2023-09-13T15:43:10,182 Created temporary directory: /tmp/pip-build-tracker-es65t3pz
2023-09-13T15:43:10,184 Initialized build tracking at /tmp/pip-build-tracker-es65t3pz
2023-09-13T15:43:10,184 Created build tracker: /tmp/pip-build-tracker-es65t3pz
2023-09-13T15:43:10,185 Entered build tracker: /tmp/pip-build-tracker-es65t3pz
2023-09-13T15:43:10,185 Created temporary directory: /tmp/pip-wheel-ih632d7p
2023-09-13T15:43:10,188 Created temporary directory: /tmp/pip-ephem-wheel-cache-qy9tsbwy
2023-09-13T15:43:10,210 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-13T15:43:10,214 2 location(s) to search for versions of isambard:
2023-09-13T15:43:10,214 * https://pypi.org/simple/isambard/
2023-09-13T15:43:10,214 * https://www.piwheels.org/simple/isambard/
2023-09-13T15:43:10,214 Fetching project page and analyzing links: https://pypi.org/simple/isambard/
2023-09-13T15:43:10,215 Getting page https://pypi.org/simple/isambard/
2023-09-13T15:43:10,217 Found index url https://pypi.org/simple/
2023-09-13T15:43:10,465 Fetched page https://pypi.org/simple/isambard/ as application/vnd.pypi.simple.v1+json
2023-09-13T15:43:10,467   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
2023-09-13T15:43:10,468   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
2023-09-13T15:43:10,468   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
2023-09-13T15:43:10,469 Fetching project page and analyzing links: https://www.piwheels.org/simple/isambard/
2023-09-13T15:43:10,470 Getting page https://www.piwheels.org/simple/isambard/
2023-09-13T15:43:10,471 Found index url https://www.piwheels.org/simple/
2023-09-13T15:43:10,729 Fetched page https://www.piwheels.org/simple/isambard/ as text/html
2023-09-13T15:43:10,737   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/)
2023-09-13T15:43:10,737   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/)
2023-09-13T15:43:10,738   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/)
2023-09-13T15:43:10,739   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/)
2023-09-13T15:43:10,739   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/)
2023-09-13T15:43:10,740   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/)
2023-09-13T15:43:10,740   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp311-cp311-linux_armv7l.whl#sha256=da0939c6735170d08c9e5c63a3d82bb9003d2457ae53546e18eca4b785976758 (from https://www.piwheels.org/simple/isambard/)
2023-09-13T15:43:10,741   Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp311-cp311-linux_armv6l.whl#sha256=da0939c6735170d08c9e5c63a3d82bb9003d2457ae53546e18eca4b785976758 (from https://www.piwheels.org/simple/isambard/)
2023-09-13T15:43:10,742   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/)
2023-09-13T15:43:10,742   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/)
2023-09-13T15:43:10,743   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/)
2023-09-13T15:43:10,743   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/)
2023-09-13T15:43:10,744   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/)
2023-09-13T15:43:10,744   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/)
2023-09-13T15:43:10,745   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/)
2023-09-13T15:43:10,745   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/)
2023-09-13T15:43:10,746   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/)
2023-09-13T15:43:10,747   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/)
2023-09-13T15:43:10,747   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/)
2023-09-13T15:43:10,748   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/)
2023-09-13T15:43:10,748   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/)
2023-09-13T15:43:10,749   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/)
2023-09-13T15:43:10,749   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/)
2023-09-13T15:43:10,750   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/)
2023-09-13T15:43:10,751   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/)
2023-09-13T15:43:10,751   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/)
2023-09-13T15:43:10,752 Skipping link: not a file: https://www.piwheels.org/simple/isambard/
2023-09-13T15:43:10,752 Skipping link: not a file: https://pypi.org/simple/isambard/
2023-09-13T15:43:10,770 Given no hashes to check 1 links for project 'isambard': discarding no candidates
2023-09-13T15:43:10,788 Collecting isambard==2.3.1
2023-09-13T15:43:10,790   Created temporary directory: /tmp/pip-unpack-s56gg0wa
2023-09-13T15:43:11,012   Downloading ISAMBARD-2.3.1.tar.gz (370 kB)
2023-09-13T15:43:11,227   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-es65t3pz'
2023-09-13T15:43:11,229   Running setup.py (path:/tmp/pip-wheel-ih632d7p/isambard_bc27d564e5924c0fa31b73d0ac0fceef/setup.py) egg_info for package isambard
2023-09-13T15:43:11,229   Created temporary directory: /tmp/pip-pip-egg-info-zhjtcb36
2023-09-13T15:43:11,230   Preparing metadata (setup.py): started
2023-09-13T15:43:11,231   Running command python setup.py egg_info
2023-09-13T15:43:13,453   /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-ih632d7p/isambard_bc27d564e5924c0fa31b73d0ac0fceef/src/isambard/specifications/ta_polypeptide.pyx
2023-09-13T15:43:13,453     tree = Parsing.p_module(s, pxd, full_module_name)
2023-09-13T15:43:14,203   Compiling src/isambard/specifications/ta_polypeptide.pyx because it changed.
2023-09-13T15:43:14,204   [1/1] Cythonizing src/isambard/specifications/ta_polypeptide.pyx
2023-09-13T15:43:14,635   running egg_info
2023-09-13T15:43:14,637   creating /tmp/pip-pip-egg-info-zhjtcb36/ISAMBARD.egg-info
2023-09-13T15:43:14,660   writing /tmp/pip-pip-egg-info-zhjtcb36/ISAMBARD.egg-info/PKG-INFO
