2025-09-09T08:48:43,580 Created temporary directory: /tmp/pip-build-tracker-lxtccpuh 2025-09-09T08:48:43,581 Initialized build tracking at /tmp/pip-build-tracker-lxtccpuh 2025-09-09T08:48:43,581 Created build tracker: /tmp/pip-build-tracker-lxtccpuh 2025-09-09T08:48:43,581 Entered build tracker: /tmp/pip-build-tracker-lxtccpuh 2025-09-09T08:48:43,582 Created temporary directory: /tmp/pip-wheel-60qdy46j 2025-09-09T08:48:43,585 Created temporary directory: /tmp/pip-ephem-wheel-cache-t0erulfc 2025-09-09T08:48:43,647 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-09T08:48:43,649 2 location(s) to search for versions of bioscrape: 2025-09-09T08:48:43,649 * https://pypi.org/simple/bioscrape/ 2025-09-09T08:48:43,649 * https://www.piwheels.org/simple/bioscrape/ 2025-09-09T08:48:43,649 Fetching project page and analyzing links: https://pypi.org/simple/bioscrape/ 2025-09-09T08:48:43,650 Getting page https://pypi.org/simple/bioscrape/ 2025-09-09T08:48:43,651 Found index url https://pypi.org/simple/ 2025-09-09T08:48:43,721 Fetched page https://pypi.org/simple/bioscrape/ as application/vnd.pypi.simple.v1+json 2025-09-09T08:48:43,724 Found link https://files.pythonhosted.org/packages/0c/22/e9fa3067657b389f96a90736bba21abacacc056c984cedcd1df82440b976/bioscrape-1.0.2.tar.gz (from https://pypi.org/simple/bioscrape/), version: 1.0.2 2025-09-09T08:48:43,724 Found link https://files.pythonhosted.org/packages/75/f5/7b5c7157119c5a3b7042e559cd20797125cb5e58cbe93046a2f3c237eb34/bioscrape-1.0.2.1.tar.gz (from https://pypi.org/simple/bioscrape/), version: 1.0.2.1 2025-09-09T08:48:43,724 Found link https://files.pythonhosted.org/packages/6b/7a/49938026e6b712ff6f93e353babcb85ac8db35d92a966ae39f30ef727eb4/bioscrape-1.0.2.2.tar.gz (from https://pypi.org/simple/bioscrape/), version: 1.0.2.2 2025-09-09T08:48:43,725 Found link https://files.pythonhosted.org/packages/44/9f/7dad2a85d729b705eb9d81bb133efa54e9d9f6fad1dd48b113524655a67c/bioscrape-1.0.3.tar.gz (from https://pypi.org/simple/bioscrape/), version: 1.0.3 2025-09-09T08:48:43,725 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/ba/1b/2ad1ffcaf9d71e67a66177ca9a3b71a5a20981f890909856dc165f8dd28c/bioscrape-1.0.4-py3.9-win-amd64.egg (from https://pypi.org/simple/bioscrape/) 2025-09-09T08:48:43,725 Found link https://files.pythonhosted.org/packages/20/c4/aef522565064181d05c470a5d3e8d7ee070792c38969041db51ee274e8a2/bioscrape-1.0.4.tar.gz (from https://pypi.org/simple/bioscrape/), version: 1.0.4 2025-09-09T08:48:43,725 Skipping link: No binaries permitted for bioscrape: https://files.pythonhosted.org/packages/3b/61/28f6981753b4c5dd0f8caae0f14b12b4ae8cdc41fe2fe457175fb2e2bbbf/bioscrape-1.1.0-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,725 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/0a/a5/1377480b761f3ed7241ae7f6e692c62a5a04209877caef36ec6b8c9364ff/bioscrape-1.1.0-py3.9-win-amd64.egg (from https://pypi.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,726 Found link https://files.pythonhosted.org/packages/bf/97/3d059aed33d22fb9ade1007310649b0c53335f76a5db010155c97d06c438/bioscrape-1.1.0.tar.gz (from https://pypi.org/simple/bioscrape/) (requires-python:>=3.6), version: 1.1.0 2025-09-09T08:48:43,726 Skipping link: No binaries permitted for bioscrape: https://files.pythonhosted.org/packages/d8/06/7520de3eebf3f564bf8b6f8dc023f45d4c99ee8b2257cc96d5736d55a2cb/bioscrape-1.2.0-cp310-cp310-win_amd64.whl (from https://pypi.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,726 Found link https://files.pythonhosted.org/packages/5e/48/73d5437aa9167e88d2452aa9e12b6ed7613a5a4b0c9c76c967eb5d6e87df/bioscrape-1.2.0.tar.gz (from https://pypi.org/simple/bioscrape/) (requires-python:>=3.6), version: 1.2.0 2025-09-09T08:48:43,726 Skipping link: No binaries permitted for bioscrape: https://files.pythonhosted.org/packages/f3/d6/88e220bd59d5c5c2980faada66cb02e4ff82450a9ba6cc00d52e530488a7/bioscrape-1.2.1-cp37-cp37m-win_amd64.whl (from https://pypi.