2025-09-08T13:30:22,804 Created temporary directory: /tmp/pip-build-tracker-plndqfou 2025-09-08T13:30:22,804 Initialized build tracking at /tmp/pip-build-tracker-plndqfou 2025-09-08T13:30:22,805 Created build tracker: /tmp/pip-build-tracker-plndqfou 2025-09-08T13:30:22,805 Entered build tracker: /tmp/pip-build-tracker-plndqfou 2025-09-08T13:30:22,805 Created temporary directory: /tmp/pip-wheel-xbj7i0r2 2025-09-08T13:30:22,808 Created temporary directory: /tmp/pip-ephem-wheel-cache-efn9u9f1 2025-09-08T13:30:22,868 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T13:30:22,870 2 location(s) to search for versions of isambard: 2025-09-08T13:30:22,870 * https://pypi.org/simple/isambard/ 2025-09-08T13:30:22,870 * https://www.piwheels.org/simple/isambard/ 2025-09-08T13:30:22,871 Fetching project page and analyzing links: https://pypi.org/simple/isambard/ 2025-09-08T13:30:22,871 Getting page https://pypi.org/simple/isambard/ 2025-09-08T13:30:22,872 Found index url https://pypi.org/simple/ 2025-09-08T13:30:22,944 Fetched page https://pypi.org/simple/isambard/ as application/vnd.pypi.simple.v1+json 2025-09-08T13:30:22,945 Found link https://files.pythonhosted.org/packages/ca/6d/9456a011721c3376fc03e77d5ea89f563dfac30660be8b2517ad1ba2c44a/ISAMBARD-2.0.1.tar.gz (from https://pypi.org/simple/isambard/), version: 2.0.1 2025-09-08T13:30:22,945 Found link https://files.pythonhosted.org/packages/9c/ba/636028b8e309e217e171016e34b2a9f5f0b37f3be916d02ad55f97cf4991/ISAMBARD-2.2.0.tar.gz (from https://pypi.org/simple/isambard/), version: 2.2.0 2025-09-08T13:30:22,946 Found link https://files.pythonhosted.org/packages/6d/5d/36e0369e6e7bdb1061074aff44dab96caf1e1809a289f41156a0a34bce49/ISAMBARD-2.3.1.tar.gz (from https://pypi.org/simple/isambard/), version: 2.3.1 2025-09-08T13:30:22,946 Fetching project page and analyzing links: https://www.piwheels.org/simple/isambard/ 2025-09-08T13:30:22,946 Getting page https://www.piwheels.org/simple/isambard/ 2025-09-08T13:30:22,947 Found index url https://www.piwheels.org/simple/ 2025-09-08T13:30:23,042 Fetched page https://www.piwheels.org/simple/isambard/ as text/html 2025-09-08T13:30:23,049 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp35-cp35m-linux_armv6l.whl#sha256=5456ca91d4e8a25515a72ce369c3dc3bd75771154926907a13ee229c5c775c90 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,049 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp35-cp35m-linux_armv7l.whl#sha256=5456ca91d4e8a25515a72ce369c3dc3bd75771154926907a13ee229c5c775c90 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,049 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp37-cp37m-linux_armv6l.whl#sha256=efae9efaebdc3a20e5d63f7004a92e689f3e6e5836be027bc95d82dfc3a96931 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,049 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp37-cp37m-linux_armv7l.whl#sha256=efae9efaebdc3a20e5d63f7004a92e689f3e6e5836be027bc95d82dfc3a96931 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,049 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp311-cp311-linux_armv6l.whl#sha256=0c3ad4f0c4a0b8169c1ea441c243457c4de16bbc36eaaa2aa170c0965e87c84e (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,050 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp311-cp311-linux_armv7l.whl#sha256=0c3ad4f0c4a0b8169c1ea441c243457c4de16bbc36eaaa2aa170c0965e87c84e (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,050 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp39-cp39-linux_armv6l.whl#sha256=697398715022626b617288089a4d8f169aba9b6a2741bb64a57baf0008f4a682 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,050 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.3.1-cp39-cp39-linux_armv7l.whl#sha256=697398715022626b617288089a4d8f169aba9b6a2741bb64a57baf0008f4a682 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,050 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp39-cp39-linux_armv6l.whl#sha256=0010224aeec40539f9f2ef43ef893a7b0735d1b3f4e95dc31708219c0337dc30 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,050 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp39-cp39-linux_armv7l.whl#sha256=0010224aeec40539f9f2ef43ef893a7b0735d1b3f4e95dc31708219c0337dc30 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,050 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp34-cp34m-linux_armv6l.whl#sha256=97c289f5089392b53f0c6d552d6d48650a1fb4dfc834cfc8b472a8a01c98dc89 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,050 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp34-cp34m-linux_armv7l.whl#sha256=97c289f5089392b53f0c6d552d6d48650a1fb4dfc834cfc8b472a8a01c98dc89 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,051 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp35-cp35m-linux_armv7l.whl#sha256=3fd2a12daa3a717fd4fcba1f02c00189966f88fdecfd4fe27a826bbc5e2e9e0d (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,051 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp35-cp35m-linux_armv6l.whl#sha256=3fd2a12daa3a717fd4fcba1f02c00189966f88fdecfd4fe27a826bbc5e2e9e0d (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,051 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp37-cp37m-linux_armv7l.whl#sha256=1ed4e4469c6a429a8d7983454afa221ed4de77c4f796928fe85b8ca9493ce9b7 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,051 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp37-cp37m-linux_armv6l.whl#sha256=1ed4e4469c6a429a8d7983454afa221ed4de77c4f796928fe85b8ca9493ce9b7 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,051 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp311-cp311-linux_armv6l.whl#sha256=da0939c6735170d08c9e5c63a3d82bb9003d2457ae53546e18eca4b785976758 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,051 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.2.0-cp311-cp311-linux_armv7l.whl#sha256=da0939c6735170d08c9e5c63a3d82bb9003d2457ae53546e18eca4b785976758 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,051 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp35-cp35m-linux_armv6l.whl#sha256=e0fc68b3f5047b9165d5153bc4dc316bab81664ff21671571b7513628b90b5a1 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,052 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp35-cp35m-linux_armv7l.whl#sha256=e0fc68b3f5047b9165d5153bc4dc316bab81664ff21671571b7513628b90b5a1 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,052 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp34-cp34m-linux_armv7l.whl#sha256=887549f381be5e2479ffed07b8c2eb4f307e592beccbe3290feba06d0c3790f9 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,052 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp34-cp34m-linux_armv6l.whl#sha256=887549f381be5e2479ffed07b8c2eb4f307e592beccbe3290feba06d0c3790f9 