2023-09-10T15:13:13,148 Created temporary directory: /tmp/pip-build-tracker-16wgowti 2023-09-10T15:13:13,149 Initialized build tracking at /tmp/pip-build-tracker-16wgowti 2023-09-10T15:13:13,149 Created build tracker: /tmp/pip-build-tracker-16wgowti 2023-09-10T15:13:13,150 Entered build tracker: /tmp/pip-build-tracker-16wgowti 2023-09-10T15:13:13,151 Created temporary directory: /tmp/pip-wheel-xwr5w3_w 2023-09-10T15:13:13,154 Created temporary directory: /tmp/pip-ephem-wheel-cache-jke6vfl1 2023-09-10T15:13:13,176 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-10T15:13:13,180 2 location(s) to search for versions of isambard: 2023-09-10T15:13:13,180 * https://pypi.org/simple/isambard/ 2023-09-10T15:13:13,180 * https://www.piwheels.org/simple/isambard/ 2023-09-10T15:13:13,181 Fetching project page and analyzing links: https://pypi.org/simple/isambard/ 2023-09-10T15:13:13,182 Getting page https://pypi.org/simple/isambard/ 2023-09-10T15:13:13,183 Found index url https://pypi.org/simple/ 2023-09-10T15:13:13,410 Fetched page https://pypi.org/simple/isambard/ as application/vnd.pypi.simple.v1+json 2023-09-10T15:13:13,411 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 2023-09-10T15:13:13,412 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 2023-09-10T15:13:13,413 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 2023-09-10T15:13:13,413 Fetching project page and analyzing links: https://www.piwheels.org/simple/isambard/ 2023-09-10T15:13:13,414 Getting page https://www.piwheels.org/simple/isambard/ 2023-09-10T15:13:13,415 Found index url https://www.piwheels.org/simple/ 2023-09-10T15:13:14,658 Fetched page https://www.piwheels.org/simple/isambard/ as text/html 2023-09-10T15:13:14,675 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/) 2023-09-10T15:13:14,676 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/) 2023-09-10T15:13:14,677 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/) 2023-09-10T15:13:14,678 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/) 2023-09-10T15:13:14,679 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/) 2023-09-10T15:13:14,680 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/) 2023-09-10T15:13:14,681 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/) 2023-09-10T15:13:14,682 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/) 2023-09-10T15:13:14,683 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/) 2023-09-10T15:13:14,684 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/) 2023-09-10T15:13:14,685 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/) 2023-09-10T15:13:14,686 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/) 2023-09-10T15:13:14,687 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/) 2023-09-10T15:13:14,687 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/) 2023-09-10T15:13:14,688 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/) 2023-09-10T15:13:14,689 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/) 2023-09-10T15:13:14,690 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/) 2023-09-10T15:13:14,691 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/) 2023-09-10T15:13:14,692 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/) 2023-09-10T15:13:14,693 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/) 2023-09-10T15:13:14,693 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/) 2023-09-10T15:13:14,694 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/) 2023-09-10T15:13:14,695 Skipping link: not a file: https://www.piwheels.org/simple/isambard/ 2023-09-10T15:13:14,696 Skipping link: not a file: https://pypi.org/simple/isambard/ 2023-09-10T15:13:14,734 Given no hashes to check 1 links for project 'isambard': discarding no candidates 2023-09-10T15:13:14,760 Collecting isambard==2.0.1 2023-09-10T15:13:14,763 Created temporary directory: /tmp/pip-unpack-t2gorpdr 2023-09-10T15:13:15,023 Downloading ISAMBARD-2.0.1.tar.gz (337 kB) 2023-09-10T15:13:15,476 Added isambard==2.0.1 from https://files.pythonhosted.org/packages/ca/6d/9456a011721c3376fc03e77d5ea89f563dfac30660be8b2517ad1ba2c44a/ISAMBARD-2.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-16wgowti' 2023-09-10T15:13:15,478 Running setup.py (path:/tmp/pip-wheel-xwr5w3_w/isambard_e8d88189a58145539ea6b4ff60d353fb/setup.py) egg_info for package isambard 2023-09-10T15:13:15,479 Created temporary directory: /tmp/pip-pip-egg-info-o62s945w 2023-09-10T15:13:15,479 Preparing metadata (setup.py): started 2023-09-10T15:13:15,481 Running command python setup.py egg_info 2023-09-10T15:13:17,732 /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-xwr5w3_w/isambard_e8d88189a58145539ea6b4ff60d353fb/src/isambard/specifications/ta_polypeptide.pyx 2023-09-10T15:13:17,732 tree = Parsing.p_module(s, pxd, full_module_name) 2023-09-10T15:13:18,486 Compiling src/isambard/specifications/ta_polypeptide.pyx because it changed. 