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,727 Found link https://files.pythonhosted.org/packages/38/98/4ba083b3b2e349c2043af33b8de46922572bf8db8cdb16fc70d633701f29/bioscrape-1.2.1.tar.gz (from https://pypi.org/simple/bioscrape/) (requires-python:>=3.6), version: 1.2.1 2025-09-09T08:48:43,727 Skipping link: No binaries permitted for bioscrape: https://files.pythonhosted.org/packages/6b/45/45613a281dd21a8772675bc7250344be5b0a33050f75c39fb1a1c4233340/Bioscrape-1.2.2-cp310-cp310-win_amd64.whl (from https://pypi.org/simple/bioscrape/) (requires-python:>=3.7) 2025-09-09T08:48:43,727 Skipping link: No binaries permitted for bioscrape: https://files.pythonhosted.org/packages/c7/7a/d632320e71f449e91d3adeadd6252841fdd750b1e65dcc86c2de564215d9/Bioscrape-1.3.0-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/bioscrape/) (requires-python:>=3.7) 2025-09-09T08:48:43,727 Fetching project page and analyzing links: https://www.piwheels.org/simple/bioscrape/ 2025-09-09T08:48:43,727 Getting page https://www.piwheels.org/simple/bioscrape/ 2025-09-09T08:48:43,728 Found index url https://www.piwheels.org/simple/ 2025-09-09T08:48:43,830 Fetched page https://www.piwheels.org/simple/bioscrape/ as text/html 2025-09-09T08:48:43,839 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.2.1-cp37-cp37m-linux_armv6l.whl#sha256=8a9fbff1a372b8f6717354b69bfa683d77c6e64a99785ab5b470702909f34a8d (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,839 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.2.1-cp37-cp37m-linux_armv7l.whl#sha256=8a9fbff1a372b8f6717354b69bfa683d77c6e64a99785ab5b470702909f34a8d (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,839 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.2.1-cp39-cp39-linux_armv6l.whl#sha256=1bcc3bec0e129bfeaf3531ce4fae15775687070c419c5c1842193fbda4130cdb (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,840 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.2.1-cp39-cp39-linux_armv7l.whl#sha256=1bcc3bec0e129bfeaf3531ce4fae15775687070c419c5c1842193fbda4130cdb (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,840 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.2.0-cp37-cp37m-linux_armv6l.whl#sha256=d6c84d98a3b5d2d28daf7910e8fd0c3e0483b14f085d123549fcc7971469da8f (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,840 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.2.0-cp37-cp37m-linux_armv7l.whl#sha256=d6c84d98a3b5d2d28daf7910e8fd0c3e0483b14f085d123549fcc7971469da8f (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,840 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.2.0-cp39-cp39-linux_armv6l.whl#sha256=81cb8b5ad98fe393427baadebaf000546f8a391fe75c474bd0266d9ccfd83f0a (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,840 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.2.0-cp39-cp39-linux_armv7l.whl#sha256=81cb8b5ad98fe393427baadebaf000546f8a391fe75c474bd0266d9ccfd83f0a (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,840 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.1.0-cp37-cp37m-linux_armv6l.whl#sha256=d6cec47dd1c48a1d8fcb0330a7dd2a5b12bc23003cc9fb3c5a1a09ffd78e6560 (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,841 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.1.0-cp37-cp37m-linux_armv7l.whl#sha256=d6cec47dd1c48a1d8fcb0330a7dd2a5b12bc23003cc9fb3c5a1a09ffd78e6560 (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,841 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.1.0-cp39-cp39-linux_armv6l.whl#sha256=22392b2f427deabfdea356b6ac55c3155afbc72435fea0a7fd29b3d06397832f (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,841 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.1.0-cp39-cp39-linux_armv7l.whl#sha256=22392b2f427deabfdea356b6ac55c3155afbc72435fea0a7fd29b3d06397832f (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,841 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.4-cp37-cp37m-linux_armv6l.whl#sha256=417e5aec8c9b4859d8b7e2fb305cf9ed077d2307a1213abdb59704db3c8d2829 (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,841 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.4-cp37-cp37m-linux_armv7l.whl#sha256=417e5aec8c9b4859d8b7e2fb305cf9ed077d2307a1213abdb59704db3c8d2829 (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,841 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.4-cp39-cp39-linux_armv6l.whl#sha256=02cae05f27f680afc960696a3bc00b3daf0a723f26220b4b852eae4ae5b651bb (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,842 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.4-cp39-cp39-linux_armv7l.whl#sha256=02cae05f27f680afc960696a3bc00b3daf0a723f26220b4b852eae4ae5b651bb (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,842 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.3-cp37-cp37m-linux_armv6l.whl#sha256=dd39f635d1c7199683227ceac02f25f922636c9885c0cb6e8158c2c8e51cb2ce (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,842 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.3-cp37-cp37m-linux_armv7l.whl#sha256=dd39f635d1c7199683227ceac02f25f922636c9885c0cb6e8158c2c8e51cb2ce (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,842 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.3-cp39-cp39-linux_armv6l.whl#sha256=74438fb5c4b8f66236ce6468f1d30c624381192f5266a672f5ba33a63a144190 (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,842 