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,052 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp37-cp37m-linux_armv7l.whl#sha256=bd0f20e61ccc5234636764d226a0798035a8fbf626bcac75c0b0ecca150f5006 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,052 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp37-cp37m-linux_armv6l.whl#sha256=bd0f20e61ccc5234636764d226a0798035a8fbf626bcac75c0b0ecca150f5006 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,052 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp311-cp311-linux_armv6l.whl#sha256=4cf86ff1923fd823d90a7bd0993af4a2a172829212bf9de92f255ee304f38307 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,053 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp311-cp311-linux_armv7l.whl#sha256=4cf86ff1923fd823d90a7bd0993af4a2a172829212bf9de92f255ee304f38307 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,053 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp39-cp39-linux_armv6l.whl#sha256=45f89745fb452c115ce88125bc0668253c3f3b887d7ece84108e217dd6760ec8 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,053 Skipping link: No binaries permitted for isambard: https://archive1.piwheels.org/simple/isambard/ISAMBARD-2.0.1-cp39-cp39-linux_armv7l.whl#sha256=45f89745fb452c115ce88125bc0668253c3f3b887d7ece84108e217dd6760ec8 (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,053 Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/isambard-2.0.1-cp313-cp313-linux_armv6l.whl#sha256=85cf289db8dc2a9066339a812cbb82449045a0dd42e40546348aa8ebb9cf841a (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,053 Skipping link: No binaries permitted for isambard: https://www.piwheels.org/simple/isambard/isambard-2.0.1-cp313-cp313-linux_armv7l.whl#sha256=85cf289db8dc2a9066339a812cbb82449045a0dd42e40546348aa8ebb9cf841a (from https://www.piwheels.org/simple/isambard/) 2025-09-08T13:30:23,053 Skipping link: not a file: https://www.piwheels.org/simple/isambard/ 2025-09-08T13:30:23,054 Skipping link: not a file: https://pypi.org/simple/isambard/ 2025-09-08T13:30:23,077 Given no hashes to check 1 links for project 'isambard': discarding no candidates 2025-09-08T13:30:23,078 Collecting isambard==2.2.0 2025-09-08T13:30:23,079 Created temporary directory: /tmp/pip-unpack-ftq83kj9 2025-09-08T13:30:23,218 Downloading ISAMBARD-2.2.0.tar.gz (359 kB) 2025-09-08T13:30:23,341 Added isambard==2.2.0 from https://files.pythonhosted.org/packages/9c/ba/636028b8e309e217e171016e34b2a9f5f0b37f3be916d02ad55f97cf4991/ISAMBARD-2.2.0.tar.gz to build tracker '/tmp/pip-build-tracker-plndqfou' 2025-09-08T13:30:23,342 Running setup.py (path:/tmp/pip-wheel-xbj7i0r2/isambard_841bfd37c27645e4b5211ac5bda8b20f/setup.py) egg_info for package isambard 2025-09-08T13:30:23,342 Created temporary directory: /tmp/pip-pip-egg-info-moxwq6jm 2025-09-08T13:30:23,342 Preparing metadata (setup.py): started 2025-09-08T13:30:23,343 Running command python setup.py egg_info 2025-09-08T13:30:25,801 Compiling src/isambard/specifications/ta_polypeptide.pyx because it changed. 2025-09-08T13:30:25,801 [1/1] Cythonizing src/isambard/specifications/ta_polypeptide.pyx 2025-09-08T13:30:26,197 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T13:30:26,197 !! 2025-09-08T13:30:26,198 ******************************************************************************** 2025-09-08T13:30:26,198 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T13:30:26,198 License :: OSI Approved :: MIT License 2025-09-08T13:30:26,198 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T13:30:26,198 ******************************************************************************** 2025-09-08T13:30:26,198 !! 2025-09-08T13:30:26,198 self._finalize_license_expression() 2025-09-08T13:30:26,274 running egg_info 2025-09-08T13:30:26,350 creating /tmp/pip-pip-egg-info-moxwq6jm/ISAMBARD.egg-info 2025-09-08T13:30:26,351 writing /tmp/pip-pip-egg-info-moxwq6jm/ISAMBARD.egg-info/PKG-INFO 2025-09-08T13:30:26,352 writing dependency_links to /tmp/pip-pip-egg-info-moxwq6jm/ISAMBARD.egg-info/dependency_links.txt 2025-09-08T13:30:26,353 writing requirements to /tmp/pip-pip-egg-info-moxwq6jm/ISAMBARD.egg-info/requires.txt 2025-09-08T13:30:26,353 writing top-level names to /tmp/pip-pip-egg-info-moxwq6jm/ISAMBARD.egg-info/top_level.txt 2025-09-08T13:30:26,353 writing manifest file '/tmp/pip-pip-egg-info-moxwq6jm/ISAMBARD.egg-info/SOURCES.txt' 2025-09-08T13:30:26,660 reading manifest file '/tmp/pip-pip-egg-info-moxwq6jm/ISAMBARD.egg-info/SOURCES.txt' 2025-09-08T13:30:26,660 reading manifest template 'MANIFEST.in' 2025-09-08T13:30:26,666 adding license file 'LICENSE.txt' 2025-09-08T13:30:26,670 writing manifest file '/tmp/pip-pip-egg-info-moxwq6jm/ISAMBARD.egg-info/SOURCES.txt' 2025-09-08T13:30:26,944 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T13:30:26,949 Source in /tmp/pip-wheel-xbj7i0r2/isambard_841bfd37c27645e4b5211ac5bda8b20f has version 2.2.0, which satisfies requirement isambard==2.2.0 from https://files.pythonhosted.org/packages/9c/ba/636028b8e309e217e171016e34b2a9f5f0b37f3be916d02ad55f97cf4991/ISAMBARD-2.2.0.tar.gz 2025-09-08T13:30:26,949 Removed isambard==2.2.0 from https://files.pythonhosted.org/packages/9c/ba/636028b8e309e217e171016e34b2a9f5f0b37f3be916d02ad55f97cf4991/ISAMBARD-2.2.0.tar.gz from build tracker '/tmp/pip-build-tracker-plndqfou' 2025-09-08T13:30:26,953 Created temporary directory: /tmp/pip-unpack-cj_or3r4 2025-09-08T13:30:26,954 Created temporary directory: /tmp/pip-unpack-rfaun8bk 2025-09-08T13:30:26,954 Building wheels for collected packages: isambard 2025-09-08T13:30:26,956 Created temporary directory: /tmp/pip-wheel-8a2yjb2o 2025-09-08T13:30:26,956 DEPRECATION: Building 'isambard' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'isambard'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T13:30:26,958 Building wheel for isambard (setup.py): started 2025-09-08T13:30:26,958 Destination directory: /tmp/pip-wheel-8a2yjb2o 2025-09-08T13:30:26,959 Running command python setup.py bdist_wheel 2025-09-08T13:30:28,467 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T13:30:28,467 !! 2025-09-08T13:30:28,467 ******************************************************************************** 2025-09-08T13:30:28,468 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T13:30:28,468 License :: OSI Approved :: MIT License 2025-09-08T13:30:28,468 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T13:30:28,468 ******************************************************************************** 2025-09-08T13:30:28,468 !! 