2023-09-10T15:13:18,487 [1/1] Cythonizing src/isambard/specifications/ta_polypeptide.pyx 2023-09-10T15:13:18,945 running egg_info 2023-09-10T15:13:18,947 creating /tmp/pip-pip-egg-info-o62s945w/ISAMBARD.egg-info 2023-09-10T15:13:18,971 writing /tmp/pip-pip-egg-info-o62s945w/ISAMBARD.egg-info/PKG-INFO 2023-09-10T15:13:18,975 writing dependency_links to /tmp/pip-pip-egg-info-o62s945w/ISAMBARD.egg-info/dependency_links.txt 2023-09-10T15:13:18,977 writing requirements to /tmp/pip-pip-egg-info-o62s945w/ISAMBARD.egg-info/requires.txt 2023-09-10T15:13:18,978 writing top-level names to /tmp/pip-pip-egg-info-o62s945w/ISAMBARD.egg-info/top_level.txt 2023-09-10T15:13:18,979 writing manifest file '/tmp/pip-pip-egg-info-o62s945w/ISAMBARD.egg-info/SOURCES.txt' 2023-09-10T15:13:19,083 reading manifest file '/tmp/pip-pip-egg-info-o62s945w/ISAMBARD.egg-info/SOURCES.txt' 2023-09-10T15:13:19,084 reading manifest template 'MANIFEST.in' 2023-09-10T15:13:19,108 adding license file 'LICENSE.txt' 2023-09-10T15:13:19,112 writing manifest file '/tmp/pip-pip-egg-info-o62s945w/ISAMBARD.egg-info/SOURCES.txt' 2023-09-10T15:13:19,358 Preparing metadata (setup.py): finished with status 'done' 2023-09-10T15:13:19,363 Source in /tmp/pip-wheel-xwr5w3_w/isambard_e8d88189a58145539ea6b4ff60d353fb has version 2.0.1, which satisfies requirement isambard==2.0.1 from https://files.pythonhosted.org/packages/ca/6d/9456a011721c3376fc03e77d5ea89f563dfac30660be8b2517ad1ba2c44a/ISAMBARD-2.0.1.tar.gz 2023-09-10T15:13:19,364 Removed isambard==2.0.1 from https://files.pythonhosted.org/packages/ca/6d/9456a011721c3376fc03e77d5ea89f563dfac30660be8b2517ad1ba2c44a/ISAMBARD-2.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-16wgowti' 2023-09-10T15:13:19,368 Created temporary directory: /tmp/pip-unpack-j1oxxmt4 2023-09-10T15:13:19,370 Created temporary directory: /tmp/pip-unpack-3hoz65ih 2023-09-10T15:13:19,378 Building wheels for collected packages: isambard 2023-09-10T15:13:19,382 Created temporary directory: /tmp/pip-wheel-ewko90lr 2023-09-10T15:13:19,383 Building wheel for isambard (setup.py): started 2023-09-10T15:13:19,384 Destination directory: /tmp/pip-wheel-ewko90lr 2023-09-10T15:13:19,385 Running command python setup.py bdist_wheel 2023-09-10T15:13:20,922 running bdist_wheel 2023-09-10T15:13:21,020 running build 2023-09-10T15:13:21,021 running build_py 2023-09-10T15:13:21,047 creating build 2023-09-10T15:13:21,048 creating build/lib.linux-armv7l-cpython-311 2023-09-10T15:13:21,048 creating build/lib.linux-armv7l-cpython-311/isambard 2023-09-10T15:13:21,050 copying src/isambard/__init__.py -> build/lib.linux-armv7l-cpython-311/isambard 2023-09-10T15:13:21,052 creating build/lib.linux-armv7l-cpython-311/isambard/specifications 2023-09-10T15:13:21,053 copying src/isambard/specifications/helix.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications 2023-09-10T15:13:21,055 copying src/isambard/specifications/nucleic_acid_duplex.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications 2023-09-10T15:13:21,057 copying src/isambard/specifications/nucleic_acid_strand.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications 2023-09-10T15:13:21,059 copying src/isambard/specifications/solenoid.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications 2023-09-10T15:13:21,061 copying src/isambard/specifications/__init__.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications 2023-09-10T15:13:21,063 copying src/isambard/specifications/coiledcoil.py -> build/lib.linux-armv7l-cpython-311/isambard/specifications 2023-09-10T15:13:21,066 creating build/lib.linux-armv7l-cpython-311/isambard/modelling 2023-09-10T15:13:21,067 copying src/isambard/modelling/non_canonical.py -> build/lib.linux-armv7l-cpython-311/isambard/modelling 2023-09-10T15:13:21,069 copying src/isambard/modelling/__init__.py -> build/lib.linux-armv7l-cpython-311/isambard/modelling 2023-09-10T15:13:21,070 copying src/isambard/modelling/scwrl.py -> build/lib.linux-armv7l-cpython-311/isambard/modelling 2023-09-10T15:13:21,073 creating build/lib.linux-armv7l-cpython-311/isambard/optimisation 2023-09-10T15:13:21,074 copying src/isambard/optimisation/mmc_optimizer.py -> build/lib.linux-armv7l-cpython-311/isambard/optimisation 2023-09-10T15:13:21,077 copying src/isambard/optimisation/__init__.py -> build/lib.linux-armv7l-cpython-311/isambard/optimisation 2023-09-10T15:13:21,078 copying src/isambard/optimisation/base_evo_opt.py -> build/lib.linux-armv7l-cpython-311/isambard/optimisation 2023-09-10T15:13:21,081 copying src/isambard/optimisation/evo_optimizers.py -> build/lib.linux-armv7l-cpython-311/isambard/optimisation 2023-09-10T15:13:21,084 creating build/lib.linux-armv7l-cpython-311/isambard/evaluation 2023-09-10T15:13:21,085 copying src/isambard/evaluation/hydrophobic_fitness.py -> build/lib.linux-armv7l-cpython-311/isambard/evaluation 2023-09-10T15:13:21,087 copying src/isambard/evaluation/__init__.py -> build/lib.linux-armv7l-cpython-311/isambard/evaluation 2023-09-10T15:13:21,089 copying src/isambard/evaluation/contact_order.py -> build/lib.linux-armv7l-cpython-311/isambard/evaluation 2023-09-10T15:13:21,091 running egg_info 2023-09-10T15:13:21,146 writing src/ISAMBARD.egg-info/PKG-INFO 2023-09-10T15:13:21,150 writing dependency_links to src/ISAMBARD.egg-info/dependency_links.txt 2023-09-10T15:13:21,152 writing requirements to src/ISAMBARD.egg-info/requires.txt 2023-09-10T15:13:21,153 writing top-level names to src/ISAMBARD.egg-info/top_level.txt 2023-09-10T15:13:21,182 reading manifest file 'src/ISAMBARD.egg-info/SOURCES.txt' 2023-09-10T15:13:21,185 reading manifest template 'MANIFEST.in' 2023-09-10T15:13:21,209 adding license file 'LICENSE.txt' 2023-09-10T15:13:21,212 writing manifest file 'src/ISAMBARD.egg-info/SOURCES.txt' 2023-09-10T15:13:21,215 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'isambard.__pycache__' is absent from the `packages` configuration. 2023-09-10T15:13:21,215 !! 2023-09-10T15:13:21,217 ******************************************************************************** 2023-09-10T15:13:21,217 ############################ 2023-09-10T15:13:21,218 # Package would be ignored # 2023-09-10T15:13:21,218 ############################ 2023-09-10T15:13:21,219 Python recognizes 'isambard.