py' 2025-09-08T12:33:09,283 adding 'isambard/optimisation/evo_optimizers.py' 2025-09-08T12:33:09,285 adding 'isambard/optimisation/mmc_optimizer.py' 2025-09-08T12:33:09,286 adding 'isambard/optimisation/__pycache__/__init__.cpython-36.pyc' 2025-09-08T12:33:09,288 adding 'isambard/optimisation/__pycache__/base_evo_opt.cpython-36.pyc' 2025-09-08T12:33:09,290 adding 'isambard/optimisation/__pycache__/evo_optimizers.cpython-36.pyc' 2025-09-08T12:33:09,292 adding 'isambard/optimisation/__pycache__/mmc_optimizer.cpython-36.pyc' 2025-09-08T12:33:09,293 adding 'isambard/specifications/__init__.py' 2025-09-08T12:33:09,294 adding 'isambard/specifications/coiledcoil.py' 2025-09-08T12:33:09,296 adding 'isambard/specifications/helix.py' 2025-09-08T12:33:09,297 adding 'isambard/specifications/nucleic_acid_duplex.py' 2025-09-08T12:33:09,298 adding 'isambard/specifications/nucleic_acid_strand.py' 2025-09-08T12:33:09,299 adding 'isambard/specifications/solenoid.py' 2025-09-08T12:33:09,351 adding 'isambard/specifications/ta_polypeptide.c' 2025-09-08T12:33:09,517 adding 'isambard/specifications/ta_polypeptide.cpython-313-arm-linux-gnueabihf.so' 2025-09-08T12:33:09,624 adding 'isambard/specifications/ta_polypeptide.cpython-36m-x86_64-linux-gnu.so' 2025-09-08T12:33:09,629 adding 'isambard/specifications/ta_polypeptide.pyx' 2025-09-08T12:33:09,630 adding 'isambard/specifications/__pycache__/__init__.cpython-36.pyc' 2025-09-08T12:33:09,632 adding 'isambard/specifications/__pycache__/coiledcoil.cpython-36.pyc' 2025-09-08T12:33:09,634 adding 'isambard/specifications/__pycache__/helix.cpython-36.pyc' 2025-09-08T12:33:09,635 adding 'isambard/specifications/__pycache__/nucleic_acid_duplex.cpython-36.pyc' 2025-09-08T12:33:09,637 adding 'isambard/specifications/__pycache__/nucleic_acid_strand.cpython-36.pyc' 2025-09-08T12:33:09,638 adding 'isambard/specifications/__pycache__/solenoid.cpython-36.pyc' 2025-09-08T12:33:09,639 adding 'isambard-2.0.1.dist-info/licenses/LICENSE.txt' 2025-09-08T12:33:09,640 adding 'isambard-2.0.1.dist-info/METADATA' 2025-09-08T12:33:09,640 adding 'isambard-2.0.1.dist-info/WHEEL' 2025-09-08T12:33:09,640 adding 'isambard-2.0.1.dist-info/top_level.txt' 2025-09-08T12:33:09,642 adding 'isambard-2.0.1.dist-info/RECORD' 2025-09-08T12:33:09,642 removing build/bdist.linux-armv7l/wheel 2025-09-08T12:33:09,796 Building wheel for isambard (setup.py): finished with status 'done' 2025-09-08T12:33:09,804 Created wheel for isambard: filename=isambard-2.0.1-cp313-cp313-linux_armv7l.whl size=710527 sha256=85cf289db8dc2a9066339a812cbb82449045a0dd42e40546348aa8ebb9cf841a 2025-09-08T12:33:09,805 Stored in directory: /tmp/pip-ephem-wheel-cache-ml1_emy6/wheels/75/ba/c3/7f3d1fdcb280e9a79ba5515898ec148f7e755ac8d6c42473a0 2025-09-08T12:33:09,816 Successfully built isambard 2025-09-08T12:33:09,819 Removed build tracker: '/tmp/pip-build-tracker-8kab71wy'