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.3-cp39-cp39-linux_armv7l.whl#sha256=74438fb5c4b8f66236ce6468f1d30c624381192f5266a672f5ba33a63a144190 (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,842 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.2.2-cp37-cp37m-linux_armv6l.whl#sha256=192f506de67a941d59aadca64e9a31a6ffa94589b367e52006db6fdc07786ea0 (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,842 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.2.2-cp37-cp37m-linux_armv7l.whl#sha256=192f506de67a941d59aadca64e9a31a6ffa94589b367e52006db6fdc07786ea0 (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,843 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.2.2-cp39-cp39-linux_armv6l.whl#sha256=ae93564915bb90732c2697229827147b8969883e0ee926b182a47b42dd1fdebc (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,843 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.2.2-cp39-cp39-linux_armv7l.whl#sha256=ae93564915bb90732c2697229827147b8969883e0ee926b182a47b42dd1fdebc (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,843 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.2.1-cp37-cp37m-linux_armv6l.whl#sha256=4fc78676dc2c35b28459fb97c39c4ba04ec574eb45c32daf551e670cedfb1f88 (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,843 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.2.1-cp37-cp37m-linux_armv7l.whl#sha256=4fc78676dc2c35b28459fb97c39c4ba04ec574eb45c32daf551e670cedfb1f88 (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,843 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.2.1-cp39-cp39-linux_armv6l.whl#sha256=1c4fb71d3cba008596f16d0b6b20e11f4750c40ffe90981fa363099463abea36 (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,843 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.2.1-cp39-cp39-linux_armv7l.whl#sha256=1c4fb71d3cba008596f16d0b6b20e11f4750c40ffe90981fa363099463abea36 (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,844 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.2-cp37-cp37m-linux_armv6l.whl#sha256=83fce4ab312032ca902c1ba08a2b50b6b5de24babe9b4140c520e235b9957704 (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,844 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.2-cp37-cp37m-linux_armv7l.whl#sha256=83fce4ab312032ca902c1ba08a2b50b6b5de24babe9b4140c520e235b9957704 (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,844 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.2-cp39-cp39-linux_armv6l.whl#sha256=f5586551025dcd3c2553db761ce5dc3eae080a4261a513128bf56e6c4004ffba (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,844 Skipping link: No binaries permitted for bioscrape: https://archive1.piwheels.org/simple/bioscrape/bioscrape-1.0.2-cp39-cp39-linux_armv7l.whl#sha256=f5586551025dcd3c2553db761ce5dc3eae080a4261a513128bf56e6c4004ffba (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,844 Skipping link: No binaries permitted for bioscrape: https://www.piwheels.org/simple/bioscrape/bioscrape-1.0.2-cp313-cp313-linux_armv6l.whl#sha256=a0779d7e1b6414bfb564a581b7bbcecf284c27c542b4f3a28a144634cbfdb48d (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,844 Skipping link: No binaries permitted for bioscrape: https://www.piwheels.org/simple/bioscrape/bioscrape-1.0.2-cp313-cp313-linux_armv7l.whl#sha256=a0779d7e1b6414bfb564a581b7bbcecf284c27c542b4f3a28a144634cbfdb48d (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-09T08:48:43,844 Skipping link: not a file: https://www.piwheels.org/simple/bioscrape/ 2025-09-09T08:48:43,845 Skipping link: not a file: https://pypi.org/simple/bioscrape/ 2025-09-09T08:48:43,870 Given no hashes to check 1 links for project 'bioscrape': discarding no candidates 2025-09-09T08:48:43,871 Collecting bioscrape==1.0.2.2 2025-09-09T08:48:43,872 Created temporary directory: /tmp/pip-unpack-ldpbuo44 2025-09-09T08:48:44,013 Downloading bioscrape-1.0.2.2.tar.gz (594 kB) 2025-09-09T08:48:44,207 Added bioscrape==1.0.2.2 from https://files.pythonhosted.org/packages/6b/7a/49938026e6b712ff6f93e353babcb85ac8db35d92a966ae39f30ef727eb4/bioscrape-1.0.2.2.tar.gz to build tracker '/tmp/pip-build-tracker-lxtccpuh' 2025-09-09T08:48:44,208 Running setup.py (path:/tmp/pip-wheel-60qdy46j/bioscrape_c496359a5d964dbfa13a78bf5df1c1c3/setup.py) egg_info for package bioscrape 2025-09-09T08:48:44,208 Created temporary directory: /tmp/pip-pip-egg-info-bni42hnm 2025-09-09T08:48:44,208 Preparing metadata (setup.py): started 2025-09-09T08:48:44,209 Running command python setup.py egg_info 2025-09-09T08:49:01,055 warning: bioscrape/types.pyx:1781:32: the result of using negative indices inside of code sections marked as 