2025-09-09T11:07:50,263 Created temporary directory: /tmp/pip-build-tracker-saglxgrv
2025-09-09T11:07:50,263 Initialized build tracking at /tmp/pip-build-tracker-saglxgrv
2025-09-09T11:07:50,263 Created build tracker: /tmp/pip-build-tracker-saglxgrv
2025-09-09T11:07:50,264 Entered build tracker: /tmp/pip-build-tracker-saglxgrv
2025-09-09T11:07:50,264 Created temporary directory: /tmp/pip-wheel-6f0se5kt
2025-09-09T11:07:50,267 Created temporary directory: /tmp/pip-ephem-wheel-cache-z6sncb2m
2025-09-09T11:07:50,327 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-09-09T11:07:50,329 2 location(s) to search for versions of isambard:
2025-09-09T11:07:50,329 * https://pypi.org/simple/isambard/
2025-09-09T11:07:50,329 * https://www.piwheels.org/simple/isambard/
2025-09-09T11:07:50,330 Fetching project page and analyzing links: https://pypi.org/simple/isambard/
2025-09-09T11:07:50,330 Getting page https://pypi.org/simple/isambard/
2025-09-09T11:07:50,331 Found index url https://pypi.org/simple/
2025-09-09T11:07:50,400 Fetched page https://pypi.org/simple/isambard/ as application/vnd.pypi.simple.v1+json
2025-09-09T11:07:50,401   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
2025-09-09T11:07:50,402   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
2025-09-09T11:07:50,402   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
2025-09-09T11:07:50,402 Fetching project page and analyzing links: https://www.piwheels.org/simple/isambard/
2025-09-09T11:07:50,402 Getting page https://www.piwheels.org/simple/isambard/
2025-09-09T11:07:50,403 Found index url https://www.piwheels.org/simple/
2025-09-09T11:07:50,627 Fetched page https://www.piwheels.org/simple/isambard/ as text/html
2025-09-09T11:07:50,641   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/)
2025-09-09T11:07:50,641   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/)
2025-09-09T11:07:50,641   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/)
2025-09-09T11:07:50,642   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/)
2025-09-09T11:07:50,642   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/)
2025-09-09T11:07:50,642   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/)
2025-09-09T11:07:50,642   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/)
2025-09-09T11:07:50,643   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/)
2025-09-09T11:07:50,643   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/)
2025-09-09T11:07:50,643   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/)
2025-09-09T11:07:50,643   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/)
2025-09-09T11:07:50,644   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/)
2025-09-09T11:07:50,644   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/)
2025-09-09T11:07:50,644   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/)
2025-09-09T11:07:50,644   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/)
2025-09-09T11:07:50,645   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/)
2025-09-09T11:07:50,645   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/)
2025-09-09T11:07:50,645   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/)
2025-09-09T11:07:50,645   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/isambard-2.2.0-cp313-cp313-linux_armv6l.whl#sha256=81833d4099d139da2f97b313c21b37564ff293048dbdb32201fd676194ea1631 (from https://www.piwheels.org/simple/isambard/)
2025-09-09T11:07:50,646   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/isambard-2.2.0-cp313-cp313-linux_armv7l.whl#sha256=81833d4099d139da2f97b313c21b37564ff293048dbdb32201fd676194ea1631 (from https://www.piwheels.org/simple/isambard/)
2025-09-09T11:07:50,646   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/)
2025-09-09T11:07:50,646   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/)
2025-09-09T11:07:50,647   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/)
2025-09-09T11:07:50,647   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/)
2025-09-09T11:07:50,647   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/)
2025-09-09T11:07:50,647   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/)
2025-09-09T11:07:50,648   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/)
2025-09-09T11:07:50,648   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/)
2025-09-09T11:07:50,648   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/)
2025-09-09T11:07:50,648   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/)
2025-09-09T11:07:50,649   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/isambard-2.0.1-cp313-cp313-linux_armv6l.whl#sha256=85cf289db8dc2a9066339a812cbb82449045a0dd42e40546348aa8ebb9cf841a (from https://www.piwheels.org/simple/isambard/)
2025-09-09T11:07:50,649   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/isambard-2.0.1-cp313-cp313-linux_armv7l.whl#sha256=85cf289db8dc2a9066339a812cbb82449045a0dd42e40546348aa8ebb9cf841a (from https://www.piwheels.org/simple/isambard/)
2025-09-09T11:07:50,649 Skipping link: not a file: https://www.piwheels.org/simple/isambard/
2025-09-09T11:07:50,649 Skipping link: not a file: https://pypi.org/simple/isambard/
2025-09-09T11:07:50,673 Given no hashes to check 1 links for project 'isambard': discarding no candidates
2025-09-09T11:07:50,674 Collecting isambard==2.3.1
2025-09-09T11:07:50,675   Created temporary directory: /tmp/pip-unpack-286qw62y
2025-09-09T11:07:50,814   Downloading ISAMBARD-2.3.1.tar.gz (370 kB)
2025-09-09T11:07:50,926   Added isambard==2.3.1 from https://files.pythonhosted.org/packages/6d/5d/36e0369e6e7bdb1061074aff44dab96caf1e1809a289f41156a0a34bce49/ISAMBARD-2.3.1.tar.gz to build tracker '/tmp/pip-build-tracker-saglxgrv'
2025-09-09T11:07:50,927   Running setup.py (path:/tmp/pip-wheel-6f0se5kt/isambard_9b59f2635fd342ac878f0ea9c800a754/setup.py) egg_info for package isambard
2025-09-09T11:07:50,928   Created temporary directory: /tmp/pip-pip-egg-info-9xdcjopz
2025-09-09T11:07:50,928   Preparing metadata (setup.py): started
2025-09-09T11:07:50,929   Running command python setup.py egg_info
2025-09-09T11:07:53,318   Compiling src/isambard/specifications/ta_polypeptide.pyx because it changed.
2025-09-09T11:07:53,318   [1/1] Cythonizing src/isambard/specifications/ta_polypeptide.pyx
2025-09-09T11:07:53,703   /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-09-09T11:07:53,703   !!

