2023-09-10T18:58:28,883 Created temporary directory: /tmp/pip-build-tracker-i5de15g4
2023-09-10T18:58:28,885 Initialized build tracking at /tmp/pip-build-tracker-i5de15g4
2023-09-10T18:58:28,885 Created build tracker: /tmp/pip-build-tracker-i5de15g4
2023-09-10T18:58:28,886 Entered build tracker: /tmp/pip-build-tracker-i5de15g4
2023-09-10T18:58:28,886 Created temporary directory: /tmp/pip-wheel-k4bbw97j
2023-09-10T18:58:28,890 Created temporary directory: /tmp/pip-ephem-wheel-cache-mutuzyct
2023-09-10T18:58:28,911 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-10T18:58:28,915 2 location(s) to search for versions of isambard:
2023-09-10T18:58:28,915 * https://pypi.org/simple/isambard/
2023-09-10T18:58:28,915 * https://www.piwheels.org/simple/isambard/
2023-09-10T18:58:28,915 Fetching project page and analyzing links: https://pypi.org/simple/isambard/
2023-09-10T18:58:28,916 Getting page https://pypi.org/simple/isambard/
2023-09-10T18:58:28,918 Found index url https://pypi.org/simple/
2023-09-10T18:58:29,059 Fetched page https://pypi.org/simple/isambard/ as application/vnd.pypi.simple.v1+json
2023-09-10T18:58:29,060   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
2023-09-10T18:58:29,061   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
2023-09-10T18:58:29,061   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
2023-09-10T18:58:29,062 Fetching project page and analyzing links: https://www.piwheels.org/simple/isambard/
2023-09-10T18:58:29,063 Getting page https://www.piwheels.org/simple/isambard/
2023-09-10T18:58:29,064 Found index url https://www.piwheels.org/simple/
2023-09-10T18:58:29,409 Fetched page https://www.piwheels.org/simple/isambard/ as text/html
2023-09-10T18:58:29,416   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp39-cp39-linux_armv7l.whl#sha256=697398715022626b617288089a4d8f169aba9b6a2741bb64a57baf0008f4a682 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,417   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp39-cp39-linux_armv6l.whl#sha256=697398715022626b617288089a4d8f169aba9b6a2741bb64a57baf0008f4a682 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,417   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp37-cp37m-linux_armv7l.whl#sha256=efae9efaebdc3a20e5d63f7004a92e689f3e6e5836be027bc95d82dfc3a96931 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,418   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp37-cp37m-linux_armv6l.whl#sha256=efae9efaebdc3a20e5d63f7004a92e689f3e6e5836be027bc95d82dfc3a96931 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,419   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp35-cp35m-linux_armv7l.whl#sha256=5456ca91d4e8a25515a72ce369c3dc3bd75771154926907a13ee229c5c775c90 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,419   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp35-cp35m-linux_armv6l.whl#sha256=5456ca91d4e8a25515a72ce369c3dc3bd75771154926907a13ee229c5c775c90 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,420   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp39-cp39-linux_armv7l.whl#sha256=0010224aeec40539f9f2ef43ef893a7b0735d1b3f4e95dc31708219c0337dc30 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,420   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp39-cp39-linux_armv6l.whl#sha256=0010224aeec40539f9f2ef43ef893a7b0735d1b3f4e95dc31708219c0337dc30 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,421   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp34-cp34m-linux_armv7l.whl#sha256=97c289f5089392b53f0c6d552d6d48650a1fb4dfc834cfc8b472a8a01c98dc89 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,422   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp34-cp34m-linux_armv6l.whl#sha256=97c289f5089392b53f0c6d552d6d48650a1fb4dfc834cfc8b472a8a01c98dc89 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,422   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp35-cp35m-linux_armv6l.whl#sha256=3fd2a12daa3a717fd4fcba1f02c00189966f88fdecfd4fe27a826bbc5e2e9e0d (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,423   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp35-cp35m-linux_armv7l.whl#sha256=3fd2a12daa3a717fd4fcba1f02c00189966f88fdecfd4fe27a826bbc5e2e9e0d (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,423   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp37-cp37m-linux_armv6l.whl#sha256=1ed4e4469c6a429a8d7983454afa221ed4de77c4f796928fe85b8ca9493ce9b7 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,424   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp37-cp37m-linux_armv7l.whl#sha256=1ed4e4469c6a429a8d7983454afa221ed4de77c4f796928fe85b8ca9493ce9b7 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,424   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp311-cp311-linux_armv7l.whl#sha256=4cf86ff1923fd823d90a7bd0993af4a2a172829212bf9de92f255ee304f38307 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,424   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp311-cp311-linux_armv6l.whl#sha256=4cf86ff1923fd823d90a7bd0993af4a2a172829212bf9de92f255ee304f38307 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,425   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp39-cp39-linux_armv7l.whl#sha256=45f89745fb452c115ce88125bc0668253c3f3b887d7ece84108e217dd6760ec8 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,426   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp39-cp39-linux_armv6l.whl#sha256=45f89745fb452c115ce88125bc0668253c3f3b887d7ece84108e217dd6760ec8 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,426   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp35-cp35m-linux_armv7l.whl#sha256=e0fc68b3f5047b9165d5153bc4dc316bab81664ff21671571b7513628b90b5a1 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,427   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp35-cp35m-linux_armv6l.whl#sha256=e0fc68b3f5047b9165d5153bc4dc316bab81664ff21671571b7513628b90b5a1 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,427   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp34-cp34m-linux_armv6l.whl#sha256=887549f381be5e2479ffed07b8c2eb4f307e592beccbe3290feba06d0c3790f9 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,428   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp34-cp34m-linux_armv7l.whl#sha256=887549f381be5e2479ffed07b8c2eb4f307e592beccbe3290feba06d0c3790f9 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,429   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp37-cp37m-linux_armv6l.whl#sha256=bd0f20e61ccc5234636764d226a0798035a8fbf626bcac75c0b0ecca150f5006 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,429   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp37-cp37m-linux_armv7l.whl#sha256=bd0f20e61ccc5234636764d226a0798035a8fbf626bcac75c0b0ecca150f5006 (from https://www.piwheels.org/simple/isambard/)
2023-09-10T18:58:29,430 Skipping link: not a file: https://www.piwheels.org/simple/isambard/
2023-09-10T18:58:29,430 Skipping link: not a file: https://pypi.org/simple/isambard/
2023-09-10T18:58:29,449 Given no hashes to check 1 links for project 'isambard': discarding no candidates
2023-09-10T18:58:29,466 Collecting isambard==2.2.0
2023-09-10T18:58:29,469   Created temporary directory: /tmp/pip-unpack-j57bfacf
2023-09-10T18:58:29,690   Downloading ISAMBARD-2.2.0.tar.gz (359 kB)