2023-09-13T15:43:14,664   writing dependency_links to /tmp/pip-pip-egg-info-zhjtcb36/ISAMBARD.egg-info/dependency_links.txt
2023-09-13T15:43:14,666   writing requirements to /tmp/pip-pip-egg-info-zhjtcb36/ISAMBARD.egg-info/requires.txt
2023-09-13T15:43:14,667   writing top-level names to /tmp/pip-pip-egg-info-zhjtcb36/ISAMBARD.egg-info/top_level.txt
2023-09-13T15:43:14,669   writing manifest file '/tmp/pip-pip-egg-info-zhjtcb36/ISAMBARD.egg-info/SOURCES.txt'
2023-09-13T15:43:14,768   reading manifest file '/tmp/pip-pip-egg-info-zhjtcb36/ISAMBARD.egg-info/SOURCES.txt'
2023-09-13T15:43:14,769   reading manifest template 'MANIFEST.in'
2023-09-13T15:43:14,788   adding license file 'LICENSE.txt'
2023-09-13T15:43:14,791   writing manifest file '/tmp/pip-pip-egg-info-zhjtcb36/ISAMBARD.egg-info/SOURCES.txt'
2023-09-13T15:43:15,035   Preparing metadata (setup.py): finished with status 'done'
2023-09-13T15:43:15,039   Source in /tmp/pip-wheel-ih632d7p/isambard_bc27d564e5924c0fa31b73d0ac0fceef 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
2023-09-13T15:43:15,040   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-es65t3pz'
2023-09-13T15:43:15,045 Created temporary directory: /tmp/pip-unpack-k25bgod5
2023-09-13T15:43:15,046 Created temporary directory: /tmp/pip-unpack-p8hsqeel
2023-09-13T15:43:15,055 Building wheels for collected packages: isambard
2023-09-13T15:43:15,059   Created temporary directory: /tmp/pip-wheel-x7zc8l8e
2023-09-13T15:43:15,059   Building wheel for isambard (setup.py): started
2023-09-13T15:43:15,061   Destination directory: /tmp/pip-wheel-x7zc8l8e
2023-09-13T15:43:15,061   Running command python setup.py bdist_wheel
2023-09-13T15:43:16,575   running bdist_wheel
2023-09-13T15:43:16,675   running build
2023-09-13T15:43:16,675   running build_py
2023-09-13T15:43:16,701   creating build
2023-09-13T15:43:16,702   creating build/lib.linux-armv7l-cpython-311
2023-09-13T15:43:16,703   creating build/lib.linux-armv7l-cpython-311/isambard
2023-09-13T15:43:16,704   copying src/isambard/__init__.py -> build/lib.linux-armv7l-cpython-311/isambard
2023-09-13T15:43:16,707   creating build/lib.linux-armv7l-cpython-311/isambard/optimisation
2023-09-13T15:43:16,708   copying src/isambard/optimisation/base_evo_opt.py -> build/lib.linux-armv7l-cpython-311/isambard/optimisation
2023-09-13T15:43:16,710   copying src/isambard/optimisation/__init__.py -> build/lib.linux-armv7l-cpython-311/isambard/optimisation
2023-09-13T15:43:16,712   copying src/isambard/optimisation/mmc_optimizer.py -> build/lib.linux-armv7l-cpython-311/isambard/optimisation
2023-09-13T15:43:16,714   copying src/isambard/optimisation/evo_optimizers.py -> build/lib.linux-armv7l-cpython-311/isambard/optimisation
2023-09-13T15:43:16,717   creating build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-13T15:43:16,718   copying src/isambard/specifications/solenoid.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-13T15:43:16,720   copying src/isambard/specifications/nucleic_acid_duplex.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-13T15:43:16,722   copying src/isambard/specifications/nucleic_acid_strand.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-13T15:43:16,724   copying src/isambard/specifications/__init__.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-13T15:43:16,726   copying src/isambard/specifications/helix.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-13T15:43:16,729   copying src/isambard/specifications/coiledcoil.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-13T15:43:16,732   creating build/lib.linux-armv7l-cpython-311/isambard/modelling
2023-09-13T15:43:16,733   copying src/isambard/modelling/scwrl.py -> build/lib.linux-armv7l-cpython-311/isambard/modelling
2023-09-13T15:43:16,735   copying src/isambard/modelling/__init__.py -> build/lib.linux-armv7l-cpython-311/isambard/modelling
2023-09-13T15:43:16,737   copying src/isambard/modelling/non_canonical.py -> build/lib.linux-armv7l-cpython-311/isambard/modelling
2023-09-13T15:43:16,739   creating build/lib.linux-armv7l-cpython-311/isambard/evaluation
2023-09-13T15:43:16,740   copying src/isambard/evaluation/pacc.py -> build/lib.linux-armv7l-cpython-311/isambard/evaluation
2023-09-13T15:43:16,742   copying src/isambard/evaluation/contact_order.py -> build/lib.linux-armv7l-cpython-311/isambard/evaluation
2023-09-13T15:43:16,744   copying src/isambard/evaluation/__init__.py -> build/lib.linux-armv7l-cpython-311/isambard/evaluation
2023-09-13T15:43:16,745   copying src/isambard/evaluation/packing_density.py -> build/lib.linux-armv7l-cpython-311/isambard/evaluation
2023-09-13T15:43:16,747   copying src/isambard/evaluation/dssp.py -> build/lib.linux-armv7l-cpython-311/isambard/evaluation
2023-09-13T15:43:16,749   copying src/isambard/evaluation/hydrophobic_fitness.py -> build/lib.linux-armv7l-cpython-311/isambard/evaluation
2023-09-13T15:43:16,751   running egg_info
2023-09-13T15:43:16,805   writing src/ISAMBARD.egg-info/PKG-INFO
2023-09-13T15:43:16,808   writing dependency_links to src/ISAMBARD.egg-info/dependency_links.txt
2023-09-13T15:43:16,809   writing requirements to src/ISAMBARD.egg-info/requires.txt
2023-09-13T15:43:16,810   writing top-level names to src/ISAMBARD.egg-info/top_level.txt
2023-09-13T15:43:16,839   reading manifest file 'src/ISAMBARD.egg-info/SOURCES.txt'
2023-09-13T15:43:16,842   reading manifest template 'MANIFEST.in'
2023-09-13T15:43:16,862   adding license file 'LICENSE.txt'
2023-09-13T15:43:16,866   writing manifest file 'src/ISAMBARD.egg-info/SOURCES.txt'
2023-09-13T15:43:16,868   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'isambard.__pycache__' is absent from the `packages` configuration.
2023-09-13T15:43:16,869   !!