2025-09-09T11:07:53,703           ********************************************************************************
2025-09-09T11:07:53,703           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-09-09T11:07:53,703           License :: OSI Approved :: MIT License

2025-09-09T11:07:53,703           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-09-09T11:07:53,703           ********************************************************************************

2025-09-09T11:07:53,704   !!
2025-09-09T11:07:53,704     self._finalize_license_expression()
2025-09-09T11:07:53,777   running egg_info
2025-09-09T11:07:53,851   creating /tmp/pip-pip-egg-info-9xdcjopz/ISAMBARD.egg-info
2025-09-09T11:07:53,851   writing /tmp/pip-pip-egg-info-9xdcjopz/ISAMBARD.egg-info/PKG-INFO
2025-09-09T11:07:53,852   writing dependency_links to /tmp/pip-pip-egg-info-9xdcjopz/ISAMBARD.egg-info/dependency_links.txt
2025-09-09T11:07:53,853   writing requirements to /tmp/pip-pip-egg-info-9xdcjopz/ISAMBARD.egg-info/requires.txt
2025-09-09T11:07:53,853   writing top-level names to /tmp/pip-pip-egg-info-9xdcjopz/ISAMBARD.egg-info/top_level.txt
2025-09-09T11:07:53,854   writing manifest file '/tmp/pip-pip-egg-info-9xdcjopz/ISAMBARD.egg-info/SOURCES.txt'
2025-09-09T11:07:54,149   reading manifest file '/tmp/pip-pip-egg-info-9xdcjopz/ISAMBARD.egg-info/SOURCES.txt'
2025-09-09T11:07:54,149   reading manifest template 'MANIFEST.in'
2025-09-09T11:07:54,154   adding license file 'LICENSE.txt'
2025-09-09T11:07:54,157   writing manifest file '/tmp/pip-pip-egg-info-9xdcjopz/ISAMBARD.egg-info/SOURCES.txt'
2025-09-09T11:07:54,426   Preparing metadata (setup.py): finished with status 'done'
2025-09-09T11:07:54,431   Source in /tmp/pip-wheel-6f0se5kt/isambard_9b59f2635fd342ac878f0ea9c800a754 has version 2.3.1, which satisfies requirement isambard==2.3.1 from https://files.pythonhosted.org/packages/6d/5d/36e0369e6e7bdb1061074aff44dab96caf1e1809a289f41156a0a34bce49/ISAMBARD-2.3.1.tar.gz
2025-09-09T11:07:54,432   Removed isambard==2.3.1 from https://files.pythonhosted.org/packages/6d/5d/36e0369e6e7bdb1061074aff44dab96caf1e1809a289f41156a0a34bce49/ISAMBARD-2.3.1.tar.gz from build tracker '/tmp/pip-build-tracker-saglxgrv'
2025-09-09T11:07:54,436 Created temporary directory: /tmp/pip-unpack-kqapgd9h
2025-09-09T11:07:54,436 Created temporary directory: /tmp/pip-unpack-w95iii9x
2025-09-09T11:07:54,436 Building wheels for collected packages: isambard
2025-09-09T11:07:54,438   Created temporary directory: /tmp/pip-wheel-7bhn_0nh
2025-09-09T11:07:54,438   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
2025-09-09T11:07:54,440   Building wheel for isambard (setup.py): started
2025-09-09T11:07:54,441   Destination directory: /tmp/pip-wheel-7bhn_0nh
2025-09-09T11:07:54,441   Running command python setup.py bdist_wheel
2025-09-09T11:07:55,885   /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-09-09T11:07:55,885   !!