__pycache__' as an importable package[^1], 2023-09-10T15:13:21,219 but it is absent from setuptools' `packages` configuration. 2023-09-10T15:13:21,220 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-10T15:13:21,221 package, please make sure that 'isambard.__pycache__' is explicitly added 2023-09-10T15:13:21,221 to the `packages` configuration field. 2023-09-10T15:13:21,222 Alternatively, you can also rely on setuptools' discovery methods 2023-09-10T15:13:21,223 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-10T15:13:21,223 instead of `find_packages(...)`/`find:`). 2023-09-10T15:13:21,224 You can read more about "package discovery" on setuptools documentation page: 2023-09-10T15:13:21,225 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-10T15:13:21,226 If you don't want 'isambard.__pycache__' to be distributed and are 2023-09-10T15:13:21,226 already explicitly excluding 'isambard.__pycache__' via 2023-09-10T15:13:21,227 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-10T15:13:21,227 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-10T15:13:21,228 combination with a more fine grained `package-data` configuration. 2023-09-10T15:13:21,230 You can read more about "package data files" on setuptools documentation page: 2023-09-10T15:13:21,235 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-10T15:13:21,236 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-10T15:13:21,237 even if it does not contain any `.py` files. 2023-09-10T15:13:21,237 On the other hand, currently there is no concept of package data 2023-09-10T15:13:21,238 directory, all directories are treated like packages. 2023-09-10T15:13:21,238 ******************************************************************************** 2023-09-10T15:13:21,239 !! 2023-09-10T15:13:21,241 check.warn(importable) 2023-09-10T15:13:21,244 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'isambard.evaluation.__pycache__' is absent from the `packages` configuration. 2023-09-10T15:13:21,247 !! 2023-09-10T15:13:21,248 ******************************************************************************** 2023-09-10T15:13:21,248 ############################ 2023-09-10T15:13:21,249 # Package would be ignored # 2023-09-10T15:13:21,249 ############################ 2023-09-10T15:13:21,250 Python recognizes 'isambard.evaluation.__pycache__' as an importable package[^1], 2023-09-10T15:13:21,250 but it is absent from setuptools' `packages` configuration. 2023-09-10T15:13:21,251 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-10T15:13:21,252 package, please make sure that 'isambard.evaluation.__pycache__' is explicitly added 2023-09-10T15:13:21,252 to the `packages` configuration field. 2023-09-10T15:13:21,253 Alternatively, you can also rely on setuptools' discovery methods 2023-09-10T15:13:21,254 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-10T15:13:21,255 instead of `find_packages(...)`/`find:`). 2023-09-10T15:13:21,256 You can read more about "package discovery" on setuptools documentation page: 2023-09-10T15:13:21,257 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-10T15:13:21,258 If you don't want 'isambard.evaluation.__pycache__' to be distributed and are 2023-09-10T15:13:21,258 already explicitly excluding 'isambard.evaluation.__pycache__' via 2023-09-10T15:13:21,259 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-10T15:13:21,259 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-10T15:13:21,260 combination with a more fine grained `package-data` configuration. 2023-09-10T15:13:21,261 You can read more about "package data files" on setuptools documentation page: 2023-09-10T15:13:21,262 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-10T15:13:21,263 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-10T15:13:21,264 even if it does not contain any `.py` files. 2023-09-10T15:13:21,264 On the other hand, currently there is no concept of package data 2023-09-10T15:13:21,265 directory, all directories are treated like packages. 2023-09-10T15:13:21,265 ******************************************************************************** 2023-09-10T15:13:21,266 !! 2023-09-10T15:13:21,267 check.warn(importable) 2023-09-10T15:13:21,268 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'isambard.modelling.__pycache__' is absent from the `packages` configuration. 2023-09-10T15:13:21,268 !! 2023-09-10T15:13:21,269 ******************************************************************************** 2023-09-10T15:13:21,270 ############################ 2023-09-10T15:13:21,271 # Package would be ignored # 2023-09-10T15:13:21,271 ############################ 2023-09-10T15:13:21,272 Python recognizes 'isambard.modelling.__pycache__' as an importable package[^1], 2023-09-10T15:13:21,272 but it is absent from setuptools' `packages` configuration. 2023-09-10T15:13:21,274 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-10T15:13:21,274 package, please make sure that 'isambard.modelling.__pycache__' is explicitly added 2023-09-10T15:13:21,275 to the `packages` configuration field. 2023-09-10T15:13:21,276 Alternatively, you can also rely on setuptools' discovery methods 2023-09-10T15:13:21,276 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-10T15:13:21,277 instead of `find_packages(...)`/`find:`). 2023-09-10T15:13:21,278 You can read more about "package discovery" on setuptools documentation page: 2023-09-10T15:13:21,279 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-10T15:13:21,280 If you don't want 'isambard.modelling.