2023-09-13T15:43:16,870           ********************************************************************************
2023-09-13T15:43:16,870           ############################
2023-09-13T15:43:16,872           # Package would be ignored #
2023-09-13T15:43:16,872           ############################
2023-09-13T15:43:16,872           Python recognizes 'isambard.__pycache__' as an importable package[^1],
2023-09-13T15:43:16,873           but it is absent from setuptools' `packages` configuration.

2023-09-13T15:43:16,874           This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-13T15:43:16,875           package, please make sure that 'isambard.__pycache__' is explicitly added
2023-09-13T15:43:16,875           to the `packages` configuration field.

2023-09-13T15:43:16,876           Alternatively, you can also rely on setuptools' discovery methods
2023-09-13T15:43:16,877           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-13T15:43:16,877           instead of `find_packages(...)`/`find:`).

2023-09-13T15:43:16,878           You can read more about "package discovery" on setuptools documentation page:

2023-09-13T15:43:16,879           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-13T15:43:16,880           If you don't want 'isambard.__pycache__' to be distributed and are
2023-09-13T15:43:16,881           already explicitly excluding 'isambard.__pycache__' via
2023-09-13T15:43:16,881           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-13T15:43:16,882           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-13T15:43:16,883           combination with a more fine grained `package-data` configuration.