2025-09-09T11:07:55,886           ********************************************************************************
2025-09-09T11:07:55,886           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-09-09T11:07:55,886           License :: OSI Approved :: MIT License

2025-09-09T11:07:55,886           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-09-09T11:07:55,886           ********************************************************************************

2025-09-09T11:07:55,886   !!
2025-09-09T11:07:55,887     self._finalize_license_expression()
2025-09-09T11:07:55,887   running bdist_wheel
2025-09-09T11:07:56,272   running build
2025-09-09T11:07:56,272   running build_py
2025-09-09T11:07:56,348   creating build/lib.linux-armv7l-cpython-313/isambard
2025-09-09T11:07:56,349   copying src/isambard/__init__.py -> build/lib.linux-armv7l-cpython-313/isambard
2025-09-09T11:07:56,350   creating build/lib.linux-armv7l-cpython-313/isambard/specifications
2025-09-09T11:07:56,350   copying src/isambard/specifications/solenoid.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications
2025-09-09T11:07:56,351   copying src/isambard/specifications/nucleic_acid_strand.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications
2025-09-09T11:07:56,351   copying src/isambard/specifications/nucleic_acid_duplex.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications
2025-09-09T11:07:56,352   copying src/isambard/specifications/helix.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications
2025-09-09T11:07:56,352   copying src/isambard/specifications/coiledcoil.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications
2025-09-09T11:07:56,353   copying src/isambard/specifications/__init__.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications
2025-09-09T11:07:56,354   creating build/lib.linux-armv7l-cpython-313/isambard/optimisation
2025-09-09T11:07:56,354   copying src/isambard/optimisation/mmc_optimizer.py -> build/lib.linux-armv7l-cpython-313/isambard/optimisation
2025-09-09T11:07:56,355   copying src/isambard/optimisation/evo_optimizers.py -> build/lib.linux-armv7l-cpython-313/isambard/optimisation
2025-09-09T11:07:56,355   copying src/isambard/optimisation/base_evo_opt.py -> build/lib.linux-armv7l-cpython-313/isambard/optimisation
2025-09-09T11:07:56,356   copying src/isambard/optimisation/__init__.py -> build/lib.linux-armv7l-cpython-313/isambard/optimisation
2025-09-09T11:07:56,356   creating build/lib.linux-armv7l-cpython-313/isambard/modelling
2025-09-09T11:07:56,357   copying src/isambard/modelling/scwrl.py -> build/lib.linux-armv7l-cpython-313/isambard/modelling
2025-09-09T11:07:56,357   copying src/isambard/modelling/non_canonical.py -> build/lib.linux-armv7l-cpython-313/isambard/modelling
2025-09-09T11:07:56,358   copying src/isambard/modelling/__init__.py -> build/lib.linux-armv7l-cpython-313/isambard/modelling
2025-09-09T11:07:56,359   creating build/lib.linux-armv7l-cpython-313/isambard/evaluation
2025-09-09T11:07:56,359   copying src/isambard/evaluation/packing_density.py -> build/lib.linux-armv7l-cpython-313/isambard/evaluation
2025-09-09T11:07:56,360   copying src/isambard/evaluation/pacc.py -> build/lib.linux-armv7l-cpython-313/isambard/evaluation
2025-09-09T11:07:56,360   copying src/isambard/evaluation/hydrophobic_fitness.py -> build/lib.linux-armv7l-cpython-313/isambard/evaluation
2025-09-09T11:07:56,361   copying src/isambard/evaluation/dssp.py -> build/lib.linux-armv7l-cpython-313/isambard/evaluation
2025-09-09T11:07:56,361   copying src/isambard/evaluation/contact_order.py -> build/lib.linux-armv7l-cpython-313/isambard/evaluation
2025-09-09T11:07:56,362   copying src/isambard/evaluation/__init__.py -> build/lib.linux-armv7l-cpython-313/isambard/evaluation
2025-09-09T11:07:56,362   running egg_info
2025-09-09T11:07:56,437   writing src/ISAMBARD.egg-info/PKG-INFO
2025-09-09T11:07:56,439   writing dependency_links to src/ISAMBARD.egg-info/dependency_links.txt
2025-09-09T11:07:56,439   writing requirements to src/ISAMBARD.egg-info/requires.txt
2025-09-09T11:07:56,440   writing top-level names to src/ISAMBARD.egg-info/top_level.txt
2025-09-09T11:07:56,518   reading manifest file 'src/ISAMBARD.egg-info/SOURCES.txt'
2025-09-09T11:07:56,521   reading manifest template 'MANIFEST.in'
2025-09-09T11:07:56,526   adding license file 'LICENSE.txt'
2025-09-09T11:07:56,530   writing manifest file 'src/ISAMBARD.egg-info/SOURCES.txt'
2025-09-09T11:07:56,531   /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.__pycache__' is absent from the `packages` configuration.
2025-09-09T11:07:56,532   !!

2025-09-09T11:07:56,532           ********************************************************************************
2025-09-09T11:07:56,532           ############################
2025-09-09T11:07:56,532           # Package would be ignored #
2025-09-09T11:07:56,532           ############################
2025-09-09T11:07:56,532           Python recognizes 'isambard.__pycache__' as an importable package[^1],
2025-09-09T11:07:56,532           but it is absent from setuptools' `packages` configuration.

2025-09-09T11:07:56,532           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-09T11:07:56,532           package, please make sure that 'isambard.__pycache__' is explicitly added
2025-09-09T11:07:56,532           to the `packages` configuration field.