__pycache__' to be distributed and are 2023-09-10T15:13:21,281 already explicitly excluding 'isambard.modelling.__pycache__' via 2023-09-10T15:13:21,282 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-10T15:13:21,282 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-10T15:13:21,283 combination with a more fine grained `package-data` configuration. 2023-09-10T15:13:21,284 You can read more about "package data files" on setuptools documentation page: 2023-09-10T15:13:21,285 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-10T15:13:21,286 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-10T15:13:21,287 even if it does not contain any `.py` files. 2023-09-10T15:13:21,287 On the other hand, currently there is no concept of package data 2023-09-10T15:13:21,288 directory, all directories are treated like packages. 2023-09-10T15:13:21,288 ******************************************************************************** 2023-09-10T15:13:21,289 !! 2023-09-10T15:13:21,290 check.warn(importable) 2023-09-10T15:13:21,290 /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. 2023-09-10T15:13:21,291 !! 2023-09-10T15:13:21,292 ******************************************************************************** 2023-09-10T15:13:21,292 ############################ 2023-09-10T15:13:21,293 # Package would be ignored # 2023-09-10T15:13:21,293 ############################ 2023-09-10T15:13:21,293 Python recognizes 'isambard.modelling.reference_ampals' as an importable package[^1], 2023-09-10T15:13:21,294 but it is absent from setuptools' `packages` configuration. 2023-09-10T15:13:21,295 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-10T15:13:21,295 package, please make sure that 'isambard.modelling.reference_ampals' is explicitly added 2023-09-10T15:13:21,296 to the `packages` configuration field. 2023-09-10T15:13:21,297 Alternatively, you can also rely on setuptools' discovery methods 2023-09-10T15:13:21,297 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-10T15:13:21,298 instead of `find_packages(...)`/`find:`). 2023-09-10T15:13:21,299 You can read more about "package discovery" on setuptools documentation page: 2023-09-10T15:13:21,299 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-10T15:13:21,301 If you don't want 'isambard.modelling.reference_ampals' to be distributed and are 2023-09-10T15:13:21,301 already explicitly excluding 'isambard.modelling.reference_ampals' via 2023-09-10T15:13:21,301 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-10T15:13:21,302 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-10T15:13:21,302 combination with a more fine grained `package-data` configuration. 2023-09-10T15:13:21,303 You can read more about "package data files" on setuptools documentation page: 2023-09-10T15:13:21,304 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-10T15:13:21,306 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-10T15:13:21,306 even if it does not contain any `.py` files. 2023-09-10T15:13:21,307 On the other hand, currently there is no concept of package data 2023-09-10T15:13:21,307 directory, all directories are treated like packages. 2023-09-10T15:13:21,308 ******************************************************************************** 2023-09-10T15:13:21,308 !! 2023-09-10T15:13:21,309 check.warn(importable) 2023-09-10T15:13:21,309 /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. 2023-09-10T15:13:21,310 !! 2023-09-10T15:13:21,311 ******************************************************************************** 2023-09-10T15:13:21,312 ############################ 2023-09-10T15:13:21,312 # Package would be ignored # 2023-09-10T15:13:21,313 ############################ 2023-09-10T15:13:21,313 Python recognizes 'isambard.modelling.reference_ampals.non_canonical_amino_acids' as an importable package[^1], 2023-09-10T15:13:21,314 but it is absent from setuptools' `packages` configuration. 2023-09-10T15:13:21,315 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-10T15:13:21,315 package, please make sure that 'isambard.modelling.reference_ampals.non_canonical_amino_acids' is explicitly added 2023-09-10T15:13:21,316 to the `packages` configuration field. 2023-09-10T15:13:21,317 Alternatively, you can also rely on setuptools' discovery methods 2023-09-10T15:13:21,318 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-10T15:13:21,318 instead of `find_packages(...)`/`find:`). 2023-09-10T15:13:21,319 You can read more about "package discovery" on setuptools documentation page: 2023-09-10T15:13:21,321 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-10T15:13:21,321 If you don't want 'isambard.modelling.reference_ampals.non_canonical_amino_acids' to be distributed and are 2023-09-10T15:13:21,322 already explicitly excluding 'isambard.modelling.reference_ampals.non_canonical_amino_acids' via 2023-09-10T15:13:21,322 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-10T15:13:21,323 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-10T15:13:21,324 combination with a more fine grained `package-data` configuration. 2023-09-10T15:13:21,325 You can read more about "package data files" on setuptools documentation page: 2023-09-10T15:13:21,326 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-10T15:13:21,327 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-10T15:13:21,327 even if it does not contain any `.py` files. 