2023-09-13T15:43:16,884           You can read more about "package data files" on setuptools documentation page:

2023-09-13T15:43:16,887           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-13T15:43:16,892           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-13T15:43:16,893                 even if it does not contain any `.py` files.
2023-09-13T15:43:16,893                 On the other hand, currently there is no concept of package data
2023-09-13T15:43:16,894                 directory, all directories are treated like packages.
2023-09-13T15:43:16,894           ********************************************************************************

2023-09-13T15:43:16,895   !!
2023-09-13T15:43:16,896     check.warn(importable)
2023-09-13T15:43:16,897   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'isambard.evaluation.__pycache__' is absent from the `packages` configuration.
2023-09-13T15:43:16,897   !!

2023-09-13T15:43:16,899           ********************************************************************************
2023-09-13T15:43:16,900           ############################
2023-09-13T15:43:16,916           # Package would be ignored #
2023-09-13T15:43:16,916           ############################
2023-09-13T15:43:16,917           Python recognizes 'isambard.evaluation.__pycache__' as an importable package[^1],
2023-09-13T15:43:16,917           but it is absent from setuptools' `packages` configuration.

2023-09-13T15:43:16,918           This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-13T15:43:16,919           package, please make sure that 'isambard.evaluation.__pycache__' is explicitly added
2023-09-13T15:43:16,919           to the `packages` configuration field.

2023-09-13T15:43:16,920           Alternatively, you can also rely on setuptools' discovery methods
2023-09-13T15:43:16,920           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-13T15:43:16,921           instead of `find_packages(...)`/`find:`).

2023-09-13T15:43:16,922           You can read more about "package discovery" on setuptools documentation page:

2023-09-13T15:43:16,922           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-13T15:43:16,923           If you don't want 'isambard.evaluation.__pycache__' to be distributed and are
2023-09-13T15:43:16,924           already explicitly excluding 'isambard.evaluation.__pycache__' via
2023-09-13T15:43:16,924           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-13T15:43:16,925           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-13T15:43:16,925           combination with a more fine grained `package-data` configuration.

2023-09-13T15:43:16,926           You can read more about "package data files" on setuptools documentation page:

2023-09-13T15:43:16,927           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-13T15:43:16,929           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-13T15:43:16,929                 even if it does not contain any `.py` files.
2023-09-13T15:43:16,929                 On the other hand, currently there is no concept of package data
2023-09-13T15:43:16,930                 directory, all directories are treated like packages.
2023-09-13T15:43:16,930           ********************************************************************************

2023-09-13T15:43:16,932   !!
2023-09-13T15:43:16,932     check.warn(importable)
2023-09-13T15:43:16,933   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'isambard.modelling.__pycache__' is absent from the `packages` configuration.
2023-09-13T15:43:16,933   !!

2023-09-13T15:43:16,934           ********************************************************************************
2023-09-13T15:43:16,934           ############################
2023-09-13T15:43:16,935           # Package would be ignored #
2023-09-13T15:43:16,935           ############################
2023-09-13T15:43:16,936           Python recognizes 'isambard.modelling.__pycache__' as an importable package[^1],
2023-09-13T15:43:16,936           but it is absent from setuptools' `packages` configuration.

2023-09-13T15:43:16,937           This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-13T15:43:16,938           package, please make sure that 'isambard.modelling.__pycache__' is explicitly added
2023-09-13T15:43:16,938           to the `packages` configuration field.

2023-09-13T15:43:16,939           Alternatively, you can also rely on setuptools' discovery methods
2023-09-13T15:43:16,940           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-13T15:43:16,940           instead of `find_packages(...)`/`find:`).

2023-09-13T15:43:16,941           You can read more about "package discovery" on setuptools documentation page:

2023-09-13T15:43:16,942           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-13T15:43:16,944           If you don't want 'isambard.modelling.__pycache__' to be distributed and are
2023-09-13T15:43:16,944           already explicitly excluding 'isambard.modelling.__pycache__' via
2023-09-13T15:43:16,944           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-13T15:43:16,945           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-13T15:43:16,945           combination with a more fine grained `package-data` configuration.

2023-09-13T15:43:16,946           You can read more about "package data files" on setuptools documentation page:

2023-09-13T15:43:16,947           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-13T15:43:16,948           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-13T15:43:16,949                 even if it does not contain any `.py` files.
2023-09-13T15:43:16,949                 On the other hand, currently there is no concept of package data
2023-09-13T15:43:16,949                 directory, all directories are treated like packages.
2023-09-13T15:43:16,950           ********************************************************************************

2023-09-13T15:43:16,951   !!
2023-09-13T15:43:16,951     check.warn(importable)
2023-09-13T15:43:16,952   /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.
2023-09-13T15:43:16,952   !!