2025-09-09T11:07:56,533           Alternatively, you can also rely on setuptools' discovery methods
2025-09-09T11:07:56,533           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-09T11:07:56,533           instead of `find_packages(...)`/`find:`).

2025-09-09T11:07:56,533           You can read more about "package discovery" on setuptools documentation page:

2025-09-09T11:07:56,533           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-09T11:07:56,533           If you don't want 'isambard.__pycache__' to be distributed and are
2025-09-09T11:07:56,533           already explicitly excluding 'isambard.__pycache__' via
2025-09-09T11:07:56,534           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-09T11:07:56,534           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-09T11:07:56,534           combination with a more fine grained `package-data` configuration.

2025-09-09T11:07:56,534           You can read more about "package data files" on setuptools documentation page:

2025-09-09T11:07:56,534           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-09T11:07:56,534           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-09T11:07:56,534                 even if it does not contain any `.py` files.
2025-09-09T11:07:56,534                 On the other hand, currently there is no concept of package data
2025-09-09T11:07:56,535                 directory, all directories are treated like packages.
2025-09-09T11:07:56,535           ********************************************************************************

2025-09-09T11:07:56,535   !!
2025-09-09T11:07:56,535     check.warn(importable)
2025-09-09T11:07:56,535   /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.evaluation.__pycache__' is absent from the `packages` configuration.
2025-09-09T11:07:56,535   !!

2025-09-09T11:07:56,535           ********************************************************************************
2025-09-09T11:07:56,535           ############################
2025-09-09T11:07:56,536           # Package would be ignored #
2025-09-09T11:07:56,536           ############################
2025-09-09T11:07:56,536           Python recognizes 'isambard.evaluation.__pycache__' as an importable package[^1],
2025-09-09T11:07:56,536           but it is absent from setuptools' `packages` configuration.

2025-09-09T11:07:56,536           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-09T11:07:56,536           package, please make sure that 'isambard.evaluation.__pycache__' is explicitly added
2025-09-09T11:07:56,536           to the `packages` configuration field.

2025-09-09T11:07:56,536           Alternatively, you can also rely on setuptools' discovery methods
2025-09-09T11:07:56,536           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-09T11:07:56,537           instead of `find_packages(...)`/`find:`).

2025-09-09T11:07:56,537           You can read more about "package discovery" on setuptools documentation page:

2025-09-09T11:07:56,537           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-09T11:07:56,537           If you don't want 'isambard.evaluation.__pycache__' to be distributed and are
2025-09-09T11:07:56,537           already explicitly excluding 'isambard.evaluation.__pycache__' via
2025-09-09T11:07:56,537           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-09T11:07:56,537           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-09T11:07:56,537           combination with a more fine grained `package-data` configuration.

2025-09-09T11:07:56,538           You can read more about "package data files" on setuptools documentation page:

2025-09-09T11:07:56,538           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-09T11:07:56,538           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-09T11:07:56,538                 even if it does not contain any `.py` files.
2025-09-09T11:07:56,538                 On the other hand, currently there is no concept of package data
2025-09-09T11:07:56,538                 directory, all directories are treated like packages.
2025-09-09T11:07:56,538           ********************************************************************************

2025-09-09T11:07:56,539   !!
2025-09-09T11:07:56,539     check.warn(importable)
2025-09-09T11:07:56,539   /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.modelling.__pycache__' is absent from the `packages` configuration.
2025-09-09T11:07:56,539   !!

2025-09-09T11:07:56,539           ********************************************************************************
2025-09-09T11:07:56,539           ############################
2025-09-09T11:07:56,539           # Package would be ignored #
2025-09-09T11:07:56,539           ############################
2025-09-09T11:07:56,539           Python recognizes 'isambard.modelling.__pycache__' as an importable package[^1],
2025-09-09T11:07:56,539           but it is absent from setuptools' `packages` configuration.

2025-09-09T11:07:56,540           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-09T11:07:56,540           package, please make sure that 'isambard.modelling.__pycache__' is explicitly added
2025-09-09T11:07:56,540           to the `packages` configuration field.

2025-09-09T11:07:56,540           Alternatively, you can also rely on setuptools' discovery methods
2025-09-09T11:07:56,540           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-09T11:07:56,540           instead of `find_packages(...)`/`find:`).

2025-09-09T11:07:56,540           You can read more about "package discovery" on setuptools documentation page:

2025-09-09T11:07:56,541           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-09T11:07:56,541           If you don't want 'isambard.modelling.__pycache__' to be distributed and are
2025-09-09T11:07:56,541           already explicitly excluding 'isambard.modelling.__pycache__' via
2025-09-09T11:07:56,541           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-09T11:07:56,541           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-09T11:07:56,541           combination with a more fine grained `package-data` configuration.