2023-09-10T18:58:29,960   Added isambard==2.2.0 from https://files.pythonhosted.org/packages/9c/ba/636028b8e309e217e171016e34b2a9f5f0b37f3be916d02ad55f97cf4991/ISAMBARD-2.2.0.tar.gz to build tracker '/tmp/pip-build-tracker-i5de15g4'
2023-09-10T18:58:29,962   Running setup.py (path:/tmp/pip-wheel-k4bbw97j/isambard_9f52acfa87ce4928ad123d7621d54cca/setup.py) egg_info for package isambard
2023-09-10T18:58:29,962   Created temporary directory: /tmp/pip-pip-egg-info-zyrj3u4z
2023-09-10T18:58:29,963   Preparing metadata (setup.py): started
2023-09-10T18:58:29,964   Running command python setup.py egg_info
2023-09-10T18:58:32,177   /usr/local/lib/python3.11/dist-packages/Cython/Compiler/Main.py:384: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-wheel-k4bbw97j/isambard_9f52acfa87ce4928ad123d7621d54cca/src/isambard/specifications/ta_polypeptide.pyx
2023-09-10T18:58:32,177     tree = Parsing.p_module(s, pxd, full_module_name)
2023-09-10T18:58:32,929   Compiling src/isambard/specifications/ta_polypeptide.pyx because it changed.
2023-09-10T18:58:32,929   [1/1] Cythonizing src/isambard/specifications/ta_polypeptide.pyx
2023-09-10T18:58:33,369   running egg_info
2023-09-10T18:58:33,371   creating /tmp/pip-pip-egg-info-zyrj3u4z/ISAMBARD.egg-info
2023-09-10T18:58:33,395   writing /tmp/pip-pip-egg-info-zyrj3u4z/ISAMBARD.egg-info/PKG-INFO
2023-09-10T18:58:33,399   writing dependency_links to /tmp/pip-pip-egg-info-zyrj3u4z/ISAMBARD.egg-info/dependency_links.txt
2023-09-10T18:58:33,401   writing requirements to /tmp/pip-pip-egg-info-zyrj3u4z/ISAMBARD.egg-info/requires.txt
2023-09-10T18:58:33,402   writing top-level names to /tmp/pip-pip-egg-info-zyrj3u4z/ISAMBARD.egg-info/top_level.txt
2023-09-10T18:58:33,404   writing manifest file '/tmp/pip-pip-egg-info-zyrj3u4z/ISAMBARD.egg-info/SOURCES.txt'
2023-09-10T18:58:33,509   reading manifest file '/tmp/pip-pip-egg-info-zyrj3u4z/ISAMBARD.egg-info/SOURCES.txt'
2023-09-10T18:58:33,511   reading manifest template 'MANIFEST.in'
2023-09-10T18:58:33,539   adding license file 'LICENSE.txt'
2023-09-10T18:58:33,542   writing manifest file '/tmp/pip-pip-egg-info-zyrj3u4z/ISAMBARD.egg-info/SOURCES.txt'
2023-09-10T18:58:33,785   Preparing metadata (setup.py): finished with status 'done'
2023-09-10T18:58:33,790   Source in /tmp/pip-wheel-k4bbw97j/isambard_9f52acfa87ce4928ad123d7621d54cca has version 2.2.0, which satisfies requirement isambard==2.2.0 from https://files.pythonhosted.org/packages/9c/ba/636028b8e309e217e171016e34b2a9f5f0b37f3be916d02ad55f97cf4991/ISAMBARD-2.2.0.tar.gz
2023-09-10T18:58:33,791   Removed isambard==2.2.0 from https://files.pythonhosted.org/packages/9c/ba/636028b8e309e217e171016e34b2a9f5f0b37f3be916d02ad55f97cf4991/ISAMBARD-2.2.0.tar.gz from build tracker '/tmp/pip-build-tracker-i5de15g4'
2023-09-10T18:58:33,796 Created temporary directory: /tmp/pip-unpack-bko0ay6x
2023-09-10T18:58:33,797 Created temporary directory: /tmp/pip-unpack-7k8w8dd_
2023-09-10T18:58:33,806 Building wheels for collected packages: isambard
2023-09-10T18:58:33,810   Created temporary directory: /tmp/pip-wheel-2g_u6obu
2023-09-10T18:58:33,810   Building wheel for isambard (setup.py): started
2023-09-10T18:58:33,812   Destination directory: /tmp/pip-wheel-2g_u6obu
2023-09-10T18:58:33,812   Running command python setup.py bdist_wheel
2023-09-10T18:58:35,338   running bdist_wheel
2023-09-10T18:58:35,433   running build
2023-09-10T18:58:35,433   running build_py
2023-09-10T18:58:35,460   creating build
2023-09-10T18:58:35,460   creating build/lib.linux-armv7l-cpython-311
2023-09-10T18:58:35,461   creating build/lib.linux-armv7l-cpython-311/isambard
2023-09-10T18:58:35,462   copying src/isambard/__init__.py -> build/lib.linux-armv7l-cpython-311/isambard
2023-09-10T18:58:35,464   creating build/lib.linux-armv7l-cpython-311/isambard/optimisation
2023-09-10T18:58:35,465   copying src/isambard/optimisation/base_evo_opt.py -> build/lib.linux-armv7l-cpython-311/isambard/optimisation
2023-09-10T18:58:35,468   copying src/isambard/optimisation/__init__.py -> build/lib.linux-armv7l-cpython-311/isambard/optimisation
2023-09-10T18:58:35,469   copying src/isambard/optimisation/evo_optimizers.py -> build/lib.linux-armv7l-cpython-311/isambard/optimisation
2023-09-10T18:58:35,472   copying src/isambard/optimisation/mmc_optimizer.py -> build/lib.linux-armv7l-cpython-311/isambard/optimisation
2023-09-10T18:58:35,476   creating build/lib.linux-armv7l-cpython-311/isambard/modelling
2023-09-10T18:58:35,476   copying src/isambard/modelling/scwrl.py -> build/lib.linux-armv7l-cpython-311/isambard/modelling
2023-09-10T18:58:35,479   copying src/isambard/modelling/__init__.py -> build/lib.linux-armv7l-cpython-311/isambard/modelling
2023-09-10T18:58:35,480   copying src/isambard/modelling/non_canonical.py -> build/lib.linux-armv7l-cpython-311/isambard/modelling
2023-09-10T18:58:35,482   creating build/lib.linux-armv7l-cpython-311/isambard/evaluation
2023-09-10T18:58:35,483   copying src/isambard/evaluation/__init__.py -> build/lib.linux-armv7l-cpython-311/isambard/evaluation
2023-09-10T18:58:35,485   copying src/isambard/evaluation/hydrophobic_fitness.py -> build/lib.linux-armv7l-cpython-311/isambard/evaluation
2023-09-10T18:58:35,487   copying src/isambard/evaluation/pacc.py -> build/lib.linux-armv7l-cpython-311/isambard/evaluation
2023-09-10T18:58:35,490   copying src/isambard/evaluation/dssp.py -> build/lib.linux-armv7l-cpython-311/isambard/evaluation
2023-09-10T18:58:35,492   copying src/isambard/evaluation/contact_order.py -> build/lib.linux-armv7l-cpython-311/isambard/evaluation
2023-09-10T18:58:35,494   creating build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-10T18:58:35,495   copying src/isambard/specifications/__init__.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-10T18:58:35,497   copying src/isambard/specifications/coiledcoil.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-10T18:58:35,499   copying src/isambard/specifications/solenoid.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-10T18:58:35,501   copying src/isambard/specifications/nucleic_acid_duplex.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-10T18:58:35,503   copying src/isambard/specifications/nucleic_acid_strand.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-10T18:58:35,505   copying src/isambard/specifications/helix.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-10T18:58:35,507   running egg_info
2023-09-10T18:58:35,561   writing src/ISAMBARD.egg-info/PKG-INFO
2023-09-10T18:58:35,564   writing dependency_links to src/ISAMBARD.egg-info/dependency_links.txt
2023-09-10T18:58:35,566   writing requirements to src/ISAMBARD.egg-info/requires.txt
2023-09-10T18:58:35,567   writing top-level names to src/ISAMBARD.egg-info/top_level.txt
2023-09-10T18:58:35,595   reading manifest file 'src/ISAMBARD.egg-info/SOURCES.txt'
2023-09-10T18:58:35,598   reading manifest template 'MANIFEST.in'
2023-09-10T18:58:35,621   adding license file 'LICENSE.txt'
2023-09-10T18:58:35,625   writing manifest file 'src/ISAMBARD.egg-info/SOURCES.txt'
2023-09-10T18:58:35,628   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'isambard.__pycache__' is absent from the `packages` configuration.
2023-09-10T18:58:35,629   !!