2025-09-08T13:30:28,468 self._finalize_license_expression() 2025-09-08T13:30:28,469 running bdist_wheel 2025-09-08T13:30:28,842 running build 2025-09-08T13:30:28,842 running build_py 2025-09-08T13:30:28,920 creating build/lib.linux-armv7l-cpython-313/isambard 2025-09-08T13:30:28,920 copying src/isambard/__init__.py -> build/lib.linux-armv7l-cpython-313/isambard 2025-09-08T13:30:28,921 creating build/lib.linux-armv7l-cpython-313/isambard/optimisation 2025-09-08T13:30:28,922 copying src/isambard/optimisation/base_evo_opt.py -> build/lib.linux-armv7l-cpython-313/isambard/optimisation 2025-09-08T13:30:28,922 copying src/isambard/optimisation/mmc_optimizer.py -> build/lib.linux-armv7l-cpython-313/isambard/optimisation 2025-09-08T13:30:28,923 copying src/isambard/optimisation/__init__.py -> build/lib.linux-armv7l-cpython-313/isambard/optimisation 2025-09-08T13:30:28,923 copying src/isambard/optimisation/evo_optimizers.py -> build/lib.linux-armv7l-cpython-313/isambard/optimisation 2025-09-08T13:30:28,924 creating build/lib.linux-armv7l-cpython-313/isambard/modelling 2025-09-08T13:30:28,925 copying src/isambard/modelling/non_canonical.py -> build/lib.linux-armv7l-cpython-313/isambard/modelling 2025-09-08T13:30:28,925 copying src/isambard/modelling/scwrl.py -> build/lib.linux-armv7l-cpython-313/isambard/modelling 2025-09-08T13:30:28,926 copying src/isambard/modelling/__init__.py -> build/lib.linux-armv7l-cpython-313/isambard/modelling 2025-09-08T13:30:28,926 creating build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T13:30:28,927 copying src/isambard/specifications/coiledcoil.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T13:30:28,927 copying src/isambard/specifications/helix.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T13:30:28,928 copying src/isambard/specifications/nucleic_acid_duplex.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T13:30:28,928 copying src/isambard/specifications/nucleic_acid_strand.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T13:30:28,929 copying src/isambard/specifications/__init__.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T13:30:28,929 copying src/isambard/specifications/solenoid.py -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T13:30:28,930 creating build/lib.linux-armv7l-cpython-313/isambard/evaluation 2025-09-08T13:30:28,930 copying src/isambard/evaluation/dssp.py -> build/lib.linux-armv7l-cpython-313/isambard/evaluation 2025-09-08T13:30:28,931 copying src/isambard/evaluation/pacc.py -> build/lib.linux-armv7l-cpython-313/isambard/evaluation 2025-09-08T13:30:28,932 copying src/isambard/evaluation/hydrophobic_fitness.py -> build/lib.linux-armv7l-cpython-313/isambard/evaluation 2025-09-08T13:30:28,932 copying src/isambard/evaluation/contact_order.py -> build/lib.linux-armv7l-cpython-313/isambard/evaluation 2025-09-08T13:30:28,933 copying src/isambard/evaluation/__init__.py -> build/lib.linux-armv7l-cpython-313/isambard/evaluation 2025-09-08T13:30:28,933 running egg_info 2025-09-08T13:30:29,009 writing src/ISAMBARD.egg-info/PKG-INFO 2025-09-08T13:30:29,010 writing dependency_links to src/ISAMBARD.egg-info/dependency_links.txt 2025-09-08T13:30:29,011 writing requirements to src/ISAMBARD.egg-info/requires.txt 2025-09-08T13:30:29,011 writing top-level names to src/ISAMBARD.egg-info/top_level.txt 2025-09-08T13:30:29,089 reading manifest file 'src/ISAMBARD.egg-info/SOURCES.txt' 2025-09-08T13:30:29,093 reading manifest template 'MANIFEST.in' 2025-09-08T13:30:29,098 adding license file 'LICENSE.txt' 2025-09-08T13:30:29,103 writing manifest file 'src/ISAMBARD.egg-info/SOURCES.txt' 2025-09-08T13:30:29,105 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.__pycache__' is absent from the `packages` configuration. 2025-09-08T13:30:29,105 !! 2025-09-08T13:30:29,105 ******************************************************************************** 2025-09-08T13:30:29,105 ############################ 2025-09-08T13:30:29,105 # Package would be ignored # 2025-09-08T13:30:29,105 ############################ 2025-09-08T13:30:29,105 Python recognizes 'isambard.__pycache__' as an importable package[^1], 2025-09-08T13:30:29,105 but it is absent from setuptools' `packages` configuration. 2025-09-08T13:30:29,106 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T13:30:29,106 package, please make sure that 'isambard.__pycache__' is explicitly added 2025-09-08T13:30:29,106 to the `packages` configuration field. 2025-09-08T13:30:29,106 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T13:30:29,106 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T13:30:29,106 instead of `find_packages(...)`/`find:`). 2025-09-08T13:30:29,106 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T13:30:29,106 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T13:30:29,107 If you don't want 'isambard.__pycache__' to be distributed and are 2025-09-08T13:30:29,107 already explicitly excluding 'isambard.__pycache__' via 2025-09-08T13:30:29,107 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T13:30:29,107 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T13:30:29,107 combination with a more fine grained `package-data` configuration. 2025-09-08T13:30:29,107 You can read more about "package data files" on setuptools documentation page: 2025-09-08T13:30:29,107 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T13:30:29,107 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T13:30:29,108 even if it does not contain any `.py` files. 2025-09-08T13:30:29,108 On the other hand, currently there is no concept of package data 2025-09-08T13:30:29,108 directory, all directories are treated like packages. 2025-09-08T13:30:29,108 ******************************************************************************** 2025-09-08T13:30:29,108 !! 2025-09-08T13:30:29,108 check.warn(importable) 2025-09-08T13:30:29,108 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.evaluation.__pycache__' is absent from the `packages` configuration. 2025-09-08T13:30:29,108 !! 2025-09-08T13:30:29,109 ******************************************************************************** 2025-09-08T13:30:29,109 ############################ 2025-09-08T13:30:29,109 # Package would be ignored # 2025-09-08T13:30:29,109 ############################ 2025-09-08T13:30:29,109 Python recognizes 'isambard.evaluation.__pycache__' as an importable package[^1], 2025-09-08T13:30:29,109 but it is absent from setuptools' `packages` configuration. 2025-09-08T13:30:29,109 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T13:30:29,109 package, please make sure that 'isambard.evaluation.__pycache__' is explicitly added 2025-09-08T13:30:29,109 to the `packages` configuration field. 2025-09-08T13:30:29,110 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T13:30:29,110 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T13:30:29,110 instead of `find_packages(...)