2025-09-09T11:07:56,541           You can read more about "package data files" on setuptools documentation page:

2025-09-09T11:07:56,541           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-09T11:07:56,542           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-09T11:07:56,542                 even if it does not contain any `.py` files.
2025-09-09T11:07:56,542                 On the other hand, currently there is no concept of package data
2025-09-09T11:07:56,542                 directory, all directories are treated like packages.
2025-09-09T11:07:56,542           ********************************************************************************

2025-09-09T11:07:56,542   !!
2025-09-09T11:07:56,542     check.warn(importable)
2025-09-09T11:07:56,542   /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.
2025-09-09T11:07:56,542   !!

2025-09-09T11:07:56,543           ********************************************************************************
2025-09-09T11:07:56,543           ############################
2025-09-09T11:07:56,543           # Package would be ignored #
2025-09-09T11:07:56,543           ############################
2025-09-09T11:07:56,543           Python recognizes 'isambard.modelling.reference_ampals' as an importable package[^1],
2025-09-09T11:07:56,543           but it is absent from setuptools' `packages` configuration.

2025-09-09T11:07:56,543           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-09T11:07:56,543           package, please make sure that 'isambard.modelling.reference_ampals' is explicitly added
2025-09-09T11:07:56,543           to the `packages` configuration field.

2025-09-09T11:07:56,544           Alternatively, you can also rely on setuptools' discovery methods
2025-09-09T11:07:56,544           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-09T11:07:56,544           instead of `find_packages(...)`/`find:`).

2025-09-09T11:07:56,544           You can read more about "package discovery" on setuptools documentation page:

2025-09-09T11:07:56,544           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-09T11:07:56,544           If you don't want 'isambard.modelling.reference_ampals' to be distributed and are
2025-09-09T11:07:56,544           already explicitly excluding 'isambard.modelling.reference_ampals' via
2025-09-09T11:07:56,545           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-09T11:07:56,545           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-09T11:07:56,545           combination with a more fine grained `package-data` configuration.

2025-09-09T11:07:56,545           You can read more about "package data files" on setuptools documentation page:

2025-09-09T11:07:56,545           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-09T11:07:56,545           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-09T11:07:56,545                 even if it does not contain any `.py` files.
2025-09-09T11:07:56,546                 On the other hand, currently there is no concept of package data
2025-09-09T11:07:56,546                 directory, all directories are treated like packages.
2025-09-09T11:07:56,546           ********************************************************************************

2025-09-09T11:07:56,546   !!
2025-09-09T11:07:56,546     check.warn(importable)
2025-09-09T11:07:56,546   /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.
2025-09-09T11:07:56,546   !!

2025-09-09T11:07:56,546           ********************************************************************************
2025-09-09T11:07:56,546           ############################
2025-09-09T11:07:56,547           # Package would be ignored #
2025-09-09T11:07:56,547           ############################
2025-09-09T11:07:56,547           Python recognizes 'isambard.modelling.reference_ampals.non_canonical_amino_acids' as an importable package[^1],
2025-09-09T11:07:56,547           but it is absent from setuptools' `packages` configuration.

2025-09-09T11:07:56,547           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-09T11:07:56,547           package, please make sure that 'isambard.modelling.reference_ampals.non_canonical_amino_acids' is explicitly added
2025-09-09T11:07:56,547           to the `packages` configuration field.

2025-09-09T11:07:56,547           Alternatively, you can also rely on setuptools' discovery methods
2025-09-09T11:07:56,547           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-09T11:07:56,548           instead of `find_packages(...)`/`find:`).

2025-09-09T11:07:56,548           You can read more about "package discovery" on setuptools documentation page:

2025-09-09T11:07:56,548           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-09T11:07:56,548           If you don't want 'isambard.modelling.reference_ampals.non_canonical_amino_acids' to be distributed and are
2025-09-09T11:07:56,548           already explicitly excluding 'isambard.modelling.reference_ampals.non_canonical_amino_acids' via
2025-09-09T11:07:56,548           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-09T11:07:56,548           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-09T11:07:56,548           combination with a more fine grained `package-data` configuration.

2025-09-09T11:07:56,549           You can read more about "package data files" on setuptools documentation page:

2025-09-09T11:07:56,549           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-09T11:07:56,549           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-09T11:07:56,549                 even if it does not contain any `.py` files.
2025-09-09T11:07:56,549                 On the other hand, currently there is no concept of package data
2025-09-09T11:07:56,549                 directory, all directories are treated like packages.
2025-09-09T11:07:56,549           ********************************************************************************