2023-09-13T15:43:16,953           ********************************************************************************
2023-09-13T15:43:16,953           ############################
2023-09-13T15:43:16,954           # Package would be ignored #
2023-09-13T15:43:16,954           ############################
2023-09-13T15:43:16,955           Python recognizes 'isambard.modelling.reference_ampals' as an importable package[^1],
2023-09-13T15:43:16,955           but it is absent from setuptools' `packages` configuration.

2023-09-13T15:43:16,956           This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-13T15:43:16,957           package, please make sure that 'isambard.modelling.reference_ampals' is explicitly added
2023-09-13T15:43:16,957           to the `packages` configuration field.

2023-09-13T15:43:16,958           Alternatively, you can also rely on setuptools' discovery methods
2023-09-13T15:43:16,959           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-13T15:43:16,959           instead of `find_packages(...)`/`find:`).

2023-09-13T15:43:16,960           You can read more about "package discovery" on setuptools documentation page:

2023-09-13T15:43:16,961           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-13T15:43:16,962           If you don't want 'isambard.modelling.reference_ampals' to be distributed and are
2023-09-13T15:43:16,963           already explicitly excluding 'isambard.modelling.reference_ampals' via
2023-09-13T15:43:16,963           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-13T15:43:16,964           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-13T15:43:16,965           combination with a more fine grained `package-data` configuration.

2023-09-13T15:43:16,966           You can read more about "package data files" on setuptools documentation page:

2023-09-13T15:43:16,967           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-13T15:43:16,969           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-13T15:43:16,970                 even if it does not contain any `.py` files.
2023-09-13T15:43:16,970                 On the other hand, currently there is no concept of package data
2023-09-13T15:43:16,971                 directory, all directories are treated like packages.
2023-09-13T15:43:16,971           ********************************************************************************

2023-09-13T15:43:16,972   !!
2023-09-13T15:43:16,973     check.warn(importable)
2023-09-13T15:43:16,973   /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.
2023-09-13T15:43:16,974   !!

2023-09-13T15:43:16,974           ********************************************************************************
2023-09-13T15:43:16,975           ############################
2023-09-13T15:43:16,975           # Package would be ignored #
2023-09-13T15:43:16,976           ############################
2023-09-13T15:43:16,976           Python recognizes 'isambard.modelling.reference_ampals.non_canonical_amino_acids' as an importable package[^1],
2023-09-13T15:43:16,977           but it is absent from setuptools' `packages` configuration.

2023-09-13T15:43:16,978           This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-13T15:43:16,978           package, please make sure that 'isambard.modelling.reference_ampals.non_canonical_amino_acids' is explicitly added
2023-09-13T15:43:16,978           to the `packages` configuration field.

2023-09-13T15:43:16,979           Alternatively, you can also rely on setuptools' discovery methods
2023-09-13T15:43:16,980           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-13T15:43:16,980           instead of `find_packages(...)`/`find:`).

2023-09-13T15:43:16,981           You can read more about "package discovery" on setuptools documentation page:

2023-09-13T15:43:16,983           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-13T15:43:16,984           If you don't want 'isambard.modelling.reference_ampals.non_canonical_amino_acids' to be distributed and are
2023-09-13T15:43:16,984           already explicitly excluding 'isambard.modelling.reference_ampals.non_canonical_amino_acids' via
2023-09-13T15:43:16,985           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-13T15:43:16,985           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-13T15:43:16,988           combination with a more fine grained `package-data` configuration.

2023-09-13T15:43:16,989           You can read more about "package data files" on setuptools documentation page:

2023-09-13T15:43:16,994           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-13T15:43:16,996           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-13T15:43:16,997                 even if it does not contain any `.py` files.
2023-09-13T15:43:16,997                 On the other hand, currently there is no concept of package data
2023-09-13T15:43:16,998                 directory, all directories are treated like packages.
2023-09-13T15:43:16,998           ********************************************************************************