`/`find:`). 2025-09-08T13:30:29,110 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T13:30:29,110 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T13:30:29,110 If you don't want 'isambard.evaluation.__pycache__' to be distributed and are 2025-09-08T13:30:29,110 already explicitly excluding 'isambard.evaluation.__pycache__' via 2025-09-08T13:30:29,110 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T13:30:29,110 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T13:30:29,111 combination with a more fine grained `package-data` configuration. 2025-09-08T13:30:29,111 You can read more about "package data files" on setuptools documentation page: 2025-09-08T13:30:29,111 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T13:30:29,111 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T13:30:29,111 even if it does not contain any `.py` files. 2025-09-08T13:30:29,111 On the other hand, currently there is no concept of package data 2025-09-08T13:30:29,111 directory, all directories are treated like packages. 2025-09-08T13:30:29,112 ******************************************************************************** 2025-09-08T13:30:29,112 !! 2025-09-08T13:30:29,112 check.warn(importable) 2025-09-08T13:30:29,112 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.modelling.__pycache__' is absent from the `packages` configuration. 2025-09-08T13:30:29,112 !! 2025-09-08T13:30:29,112 ******************************************************************************** 2025-09-08T13:30:29,112 ############################ 2025-09-08T13:30:29,112 # Package would be ignored # 2025-09-08T13:30:29,112 ############################ 2025-09-08T13:30:29,113 Python recognizes 'isambard.modelling.__pycache__' as an importable package[^1], 2025-09-08T13:30:29,113 but it is absent from setuptools' `packages` configuration. 2025-09-08T13:30:29,113 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T13:30:29,113 package, please make sure that 'isambard.modelling.__pycache__' is explicitly added 2025-09-08T13:30:29,113 to the `packages` configuration field. 2025-09-08T13:30:29,113 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T13:30:29,113 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T13:30:29,113 instead of `find_packages(...)`/`find:`). 2025-09-08T13:30:29,114 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T13:30:29,114 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T13:30:29,114 If you don't want 'isambard.modelling.__pycache__' to be distributed and are 2025-09-08T13:30:29,114 already explicitly excluding 'isambard.modelling.__pycache__' via 2025-09-08T13:30:29,114 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T13:30:29,114 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T13:30:29,114 combination with a more fine grained `package-data` configuration. 2025-09-08T13:30:29,114 You can read more about "package data files" on setuptools documentation page: 2025-09-08T13:30:29,115 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T13:30:29,115 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T13:30:29,115 even if it does not contain any `.py` files. 2025-09-08T13:30:29,115 On the other hand, currently there is no concept of package data 2025-09-08T13:30:29,115 directory, all directories are treated like packages. 2025-09-08T13:30:29,115 ******************************************************************************** 2025-09-08T13:30:29,115 !! 2025-09-08T13:30:29,116 check.warn(importable) 2025-09-08T13:30:29,116 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.modelling.reference_ampals' is absent from the `packages` configuration. 2025-09-08T13:30:29,116 !! 2025-09-08T13:30:29,116 ******************************************************************************** 2025-09-08T13:30:29,116 ############################ 2025-09-08T13:30:29,116 # Package would be ignored # 2025-09-08T13:30:29,116 ############################ 2025-09-08T13:30:29,116 Python recognizes 'isambard.modelling.reference_ampals' as an importable package[^1], 2025-09-08T13:30:29,116 but it is absent from setuptools' `packages` configuration. 2025-09-08T13:30:29,116 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T13:30:29,117 package, please make sure that 'isambard.modelling.reference_ampals' is explicitly added 2025-09-08T13:30:29,117 to the `packages` configuration field. 2025-09-08T13:30:29,117 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T13:30:29,117 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T13:30:29,117 instead of `find_packages(...)`/`find:`). 2025-09-08T13:30:29,117 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T13:30:29,117 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T13:30:29,118 If you don't want 'isambard.modelling.reference_ampals' to be distributed and are 2025-09-08T13:30:29,118 already explicitly excluding 'isambard.modelling.reference_ampals' via 2025-09-08T13:30:29,118 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T13:30:29,118 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T13:30:29,118 combination with a more fine grained `package-data` configuration. 2025-09-08T13:30:29,118 You can read more about "package data files" on setuptools documentation page: 2025-09-08T13:30:29,118 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T13:30:29,118 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T13:30:29,119 even if it does not contain any `.py` files. 2025-09-08T13:30:29,119 On the other hand, currently there is no concept of package data 2025-09-08T13:30:29,119 directory, all directories are treated like packages. 2025-09-08T13:30:29,119 ******************************************************************************** 2025-09-08T13:30:29,119 !! 2025-09-08T13:30:29,119 check.warn(importable) 2025-09-08T13:30:29,119 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.modelling.reference_ampals.non_canonical_amino_acids' is absent from the `packages` configuration. 2025-09-08T13:30:29,119 !! 2025-09-08T13:30:29,119 ******************************************************************************** 2025-09-08T13:30:29,120 ############################ 2025-09-08T13:30:29,120 # Package would be ignored # 2025-09-08T13:30:29,120 ############################ 2025-09-08T13:30:29,120 Python recognizes 'isambard.modelling.reference_ampals.non_canonical_amino_acids' as an importable package[^1], 2025-09-08T13:30:29,120 but it is absent from setuptools' `packages` configuration. 2025-09-08T13:30:29,120 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T13:30:29,120 package, please make sure that 'isambard.modelling.reference_ampals.non_canonical_amino_acids' is explicitly added 2025-09-08T13:30:29,120 to the `packages` configuration field. 