2025-09-09T11:07:56,550   !!
2025-09-09T11:07:56,550     check.warn(importable)
2025-09-09T11:07:56,550   creating build/lib.linux-armv7l-cpython-313/isambard/__pycache__
2025-09-09T11:07:56,550   copying src/isambard/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/isambard/__pycache__
2025-09-09T11:07:56,550   copying src/isambard/specifications/ta_polypeptide.c -> build/lib.linux-armv7l-cpython-313/isambard/specifications
2025-09-09T11:07:56,550   copying src/isambard/specifications/ta_polypeptide.cpython-37m-x86_64-linux-gnu.so -> build/lib.linux-armv7l-cpython-313/isambard/specifications
2025-09-09T11:07:56,550   copying src/isambard/specifications/ta_polypeptide.pyx -> build/lib.linux-armv7l-cpython-313/isambard/specifications
2025-09-09T11:07:56,550   creating build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__
2025-09-09T11:07:56,550   copying src/isambard/modelling/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__
2025-09-09T11:07:56,550   copying src/isambard/modelling/__pycache__/create_loop_database.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__
2025-09-09T11:07:56,551   copying src/isambard/modelling/__pycache__/extract_loop_data.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__
2025-09-09T11:07:56,551   copying src/isambard/modelling/__pycache__/non_canonical.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__
2025-09-09T11:07:56,551   copying src/isambard/modelling/__pycache__/scwrl.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__
2025-09-09T11:07:56,551   creating build/lib.linux-armv7l-cpython-313/isambard/modelling/reference_ampals
2025-09-09T11:07:56,551   copying src/isambard/modelling/reference_ampals/README.md -> build/lib.linux-armv7l-cpython-313/isambard/modelling/reference_ampals
2025-09-09T11:07:56,551   creating build/lib.linux-armv7l-cpython-313/isambard/modelling/reference_ampals/non_canonical_amino_acids
2025-09-09T11:07:56,551   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
2025-09-09T11:07:56,551   creating build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__
2025-09-09T11:07:56,551   copying src/isambard/evaluation/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__
2025-09-09T11:07:56,551   copying src/isambard/evaluation/__pycache__/contact_order.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__
2025-09-09T11:07:56,551   copying src/isambard/evaluation/__pycache__/dssp.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__
2025-09-09T11:07:56,552   copying src/isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__
2025-09-09T11:07:56,552   copying src/isambard/evaluation/__pycache__/pacc.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__
2025-09-09T11:07:56,552   copying src/isambard/evaluation/__pycache__/packing_density.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__
2025-09-09T11:07:56,554   running build_ext
2025-09-09T11:07:56,561   building 'isambard.specifications.ta_polypeptide' extension
2025-09-09T11:07:56,562   creating build/temp.linux-armv7l-cpython-313/src/isambard/specifications
2025-09-09T11:07:56,562   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
2025-09-09T11:08:13,858   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
2025-09-09T11:08:14,145   /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-09-09T11:08:14,145   !!

2025-09-09T11:08:14,146           ********************************************************************************
2025-09-09T11:08:14,146           Please avoid running ``setup.py`` directly.
2025-09-09T11:08:14,146           Instead, use pypa/build, pypa/installer or other
2025-09-09T11:08:14,146           standards-based tools.

2025-09-09T11:08:14,146           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-09-09T11:08:14,146           or your builds will no longer be supported.

2025-09-09T11:08:14,147           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-09-09T11:08:14,147           ********************************************************************************