2023-09-10T15:13:21,328 On the other hand, currently there is no concept of package data 2023-09-10T15:13:21,328 directory, all directories are treated like packages. 2023-09-10T15:13:21,329 ******************************************************************************** 2023-09-10T15:13:21,330 !! 2023-09-10T15:13:21,330 check.warn(importable) 2023-09-10T15:13:21,331 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'isambard.optimisation.__pycache__' is absent from the `packages` configuration. 2023-09-10T15:13:21,331 !! 2023-09-10T15:13:21,332 ******************************************************************************** 2023-09-10T15:13:21,333 ############################ 2023-09-10T15:13:21,333 # Package would be ignored # 2023-09-10T15:13:21,334 ############################ 2023-09-10T15:13:21,334 Python recognizes 'isambard.optimisation.__pycache__' as an importable package[^1], 2023-09-10T15:13:21,335 but it is absent from setuptools' `packages` configuration. 2023-09-10T15:13:21,336 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-10T15:13:21,336 package, please make sure that 'isambard.optimisation.__pycache__' is explicitly added 2023-09-10T15:13:21,336 to the `packages` configuration field. 2023-09-10T15:13:21,337 Alternatively, you can also rely on setuptools' discovery methods 2023-09-10T15:13:21,338 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-10T15:13:21,338 instead of `find_packages(...)`/`find:`). 2023-09-10T15:13:21,339 You can read more about "package discovery" on setuptools documentation page: 2023-09-10T15:13:21,341 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-10T15:13:21,342 If you don't want 'isambard.optimisation.__pycache__' to be distributed and are 2023-09-10T15:13:21,342 already explicitly excluding 'isambard.optimisation.__pycache__' via 2023-09-10T15:13:21,343 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-10T15:13:21,343 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-10T15:13:21,344 combination with a more fine grained `package-data` configuration. 2023-09-10T15:13:21,345 You can read more about "package data files" on setuptools documentation page: 2023-09-10T15:13:21,346 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-10T15:13:21,347 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-10T15:13:21,348 even if it does not contain any `.py` files. 2023-09-10T15:13:21,349 On the other hand, currently there is no concept of package data 2023-09-10T15:13:21,349 directory, all directories are treated like packages. 2023-09-10T15:13:21,350 ******************************************************************************** 2023-09-10T15:13:21,351 !! 2023-09-10T15:13:21,351 check.warn(importable) 2023-09-10T15:13:21,352 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'isambard.specifications.__pycache__' is absent from the `packages` configuration. 2023-09-10T15:13:21,352 !! 2023-09-10T15:13:21,353 ******************************************************************************** 2023-09-10T15:13:21,354 ############################ 2023-09-10T15:13:21,354 # Package would be ignored # 2023-09-10T15:13:21,355 ############################ 2023-09-10T15:13:21,355 Python recognizes 'isambard.specifications.__pycache__' as an importable package[^1], 2023-09-10T15:13:21,356 but it is absent from setuptools' `packages` configuration. 2023-09-10T15:13:21,356 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-10T15:13:21,357 package, please make sure that 'isambard.specifications.__pycache__' is explicitly added 2023-09-10T15:13:21,358 to the `packages` configuration field. 2023-09-10T15:13:21,359 Alternatively, you can also rely on setuptools' discovery methods 2023-09-10T15:13:21,359 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-10T15:13:21,360 instead of `find_packages(...)`/`find:`). 2023-09-10T15:13:21,361 You can read more about "package discovery" on setuptools documentation page: 2023-09-10T15:13:21,362 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-10T15:13:21,363 If you don't want 'isambard.specifications.__pycache__' to be distributed and are 2023-09-10T15:13:21,363 already explicitly excluding 'isambard.specifications.__pycache__' via 2023-09-10T15:13:21,364 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-10T15:13:21,364 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-10T15:13:21,365 combination with a more fine grained `package-data` configuration. 2023-09-10T15:13:21,367 You can read more about "package data files" on setuptools documentation page: 2023-09-10T15:13:21,368 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-10T15:13:21,370 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-10T15:13:21,370 even if it does not contain any `.py` files. 2023-09-10T15:13:21,371 On the other hand, currently there is no concept of package data 2023-09-10T15:13:21,372 directory, all directories are treated like packages. 2023-09-10T15:13:21,373 ******************************************************************************** 2023-09-10T15:13:21,375 !! 2023-09-10T15:13:21,377 check.warn(importable) 2023-09-10T15:13:21,378 creating build/lib.linux-armv7l-cpython-311/isambard/__pycache__ 2023-09-10T15:13:21,378 copying src/isambard/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/__pycache__ 2023-09-10T15:13:21,379 copying src/isambard/specifications/ta_polypeptide.c -> build/lib.linux-armv7l-cpython-311/isambard/specifications 2023-09-10T15:13:21,379 copying src/isambard/specifications/ta_polypeptide.cpython-36m-x86_64-linux-gnu.so -> build/lib.linux-armv7l-cpython-311/isambard/specifications 2023-09-10T15:13:21,380 copying src/isambard/specifications/ta_polypeptide.pyx -> build/lib.linux-armv7l-cpython-311/isambard/specifications 2023-09-10T15:13:21,380 creating build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__ 2023-09-10T15:13:21,381 copying src/isambard/specifications/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__ 2023-09-10T15:13:21,382 copying src/isambard/specifications/__pycache__/coiledcoil.