2025-09-08T13:30:29,120 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T13:30:29,121 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T13:30:29,121 instead of `find_packages(...)`/`find:`). 2025-09-08T13:30:29,121 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T13:30:29,121 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T13:30:29,121 If you don't want 'isambard.modelling.reference_ampals.non_canonical_amino_acids' to be distributed and are 2025-09-08T13:30:29,121 already explicitly excluding 'isambard.modelling.reference_ampals.non_canonical_amino_acids' via 2025-09-08T13:30:29,121 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T13:30:29,121 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T13:30:29,121 combination with a more fine grained `package-data` configuration. 2025-09-08T13:30:29,122 You can read more about "package data files" on setuptools documentation page: 2025-09-08T13:30:29,122 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T13:30:29,122 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T13:30:29,122 even if it does not contain any `.py` files. 2025-09-08T13:30:29,122 On the other hand, currently there is no concept of package data 2025-09-08T13:30:29,122 directory, all directories are treated like packages. 2025-09-08T13:30:29,123 ******************************************************************************** 2025-09-08T13:30:29,123 !! 2025-09-08T13:30:29,123 check.warn(importable) 2025-09-08T13:30:29,123 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.optimisation.__pycache__' is absent from the `packages` configuration. 2025-09-08T13:30:29,123 !! 2025-09-08T13:30:29,123 ******************************************************************************** 2025-09-08T13:30:29,123 ############################ 2025-09-08T13:30:29,123 # Package would be ignored # 2025-09-08T13:30:29,123 ############################ 2025-09-08T13:30:29,124 Python recognizes 'isambard.optimisation.__pycache__' as an importable package[^1], 2025-09-08T13:30:29,124 but it is absent from setuptools' `packages` configuration. 2025-09-08T13:30:29,124 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T13:30:29,124 package, please make sure that 'isambard.optimisation.__pycache__' is explicitly added 2025-09-08T13:30:29,124 to the `packages` configuration field. 2025-09-08T13:30:29,124 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T13:30:29,124 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T13:30:29,124 instead of `find_packages(...)`/`find:`). 2025-09-08T13:30:29,124 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T13:30:29,125 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T13:30:29,125 If you don't want 'isambard.optimisation.__pycache__' to be distributed and are 2025-09-08T13:30:29,125 already explicitly excluding 'isambard.optimisation.__pycache__' via 2025-09-08T13:30:29,125 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T13:30:29,125 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T13:30:29,125 combination with a more fine grained `package-data` configuration. 2025-09-08T13:30:29,125 You can read more about "package data files" on setuptools documentation page: 2025-09-08T13:30:29,126 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T13:30:29,126 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T13:30:29,126 even if it does not contain any `.py` files. 2025-09-08T13:30:29,126 On the other hand, currently there is no concept of package data 2025-09-08T13:30:29,126 directory, all directories are treated like packages. 2025-09-08T13:30:29,126 ******************************************************************************** 2025-09-08T13:30:29,126 !! 2025-09-08T13:30:29,126 check.warn(importable) 2025-09-08T13:30:29,126 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'isambard.specifications.__pycache__' is absent from the `packages` configuration. 2025-09-08T13:30:29,127 !! 2025-09-08T13:30:29,127 ******************************************************************************** 2025-09-08T13:30:29,127 ############################ 2025-09-08T13:30:29,127 # Package would be ignored # 2025-09-08T13:30:29,127 ############################ 2025-09-08T13:30:29,127 Python recognizes 'isambard.specifications.__pycache__' as an importable package[^1], 2025-09-08T13:30:29,127 but it is absent from setuptools' `packages` configuration. 2025-09-08T13:30:29,127 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T13:30:29,127 package, please make sure that 'isambard.specifications.__pycache__' is explicitly added 2025-09-08T13:30:29,127 to the `packages` configuration field. 2025-09-08T13:30:29,128 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T13:30:29,128 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T13:30:29,128 instead of `find_packages(...)`/`find:`). 2025-09-08T13:30:29,128 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T13:30:29,128 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T13:30:29,128 If you don't want 'isambard.specifications.__pycache__' to be distributed and are 2025-09-08T13:30:29,128 already explicitly excluding 'isambard.specifications.__pycache__' via 2025-09-08T13:30:29,129 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T13:30:29,129 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T13:30:29,129 combination with a more fine grained `package-data` configuration. 2025-09-08T13:30:29,129 You can read more about "package data files" on setuptools documentation page: 2025-09-08T13:30:29,129 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T13:30:29,129 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T13:30:29,129 even if it does not contain any `.py` files. 2025-09-08T13:30:29,129 On the other hand, currently there is no concept of package data 2025-09-08T13:30:29,130 directory, all directories are treated like packages. 2025-09-08T13:30:29,130 ******************************************************************************** 2025-09-08T13:30:29,130 !! 2025-09-08T13:30:29,130 check.warn(importable) 2025-09-08T13:30:29,130 creating build/lib.linux-armv7l-cpython-313/isambard/__pycache__ 2025-09-08T13:30:29,130 copying src/isambard/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/__pycache__ 2025-09-08T13:30:29,130 creating build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__ 2025-09-08T13:30:29,130 copying src/isambard/optimisation/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__ 2025-09-08T13:30:29,130 copying src/isambard/optimisation/__pycache__/base_evo_opt.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__ 2025-09-08T13:30:29,130 copying src/isambard/optimisation/__pycache__/evo_optimizers.