'wraparound=False' is undefined 2025-09-09T08:49:01,056 warning: bioscrape/types.pyx:1787:32: the result of using negative indices inside of code sections marked as 'wraparound=False' is undefined 2025-09-09T08:49:01,058 warning: bioscrape/types.pyx:1796:40: the result of using negative indices inside of code sections marked as 'wraparound=False' is undefined 2025-09-09T08:49:01,059 warning: bioscrape/types.pyx:1803:40: the result of using negative indices inside of code sections marked as 'wraparound=False' is undefined 2025-09-09T08:49:01,074 warning: bioscrape/types.pyx:1912:44: the result of using negative indices inside of code sections marked as 'wraparound=False' is undefined 2025-09-09T08:49:03,903 Installing Bioscrape... 2025-09-09T08:49:03,904 Compiling bioscrape/random.pyx because it changed. 2025-09-09T08:49:03,904 Compiling bioscrape/types.pyx because it changed. 2025-09-09T08:49:03,904 Compiling bioscrape/simulator.pyx because it changed. 2025-09-09T08:49:03,904 Compiling bioscrape/inference.pyx because it changed. 2025-09-09T08:49:03,904 [1/4] Cythonizing bioscrape/inference.pyx 2025-09-09T08:49:03,904 [2/4] Cythonizing bioscrape/random.pyx 2025-09-09T08:49:03,904 [3/4] Cythonizing bioscrape/simulator.pyx 2025-09-09T08:49:03,904 [4/4] Cythonizing bioscrape/types.pyx 2025-09-09T08:49:04,510 warning: lineage/lineage.pyx:729:32: Unreachable code 2025-09-09T08:49:08,400 warning: lineage/lineage.pyx:3027:39: the result of using negative indices inside of code sections marked as 'wraparound=False' is undefined 2025-09-09T08:49:11,688 Bioscrape Cythonized. 2025-09-09T08:49:11,688 Installing Lineage... 2025-09-09T08:49:11,688 Compiling lineage/lineage.pyx because it changed. 2025-09-09T08:49:11,688 [1/1] Cythonizing lineage/lineage.pyx 2025-09-09T08:49:11,862 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-09-09T08:49:11,862 warnings.warn(msg) 2025-09-09T08:49:12,734 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-09T08:49:12,734 !! 2025-09-09T08:49:12,734 ******************************************************************************** 2025-09-09T08:49:12,735 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-09T08:49:12,735 License :: OSI Approved :: BSD License 2025-09-09T08:49:12,735 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-09T08:49:12,735 ******************************************************************************** 2025-09-09T08:49:12,735 !! 2025-09-09T08:49:12,735 self._finalize_license_expression() 2025-09-09T08:49:13,207 Lineage Cythonized. 2025-09-09T08:49:14,403 Preparing metadata (setup.py): finished with status 'done' 2025-09-09T08:49:14,408 Source in /tmp/pip-wheel-60qdy46j/bioscrape_c496359a5d964dbfa13a78bf5df1c1c3 has version 1.0.2.2, which satisfies requirement bioscrape==1.0.2.2 from https://files.pythonhosted.org/packages/6b/7a/49938026e6b712ff6f93e353babcb85ac8db35d92a966ae39f30ef727eb4/bioscrape-1.0.2.2.tar.gz 2025-09-09T08:49:14,408 Removed bioscrape==1.0.2.2 from https://files.pythonhosted.org/packages/6b/7a/49938026e6b712ff6f93e353babcb85ac8db35d92a966ae39f30ef727eb4/bioscrape-1.0.2.2.tar.gz from build tracker '/tmp/pip-build-tracker-lxtccpuh' 2025-09-09T08:49:14,414 Created temporary directory: /tmp/pip-unpack-preptm41 2025-09-09T08:49:14,414 Created temporary directory: /tmp/pip-unpack-az_vvpl8 2025-09-09T08:49:14,414 Building wheels for collected packages: bioscrape 2025-09-09T08:49:14,416 Created temporary directory: /tmp/pip-wheel-xxwrxmt0 2025-09-09T08:49:14,416 DEPRECATION: Building 'bioscrape' 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 'bioscrape'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-09T08:49:14,417 Building wheel for bioscrape (setup.py): started 2025-09-09T08:49:14,418 Destination directory: /tmp/pip-wheel-xxwrxmt0 2025-09-09T08:49:14,418 Running command python setup.py bdist_wheel 2025-09-09T08:49:15,377 Installing Bioscrape... 2025-09-09T08:49:15,976 Bioscrape Cythonized. 2025-09-09T08:49:15,977 Installing Lineage... 2025-09-09T08:49:16,043 Lineage Cythonized. 2025-09-09T08:49:16,133 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-09-09T08:49:16,133 warnings.warn(msg) 2025-09-09T08:49:16,352 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-09T08:49:16,352 !! 2025-09-09T08:49:16,352 ******************************************************************************** 2025-09-09T08:49:16,352 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-09T08:49:16,352 License :: OSI Approved :: BSD License 2025-09-09T08:49:16,352 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-09T08:49:16,353 ******************************************************************************** 2025-09-09T08:49:16,353 !! 