2023-09-10T18:58:35,630           ********************************************************************************
2023-09-10T18:58:35,630           ############################
2023-09-10T18:58:35,631           # Package would be ignored #
2023-09-10T18:58:35,631           ############################
2023-09-10T18:58:35,632           Python recognizes 'isambard.__pycache__' as an importable package[^1],
2023-09-10T18:58:35,632           but it is absent from setuptools' `packages` configuration.

2023-09-10T18:58:35,633           This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-10T18:58:35,634           package, please make sure that 'isambard.__pycache__' is explicitly added
2023-09-10T18:58:35,634           to the `packages` configuration field.

2023-09-10T18:58:35,635           Alternatively, you can also rely on setuptools' discovery methods
2023-09-10T18:58:35,635           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-10T18:58:35,636           instead of `find_packages(...)`/`find:`).

2023-09-10T18:58:35,637           You can read more about "package discovery" on setuptools documentation page:

2023-09-10T18:58:35,638           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-10T18:58:35,639           If you don't want 'isambard.__pycache__' to be distributed and are
2023-09-10T18:58:35,639           already explicitly excluding 'isambard.__pycache__' via
2023-09-10T18:58:35,640           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-10T18:58:35,640           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-10T18:58:35,641           combination with a more fine grained `package-data` configuration.

2023-09-10T18:58:35,642           You can read more about "package data files" on setuptools documentation page:

2023-09-10T18:58:35,643           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-10T18:58:35,645           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-10T18:58:35,645                 even if it does not contain any `.py` files.
2023-09-10T18:58:35,646                 On the other hand, currently there is no concept of package data
2023-09-10T18:58:35,647                 directory, all directories are treated like packages.
2023-09-10T18:58:35,647           ********************************************************************************

2023-09-10T18:58:35,648   !!
2023-09-10T18:58:35,649     check.warn(importable)
2023-09-10T18:58:35,650   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'isambard.evaluation.__pycache__' is absent from the `packages` configuration.
2023-09-10T18:58:35,650   !!

2023-09-10T18:58:35,652           ********************************************************************************
2023-09-10T18:58:35,652           ############################
2023-09-10T18:58:35,652           # Package would be ignored #
2023-09-10T18:58:35,653           ############################
2023-09-10T18:58:35,653           Python recognizes 'isambard.evaluation.__pycache__' as an importable package[^1],
2023-09-10T18:58:35,654           but it is absent from setuptools' `packages` configuration.

2023-09-10T18:58:35,655           This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-10T18:58:35,655           package, please make sure that 'isambard.evaluation.__pycache__' is explicitly added
2023-09-10T18:58:35,656           to the `packages` configuration field.