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__ 2025-09-08T13:30:29,131 copying src/isambard/optimisation/__pycache__/mmc_optimizer.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__ 2025-09-08T13:30:29,131 creating build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__ 2025-09-08T13:30:29,131 copying src/isambard/modelling/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__ 2025-09-08T13:30:29,131 copying src/isambard/modelling/__pycache__/create_loop_data.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__ 2025-09-08T13:30:29,131 copying src/isambard/modelling/__pycache__/create_loop_database.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__ 2025-09-08T13:30:29,131 copying src/isambard/modelling/__pycache__/create_loop_db.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__ 2025-09-08T13:30:29,131 copying src/isambard/modelling/__pycache__/extract_loop_data.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__ 2025-09-08T13:30:29,131 copying src/isambard/modelling/__pycache__/loop_fitter.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__ 2025-09-08T13:30:29,131 copying src/isambard/modelling/__pycache__/loop_fitting.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__ 2025-09-08T13:30:29,131 copying src/isambard/modelling/__pycache__/non_canonical.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__ 2025-09-08T13:30:29,131 copying src/isambard/modelling/__pycache__/scwrl.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__ 2025-09-08T13:30:29,132 creating build/lib.linux-armv7l-cpython-313/isambard/modelling/reference_ampals 2025-09-08T13:30:29,132 copying src/isambard/modelling/reference_ampals/README.md -> build/lib.linux-armv7l-cpython-313/isambard/modelling/reference_ampals 2025-09-08T13:30:29,132 creating build/lib.linux-armv7l-cpython-313/isambard/modelling/reference_ampals/non_canonical_amino_acids 2025-09-08T13:30:29,132 copying src/isambard/modelling/reference_ampals/non_canonical_amino_acids/hydroxyproline_ref_1bkv_0_6.pickle -> build/lib.linux-armv7l-cpython-313/isambard/modelling/reference_ampals/non_canonical_amino_acids 2025-09-08T13:30:29,132 copying src/isambard/specifications/ta_polypeptide.c -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T13:30:29,132 copying src/isambard/specifications/ta_polypeptide.cpython-36m-x86_64-linux-gnu.so -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T13:30:29,132 copying src/isambard/specifications/ta_polypeptide.pyx -> build/lib.linux-armv7l-cpython-313/isambard/specifications 2025-09-08T13:30:29,132 creating build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__ 2025-09-08T13:30:29,132 copying src/isambard/specifications/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__ 2025-09-08T13:30:29,132 copying src/isambard/specifications/__pycache__/coiledcoil.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__ 2025-09-08T13:30:29,133 copying src/isambard/specifications/__pycache__/helix.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__ 2025-09-08T13:30:29,133 copying src/isambard/specifications/__pycache__/nucleic_acid_duplex.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__ 2025-09-08T13:30:29,133 copying src/isambard/specifications/__pycache__/nucleic_acid_strand.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__ 2025-09-08T13:30:29,133 copying src/isambard/specifications/__pycache__/solenoid.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__ 2025-09-08T13:30:29,133 creating build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__ 2025-09-08T13:30:29,133 copying src/isambard/evaluation/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__ 2025-09-08T13:30:29,133 copying src/isambard/evaluation/__pycache__/contact_order.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__ 2025-09-08T13:30:29,133 copying src/isambard/evaluation/__pycache__/dssp.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__ 2025-09-08T13:30:29,134 copying src/isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__ 2025-09-08T13:30:29,134 copying src/isambard/evaluation/__pycache__/pacc.cpython-36.pyc -> build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__ 2025-09-08T13:30:29,136 running build_ext 2025-09-08T13:30:29,144 building 'isambard.specifications.ta_polypeptide' extension 2025-09-08T13:30:29,145 creating build/temp.linux-armv7l-cpython-313/src/isambard/specifications 2025-09-08T13:30:29,145 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/python3.13 -c src/isambard/specifications/ta_polypeptide.c -o build/temp.linux-armv7l-cpython-313/src/isambard/specifications/ta_polypeptide.o 2025-09-08T13:30:46,510 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/src/isambard/specifications/ta_polypeptide.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/isambard/specifications/ta_polypeptide.cpython-313-arm-linux-gnueabihf.so 2025-09-08T13:30:46,780 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-08T13:30:46,780 !! 2025-09-08T13:30:46,781 ******************************************************************************** 2025-09-08T13:30:46,781 Please avoid running ``setup.py`` directly. 2025-09-08T13:30:46,781 Instead, use pypa/build, pypa/installer or other 2025-09-08T13:30:46,781 standards-based tools. 2025-09-08T13:30:46,781 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T13:30:46,781 or your builds will no longer be supported. 2025-09-08T13:30:46,781 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-08T13:30:46,782 ******************************************************************************** 2025-09-08T13:30:46,782 !! 2025-09-08T13:30:46,782 self.initialize_options() 2025-09-08T13:30:46,856 installing to build/bdist.linux-armv7l/wheel 2025-09-08T13:30:46,856 running install 2025-09-08T13:30:46,878 running install_lib 2025-09-08T13:30:46,952 creating build/bdist.linux-armv7l/wheel 2025-09-08T13:30:46,952 creating build/bdist.linux-armv7l/wheel/isambard 2025-09-08T13:30:46,953 creating build/bdist.linux-armv7l/wheel/isambard/__pycache__ 2025-09-08T13:30:46,953 copying build/lib.linux-armv7l-cpython-313/isambard/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/__pycache__ 2025-09-08T13:30:46,953 creating build/bdist.linux-armv7l/wheel/isambard/evaluation 2025-09-08T13:30:46,954 creating build/bdist.linux-armv7l/wheel/isambard/evaluation/__pycache__ 2025-09-08T13:30:46,954 copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__/pacc.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/evaluation/__pycache__ 2025-09-08T13:30:46,955 copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/evaluation/__pycache__ 2025-09-08T13:30:46,955 copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__/dssp.