2025-09-09T11:08:14,147   !!
2025-09-09T11:08:14,147     self.initialize_options()
2025-09-09T11:08:14,221   installing to build/bdist.linux-armv7l/wheel
2025-09-09T11:08:14,222   running install
2025-09-09T11:08:14,244   running install_lib
2025-09-09T11:08:14,317   creating build/bdist.linux-armv7l/wheel
2025-09-09T11:08:14,318   creating build/bdist.linux-armv7l/wheel/isambard
2025-09-09T11:08:14,318   creating build/bdist.linux-armv7l/wheel/isambard/__pycache__
2025-09-09T11:08:14,319   copying build/lib.linux-armv7l-cpython-313/isambard/__pycache__/__init__.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/./isambard/__pycache__
2025-09-09T11:08:14,319   creating build/bdist.linux-armv7l/wheel/isambard/evaluation
2025-09-09T11:08:14,319   creating build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__
2025-09-09T11:08:14,320   copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__/packing_density.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/./isambard/evaluation/__pycache__
2025-09-09T11:08:14,320   copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__/pacc.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/./isambard/evaluation/__pycache__
2025-09-09T11:08:14,321   copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/./isambard/evaluation/__pycache__
2025-09-09T11:08:14,321   copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__/dssp.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/./isambard/evaluation/__pycache__
2025-09-09T11:08:14,321   copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__/contact_order.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/./isambard/evaluation/__pycache__
2025-09-09T11:08:14,322   copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__/__init__.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/./isambard/evaluation/__pycache__
2025-09-09T11:08:14,322   copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__init__.py -> build/bdist.linux-armv7l/wheel/./isambard/evaluation
2025-09-09T11:08:14,322   copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/contact_order.py -> build/bdist.linux-armv7l/wheel/./isambard/evaluation
2025-09-09T11:08:14,323   copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/dssp.py -> build/bdist.linux-armv7l/wheel/./isambard/evaluation
2025-09-09T11:08:14,323   copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/hydrophobic_fitness.py -> build/bdist.linux-armv7l/wheel/./isambard/evaluation
2025-09-09T11:08:14,324   copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/pacc.py -> build/bdist.linux-armv7l/wheel/./isambard/evaluation
2025-09-09T11:08:14,324   copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/packing_density.py -> build/bdist.linux-armv7l/wheel/./isambard/evaluation
2025-09-09T11:08:14,325   creating build/bdist.linux-armv7l/wheel/isambard/modelling
2025-09-09T11:08:14,325   creating build/bdist.linux-armv7l/wheel/isambard/modelling/reference_ampals
2025-09-09T11:08:14,325   creating build/bdist.linux-armv7l/wheel/isambard/modelling/reference_ampals/non_canonical_amino_acids
2025-09-09T11:08:14,326   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
2025-09-09T11:08:14,326   copying build/lib.linux-armv7l-cpython-313/isambard/modelling/reference_ampals/README.md -> build/bdist.linux-armv7l/wheel/./isambard/modelling/reference_ampals
2025-09-09T11:08:14,327   creating build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2025-09-09T11:08:14,327   copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/scwrl.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__
2025-09-09T11:08:14,327   copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/non_canonical.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__
2025-09-09T11:08:14,328   copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/extract_loop_data.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__
2025-09-09T11:08:14,328   copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/create_loop_database.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__
2025-09-09T11:08:14,329   copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/__init__.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__
2025-09-09T11:08:14,329   copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__init__.py -> build/bdist.linux-armv7l/wheel/./isambard/modelling
2025-09-09T11:08:14,329   copying build/lib.linux-armv7l-cpython-313/isambard/modelling/non_canonical.py -> build/bdist.linux-armv7l/wheel/./isambard/modelling
2025-09-09T11:08:14,330   copying build/lib.linux-armv7l-cpython-313/isambard/modelling/scwrl.py -> build/bdist.linux-armv7l/wheel/./isambard/modelling
2025-09-09T11:08:14,330   creating build/bdist.linux-armv7l/wheel/isambard/optimisation
2025-09-09T11:08:14,330   copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/__init__.py -> build/bdist.linux-armv7l/wheel/./isambard/optimisation
2025-09-09T11:08:14,331   copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/base_evo_opt.py -> build/bdist.linux-armv7l/wheel/./isambard/optimisation
2025-09-09T11:08:14,331   copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/evo_optimizers.py -> build/bdist.linux-armv7l/wheel/./isambard/optimisation
2025-09-09T11:08:14,332   copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/mmc_optimizer.py -> build/bdist.linux-armv7l/wheel/./isambard/optimisation
2025-09-09T11:08:14,332   creating build/bdist.linux-armv7l/wheel/isambard/specifications
2025-09-09T11:08:14,333   copying build/lib.linux-armv7l-cpython-313/isambard/specifications/ta_polypeptide.cpython-313-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./isambard/specifications
2025-09-09T11:08:14,336   copying build/lib.linux-armv7l-cpython-313/isambard/specifications/ta_polypeptide.pyx -> build/bdist.linux-armv7l/wheel/./isambard/specifications
2025-09-09T11:08:14,336   copying build/lib.linux-armv7l-cpython-313/isambard/specifications/ta_polypeptide.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./isambard/specifications