2023-09-10T18:58:35,657           Alternatively, you can also rely on setuptools' discovery methods
2023-09-10T18:58:35,658           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-10T18:58:35,658           instead of `find_packages(...)`/`find:`).

2023-09-10T18:58:35,659           You can read more about "package discovery" on setuptools documentation page:

2023-09-10T18:58:35,660           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-10T18:58:35,661           If you don't want 'isambard.evaluation.__pycache__' to be distributed and are
2023-09-10T18:58:35,661           already explicitly excluding 'isambard.evaluation.__pycache__' via
2023-09-10T18:58:35,662           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-10T18:58:35,662           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-10T18:58:35,662           combination with a more fine grained `package-data` configuration.

2023-09-10T18:58:35,663           You can read more about "package data files" on setuptools documentation page:

2023-09-10T18:58:35,664           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-10T18:58:35,666           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-10T18:58:35,666                 even if it does not contain any `.py` files.
2023-09-10T18:58:35,667                 On the other hand, currently there is no concept of package data
2023-09-10T18:58:35,667                 directory, all directories are treated like packages.
2023-09-10T18:58:35,668           ********************************************************************************

2023-09-10T18:58:35,669   !!
2023-09-10T18:58:35,669     check.warn(importable)
2023-09-10T18:58:35,670   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'isambard.modelling.__pycache__' is absent from the `packages` configuration.
2023-09-10T18:58:35,670   !!

2023-09-10T18:58:35,671           ********************************************************************************
2023-09-10T18:58:35,672           ############################
2023-09-10T18:58:35,672           # Package would be ignored #
2023-09-10T18:58:35,673           ############################
2023-09-10T18:58:35,673           Python recognizes 'isambard.modelling.__pycache__' as an importable package[^1],
2023-09-10T18:58:35,674           but it is absent from setuptools' `packages` configuration.

2023-09-10T18:58:35,675           This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-10T18:58:35,675           package, please make sure that 'isambard.modelling.__pycache__' is explicitly added
2023-09-10T18:58:35,676           to the `packages` configuration field.

2023-09-10T18:58:35,677           Alternatively, you can also rely on setuptools' discovery methods
2023-09-10T18:58:35,677           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-10T18:58:35,678           instead of `find_packages(...)`/`find:`).

2023-09-10T18:58:35,679           You can read more about "package discovery" on setuptools documentation page:

2023-09-10T18:58:35,680           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-10T18:58:35,681           If you don't want 'isambard.modelling.__pycache__' to be distributed and are
2023-09-10T18:58:35,682           already explicitly excluding 'isambard.modelling.__pycache__' via
2023-09-10T18:58:35,682           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-10T18:58:35,682           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-10T18:58:35,683           combination with a more fine grained `package-data` configuration.

2023-09-10T18:58:35,684           You can read more about "package data files" on setuptools documentation page:

2023-09-10T18:58:35,685           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-10T18:58:35,686           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-10T18:58:35,687                 even if it does not contain any `.py` files.
2023-09-10T18:58:35,687                 On the other hand, currently there is no concept of package data
2023-09-10T18:58:35,688                 directory, all directories are treated like packages.
2023-09-10T18:58:35,688           ********************************************************************************

2023-09-10T18:58:35,689   !!
2023-09-10T18:58:35,689     check.warn(importable)
2023-09-10T18:58:35,690   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'isambard.modelling.reference_ampals' is absent from the `packages` configuration.
2023-09-10T18:58:35,690   !!

2023-09-10T18:58:35,691           ********************************************************************************
2023-09-10T18:58:35,692           ############################
2023-09-10T18:58:35,692           # Package would be ignored #
2023-09-10T18:58:35,692           ############################
2023-09-10T18:58:35,693           Python recognizes 'isambard.modelling.reference_ampals' as an importable package[^1],
2023-09-10T18:58:35,693           but it is absent from setuptools' `packages` configuration.

2023-09-10T18:58:35,694           This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-10T18:58:35,695           package, please make sure that 'isambard.modelling.reference_ampals' is explicitly added
2023-09-10T18:58:35,695           to the `packages` configuration field.

2023-09-10T18:58:35,696           Alternatively, you can also rely on setuptools' discovery methods
2023-09-10T18:58:35,697           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-10T18:58:35,697           instead of `find_packages(...)`/`find:`).

2023-09-10T18:58:35,698           You can read more about "package discovery" on setuptools documentation page:

2023-09-10T18:58:35,699           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-10T18:58:35,700           If you don't want 'isambard.modelling.reference_ampals' to be distributed and are
2023-09-10T18:58:35,701           already explicitly excluding 'isambard.modelling.reference_ampals' via
2023-09-10T18:58:35,703           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-10T18:58:35,704           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-10T18:58:35,705           combination with a more fine grained `package-data` configuration.

2023-09-10T18:58:35,706           You can read more about "package data files" on setuptools documentation page:

2023-09-10T18:58:35,707           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-10T18:58:35,709           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-10T18:58:35,710                 even if it does not contain any `.py` files.
2023-09-10T18:58:35,710                 On the other hand, currently there is no concept of package data
2023-09-10T18:58:35,711                 directory, all directories are treated like packages.
2023-09-10T18:58:35,712           ********************************************************************************

2023-09-10T18:58:35,713   !!
2023-09-10T18:58:35,713     check.warn(importable)
2023-09-10T18:58:35,714   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'isambard.modelling.reference_ampals.non_canonical_amino_acids' is absent from the `packages` configuration.
2023-09-10T18:58:35,714   !!

2023-09-10T18:58:35,715           ********************************************************************************
2023-09-10T18:58:35,716           ############################
2023-09-10T18:58:35,716           # Package would be ignored #
2023-09-10T18:58:35,717           ############################
2023-09-10T18:58:35,718           Python recognizes 'isambard.modelling.reference_ampals.non_canonical_amino_acids' as an importable package[^1],
2023-09-10T18:58:35,719           but it is absent from setuptools' `packages` configuration.

2023-09-10T18:58:35,720           This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-10T18:58:35,720           package, please make sure that 'isambard.modelling.reference_ampals.non_canonical_amino_acids' is explicitly added
2023-09-10T18:58:35,721           to the `packages` configuration field.