2023-09-13T15:43:16,999   !!
2023-09-13T15:43:17,000     check.warn(importable)
2023-09-13T15:43:17,000   creating build/lib.linux-armv7l-cpython-311/isambard/__pycache__
2023-09-13T15:43:17,001   copying src/isambard/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/isambard/__pycache__
2023-09-13T15:43:17,001   copying src/isambard/specifications/ta_polypeptide.c -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-13T15:43:17,002   copying src/isambard/specifications/ta_polypeptide.cpython-37m-x86_64-linux-gnu.so -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-13T15:43:17,002   copying src/isambard/specifications/ta_polypeptide.pyx -> build/lib.linux-armv7l-cpython-311/isambard/specifications
2023-09-13T15:43:17,003   creating build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__
2023-09-13T15:43:17,003   copying src/isambard/modelling/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__
2023-09-13T15:43:17,004   copying src/isambard/modelling/__pycache__/create_loop_database.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__
2023-09-13T15:43:17,005   copying src/isambard/modelling/__pycache__/extract_loop_data.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__
2023-09-13T15:43:17,005   copying src/isambard/modelling/__pycache__/non_canonical.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__
2023-09-13T15:43:17,006   copying src/isambard/modelling/__pycache__/scwrl.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__
2023-09-13T15:43:17,006   creating build/lib.linux-armv7l-cpython-311/isambard/modelling/reference_ampals
2023-09-13T15:43:17,007   copying src/isambard/modelling/reference_ampals/README.md -> build/lib.linux-armv7l-cpython-311/isambard/modelling/reference_ampals
2023-09-13T15:43:17,007   creating build/lib.linux-armv7l-cpython-311/isambard/modelling/reference_ampals/non_canonical_amino_acids
2023-09-13T15:43:17,007   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
2023-09-13T15:43:17,008   creating build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__
2023-09-13T15:43:17,008   copying src/isambard/evaluation/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__
2023-09-13T15:43:17,009   copying src/isambard/evaluation/__pycache__/contact_order.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__
2023-09-13T15:43:17,009   copying src/isambard/evaluation/__pycache__/dssp.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__
2023-09-13T15:43:17,010   copying src/isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__
2023-09-13T15:43:17,010   copying src/isambard/evaluation/__pycache__/pacc.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__
2023-09-13T15:43:17,010   copying src/isambard/evaluation/__pycache__/packing_density.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__
2023-09-13T15:43:17,011   running build_ext
2023-09-13T15:43:17,012   building 'isambard.specifications.ta_polypeptide' extension
2023-09-13T15:43:17,012   creating build/temp.linux-armv7l-cpython-311
2023-09-13T15:43:17,013   creating build/temp.linux-armv7l-cpython-311/src
2023-09-13T15:43:17,013   creating build/temp.linux-armv7l-cpython-311/src/isambard
2023-09-13T15:43:17,014   creating build/temp.linux-armv7l-cpython-311/src/isambard/specifications
2023-09-13T15:43:17,014   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
2023-09-13T15:43:36,811   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
2023-09-13T15:43:36,953   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2023-09-13T15:43:36,954   !!

2023-09-13T15:43:36,955           ********************************************************************************
2023-09-13T15:43:36,955           Please avoid running ``setup.py`` directly.
2023-09-13T15:43:36,956           Instead, use pypa/build, pypa/installer or other
2023-09-13T15:43:36,957           standards-based tools.

2023-09-13T15:43:36,958           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2023-09-13T15:43:36,958           ********************************************************************************