2025-09-09T08:49:16,353 self._finalize_license_expression() 2025-09-09T08:49:19,075 bioscrape/random.cpp: In function ‘long long unsigned int __pyx_f_9bioscrape_6random_genrand64()’: 2025-09-09T08:49:19,075 bioscrape/random.cpp:4928:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T08:49:19,075 4928 | for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { 2025-09-09T08:49:19,075 | ~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:49:31,904 bioscrape/types.cpp: In function ‘PyObject* __pyx_pf_9bioscrape_5types_7Schnitz_20get_sub_lineage(__pyx_obj_9bioscrape_5types_Schnitz*, PyObject*)’: 2025-09-09T08:49:31,904 bioscrape/types.cpp:69985:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:49:31,904 69985 | __pyx_t_1 = (__pyx_v_index < __pyx_t_7); 2025-09-09T08:49:31,904 | ~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:49:31,907 bioscrape/types.cpp:70088:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:49:31,908 70088 | for (__pyx_t_10 = 0; __pyx_t_10 < __pyx_t_9; __pyx_t_10+=1) { 2025-09-09T08:49:31,908 | ~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:51:52,292 bioscrape/simulator.cpp: In function ‘__pyx_obj_9bioscrape_5types_Lineage* __pyx_f_9bioscrape_9simulator_simulate_cell_lineage(__pyx_obj_9bioscrape_9simulator_CSimInterface*, __pyx_obj_9bioscrape_5types_Volume*, PyArrayObject*, __pyx_obj_9bioscrape_9simulator_VolumeSimulator*, __pyx_obj_9bioscrape_9simulator_VolumeSplitter*)’: 2025-09-09T08:51:52,292 bioscrape/simulator.cpp:44269:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:51:52,292 44269 | __pyx_t_7 = (__pyx_v_list_index < __pyx_t_9); 2025-09-09T08:51:52,292 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:51:52,336 bioscrape/simulator.cpp: In function ‘__pyx_obj_9bioscrape_5types_Lineage* __pyx_f_9bioscrape_9simulator_simulate_delay_cell_lineage(__pyx_obj_9bioscrape_9simulator_CSimInterface*, __pyx_obj_9bioscrape_9simulator_DelayQueue*, __pyx_obj_9bioscrape_5types_Volume*, PyArrayObject*, __pyx_obj_9bioscrape_9simulator_DelayVolumeSimulator*, __pyx_obj_9bioscrape_9simulator_DelayVolumeSplitter*)’: 2025-09-09T08:51:52,336 bioscrape/simulator.cpp:45136:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:51:52,336 45136 | __pyx_t_7 = (__pyx_v_list_index < __pyx_t_9); 2025-09-09T08:51:52,337 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:51:52,685 bioscrape/simulator.cpp: In function ‘PyObject* __pyx_pf_9bioscrape_9simulator_22DeterministicSimulator_6_helper_simulate(__pyx_obj_9bioscrape_9simulator_DeterministicSimulator*, __pyx_obj_9bioscrape_9simulator_CSimInterface*, PyArrayObject*)’: 2025-09-09T08:51:52,685 bioscrape/simulator.cpp:53134:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘npy_intp’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:51:52,685 53134 | for (__pyx_t_16 = 0; __pyx_t_16 < __pyx_t_18; __pyx_t_16+=1) { 2025-09-09T08:51:52,685 | ~~~~~~~~~~~^~~~~~~~~~~~ 2025-09-09T08:51:52,776 bioscrape/simulator.cpp: In function ‘PyObject* __pyx_pf_9bioscrape_9simulator_30DeterministicDilutionSimulator_8_helper_simulate(__pyx_obj_9bioscrape_9simulator_DeterministicDilutionSimulator*, __pyx_obj_9bioscrape_9simulator_CSimInterface*, PyArrayObject*)’: 2025-09-09T08:51:52,777 bioscrape/simulator.cpp:55053:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘npy_intp’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:51:52,777 55053 | for (__pyx_t_15 = 0; __pyx_t_15 < __pyx_t_17; __pyx_t_15+=1) { 2025-09-09T08:51:52,777 | ~~~~~~~~~~~^~~~~~~~~~~~ 2025-09-09T08:53:38,846 bioscrape/inference.cpp: In function ‘PyObject* __pyx_pf_9bioscrape_9inference_8BulkData_set_data(__pyx_obj_9bioscrape_9inference_BulkData*, PyArrayObject*, PyArrayObject*, PyObject*, unsigned int)’: 2025-09-09T08:53:38,846 bioscrape/inference.cpp:28009:30: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2025-09-09T08:53:38,847 28009 | __pyx_t_2 = (__pyx_t_3 == __pyx_v_N); 2025-09-09T08:53:38,847 | ~~~~~~~~~~^~~~~~~~~~~~ 2025-09-09T08:53:38,887 bioscrape/inference.cpp: In function ‘PyObject* __pyx_pf_9bioscrape_9inference_8FlowData_set_data(__pyx_obj_9bioscrape_9inference_FlowData*, PyArrayObject*, PyArrayObject*, PyObject*, unsigned int)’: 2025-09-09T08:53:38,887 bioscrape/inference.cpp:28984:80: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2025-09-09T08:53:38,887 28984 | __pyx_t_1 = ((__pyx_f_5numpy_7ndarray_5shape_shape(__pyx_v_measurements)[1]) != __pyx_v_self->__pyx_base.M); 2025-09-09T08:53:38,888 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T08:53:38,923 bioscrape/inference.cpp: In function ‘PyObject* __pyx_pf_9bioscrape_9inference_22StochasticTrajectories_set_data(__pyx_obj_9bioscrape_9inference_StochasticTrajectories*, PyArrayObject*, PyArrayObject*, PyObject*, unsigned int)’: 2025-09-09T08:53:38,923 bioscrape/inference.cpp:29779:80: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2025-09-09T08:53:38,923 29779 | __pyx_t_3 = ((__pyx_f_5numpy_7ndarray_5shape_shape(__pyx_v_measurements)[2]) == __pyx_v_self->__pyx_base.M); 2025-09-09T08:53:38,923 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T08:53:38,929 bioscrape/inference.cpp:29901:78: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2025-09-09T08:53:38,930 29901 | __pyx_t_3 = ((__pyx_f_5numpy_7ndarray_5shape_shape(__pyx_v_timepoints)[0]) == __pyx_v_self->nT); 2025-09-09T08:53:38,930 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-09-09T08:53:38,931 bioscrape/inference.cpp:29943:79: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2025-09-09T08:53:38,931 29943 | __pyx_t_11 = ((__pyx_f_5numpy_7ndarray_5shape_shape(__pyx_v_timepoints)[0]) == __pyx_v_self->__pyx_base.N); 2025-09-09T08:53:38,931 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T08:53:38,932 bioscrape/inference.cpp:29949:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘npy_intp’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:53:38,932 29949 | __pyx_t_11 = (__pyx_v_self->nT == (__pyx_f_5numpy_7ndarray_5shape_shape(__pyx_v_timepoints)[1])); 2025-09-09T08:53:38,932 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T08:53:39,175 bioscrape/inference.cpp: In function ‘double __pyx_f_9bioscrape_9inference_23DeterministicLikelihood_get_log_likelihood(__pyx_obj_9bioscrape_9inference_DeterministicLikelihood*)’: 2025-09-09T08:53:39,175 bioscrape/inference.cpp:35287:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘npy_intp’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:53:39,175 35287 | for (__pyx_t_15 = 0; __pyx_t_15 < __pyx_t_14; __pyx_t_15+=1) { 2025-09-09T08:53:39,175 | ~~~~~~~~~~~^~~~~~~~~~~~ 2025-09-09T08:53:39,188 bioscrape/inference.cpp:35493:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:53:39,188 35493 | for (__pyx_t_21 = 0; __pyx_t_21 < __pyx_t_20; __pyx_t_21+=1) { 2025-09-09T08:53:39,188 | ~~~~~~~~~~~^~~~~~~~~~~~ 2025-09-09T08:53:39,314 bioscrape/inference.cpp: In function ‘double __pyx_f_9bioscrape_9inference_32StochasticTrajectoriesLikelihood_get_log_likelihood(__pyx_obj_9bioscrape_9inference_StochasticTrajectoriesLikelihood*)’: 2025-09-09T08:53:39,314 bioscrape/inference.cpp:37707:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘npy_intp’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:53:39,314 37707 | for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_17; __pyx_t_18+=1) { 2025-09-09T08:53:39,314 | ~~~~~~~~~~~^~~~~~~~~~~~ 2025-09-09T08:54:40,264 lineage/lineage.cpp: In function ‘double __pyx_f_9bioscrape_7lineage_20LineageCSimInterface_apply_volume_rules(__pyx_obj_9bioscrape_7lineage_LineageCSimInterface*, double*, double, double, double)’: 2025-09-09T08:54:40,265 lineage/lineage.cpp:57956:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T08:54:40,265 57956 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 2025-09-09T08:54:40,265 | ~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:54:40,268 lineage/lineage.cpp: In function ‘int __pyx_f_9bioscrape_7lineage_20LineageCSimInterface_apply_death_rules(__pyx_obj_9bioscrape_7lineage_LineageCSimInterface*, double*, double, double, double, double)’: 2025-09-09T08:54:40,268 lineage/lineage.cpp:58037:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T08:54:40,268 58037 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 2025-09-09T08:54:40,268 | ~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:54:40,271 lineage/lineage.cpp: In function ‘int __pyx_f_9bioscrape_7lineage_20LineageCSimInterface_apply_division_rules(__pyx_obj_9bioscrape_7lineage_LineageCSimInterface*, double*, double, double, double, double)’: 2025-09-09T08:54:40,271 lineage/lineage.cpp:58147:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T08:54:40,271 58147 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 2025-09-09T08:54:40,271 | ~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:54:40,275 lineage/lineage.cpp: In function ‘PyArrayObject* __pyx_f_9bioscrape_7lineage_20LineageCSimInterface_partition(__pyx_obj_9bioscrape_7lineage_LineageCSimInterface*, int, __pyx_obj_9bioscrape_7lineage_LineageVolumeCellState*)’: 2025-09-09T08:54:40,276 lineage/lineage.cpp:58302:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T08:54:40,276 58302 | __pyx_t_2 = (__pyx_v_vsplit_ind >= __pyx_v_self->num_division_rules); 2025-09-09T08:54:40,276 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T08:54:40,278 