2023-09-10T18:58:35,722           Alternatively, you can also rely on setuptools' discovery methods
2023-09-10T18:58:35,723           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-10T18:58:35,723           instead of `find_packages(...)`/`find:`).

2023-09-10T18:58:35,724           You can read more about "package discovery" on setuptools documentation page:

2023-09-10T18:58:35,725           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-10T18:58:35,726           If you don't want 'isambard.modelling.reference_ampals.non_canonical_amino_acids' to be distributed and are
2023-09-10T18:58:35,727           already explicitly excluding 'isambard.modelling.reference_ampals.non_canonical_amino_acids' via
2023-09-10T18:58:35,727           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-10T18:58:35,728           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-10T18:58:35,728           combination with a more fine grained `package-data` configuration.

2023-09-10T18:58:35,729           You can read more about "package data files" on setuptools documentation page:

2023-09-10T18:58:35,731           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-10T18:58:35,733           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-10T18:58:35,733                 even if it does not contain any `.py` files.
2023-09-10T18:58:35,734                 On the other hand, currently there is no concept of package data
2023-09-10T18:58:35,734                 directory, all directories are treated like packages.
2023-09-10T18:58:35,735           ********************************************************************************

2023-09-10T18:58:35,736   !!
2023-09-10T18:58:35,736     check.warn(importable)
2023-09-10T18:58:35,737   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'isambard.optimisation.__pycache__' is absent from the `packages` configuration.
2023-09-10T18:58:35,737   !!

2023-09-10T18:58:35,738           ********************************************************************************
2023-09-10T18:58:35,739           ############################
2023-09-10T18:58:35,740           # Package would be ignored #
2023-09-10T18:58:35,740           ############################
2023-09-10T18:58:35,741           Python recognizes 'isambard.optimisation.__pycache__' as an importable package[^1],
2023-09-10T18:58:35,741           but it is absent from setuptools' `packages` configuration.

2023-09-10T18:58:35,742           This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-10T18:58:35,743           package, please make sure that 'isambard.optimisation.__pycache__' is explicitly added
2023-09-10T18:58:35,743           to the `packages` configuration field.

2023-09-10T18:58:35,744           Alternatively, you can also rely on setuptools' discovery methods
2023-09-10T18:58:35,745           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-10T18:58:35,745           instead of `find_packages(...)`/`find:`).

2023-09-10T18:58:35,747           You can read more about "package discovery" on setuptools documentation page:

2023-09-10T18:58:35,748           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-10T18:58:35,749           If you don't want 'isambard.optimisation.__pycache__' to be distributed and are
2023-09-10T18:58:35,750           already explicitly excluding 'isambard.optimisation.__pycache__' via
2023-09-10T18:58:35,750           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-10T18:58:35,751           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-10T18:58:35,751           combination with a more fine grained `package-data` configuration.

2023-09-10T18:58:35,752           You can read more about "package data files" on setuptools documentation page:

2023-09-10T18:58:35,753           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-10T18:58:35,754           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-10T18:58:35,755                 even if it does not contain any `.py` files.
2023-09-10T18:58:35,755                 On the other hand, currently there is no concept of package data
2023-09-10T18:58:35,756                 directory, all directories are treated like packages.
2023-09-10T18:58:35,756           ********************************************************************************

2023-09-10T18:58:35,757   !!
2023-09-10T18:58:35,758     check.warn(importable)
2023-09-10T18:58:35,758   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'isambard.specifications.__pycache__' is absent from the `packages` configuration.
2023-09-10T18:58:35,759   !!

2023-09-10T18:58:35,759           ********************************************************************************
2023-09-10T18:58:35,760           ############################
2023-09-10T18:58:35,761           # Package would be ignored #
2023-09-10T18:58:35,761           ############################
2023-09-10T18:58:35,762           Python recognizes 'isambard.specifications.__pycache__' as an importable package[^1],
2023-09-10T18:58:35,762           but it is absent from setuptools' `packages` configuration.

2023-09-10T18:58:35,763           This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-10T18:58:35,764           package, please make sure that 'isambard.specifications.__pycache__' is explicitly added
2023-09-10T18:58:35,764           to the `packages` configuration field.

2023-09-10T18:58:35,765           Alternatively, you can also rely on setuptools' discovery methods
2023-09-10T18:58:35,766           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-10T18:58:35,766           instead of `find_packages(...)`/`find:`).

2023-09-10T18:58:35,768           You can read more about "package discovery" on setuptools documentation page:

2023-09-10T18:58:35,769           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-10T18:58:35,770           If you don't want 'isambard.specifications.__pycache__' to be distributed and are
2023-09-10T18:58:35,771           already explicitly excluding 'isambard.specifications.__pycache__' via
2023-09-10T18:58:35,772           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-10T18:58:35,772           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-10T18:58:35,773           combination with a more fine grained `package-data` configuration.

2023-09-10T18:58:35,774           You can read more about "package data files" on setuptools documentation page:

2023-09-10T18:58:35,775           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-10T18:58:35,776           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-10T18:58:35,777                 even if it does not contain any `.py` files.
2023-09-10T18:58:35,777                 On the other hand, currently there is no concept of package data
2023-09-10T18:58:35,778                 directory, all directories are treated like packages.
2023-09-10T18:58:35,779           ********************************************************************************