2023-09-13T15:43:36,959   !!
2023-09-13T15:43:36,959     self.initialize_options()
2023-09-13T15:43:36,978   installing to build/bdist.linux-armv7l/wheel
2023-09-13T15:43:36,978   running install
2023-09-13T15:43:37,002   running install_lib
2023-09-13T15:43:37,027   creating build/bdist.linux-armv7l
2023-09-13T15:43:37,027   creating build/bdist.linux-armv7l/wheel
2023-09-13T15:43:37,029   creating build/bdist.linux-armv7l/wheel/isambard
2023-09-13T15:43:37,030   creating build/bdist.linux-armv7l/wheel/isambard/optimisation
2023-09-13T15:43:37,031   copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/base_evo_opt.py -> build/bdist.linux-armv7l/wheel/isambard/optimisation
2023-09-13T15:43:37,033   copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/__init__.py -> build/bdist.linux-armv7l/wheel/isambard/optimisation
2023-09-13T15:43:37,035   copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/mmc_optimizer.py -> build/bdist.linux-armv7l/wheel/isambard/optimisation
2023-09-13T15:43:37,037   copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/evo_optimizers.py -> build/bdist.linux-armv7l/wheel/isambard/optimisation
2023-09-13T15:43:37,040   copying build/lib.linux-armv7l-cpython-311/isambard/__init__.py -> build/bdist.linux-armv7l/wheel/isambard
2023-09-13T15:43:37,042   creating build/bdist.linux-armv7l/wheel/isambard/__pycache__
2023-09-13T15:43:37,043   copying build/lib.linux-armv7l-cpython-311/isambard/__pycache__/__init__.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/isambard/__pycache__
2023-09-13T15:43:37,045   creating build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-13T15:43:37,046   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/solenoid.py -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-13T15:43:37,049   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/ta_polypeptide.pyx -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-13T15:43:37,051   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/nucleic_acid_duplex.py -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-13T15:43:37,053   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/ta_polypeptide.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-13T15:43:37,065   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/nucleic_acid_strand.py -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-13T15:43:37,067   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/__init__.py -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-13T15:43:37,069   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/helix.py -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-13T15:43:37,072   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/coiledcoil.py -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-13T15:43:37,074   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/ta_polypeptide.cpython-37m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-13T15:43:37,088   copying build/lib.linux-armv7l-cpython-311/isambard/specifications/ta_polypeptide.c -> build/bdist.linux-armv7l/wheel/isambard/specifications
2023-09-13T15:43:37,099   creating build/bdist.linux-armv7l/wheel/isambard/modelling
2023-09-13T15:43:37,100   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/scwrl.py -> build/bdist.linux-armv7l/wheel/isambard/modelling
2023-09-13T15:43:37,103   creating build/bdist.linux-armv7l/wheel/isambard/modelling/reference_ampals
2023-09-13T15:43:37,104   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/reference_ampals/README.md -> build/bdist.linux-armv7l/wheel/isambard/modelling/reference_ampals
2023-09-13T15:43:37,107   creating build/bdist.linux-armv7l/wheel/isambard/modelling/reference_ampals/non_canonical_amino_acids
2023-09-13T15:43:37,108   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
2023-09-13T15:43:37,110   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__init__.py -> build/bdist.linux-armv7l/wheel/isambard/modelling
2023-09-13T15:43:37,113   creating build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2023-09-13T15:43:37,114   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/create_loop_database.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2023-09-13T15:43:37,116   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/scwrl.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2023-09-13T15:43:37,119   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/non_canonical.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2023-09-13T15:43:37,121   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/extract_loop_data.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2023-09-13T15:43:37,123   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/__init__.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__
2023-09-13T15:43:37,125   copying build/lib.linux-armv7l-cpython-311/isambard/modelling/non_canonical.py -> build/bdist.linux-armv7l/wheel/isambard/modelling
2023-09-13T15:43:37,128   creating build/bdist.linux-armv7l/wheel/isambard/evaluation
2023-09-13T15:43:37,129   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/pacc.py -> build/bdist.linux-armv7l/wheel/isambard/evaluation
2023-09-13T15:43:37,131   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/contact_order.py -> build/bdist.linux-armv7l/wheel/isambard/evaluation
2023-09-13T15:43:37,133   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__init__.py -> build/bdist.linux-armv7l/wheel/isambard/evaluation
2023-09-13T15:43:37,135   creating build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__
2023-09-13T15:43:37,137   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__/contact_order.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__