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/evaluation/__pycache__ 2025-09-08T13:30:46,955 copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__/contact_order.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/evaluation/__pycache__ 2025-09-08T13:30:46,956 copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/evaluation/__pycache__ 2025-09-08T13:30:46,956 copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/__init__.py -> build/bdist.linux-armv7l/wheel/./isambard/evaluation 2025-09-08T13:30:46,956 copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/contact_order.py -> build/bdist.linux-armv7l/wheel/./isambard/evaluation 2025-09-08T13:30:46,957 copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/hydrophobic_fitness.py -> build/bdist.linux-armv7l/wheel/./isambard/evaluation 2025-09-08T13:30:46,957 copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/pacc.py -> build/bdist.linux-armv7l/wheel/./isambard/evaluation 2025-09-08T13:30:46,958 copying build/lib.linux-armv7l-cpython-313/isambard/evaluation/dssp.py -> build/bdist.linux-armv7l/wheel/./isambard/evaluation 2025-09-08T13:30:46,958 creating build/bdist.linux-armv7l/wheel/isambard/specifications 2025-09-08T13:30:46,958 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/ta_polypeptide.cpython-313-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T13:30:46,962 creating build/bdist.linux-armv7l/wheel/isambard/specifications/__pycache__ 2025-09-08T13:30:46,962 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__/solenoid.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/specifications/__pycache__ 2025-09-08T13:30:46,963 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__/nucleic_acid_strand.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/specifications/__pycache__ 2025-09-08T13:30:46,963 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__/nucleic_acid_duplex.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/specifications/__pycache__ 2025-09-08T13:30:46,963 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__/helix.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/specifications/__pycache__ 2025-09-08T13:30:46,964 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__/coiledcoil.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/specifications/__pycache__ 2025-09-08T13:30:46,964 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/specifications/__pycache__ 2025-09-08T13:30:46,965 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/ta_polypeptide.pyx -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T13:30:46,965 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/ta_polypeptide.cpython-36m-x86_64-linux-gnu.so -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T13:30:46,968 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/ta_polypeptide.c -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T13:30:46,971 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/solenoid.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T13:30:46,971 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/__init__.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T13:30:46,971 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/nucleic_acid_strand.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T13:30:46,972 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/nucleic_acid_duplex.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T13:30:46,972 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/helix.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T13:30:46,973 copying build/lib.linux-armv7l-cpython-313/isambard/specifications/coiledcoil.py -> build/bdist.linux-armv7l/wheel/./isambard/specifications 2025-09-08T13:30:46,973 creating build/bdist.linux-armv7l/wheel/isambard/modelling 2025-09-08T13:30:46,974 creating build/bdist.linux-armv7l/wheel/isambard/modelling/reference_ampals 2025-09-08T13:30:46,974 creating build/bdist.linux-armv7l/wheel/isambard/modelling/reference_ampals/non_canonical_amino_acids 2025-09-08T13:30:46,974 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/reference_ampals/non_canonical_amino_acids/hydroxyproline_ref_1bkv_0_6.pickle -> build/bdist.linux-armv7l/wheel/./isambard/modelling/reference_ampals/non_canonical_amino_acids 2025-09-08T13:30:46,975 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/reference_ampals/README.md -> build/bdist.linux-armv7l/wheel/./isambard/modelling/reference_ampals 2025-09-08T13:30:46,975 creating build/bdist.linux-armv7l/wheel/isambard/modelling/__pycache__ 2025-09-08T13:30:46,976 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/scwrl.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__ 2025-09-08T13:30:46,976 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/non_canonical.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__ 2025-09-08T13:30:46,976 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/loop_fitting.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__ 2025-09-08T13:30:46,977 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/loop_fitter.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__ 2025-09-08T13:30:46,977 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/extract_loop_data.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__ 2025-09-08T13:30:46,978 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/create_loop_db.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__ 2025-09-08T13:30:46,978 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/create_loop_database.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__ 2025-09-08T13:30:46,978 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/create_loop_data.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__ 2025-09-08T13:30:46,979 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/modelling/__pycache__ 2025-09-08T13:30:46,979 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/__init__.py -> build/bdist.linux-armv7l/wheel/./isambard/modelling 2025-09-08T13:30:46,979 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/scwrl.py -> build/bdist.linux-armv7l/wheel/./isambard/modelling 2025-09-08T13:30:46,980 copying build/lib.linux-armv7l-cpython-313/isambard/modelling/non_canonical.py -> build/bdist.linux-armv7l/wheel/./isambard/modelling 2025-09-08T13:30:46,980 creating build/bdist.linux-armv7l/wheel/isambard/optimisation 2025-09-08T13:30:46,981 creating build/bdist.linux-armv7l/wheel/isambard/optimisation/__pycache__ 2025-09-08T13:30:46,981 copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__/mmc_optimizer.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/optimisation/__pycache__ 2025-09-08T13:30:46,981 copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__/evo_optimizers.