lineage/lineage.cpp:58308:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T08:54:40,278 58308 | __pyx_t_2 = (__pyx_v_vsplit_ind < (__pyx_v_self->num_division_rules + __pyx_v_self->num_division_events)); 2025-09-09T08:54:40,278 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T08:54:40,281 lineage/lineage.cpp:58356:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T08:54:40,281 58356 | __pyx_t_2 = (__pyx_v_vsplit_ind < __pyx_v_self->num_division_rules); 2025-09-09T08:54:40,282 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T08:54:40,780 lineage/lineage.cpp: In function ‘__Pyx_memviewslice __pyx_f_9bioscrape_7lineage_19LineageSSASimulator_truncate_timepoints_less_than(__pyx_obj_9bioscrape_7lineage_LineageSSASimulator*, __Pyx_memviewslice, double)’: 2025-09-09T08:54:40,780 lineage/lineage.cpp:69176:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:54:40,780 69176 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 2025-09-09T08:54:40,780 | ~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:54:40,784 lineage/lineage.cpp: In function ‘__Pyx_memviewslice __pyx_f_9bioscrape_7lineage_19LineageSSASimulator_truncate_timepoints_greater_than(__pyx_obj_9bioscrape_7lineage_LineageSSASimulator*, __Pyx_memviewslice, double)’: 2025-09-09T08:54:40,784 lineage/lineage.cpp:69317:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:54:40,784 69317 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 2025-09-09T08:54:40,784 | ~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:54:40,789 lineage/lineage.cpp: In function ‘void __pyx_f_9bioscrape_7lineage_19LineageSSASimulator_simulate_cell_list(__pyx_obj_9bioscrape_7lineage_LineageSSASimulator*, PyObject*, __Pyx_memviewslice, unsigned int, unsigned int)’: 2025-09-09T08:54:40,790 lineage/lineage.cpp:69540:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:54:40,790 69540 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { 2025-09-09T08:54:40,790 | ~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:54:40,828 lineage/lineage.cpp: In function ‘__pyx_obj_9bioscrape_5types_Lineage* __pyx_f_9bioscrape_7lineage_19LineageSSASimulator_SimulateCellLineage(__pyx_obj_9bioscrape_7lineage_LineageSSASimulator*, PyObject*, __Pyx_memviewslice)’: 2025-09-09T08:54:40,828 lineage/lineage.cpp:70579:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:54:40,828 70579 | __pyx_t_1 = (__pyx_v_list_index < __pyx_t_7); 2025-09-09T08:54:40,828 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:54:40,864 lineage/lineage.cpp: In function ‘PyObject* __pyx_f_9bioscrape_7lineage_19LineageSSASimulator_PropagateCells(__pyx_obj_9bioscrape_7lineage_LineageSSASimulator*, PyObject*, __Pyx_memviewslice, __Pyx_memviewslice, unsigned int)’: 2025-09-09T08:54:40,864 lineage/lineage.cpp:71446:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:54:40,864 71446 | for (__pyx_t_14 = 0; __pyx_t_14 < __pyx_t_13; __pyx_t_14+=1) { 2025-09-09T08:54:40,864 | ~~~~~~~~~~~^~~~~~~~~~~~ 2025-09-09T08:54:40,868 lineage/lineage.cpp:71526:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:54:40,868 71526 | __pyx_t_4 = (__pyx_v_list_index < __pyx_t_15); 2025-09-09T08:54:40,868 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2025-09-09T08:54:40,906 lineage/lineage.cpp: In function ‘PyObject* __pyx_f_9bioscrape_7lineage_19LineageSSASimulator_SingleCellLineage(__pyx_obj_9bioscrape_7lineage_LineageSSASimulator*, __pyx_obj_9bioscrape_7lineage_LineageVolumeCellState*, __Pyx_memviewslice)’: 2025-09-09T08:54:40,906 lineage/lineage.cpp:72279:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:54:40,906 72279 | __pyx_t_5 = (__pyx_v_list_index < __pyx_t_4); 2025-09-09T08:54:40,906 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:54:41,214 lineage/lineage.cpp: In function ‘void __pyx_f_9bioscrape_7lineage_30InteractingLineageSSASimulator_calculate_global_volumes(__pyx_obj_9bioscrape_7lineage_InteractingLineageSSASimulator*)’: 2025-09-09T08:54:41,214 lineage/lineage.cpp:78486:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:54:41,214 78486 | for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2025-09-09T08:54:41,214 | ~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:54:41,224 lineage/lineage.cpp:78721:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:54:41,224 78721 | for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2025-09-09T08:54:41,224 | ~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:54:41,234 lineage/lineage.cpp: In function ‘void __pyx_f_9bioscrape_7lineage_30InteractingLineageSSASimulator_calculate_global_species_totals(__pyx_obj_9bioscrape_7lineage_InteractingLineageSSASimulator*)’: 