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__ 2023-09-10T15:13:21,382 copying src/isambard/specifications/__pycache__/helix.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__ 2023-09-10T15:13:21,382 copying src/isambard/specifications/__pycache__/nucleic_acid_duplex.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__ 2023-09-10T15:13:21,383 copying src/isambard/specifications/__pycache__/nucleic_acid_strand.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__ 2023-09-10T15:13:21,383 copying src/isambard/specifications/__pycache__/solenoid.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__ 2023-09-10T15:13:21,384 creating build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__ 2023-09-10T15:13:21,384 copying src/isambard/modelling/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__ 2023-09-10T15:13:21,385 copying src/isambard/modelling/__pycache__/non_canonical.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__ 2023-09-10T15:13:21,385 copying src/isambard/modelling/__pycache__/scwrl.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__ 2023-09-10T15:13:21,386 creating build/lib.linux-armv7l-cpython-311/isambard/modelling/reference_ampals 2023-09-10T15:13:21,386 copying src/isambard/modelling/reference_ampals/README.md -> build/lib.linux-armv7l-cpython-311/isambard/modelling/reference_ampals 2023-09-10T15:13:21,387 creating build/lib.linux-armv7l-cpython-311/isambard/modelling/reference_ampals/non_canonical_amino_acids 2023-09-10T15:13:21,387 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 2023-09-10T15:13:21,388 creating build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__ 2023-09-10T15:13:21,388 copying src/isambard/optimisation/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__ 2023-09-10T15:13:21,388 copying src/isambard/optimisation/__pycache__/base_evo_opt.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__ 2023-09-10T15:13:21,389 copying src/isambard/optimisation/__pycache__/evo_optimizers.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__ 2023-09-10T15:13:21,389 copying src/isambard/optimisation/__pycache__/mmc_optimizer.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__ 2023-09-10T15:13:21,390 creating build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__ 2023-09-10T15:13:21,390 copying src/isambard/evaluation/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__ 2023-09-10T15:13:21,391 copying src/isambard/evaluation/__pycache__/contact_order.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__ 2023-09-10T15:13:21,392 copying src/isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-36.pyc -> build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__ 2023-09-10T15:13:21,392 running build_ext 2023-09-10T15:13:21,393 building 'isambard.specifications.ta_polypeptide' extension 2023-09-10T15:13:21,393 creating build/temp.linux-armv7l-cpython-311 2023-09-10T15:13:21,394 creating build/temp.linux-armv7l-cpython-311/src 2023-09-10T15:13:21,395 creating build/temp.linux-armv7l-cpython-311/src/isambard 2023-09-10T15:13:21,395 creating build/temp.linux-armv7l-cpython-311/src/isambard/specifications 2023-09-10T15:13:21,396 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 2023-09-10T15:13:41,144 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 2023-09-10T15:13:41,286 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-09-10T15:13:41,287 !! 2023-09-10T15:13:41,288 ******************************************************************************** 2023-09-10T15:13:41,288 Please avoid running ``setup.py`` directly. 2023-09-10T15:13:41,289 Instead, use pypa/build, pypa/installer or other 2023-09-10T15:13:41,289 standards-based tools. 2023-09-10T15:13:41,290 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-09-10T15:13:41,291 ******************************************************************************** 2023-09-10T15:13:41,291 !! 2023-09-10T15:13:41,292 self.initialize_options() 2023-09-10T15:13:41,310 installing to build/bdist.linux-armv7l/wheel 2023-09-10T15:13:41,311 running install 2023-09-10T15:13:41,334 running install_lib 2023-09-10T15:13:41,357 creating build/bdist.linux-armv7l 2023-09-10T15:13:41,358 creating build/bdist.linux-armv7l/wheel 2023-09-10T15:13:41,359 creating build/bdist.linux-armv7l/wheel/isambard 2023-09-10T15:13:41,361 creating build/bdist.linux-armv7l/wheel/isambard/__pycache__ 2023-09-10T15:13:41,362 copying build/lib.linux-armv7l-cpython-311/isambard/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/__pycache__ 2023-09-10T15:13:41,364 creating build/bdist.linux-armv7l/wheel/isambard/specifications 2023-09-10T15:13:41,365 creating build/bdist.linux-armv7l/wheel/isambard/specifications/__pycache__ 2023-09-10T15:13:41,366 copying build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__/helix.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/specifications/__pycache__ 2023-09-10T15:13:41,369 copying build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__/nucleic_acid_duplex.