2025-09-09T11:08:14,340   copying build/lib.linux-armv7l-cpython-313/isambard/specifications/ta_polypeptide.c -> build/bdist.linux-armv7l/wheel/./isambard/specifications
2025-09-09T11:08:14,343   copying build/lib.linux-armv7l-cpython-313/isambard/specifications/__init__.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications
2025-09-09T11:08:14,343   copying build/lib.linux-armv7l-cpython-313/isambard/specifications/coiledcoil.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications
2025-09-09T11:08:14,343   copying build/lib.linux-armv7l-cpython-313/isambard/specifications/helix.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications
2025-09-09T11:08:14,344   copying build/lib.linux-armv7l-cpython-313/isambard/specifications/nucleic_acid_duplex.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications
2025-09-09T11:08:14,344   copying build/lib.linux-armv7l-cpython-313/isambard/specifications/nucleic_acid_strand.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications
2025-09-09T11:08:14,345   copying build/lib.linux-armv7l-cpython-313/isambard/specifications/solenoid.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications
2025-09-09T11:08:14,345   copying build/lib.linux-armv7l-cpython-313/isambard/__init__.py -> build/bdist.linux-armv7l/wheel/./isambard
2025-09-09T11:08:14,345   running install_egg_info
2025-09-09T11:08:14,424   Copying src/ISAMBARD.egg-info to build/bdist.linux-armv7l/wheel/./ISAMBARD-2.3.1-py3.13.egg-info
2025-09-09T11:08:14,426   running install_scripts
2025-09-09T11:08:14,476   creating build/bdist.linux-armv7l/wheel/isambard-2.3.1.dist-info/WHEEL
2025-09-09T11:08:14,477   creating '/tmp/pip-wheel-7bhn_0nh/isambard-2.3.1-cp313-cp313-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-09-09T11:08:14,478   adding 'isambard/__init__.py'
2025-09-09T11:08:14,479   adding 'isambard/__pycache__/__init__.cpython-37.pyc'
2025-09-09T11:08:14,479   adding 'isambard/evaluation/__init__.py'
2025-09-09T11:08:14,480   adding 'isambard/evaluation/contact_order.py'
2025-09-09T11:08:14,481   adding 'isambard/evaluation/dssp.py'
2025-09-09T11:08:14,482   adding 'isambard/evaluation/hydrophobic_fitness.py'
2025-09-09T11:08:14,483   adding 'isambard/evaluation/pacc.py'
2025-09-09T11:08:14,484   adding 'isambard/evaluation/packing_density.py'
2025-09-09T11:08:14,485   adding 'isambard/evaluation/__pycache__/__init__.cpython-37.pyc'
2025-09-09T11:08:14,486   adding 'isambard/evaluation/__pycache__/contact_order.cpython-37.pyc'
2025-09-09T11:08:14,487   adding 'isambard/evaluation/__pycache__/dssp.cpython-37.pyc'
2025-09-09T11:08:14,488   adding 'isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-37.pyc'
2025-09-09T11:08:14,489   adding 'isambard/evaluation/__pycache__/pacc.cpython-37.pyc'
2025-09-09T11:08:14,490   adding 'isambard/evaluation/__pycache__/packing_density.cpython-37.pyc'
2025-09-09T11:08:14,490   adding 'isambard/modelling/__init__.py'
2025-09-09T11:08:14,491   adding 'isambard/modelling/non_canonical.py'
2025-09-09T11:08:14,492   adding 'isambard/modelling/scwrl.py'
2025-09-09T11:08:14,493   adding 'isambard/modelling/__pycache__/__init__.cpython-37.pyc'
2025-09-09T11:08:14,494   adding 'isambard/modelling/__pycache__/create_loop_database.cpython-37.pyc'
2025-09-09T11:08:14,496   adding 'isambard/modelling/__pycache__/extract_loop_data.cpython-37.pyc'
2025-09-09T11:08:14,497   adding 'isambard/modelling/__pycache__/non_canonical.cpython-37.pyc'
2025-09-09T11:08:14,498   adding 'isambard/modelling/__pycache__/scwrl.cpython-37.pyc'
2025-09-09T11:08:14,498   adding 'isambard/modelling/reference_ampals/README.md'
2025-09-09T11:08:14,499   adding 'isambard/modelling/reference_ampals/non_canonical_amino_acids/hydroxyproline_ref_1bkv_0_6.pickle'
2025-09-09T11:08:14,500   adding 'isambard/optimisation/__init__.py'
2025-09-09T11:08:14,502   adding 'isambard/optimisation/base_evo_opt.py'
2025-09-09T11:08:14,504   adding 'isambard/optimisation/evo_optimizers.py'
2025-09-09T11:08:14,505   adding 'isambard/optimisation/mmc_optimizer.py'
2025-09-09T11:08:14,506   adding 'isambard/specifications/__init__.py'
2025-09-09T11:08:14,507   adding 'isambard/specifications/coiledcoil.py'
2025-09-09T11:08:14,509   adding 'isambard/specifications/helix.py'
2025-09-09T11:08:14,510   adding 'isambard/specifications/nucleic_acid_duplex.py'
2025-09-09T11:08:14,512   adding 'isambard/specifications/nucleic_acid_strand.py'
2025-09-09T11:08:14,513   adding 'isambard/specifications/solenoid.py'
2025-09-09T11:08:14,565   adding 'isambard/specifications/ta_polypeptide.c'
2025-09-09T11:08:14,730   adding 'isambard/specifications/ta_polypeptide.cpython-313-arm-linux-gnueabihf.so'
2025-09-09T11:08:14,857   adding 'isambard/specifications/ta_polypeptide.cpython-37m-x86_64-linux-gnu.so'
2025-09-09T11:08:14,863   adding 'isambard/specifications/ta_polypeptide.pyx'
2025-09-09T11:08:14,864   adding 'isambard-2.3.1.dist-info/licenses/LICENSE.txt'
2025-09-09T11:08:14,865   adding 'isambard-2.3.1.dist-info/METADATA'
2025-09-09T11:08:14,866   adding 'isambard-2.3.1.dist-info/WHEEL'
2025-09-09T11:08:14,866   adding 'isambard-2.3.1.dist-info/top_level.txt'
2025-09-09T11:08:14,867   adding 'isambard-2.3.1.dist-info/RECORD'
2025-09-09T11:08:14,868   removing build/bdist.linux-armv7l/wheel
2025-09-09T11:08:15,016   Building wheel for isambard (setup.py): finished with status 'done'
2025-09-09T11:08:15,025   Created wheel for isambard: filename=isambard-2.3.1-cp313-cp313-linux_armv7l.whl size=739948 sha256=da20d79d121b5930635e3ad7c23934818c47bcb980942956f5cf088194f85711
2025-09-09T11:08:15,026   Stored in directory: /tmp/pip-ephem-wheel-cache-z6sncb2m/wheels/22/04/d9/15b1f16da06a498642989b52d0ecc3e182347ea591ded13abe
2025-09-09T11:08:15,037 Successfully built isambard
2025-09-09T11:08:15,041 Removed build tracker: '/tmp/pip-build-tracker-saglxgrv'