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/optimisation/__pycache__ 2025-09-08T13:30:46,982 copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__/base_evo_opt.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/optimisation/__pycache__ 2025-09-08T13:30:46,982 copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/./isambard/optimisation/__pycache__ 2025-09-08T13:30:46,983 copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/evo_optimizers.py -> build/bdist.linux-armv7l/wheel/./isambard/optimisation 2025-09-08T13:30:46,983 copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/__init__.py -> build/bdist.linux-armv7l/wheel/./isambard/optimisation 2025-09-08T13:30:46,984 copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/mmc_optimizer.py -> build/bdist.linux-armv7l/wheel/./isambard/optimisation 2025-09-08T13:30:46,984 copying build/lib.linux-armv7l-cpython-313/isambard/optimisation/base_evo_opt.py -> build/bdist.linux-armv7l/wheel/./isambard/optimisation 2025-09-08T13:30:46,985 copying build/lib.linux-armv7l-cpython-313/isambard/__init__.py -> build/bdist.linux-armv7l/wheel/./isambard 2025-09-08T13:30:46,985 running install_egg_info 2025-09-08T13:30:47,063 Copying src/ISAMBARD.egg-info to build/bdist.linux-armv7l/wheel/./ISAMBARD-2.2.0-py3.13.egg-info 2025-09-08T13:30:47,065 running install_scripts 2025-09-08T13:30:47,116 creating build/bdist.linux-armv7l/wheel/isambard-2.2.0.dist-info/WHEEL 2025-09-08T13:30:47,117 creating '/tmp/pip-wheel-8a2yjb2o/isambard-2.2.0-cp313-cp313-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-09-08T13:30:47,118 adding 'isambard/__init__.py' 2025-09-08T13:30:47,119 adding 'isambard/__pycache__/__init__.cpython-36.pyc' 2025-09-08T13:30:47,119 adding 'isambard/evaluation/__init__.py' 2025-09-08T13:30:47,120 adding 'isambard/evaluation/contact_order.py' 2025-09-08T13:30:47,121 adding 'isambard/evaluation/dssp.py' 2025-09-08T13:30:47,122 adding 'isambard/evaluation/hydrophobic_fitness.py' 2025-09-08T13:30:47,123 adding 'isambard/evaluation/pacc.py' 2025-09-08T13:30:47,124 adding 'isambard/evaluation/__pycache__/__init__.cpython-36.pyc' 2025-09-08T13:30:47,125 adding 'isambard/evaluation/__pycache__/contact_order.cpython-36.pyc' 2025-09-08T13:30:47,126 adding 'isambard/evaluation/__pycache__/dssp.cpython-36.pyc' 2025-09-08T13:30:47,127 adding 'isambard/evaluation/__pycache__/hydrophobic_fitness.cpython-36.pyc' 2025-09-08T13:30:47,128 adding 'isambard/evaluation/__pycache__/pacc.cpython-36.pyc' 2025-09-08T13:30:47,129 adding 'isambard/modelling/__init__.py' 2025-09-08T13:30:47,130 adding 'isambard/modelling/non_canonical.py' 2025-09-08T13:30:47,131 adding 'isambard/modelling/scwrl.py' 2025-09-08T13:30:47,131 adding 'isambard/modelling/__pycache__/__init__.cpython-36.pyc' 2025-09-08T13:30:47,133 adding 'isambard/modelling/__pycache__/create_loop_data.cpython-36.pyc' 2025-09-08T13:30:47,134 adding 'isambard/modelling/__pycache__/create_loop_database.cpython-36.pyc' 2025-09-08T13:30:47,135 adding 'isambard/modelling/__pycache__/create_loop_db.cpython-36.pyc' 2025-09-08T13:30:47,136 adding 'isambard/modelling/__pycache__/extract_loop_data.cpython-36.pyc' 2025-09-08T13:30:47,138 adding 'isambard/modelling/__pycache__/loop_fitter.cpython-36.pyc' 2025-09-08T13:30:47,139 adding 'isambard/modelling/__pycache__/loop_fitting.cpython-36.pyc' 2025-09-08T13:30:47,140 adding 'isambard/modelling/__pycache__/non_canonical.cpython-36.pyc' 2025-09-08T13:30:47,141 adding 'isambard/modelling/__pycache__/scwrl.cpython-36.pyc' 2025-09-08T13:30:47,141 adding 'isambard/modelling/reference_ampals/README.md' 2025-09-08T13:30:47,142 adding 'isambard/modelling/reference_ampals/non_canonical_amino_acids/hydroxyproline_ref_1bkv_0_6.pickle' 2025-09-08T13:30:47,143 adding 'isambard/optimisation/__init__.py' 2025-09-08T13:30:47,145 adding 'isambard/optimisation/base_evo_opt.py' 2025-09-08T13:30:47,147 adding 'isambard/optimisation/evo_optimizers.py' 2025-09-08T13:30:47,148 adding 'isambard/optimisation/mmc_optimizer.py' 2025-09-08T13:30:47,149 adding 'isambard/optimisation/__pycache__/__init__.cpython-36.pyc' 2025-09-08T13:30:47,151 adding 'isambard/optimisation/__pycache__/base_evo_opt.cpython-36.pyc' 2025-09-08T13:30:47,154 adding 'isambard/optimisation/__pycache__/evo_optimizers.cpython-36.pyc' 2025-09-08T13:30:47,156 adding 'isambard/optimisation/__pycache__/mmc_optimizer.cpython-36.pyc' 2025-09-08T13:30:47,157 adding 'isambard/specifications/__init__.py' 2025-09-08T13:30:47,158 adding 'isambard/specifications/coiledcoil.py' 2025-09-08T13:30:47,160 adding 'isambard/specifications/helix.py' 2025-09-08T13:30:47,161 adding 'isambard/specifications/nucleic_acid_duplex.py' 2025-09-08T13:30:47,162 adding 'isambard/specifications/nucleic_acid_strand.py' 2025-09-08T13:30:47,163 adding 'isambard/specifications/solenoid.py' 2025-09-08T13:30:47,215 adding 'isambard/specifications/ta_polypeptide.c' 2025-09-08T13:30:47,382 adding 'isambard/specifications/ta_polypeptide.cpython-313-arm-linux-gnueabihf.so' 2025-09-08T13:30:47,488 adding 'isambard/specifications/ta_polypeptide.cpython-36m-x86_64-linux-gnu.so' 2025-09-08T13:30:47,494 adding 'isambard/specifications/ta_polypeptide.pyx' 2025-09-08T13:30:47,495 adding 'isambard/specifications/__pycache__/__init__.cpython-36.pyc' 2025-09-08T13:30:47,496 adding 'isambard/specifications/__pycache__/coiledcoil.cpython-36.pyc' 2025-09-08T13:30:47,498 adding 'isambard/specifications/__pycache__/helix.cpython-36.pyc' 2025-09-08T13:30:47,499 adding 'isambard/specifications/__pycache__/nucleic_acid_duplex.cpython-36.pyc' 2025-09-08T13:30:47,501 adding 'isambard/specifications/__pycache__/nucleic_acid_strand.cpython-36.pyc' 2025-09-08T13:30:47,502 adding 'isambard/specifications/__pycache__/solenoid.cpython-36.pyc' 2025-09-08T13:30:47,503 adding 'isambard-2.2.0.dist-info/licenses/LICENSE.txt' 2025-09-08T13:30:47,504 adding 'isambard-2.2.0.dist-info/METADATA' 2025-09-08T13:30:47,505 adding 'isambard-2.2.0.dist-info/WHEEL' 2025-09-08T13:30:47,505 adding 'isambard-2.2.0.dist-info/top_level.txt' 2025-09-08T13:30:47,506 adding 'isambard-2.2.0.dist-info/RECORD' 2025-09-08T13:30:47,507 removing build/bdist.linux-armv7l/wheel 2025-09-08T13:30:47,659 Building wheel for isambard (setup.py): finished with status 'done' 2025-09-08T13:30:47,668 Created wheel for isambard: filename=isambard-2.2.0-cp313-cp313-linux_armv7l.whl size=741291 sha256=81833d4099d139da2f97b313c21b37564ff293048dbdb32201fd676194ea1631 2025-09-08T13:30:47,669 Stored in directory: /tmp/pip-ephem-wheel-cache-efn9u9f1/wheels/16/00/78/767d4e3b63936266458392b02db647eb153c1d3c4af609e580 2025-09-08T13:30:47,679 Successfully built isambard 2025-09-08T13:30:47,682 Removed build tracker: '/tmp/pip-build-tracker-plndqfou'