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/specifications/__pycache__ 2023-09-10T15:13:41,370 copying build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__/nucleic_acid_strand.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/specifications/__pycache__ 2023-09-10T15:13:41,373 copying build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__/coiledcoil.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/specifications/__pycache__ 2023-09-10T15:13:41,375 copying build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__/solenoid.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/specifications/__pycache__ 2023-09-10T15:13:41,377 copying build/lib.linux-armv7l-cpython-311/isambard/specifications/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/specifications/__pycache__ 2023-09-10T15:13:41,379 copying build/lib.linux-armv7l-cpython-311/isambard/specifications/helix.py -> build/bdist.linux-armv7l/wheel/isambard/specifications 2023-09-10T15:13:41,381 copying build/lib.linux-armv7l-cpython-311/isambard/specifications/ta_polypeptide.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/isambard/specifications 2023-09-10T15:13:41,392 copying build/lib.linux-armv7l-cpython-311/isambard/specifications/ta_polypeptide.pyx -> build/bdist.linux-armv7l/wheel/isambard/specifications 2023-09-10T15:13:41,395 copying build/lib.linux-armv7l-cpython-311/isambard/specifications/nucleic_acid_duplex.py -> build/bdist.linux-armv7l/wheel/isambard/specifications 2023-09-10T15:13:41,396 copying build/lib.linux-armv7l-cpython-311/isambard/specifications/nucleic_acid_strand.py -> build/bdist.linux-armv7l/wheel/isambard/specifications 2023-09-10T15:13:41,398 copying build/lib.linux-armv7l-cpython-311/isambard/specifications/solenoid.py -> build/bdist.linux-armv7l/wheel/isambard/specifications 2023-09-10T15:13:41,400 copying build/lib.linux-armv7l-cpython-311/isambard/specifications/__init__.py -> build/bdist.linux-armv7l/wheel/isambard/specifications 2023-09-10T15:13:41,402 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 2023-09-10T15:13:41,415 copying build/lib.linux-armv7l-cpython-311/isambard/specifications/ta_polypeptide.c -> build/bdist.linux-armv7l/wheel/isambard/specifications 2023-09-10T15:13:41,431 copying build/lib.linux-armv7l-cpython-311/isambard/specifications/coiledcoil.py -> build/bdist.linux-armv7l/wheel/isambard/specifications 2023-09-10T15:13:41,433 copying build/lib.linux-armv7l-cpython-311/isambard/__init__.py -> build/bdist.linux-armv7l/wheel/isambard 2023-09-10T15:13:41,435 creating build/bdist.linux-armv7l/wheel/isambard/modelling 2023-09-10T15:13:41,436 creating build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__ 2023-09-10T15:13:41,437 copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/scwrl.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__ 2023-09-10T15:13:41,439 copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/non_canonical.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__ 2023-09-10T15:13:41,441 copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__ 2023-09-10T15:13:41,443 copying build/lib.linux-armv7l-cpython-311/isambard/modelling/non_canonical.py -> build/bdist.linux-armv7l/wheel/isambard/modelling 2023-09-10T15:13:41,445 creating build/bdist.linux-armv7l/wheel/isambard/modelling/reference_ampals 2023-09-10T15:13:41,446 copying build/lib.linux-armv7l-cpython-311/isambard/modelling/reference_ampals/README.md -> build/bdist.linux-armv7l/wheel/isambard/modelling/reference_ampals 2023-09-10T15:13:41,448 creating build/bdist.linux-armv7l/wheel/isambard/modelling/reference_ampals/non_canonical_amino_acids 2023-09-10T15:13:41,450 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 2023-09-10T15:13:41,452 copying build/lib.linux-armv7l-cpython-311/isambard/modelling/__init__.py -> build/bdist.linux-armv7l/wheel/isambard/modelling 2023-09-10T15:13:41,453 copying build/lib.linux-armv7l-cpython-311/isambard/modelling/scwrl.py -> build/bdist.linux-armv7l/wheel/isambard/modelling 2023-09-10T15:13:41,456 creating build/bdist.linux-armv7l/wheel/isambard/optimisation 2023-09-10T15:13:41,457 creating build/bdist.linux-armv7l/wheel/isambard/optimisation/__pycache__ 2023-09-10T15:13:41,458 copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__/base_evo_opt.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/optimisation/__pycache__ 2023-09-10T15:13:41,461 copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__/evo_optimizers.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/optimisation/__pycache__ 2023-09-10T15:13:41,464 copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__/mmc_optimizer.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/optimisation/__pycache__ 2023-09-10T15:13:41,466 copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/optimisation/__pycache__ 2023-09-10T15:13:41,467 copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/mmc_optimizer.py -> build/bdist.linux-armv7l/wheel/isambard/optimisation 2023-09-10T15:13:41,470 copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/__init__.py -> build/bdist.linux-armv7l/wheel/isambard/optimisation 2023-09-10T15:13:41,471 copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/base_evo_opt.py -> build/bdist.linux-armv7l/wheel/isambard/optimisation 2023-09-10T15:13:41,474 copying build/lib.linux-armv7l-cpython-311/isambard/optimisation/evo_optimizers.py -> build/bdist.linux-armv7l/wheel/isambard/optimisation 2023-09-10T15:13:41,476 creating build/bdist.linux-armv7l/wheel/isambard/evaluation 2023-09-10T15:13:41,478 creating build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__ 2023-09-10T15:13:41,478 copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__/contact_order.