2023-09-10T18:58:35,780   !!
2023-09-10T18:58:35,780     check.warn(importable)
2023-09-10T18:58:35,781   creating build/lib.linux-armv7l-cpython-311/isambard/__pycache__
2023-09-10T18:58:35,781   copying src/isambard/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/__pycache__
2023-09-10T18:58:35,782   creating build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__
2023-09-10T18:58:35,782   copying src/isambard/optimisation/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__
2023-09-10T18:58:35,782   copying src/isambard/optimisation/__pycache__/base_evo_opt.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__
2023-09-10T18:58:35,783   copying src/isambard/optimisation/__pycache__/evo_optimizers.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__
2023-09-10T18:58:35,783   copying src/isambard/optimisation/__pycache__/mmc_optimizer.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__
2023-09-10T18:58:35,784   creating build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__
2023-09-10T18:58:35,784   copying src/isambard/modelling/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__
2023-09-10T18:58:35,785   copying src/isambard/modelling/__pycache__/create_loop_data.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__
2023-09-10T18:58:35,785   copying src/isambard/modelling/__pycache__/create_loop_database.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__
2023-09-10T18:58:35,786   copying src/isambard/modelling/__pycache__/create_loop_db.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__
2023-09-10T18:58:35,786   copying src/isambard/modelling/__pycache__/extract_loop_data.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__
2023-09-10T18:58:35,787   copying src/isambard/modelling/__pycache__/loop_fitter.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__
2023-09-10T18:58:35,787   copying src/isambard/modelling/__pycache__/loop_fitting.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__
2023-09-10T18:58:35,788   copying src/isambard/modelling/__pycache__/non_canonical.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__
2023-09-10T18:58:35,788   copying src/isambard/modelling/__pycache__/scwrl.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__
2023-09-10T18:58:35,789   creating build/lib.linux-armv7l-cpython-311/isambard/modelling/reference_ampals
2023-09-10T18:58:35,789   copying src/isambard/modelling/reference_ampals/README.md -> build/lib.linux-armv7l-cpython-311/isambard/modelling/reference_ampals
2023-09-10T18:58:35,790   creating build/lib.linux-armv7l-cpython-311/isambard/modelling/reference_ampals/non_canonical_amino_acids
2023-09-10T18:58:35,790   copying src/isambard/modelling/reference_ampals/non_canonical_amino_acids/hydroxyproline_ref_1bkv_0_6.pickle -> build/lib.linux-armv7l-cpython-311/isambard/modelling/reference_ampals/non_canonical_amino_acids
2023-09-10T18:58:35,791   creating build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__
2023-09-10T18:58:35,791   copying src/isambard/evaluation/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__
2023-09-10T18:58:35,792   copying src/isambard/evaluation/__pycache__/contact_order.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__
2023-09-10T18:58:35,793   copying src/isambard/evaluation/__pycache__/dssp.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__
2023-09-10T18:58:35,793   copying src/isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__
2023-09-10T18:58:35,794   copying src/isambard/evaluation/__pycache__/pacc.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__
2023-09-10T18:58:35,795   copying src/isambard/specifications/ta_polypeptide.c -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-10T18:58:35,795   copying src/isambard/specifications/ta_polypeptide.cpython-36m-x86_64-linux-gnu.so -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-10T18:58:35,796   copying src/isambard/specifications/ta_polypeptide.pyx -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-10T18:58:35,796   creating build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__
2023-09-10T18:58:35,796   copying src/isambard/specifications/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__
2023-09-10T18:58:35,797   copying src/isambard/specifications/__pycache__/coiledcoil.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__
2023-09-10T18:58:35,797   copying src/isambard/specifications/__pycache__/helix.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__
2023-09-10T18:58:35,798   copying src/isambard/specifications/__pycache__/nucleic_acid_duplex.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__
2023-09-10T18:58:35,799   copying src/isambard/specifications/__pycache__/nucleic_acid_strand.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__
2023-09-10T18:58:35,799   copying src/isambard/specifications/__pycache__/solenoid.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__
2023-09-10T18:58:35,800   running build_ext
2023-09-10T18:58:35,800   building 'isambard.specifications.ta_polypeptide' extension
2023-09-10T18:58:35,801   creating build/temp.linux-armv7l-cpython-311
2023-09-10T18:58:35,801   creating build/temp.linux-armv7l-cpython-311/src
2023-09-10T18:58:35,802   creating build/temp.linux-armv7l-cpython-311/src/isambard
2023-09-10T18:58:35,803   creating build/temp.linux-armv7l-cpython-311/src/isambard/specifications
2023-09-10T18:58:35,803   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.11 -c src/isambard/specifications/ta_polypeptide.c -o build/temp.linux-armv7l-cpython-311/src/isambard/specifications/ta_polypeptide.o
2023-09-10T18:58:55,586   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/src/isambard/specifications/ta_polypeptide.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/isambard/specifications/ta_polypeptide.cpython-311-arm-linux-gnueabihf.so
2023-09-10T18:58:55,730   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2023-09-10T18:58:55,731   !!

2023-09-10T18:58:55,732           ********************************************************************************
2023-09-10T18:58:55,732           Please avoid running ``setup.py`` directly.
2023-09-10T18:58:55,733           Instead, use pypa/build, pypa/installer or other
2023-09-10T18:58:55,733           standards-based tools.

2023-09-10T18:58:55,735           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2023-09-10T18:58:55,735           ********************************************************************************