2025-09-09T08:54:41,234 lineage/lineage.cpp:78939:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:54:41,234 78939 | for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { 2025-09-09T08:54:41,234 | ~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:54:41,250 lineage/lineage.cpp: In function ‘double __pyx_f_9bioscrape_7lineage_30InteractingLineageSSASimulator_distribute_global_species_average(__pyx_obj_9bioscrape_7lineage_InteractingLineageSSASimulator*, double, unsigned int)’: 2025-09-09T08:54:41,250 lineage/lineage.cpp:79427:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:54:41,250 79427 | for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2025-09-09T08:54:41,250 | ~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:54:41,258 lineage/lineage.cpp: In function ‘double __pyx_f_9bioscrape_7lineage_30InteractingLineageSSASimulator_distribute_global_species_multinomial(__pyx_obj_9bioscrape_7lineage_InteractingLineageSSASimulator*, double, unsigned int)’: 2025-09-09T08:54:41,259 lineage/lineage.cpp:79794:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:54:41,259 79794 | for (__pyx_t_11 = 0; __pyx_t_11 < __pyx_t_10; __pyx_t_11+=1) { 2025-09-09T08:54:41,259 | ~~~~~~~~~~~^~~~~~~~~~~~ 2025-09-09T08:54:41,301 lineage/lineage.cpp: In function ‘void __pyx_f_9bioscrape_7lineage_30InteractingLineageSSASimulator_simulate_interacting_lineage_period(__pyx_obj_9bioscrape_7lineage_InteractingLineageSSASimulator*, __Pyx_memviewslice, unsigned int)’: 2025-09-09T08:54:41,301 lineage/lineage.cpp:80696:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:54:41,302 80696 | __pyx_t_6 = (__pyx_v_list_index < __pyx_t_7); 2025-09-09T08:54:41,302 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T08:54:41,403 lineage/lineage.cpp: In function ‘PyObject* __pyx_f_9bioscrape_7lineage_30InteractingLineageSSASimulator_SimulateInteractingCellLineage(__pyx_obj_9bioscrape_7lineage_InteractingLineageSSASimulator*, PyObject*, PyObject*, PyArrayObject*, double, PyArrayObject*, double, double)’: 2025-09-09T08:54:41,403 lineage/lineage.cpp:82882:48: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘npy_intp’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:54:41,404 82882 | __pyx_t_19 = (__pyx_v_current_time_index < (__pyx_f_5numpy_7ndarray_5shape_shape(__pyx_v_timepoints)[0])); 2025-09-09T08:54:41,404 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T08:54:41,410 lineage/lineage.cpp:82976:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2025-09-09T08:54:41,410 82976 | for (__pyx_t_28 = 0; __pyx_t_28 < __pyx_t_27; __pyx_t_28+=1) { 2025-09-09T08:54:41,410 | ~~~~~~~~~~~^~~~~~~~~~~~ 2025-09-09T08:56:43,838 lineage/lineage.cpp: In function ‘__pyx_obj_9bioscrape_7lineage_SingleCellSSAResult* __pyx_f_9bioscrape_7lineage_19LineageSSASimulator_SimulateSingleCell(__pyx_obj_9bioscrape_7lineage_LineageSSASimulator*, __pyx_obj_9bioscrape_7lineage_LineageVolumeCellState*, __Pyx_memviewslice, unsigned int)’: 2025-09-09T08:56:43,838 lineage/lineage.cpp:66423:21: warning: ‘__pyx_pybuffernd_dummy_r.__Pyx_LocalBuf_ND::diminfo[1].__Pyx_Buf_DimInfo::strides’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T08:56:43,838 66423 | __Pyx_LocalBuf_ND __pyx_pybuffernd_dummy_r; 2025-09-09T08:56:43,838 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T08:57:13,191 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-09T08:57:13,191 !! 2025-09-09T08:57:13,191 ******************************************************************************** 2025-09-09T08:57:13,191 Please avoid running ``setup.py`` directly. 2025-09-09T08:57:13,191 Instead, use pypa/build, pypa/installer or other 2025-09-09T08:57:13,192 standards-based tools. 2025-09-09T08:57:13,192 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-09T08:57:13,192 or your builds will no longer be supported. 2025-09-09T08:57:13,192 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-09T08:57:13,192 ******************************************************************************** 2025-09-09T08:57:13,192 !! 2025-09-09T08:57:13,193 self.initialize_options() 2025-09-09T08:57:17,979 Building wheel for bioscrape (setup.py): finished with status 'done' 2025-09-09T08:57:18,061 Created wheel for bioscrape: filename=bioscrape-1.0.2.2-cp313-cp313-linux_armv7l.whl size=8016739 sha256=72ec72d28f5276035cf34258be2bccad2cd599c550b6ab596cb6a94601a8ce4f 2025-09-09T08:57:18,062 Stored in directory: /tmp/pip-ephem-wheel-cache-t0erulfc/wheels/5c/2f/2e/fc9e4f06696ce14d127da674b23403262a1d085fca448e9a86 2025-09-09T08:57:18,070 Successfully built bioscrape 2025-09-09T08:57:18,088 Removed build tracker: '/tmp/pip-build-tracker-lxtccpuh'