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__ 2023-09-10T15:13:41,481 copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__ 2023-09-10T15:13:41,483 copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__ 2023-09-10T15:13:41,484 copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/hydrophobic_fitness.py -> build/bdist.linux-armv7l/wheel/isambard/evaluation 2023-09-10T15:13:41,487 copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/__init__.py -> build/bdist.linux-armv7l/wheel/isambard/evaluation 2023-09-10T15:13:41,488 copying build/lib.linux-armv7l-cpython-311/isambard/evaluation/contact_order.py -> build/bdist.linux-armv7l/wheel/isambard/evaluation 2023-09-10T15:13:41,490 running install_egg_info 2023-09-10T15:13:41,519 Copying src/ISAMBARD.egg-info to build/bdist.linux-armv7l/wheel/ISAMBARD-2.0.1-py3.11.egg-info 2023-09-10T15:13:41,531 running install_scripts 2023-09-10T15:13:41,581 creating build/bdist.linux-armv7l/wheel/ISAMBARD-2.0.1.dist-info/WHEEL 2023-09-10T15:13:41,583 creating '/tmp/pip-wheel-ewko90lr/ISAMBARD-2.0.1-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-10T15:13:41,586 adding 'isambard/__init__.py' 2023-09-10T15:13:41,588 adding 'isambard/__pycache__/__init__.cpython-36.pyc' 2023-09-10T15:13:41,589 adding 'isambard/evaluation/__init__.py' 2023-09-10T15:13:41,591 adding 'isambard/evaluation/contact_order.py' 2023-09-10T15:13:41,593 adding 'isambard/evaluation/hydrophobic_fitness.py' 2023-09-10T15:13:41,594 adding 'isambard/evaluation/__pycache__/__init__.cpython-36.pyc' 2023-09-10T15:13:41,596 adding 'isambard/evaluation/__pycache__/contact_order.cpython-36.pyc' 2023-09-10T15:13:41,597 adding 'isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-36.pyc' 2023-09-10T15:13:41,599 adding 'isambard/modelling/__init__.py' 2023-09-10T15:13:41,601 adding 'isambard/modelling/non_canonical.py' 2023-09-10T15:13:41,602 adding 'isambard/modelling/scwrl.py' 2023-09-10T15:13:41,604 adding 'isambard/modelling/__pycache__/__init__.cpython-36.pyc' 2023-09-10T15:13:41,605 adding 'isambard/modelling/__pycache__/non_canonical.cpython-36.pyc' 2023-09-10T15:13:41,607 adding 'isambard/modelling/__pycache__/scwrl.cpython-36.pyc' 2023-09-10T15:13:41,609 adding 'isambard/modelling/reference_ampals/README.md' 2023-09-10T15:13:41,611 adding 'isambard/modelling/reference_ampals/non_canonical_amino_acids/hydroxyproline_ref_1bkv_0_6.pickle' 2023-09-10T15:13:41,612 adding 'isambard/optimisation/__init__.py' 2023-09-10T15:13:41,615 adding 'isambard/optimisation/base_evo_opt.py' 2023-09-10T15:13:41,618 adding 'isambard/optimisation/evo_optimizers.py' 2023-09-10T15:13:41,620 adding 'isambard/optimisation/mmc_optimizer.py' 2023-09-10T15:13:41,622 adding 'isambard/optimisation/__pycache__/__init__.cpython-36.pyc' 2023-09-10T15:13:41,624 adding 'isambard/optimisation/__pycache__/base_evo_opt.cpython-36.pyc' 2023-09-10T15:13:41,628 adding 'isambard/optimisation/__pycache__/evo_optimizers.cpython-36.pyc' 2023-09-10T15:13:41,630 adding 'isambard/optimisation/__pycache__/mmc_optimizer.cpython-36.pyc' 2023-09-10T15:13:41,632 adding 'isambard/specifications/__init__.py' 2023-09-10T15:13:41,633 adding 'isambard/specifications/coiledcoil.py' 2023-09-10T15:13:41,636 adding 'isambard/specifications/helix.py' 2023-09-10T15:13:41,638 adding 'isambard/specifications/nucleic_acid_duplex.py' 2023-09-10T15:13:41,639 adding 'isambard/specifications/nucleic_acid_strand.py' 2023-09-10T15:13:41,641 adding 'isambard/specifications/solenoid.py' 2023-09-10T15:13:41,690 adding 'isambard/specifications/ta_polypeptide.c' 2023-09-10T15:13:41,833 adding 'isambard/specifications/ta_polypeptide.cpython-311-arm-linux-gnueabihf.so' 2023-09-10T15:13:41,942 adding 'isambard/specifications/ta_polypeptide.cpython-36m-x86_64-linux-gnu.so' 2023-09-10T15:13:41,949 adding 'isambard/specifications/ta_polypeptide.pyx' 2023-09-10T15:13:41,951 adding 'isambard/specifications/__pycache__/__init__.cpython-36.pyc' 2023-09-10T15:13:41,952 adding 'isambard/specifications/__pycache__/coiledcoil.cpython-36.pyc' 2023-09-10T15:13:41,955 adding 'isambard/specifications/__pycache__/helix.cpython-36.pyc' 2023-09-10T15:13:41,957 adding 'isambard/specifications/__pycache__/nucleic_acid_duplex.cpython-36.pyc' 2023-09-10T15:13:41,959 adding 'isambard/specifications/__pycache__/nucleic_acid_strand.cpython-36.pyc' 2023-09-10T15:13:41,961 adding 'isambard/specifications/__pycache__/solenoid.cpython-36.pyc' 2023-09-10T15:13:41,962 adding 'ISAMBARD-2.0.1.dist-info/LICENSE.txt' 2023-09-10T15:13:41,964 adding 'ISAMBARD-2.0.1.dist-info/METADATA' 2023-09-10T15:13:41,965 adding 'ISAMBARD-2.0.1.dist-info/WHEEL' 2023-09-10T15:13:41,966 adding 'ISAMBARD-2.0.1.dist-info/top_level.txt' 2023-09-10T15:13:41,967 adding 'ISAMBARD-2.0.1.dist-info/RECORD' 2023-09-10T15:13:41,975 removing build/bdist.linux-armv7l/wheel 2023-09-10T15:13:42,134 Building wheel for isambard (setup.py): finished with status 'done' 2023-09-10T15:13:42,144 Created wheel for isambard: filename=ISAMBARD-2.0.1-cp311-cp311-linux_armv7l.whl size=666233 sha256=4cf86ff1923fd823d90a7bd0993af4a2a172829212bf9de92f255ee304f38307 2023-09-10T15:13:42,146 Stored in directory: /tmp/pip-ephem-wheel-cache-jke6vfl1/wheels/5a/be/b7/1c0bd968d44f3771b3082d8af1adf6141d7262b8cdbdba45a9 2023-09-10T15:13:42,157 Successfully built isambard 2023-09-10T15:13:42,176 Removed build tracker: '/tmp/pip-build-tracker-16wgowti'