2023-09-10T18:58:55,736   !!
2023-09-10T18:58:55,737     self.initialize_options()
2023-09-10T18:58:55,754   installing to build/bdist.linux-armv7l/wheel
2023-09-10T18:58:55,755   running install
2023-09-10T18:58:55,779   running install_lib
2023-09-10T18:58:55,803   creating build/bdist.linux-armv7l
2023-09-10T18:58:55,803   creating build/bdist.linux-armv7l/wheel
2023-09-10T18:58:55,805   creating build/bdist.linux-armv7l/wheel/isambard
2023-09-10T18:58:55,807   creating build/bdist.linux-armv7l/wheel/isambard/optimisation
2023-09-10T18:58:55,808   copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/base_evo_opt.py -> build/bdist.linux-armv7l/wheel/isambard/optimisation
2023-09-10T18:58:55,810   copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/__init__.py -> build/bdist.linux-armv7l/wheel/isambard/optimisation
2023-09-10T18:58:55,812   copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/evo_optimizers.py -> build/bdist.linux-armv7l/wheel/isambard/optimisation
2023-09-10T18:58:55,815   creating build/bdist.linux-armv7l/wheel/isambard/optimisation/__pycache__
2023-09-10T18:58:55,816   copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__/mmc_optimizer.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/optimisation/__pycache__
2023-09-10T18:58:55,818   copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__/base_evo_opt.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/optimisation/__pycache__
2023-09-10T18:58:55,820   copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__/evo_optimizers.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/optimisation/__pycache__
2023-09-10T18:58:55,823   copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/optimisation/__pycache__
2023-09-10T18:58:55,824   copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/mmc_optimizer.py -> build/bdist.linux-armv7l/wheel/isambard/optimisation
2023-09-10T18:58:55,826   copying build/lib.linux-armv7l-cpython-311/isambard/__init__.py -> build/bdist.linux-armv7l/wheel/isambard
2023-09-10T18:58:55,829   creating build/bdist.linux-armv7l/wheel/isambard/modelling
2023-09-10T18:58:55,829   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/scwrl.py -> build/bdist.linux-armv7l/wheel/isambard/modelling
2023-09-10T18:58:55,832   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__init__.py -> build/bdist.linux-armv7l/wheel/isambard/modelling
2023-09-10T18:58:55,834   creating build/bdist.linux-armv7l/wheel/isambard/modelling/reference_ampals
2023-09-10T18:58:55,835   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/reference_ampals/README.md -> build/bdist.linux-armv7l/wheel/isambard/modelling/reference_ampals
2023-09-10T18:58:55,837   creating build/bdist.linux-armv7l/wheel/isambard/modelling/reference_ampals/non_canonical_amino_acids
2023-09-10T18:58:55,838   copying build/lib.linux-armv7l-cpython-311/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
2023-09-10T18:58:55,840   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/non_canonical.py -> build/bdist.linux-armv7l/wheel/isambard/modelling
2023-09-10T18:58:55,842   creating build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2023-09-10T18:58:55,843   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/extract_loop_data.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2023-09-10T18:58:55,845   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/non_canonical.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2023-09-10T18:58:55,847   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/create_loop_database.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2023-09-10T18:58:55,849   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/create_loop_db.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2023-09-10T18:58:55,851   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/create_loop_data.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2023-09-10T18:58:55,853   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/loop_fitter.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2023-09-10T18:58:55,856   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/scwrl.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2023-09-10T18:58:55,858   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/loop_fitting.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2023-09-10T18:58:55,860   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2023-09-10T18:58:55,862   creating build/bdist.linux-armv7l/wheel/isambard/evaluation
2023-09-10T18:58:55,863   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__init__.py -> build/bdist.linux-armv7l/wheel/isambard/evaluation
2023-09-10T18:58:55,865   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/hydrophobic_fitness.py -> build/bdist.linux-armv7l/wheel/isambard/evaluation
2023-09-10T18:58:55,867   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/pacc.py -> build/bdist.linux-armv7l/wheel/isambard/evaluation
2023-09-10T18:58:55,869   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/dssp.py -> build/bdist.linux-armv7l/wheel/isambard/evaluation
2023-09-10T18:58:55,871   creating build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__
2023-09-10T18:58:55,872   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__/pacc.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__
2023-09-10T18:58:55,874   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__/dssp.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__
2023-09-10T18:58:55,877   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__/contact_order.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__
2023-09-10T18:58:55,878   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__
2023-09-10T18:58:55,881   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__
2023-09-10T18:58:55,882   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/contact_order.py -> build/bdist.linux-armv7l/wheel/isambard/evaluation
2023-09-10T18:58:55,885   creating build/bdist.linux-armv7l/wheel/isambard/__pycache__
2023-09-10T18:58:55,886   copying build/lib.linux-armv7l-cpython-311/isambard/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/__pycache__
2023-09-10T18:58:55,888   creating build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-10T18:58:55,889   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/ta_polypeptide.c -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-10T18:58:55,901   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/__init__.py -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-10T18:58:55,902   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/coiledcoil.py -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-10T18:58:55,905   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/solenoid.py -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-10T18:58:55,907   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/nucleic_acid_duplex.py -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-10T18:58:55,908   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/nucleic_acid_strand.py -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-10T18:58:55,911   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/ta_polypeptide.cpython-36m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-10T18:58:55,929   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/helix.py -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-10T18:58:55,932   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/ta_polypeptide.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-10T18:58:55,949   creating build/bdist.linux-armv7l/wheel/isambard/specifications/__pycache__