2023-09-13T15:43:37,139   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__/__init__.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__
2023-09-13T15:43:37,140   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__
2023-09-13T15:43:37,143   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__/dssp.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__
2023-09-13T15:43:37,145   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__/packing_density.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__
2023-09-13T15:43:37,147   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__/pacc.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__
2023-09-13T15:43:37,150   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/packing_density.py -> build/bdist.linux-armv7l/wheel/isambard/evaluation
2023-09-13T15:43:37,151   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/dssp.py -> build/bdist.linux-armv7l/wheel/isambard/evaluation
2023-09-13T15:43:37,154   copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/hydrophobic_fitness.py -> build/bdist.linux-armv7l/wheel/isambard/evaluation
2023-09-13T15:43:37,156   running install_egg_info
2023-09-13T15:43:37,186   Copying src/ISAMBARD.egg-info to build/bdist.linux-armv7l/wheel/ISAMBARD-2.3.1-py3.11.egg-info
2023-09-13T15:43:37,199   running install_scripts
2023-09-13T15:43:37,250   creating build/bdist.linux-armv7l/wheel/ISAMBARD-2.3.1.dist-info/WHEEL
2023-09-13T15:43:37,253   creating '/tmp/pip-wheel-x7zc8l8e/ISAMBARD-2.3.1-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-09-13T15:43:37,256   adding 'isambard/__init__.py'
2023-09-13T15:43:37,258   adding 'isambard/__pycache__/__init__.cpython-37.pyc'
2023-09-13T15:43:37,260   adding 'isambard/evaluation/__init__.py'
2023-09-13T15:43:37,262   adding 'isambard/evaluation/contact_order.py'
2023-09-13T15:43:37,263   adding 'isambard/evaluation/dssp.py'
2023-09-13T15:43:37,265   adding 'isambard/evaluation/hydrophobic_fitness.py'
2023-09-13T15:43:37,267   adding 'isambard/evaluation/pacc.py'
2023-09-13T15:43:37,269   adding 'isambard/evaluation/packing_density.py'
2023-09-13T15:43:37,271   adding 'isambard/evaluation/__pycache__/__init__.cpython-37.pyc'
2023-09-13T15:43:37,273   adding 'isambard/evaluation/__pycache__/contact_order.cpython-37.pyc'
2023-09-13T15:43:37,275   adding 'isambard/evaluation/__pycache__/dssp.cpython-37.pyc'
2023-09-13T15:43:37,276   adding 'isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-37.pyc'
2023-09-13T15:43:37,279   adding 'isambard/evaluation/__pycache__/pacc.cpython-37.pyc'
2023-09-13T15:43:37,280   adding 'isambard/evaluation/__pycache__/packing_density.cpython-37.pyc'
2023-09-13T15:43:37,282   adding 'isambard/modelling/__init__.py'
2023-09-13T15:43:37,284   adding 'isambard/modelling/non_canonical.py'
2023-09-13T15:43:37,285   adding 'isambard/modelling/scwrl.py'
2023-09-13T15:43:37,287   adding 'isambard/modelling/__pycache__/__init__.cpython-37.pyc'
2023-09-13T15:43:37,290   adding 'isambard/modelling/__pycache__/create_loop_database.cpython-37.pyc'
2023-09-13T15:43:37,292   adding 'isambard/modelling/__pycache__/extract_loop_data.cpython-37.pyc'
2023-09-13T15:43:37,294   adding 'isambard/modelling/__pycache__/non_canonical.cpython-37.pyc'
2023-09-13T15:43:37,296   adding 'isambard/modelling/__pycache__/scwrl.cpython-37.pyc'
2023-09-13T15:43:37,298   adding 'isambard/modelling/reference_ampals/README.md'
2023-09-13T15:43:37,300   adding 'isambard/modelling/reference_ampals/non_canonical_amino_acids/hydroxyproline_ref_1bkv_0_6.pickle'
2023-09-13T15:43:37,302   adding 'isambard/optimisation/__init__.py'
2023-09-13T15:43:37,304   adding 'isambard/optimisation/base_evo_opt.py'
2023-09-13T15:43:37,307   adding 'isambard/optimisation/evo_optimizers.py'
2023-09-13T15:43:37,310   adding 'isambard/optimisation/mmc_optimizer.py'
2023-09-13T15:43:37,312   adding 'isambard/specifications/__init__.py'
2023-09-13T15:43:37,313   adding 'isambard/specifications/coiledcoil.py'
2023-09-13T15:43:37,316   adding 'isambard/specifications/helix.py'
2023-09-13T15:43:37,318   adding 'isambard/specifications/nucleic_acid_duplex.py'
2023-09-13T15:43:37,320   adding 'isambard/specifications/nucleic_acid_strand.py'
2023-09-13T15:43:37,322   adding 'isambard/specifications/solenoid.py'
2023-09-13T15:43:37,371   adding 'isambard/specifications/ta_polypeptide.c'
2023-09-13T15:43:37,514   adding 'isambard/specifications/ta_polypeptide.cpython-311-arm-linux-gnueabihf.so'
2023-09-13T15:43:37,644   adding 'isambard/specifications/ta_polypeptide.cpython-37m-x86_64-linux-gnu.so'
2023-09-13T15:43:37,653   adding 'isambard/specifications/ta_polypeptide.pyx'
2023-09-13T15:43:37,655   adding 'ISAMBARD-2.3.1.dist-info/LICENSE.txt'
2023-09-13T15:43:37,656   adding 'ISAMBARD-2.3.1.dist-info/METADATA'
2023-09-13T15:43:37,658   adding 'ISAMBARD-2.3.1.dist-info/WHEEL'
2023-09-13T15:43:37,659   adding 'ISAMBARD-2.3.1.dist-info/top_level.txt'
2023-09-13T15:43:37,660   adding 'ISAMBARD-2.3.1.dist-info/RECORD'
2023-09-13T15:43:37,670   removing build/bdist.linux-armv7l/wheel
2023-09-13T15:43:37,827   Building wheel for isambard (setup.py): finished with status 'done'
2023-09-13T15:43:37,838   Created wheel for isambard: filename=ISAMBARD-2.3.1-cp311-cp311-linux_armv7l.whl size=695650 sha256=0c3ad4f0c4a0b8169c1ea441c243457c4de16bbc36eaaa2aa170c0965e87c84e
2023-09-13T15:43:37,839   Stored in directory: /tmp/pip-ephem-wheel-cache-qy9tsbwy/wheels/6b/4b/a7/78db3cba9b02720d1202c72299d9d6ce57cc04df0142ee8431
2023-09-13T15:43:37,851 Successfully built isambard
2023-09-13T15:43:37,880 Removed build tracker: '/tmp/pip-build-tracker-es65t3pz'