2023-09-10T18:58:55,950   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__/nucleic_acid_duplex.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/specifications/__pycache__
2023-09-10T18:58:55,951   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__/nucleic_acid_strand.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/specifications/__pycache__
2023-09-10T18:58:55,954   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__/solenoid.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/specifications/__pycache__
2023-09-10T18:58:55,956   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__/helix.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/specifications/__pycache__
2023-09-10T18:58:55,958   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__/coiledcoil.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/specifications/__pycache__
2023-09-10T18:58:55,960   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/specifications/__pycache__
2023-09-10T18:58:55,962   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/ta_polypeptide.pyx -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-10T18:58:55,964   running install_egg_info
2023-09-10T18:58:55,995   Copying src/ISAMBARD.egg-info to build/bdist.linux-armv7l/wheel/ISAMBARD-2.2.0-py3.11.egg-info
2023-09-10T18:58:56,006   running install_scripts
2023-09-10T18:58:56,057   creating build/bdist.linux-armv7l/wheel/ISAMBARD-2.2.0.dist-info/WHEEL
2023-09-10T18:58:56,060   creating '/tmp/pip-wheel-2g_u6obu/ISAMBARD-2.2.0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-09-10T18:58:56,063   adding 'isambard/__init__.py'
2023-09-10T18:58:56,065   adding 'isambard/__pycache__/__init__.cpython-36.pyc'
2023-09-10T18:58:56,067   adding 'isambard/evaluation/__init__.py'
2023-09-10T18:58:56,068   adding 'isambard/evaluation/contact_order.py'
2023-09-10T18:58:56,070   adding 'isambard/evaluation/dssp.py'
2023-09-10T18:58:56,072   adding 'isambard/evaluation/hydrophobic_fitness.py'
2023-09-10T18:58:56,074   adding 'isambard/evaluation/pacc.py'
2023-09-10T18:58:56,076   adding 'isambard/evaluation/__pycache__/__init__.cpython-36.pyc'
2023-09-10T18:58:56,077   adding 'isambard/evaluation/__pycache__/contact_order.cpython-36.pyc'
2023-09-10T18:58:56,079   adding 'isambard/evaluation/__pycache__/dssp.cpython-36.pyc'
2023-09-10T18:58:56,080   adding 'isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-36.pyc'
2023-09-10T18:58:56,082   adding 'isambard/evaluation/__pycache__/pacc.cpython-36.pyc'
2023-09-10T18:58:56,084   adding 'isambard/modelling/__init__.py'
2023-09-10T18:58:56,085   adding 'isambard/modelling/non_canonical.py'
2023-09-10T18:58:56,087   adding 'isambard/modelling/scwrl.py'
2023-09-10T18:58:56,088   adding 'isambard/modelling/__pycache__/__init__.cpython-36.pyc'
2023-09-10T18:58:56,090   adding 'isambard/modelling/__pycache__/create_loop_data.cpython-36.pyc'
2023-09-10T18:58:56,092   adding 'isambard/modelling/__pycache__/create_loop_database.cpython-36.pyc'
2023-09-10T18:58:56,094   adding 'isambard/modelling/__pycache__/create_loop_db.cpython-36.pyc'
2023-09-10T18:58:56,096   adding 'isambard/modelling/__pycache__/extract_loop_data.cpython-36.pyc'
2023-09-10T18:58:56,098   adding 'isambard/modelling/__pycache__/loop_fitter.cpython-36.pyc'
2023-09-10T18:58:56,099   adding 'isambard/modelling/__pycache__/loop_fitting.cpython-36.pyc'
2023-09-10T18:58:56,101   adding 'isambard/modelling/__pycache__/non_canonical.cpython-36.pyc'
2023-09-10T18:58:56,102   adding 'isambard/modelling/__pycache__/scwrl.cpython-36.pyc'
2023-09-10T18:58:56,104   adding 'isambard/modelling/reference_ampals/README.md'
2023-09-10T18:58:56,105   adding 'isambard/modelling/reference_ampals/non_canonical_amino_acids/hydroxyproline_ref_1bkv_0_6.pickle'
2023-09-10T18:58:56,107   adding 'isambard/optimisation/__init__.py'
2023-09-10T18:58:56,109   adding 'isambard/optimisation/base_evo_opt.py'
2023-09-10T18:58:56,112   adding 'isambard/optimisation/evo_optimizers.py'
2023-09-10T18:58:56,114   adding 'isambard/optimisation/mmc_optimizer.py'
2023-09-10T18:58:56,115   adding 'isambard/optimisation/__pycache__/__init__.cpython-36.pyc'
2023-09-10T18:58:56,118   adding 'isambard/optimisation/__pycache__/base_evo_opt.cpython-36.pyc'
2023-09-10T18:58:56,121   adding 'isambard/optimisation/__pycache__/evo_optimizers.cpython-36.pyc'
2023-09-10T18:58:56,123   adding 'isambard/optimisation/__pycache__/mmc_optimizer.cpython-36.pyc'
2023-09-10T18:58:56,125   adding 'isambard/specifications/__init__.py'
2023-09-10T18:58:56,126   adding 'isambard/specifications/coiledcoil.py'
2023-09-10T18:58:56,129   adding 'isambard/specifications/helix.py'
2023-09-10T18:58:56,130   adding 'isambard/specifications/nucleic_acid_duplex.py'
2023-09-10T18:58:56,132   adding 'isambard/specifications/nucleic_acid_strand.py'
2023-09-10T18:58:56,134   adding 'isambard/specifications/solenoid.py'
2023-09-10T18:58:56,182   adding 'isambard/specifications/ta_polypeptide.c'
2023-09-10T18:58:56,322   adding 'isambard/specifications/ta_polypeptide.cpython-311-arm-linux-gnueabihf.so'
2023-09-10T18:58:56,428   adding 'isambard/specifications/ta_polypeptide.cpython-36m-x86_64-linux-gnu.so'
2023-09-10T18:58:56,436   adding 'isambard/specifications/ta_polypeptide.pyx'
2023-09-10T18:58:56,437   adding 'isambard/specifications/__pycache__/__init__.cpython-36.pyc'
2023-09-10T18:58:56,439   adding 'isambard/specifications/__pycache__/coiledcoil.cpython-36.pyc'
2023-09-10T18:58:56,442   adding 'isambard/specifications/__pycache__/helix.cpython-36.pyc'
2023-09-10T18:58:56,444   adding 'isambard/specifications/__pycache__/nucleic_acid_duplex.cpython-36.pyc'
2023-09-10T18:58:56,446   adding 'isambard/specifications/__pycache__/nucleic_acid_strand.cpython-36.pyc'
2023-09-10T18:58:56,448   adding 'isambard/specifications/__pycache__/solenoid.cpython-36.pyc'
2023-09-10T18:58:56,449   adding 'ISAMBARD-2.2.0.dist-info/LICENSE.txt'
2023-09-10T18:58:56,450   adding 'ISAMBARD-2.2.0.dist-info/METADATA'
2023-09-10T18:58:56,451   adding 'ISAMBARD-2.2.0.dist-info/WHEEL'
2023-09-10T18:58:56,452   adding 'ISAMBARD-2.2.0.dist-info/top_level.txt'
2023-09-10T18:58:56,454   adding 'ISAMBARD-2.2.0.dist-info/RECORD'
2023-09-10T18:58:56,465   removing build/bdist.linux-armv7l/wheel
2023-09-10T18:58:56,624   Building wheel for isambard (setup.py): finished with status 'done'
2023-09-10T18:58:56,635   Created wheel for isambard: filename=ISAMBARD-2.2.0-cp311-cp311-linux_armv7l.whl size=697003 sha256=da0939c6735170d08c9e5c63a3d82bb9003d2457ae53546e18eca4b785976758
2023-09-10T18:58:56,637   Stored in directory: /tmp/pip-ephem-wheel-cache-mutuzyct/wheels/f3/5f/7e/98e865d20b7a57c53e8ae921ca1f52a5de61565ec9ac4286a8
2023-09-10T18:58:56,648 Successfully built isambard
2023-09-10T18:58:56,670 Removed build tracker: '/tmp/pip-build-tracker-i5de15g4'