2025-09-11T10:18:57,273 Created temporary directory: /tmp/pip-build-tracker-g_in6l9f 2025-09-11T10:18:57,273 Initialized build tracking at /tmp/pip-build-tracker-g_in6l9f 2025-09-11T10:18:57,274 Created build tracker: /tmp/pip-build-tracker-g_in6l9f 2025-09-11T10:18:57,274 Entered build tracker: /tmp/pip-build-tracker-g_in6l9f 2025-09-11T10:18:57,274 Created temporary directory: /tmp/pip-wheel-9sjhv7p8 2025-09-11T10:18:57,277 Created temporary directory: /tmp/pip-ephem-wheel-cache-8ff70lp5 2025-09-11T10:18:57,342 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-11T10:18:57,345 2 location(s) to search for versions of bioscrape: 2025-09-11T10:18:57,345 * https://pypi.org/simple/bioscrape/ 2025-09-11T10:18:57,345 * https://www.piwheels.org/simple/bioscrape/ 2025-09-11T10:18:57,345 Fetching project page and analyzing links: https://pypi.org/simple/bioscrape/ 2025-09-11T10:18:57,346 Getting page https://pypi.org/simple/bioscrape/ 2025-09-11T10:18:57,347 Found index url https://pypi.org/simple/ 2025-09-11T10:18:57,496 Fetched page https://pypi.org/simple/bioscrape/ as application/vnd.pypi.simple.v1+json 2025-09-11T10:18:57,499 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 2025-09-11T10:18:57,500 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 2025-09-11T10:18:57,500 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 2025-09-11T10:18:57,500 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 2025-09-11T10:18:57,501 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/) 2025-09-11T10:18:57,501 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 2025-09-11T10:18:57,501 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) 2025-09-11T10:18:57,501 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) 2025-09-11T10:18:57,502 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 2025-09-11T10:18:57,502 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) 2025-09-11T10:18:57,503 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 2025-09-11T10:18:57,503 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) 2025-09-11T10:18:57,503 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 2025-09-11T10:18:57,503 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) 2025-09-11T10:18:57,503 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) 2025-09-11T10:18:57,504 Fetching project page and analyzing links: https://www.piwheels.org/simple/bioscrape/ 2025-09-11T10:18:57,504 Getting page https://www.piwheels.org/simple/bioscrape/ 2025-09-11T10:18:57,505 Found index url https://www.piwheels.org/simple/ 2025-09-11T10:18:57,601 Fetched page https://www.piwheels.org/simple/bioscrape/ as text/html 2025-09-11T10:18:57,610 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) 2025-09-11T10:18:57,611 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) 2025-09-11T10:18:57,611 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) 2025-09-11T10:18:57,611 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) 2025-09-11T10:18:57,611 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) 2025-09-11T10:18:57,611 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) 2025-09-11T10:18:57,612 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) 2025-09-11T10:18:57,612 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) 2025-09-11T10:18:57,612 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) 2025-09-11T10:18:57,612 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) 2025-09-11T10:18:57,612 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) 2025-09-11T10:18:57,612 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) 2025-09-11T10:18:57,613 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) 2025-09-11T10:18:57,613 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) 2025-09-11T10:18:57,613 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) 2025-09-11T10:18:57,613 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) 2025-09-11T10:18:57,613 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) 2025-09-11T10:18:57,613 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) 2025-09-11T10:18:57,613 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) 2025-09-11T10:18:57,614 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) 2025-09-11T10:18:57,614 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) 2025-09-11T10:18:57,614 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) 2025-09-11T10:18:57,614 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) 2025-09-11T10:18:57,614 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) 2025-09-11T10:18:57,614 Skipping link: No binaries permitted for bioscrape: https://www.piwheels.org/simple/bioscrape/bioscrape-1.0.2.2-cp313-cp313-linux_armv6l.whl#sha256=72ec72d28f5276035cf34258be2bccad2cd599c550b6ab596cb6a94601a8ce4f (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-11T10:18:57,615 Skipping link: No binaries permitted for bioscrape: https://www.piwheels.org/simple/bioscrape/bioscrape-1.0.2.2-cp313-cp313-linux_armv7l.whl#sha256=72ec72d28f5276035cf34258be2bccad2cd599c550b6ab596cb6a94601a8ce4f (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-11T10:18:57,615 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) 2025-09-11T10:18:57,615 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) 2025-09-11T10:18:57,615 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) 2025-09-11T10:18:57,615 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) 2025-09-11T10:18:57,615 Skipping link: No binaries permitted for bioscrape: https://www.piwheels.org/simple/bioscrape/bioscrape-1.0.2.1-cp313-cp313-linux_armv6l.whl#sha256=d2444c901afe4b9ef7108cbfddcae6ce39be9a764e7b584389f2faaa69f0ee01 (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-11T10:18:57,615 Skipping link: No binaries permitted for bioscrape: https://www.piwheels.org/simple/bioscrape/bioscrape-1.0.2.1-cp313-cp313-linux_armv7l.whl#sha256=d2444c901afe4b9ef7108cbfddcae6ce39be9a764e7b584389f2faaa69f0ee01 (from https://www.piwheels.org/simple/bioscrape/) (requires-python:>=3.6) 2025-09-11T10:18:57,616 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) 2025-09-11T10:18:57,616 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) 2025-09-11T10:18:57,616 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) 2025-09-11T10:18:57,616 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) 2025-09-11T10:18:57,616 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) 2025-09-11T10:18:57,616 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) 2025-09-11T10:18:57,617 Skipping link: not a file: https://www.piwheels.org/simple/bioscrape/ 2025-09-11T10:18:57,617 Skipping link: not a file: https://pypi.org/simple/bioscrape/ 2025-09-11T10:18:57,642 Given no hashes to check 1 links for project 'bioscrape': discarding no candidates 2025-09-11T10:18:57,644 Collecting bioscrape==1.1.0 2025-09-11T10:18:57,645 Created temporary directory: /tmp/pip-unpack-hrwoows8 2025-09-11T10:18:57,873 Downloading bioscrape-1.1.0.tar.gz (557 kB) 2025-09-11T10:18:58,084 Added bioscrape==1.1.0 from https://files.pythonhosted.org/packages/bf/97/3d059aed33d22fb9ade1007310649b0c53335f76a5db010155c97d06c438/bioscrape-1.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-g_in6l9f' 2025-09-11T10:18:58,086 Running setup.py (path:/tmp/pip-wheel-9sjhv7p8/bioscrape_6ac83037eb0e4716a062cbbe0cb83dc0/setup.py) egg_info for package bioscrape 2025-09-11T10:18:58,087 Created temporary directory: /tmp/pip-pip-egg-info-m81cx46a 2025-09-11T10:18:58,087 Preparing metadata (setup.py): started 2025-09-11T10:18:58,088 Running command python setup.py egg_info 2025-09-11T10:19:09,437 Error compiling Cython file: 2025-09-11T10:19:09,437 ------------------------------------------------------------ 2025-09-11T10:19:09,438 ... 2025-09-11T10:19:09,438 cdef unsigned s, t, ind, prod 2025-09-11T10:19:09,438 cdef unsigned tstart = len(self.timepoints[self.timepoints < start_time]) 2025-09-11T10:19:09,438 cdef unsigned tend = len(self.timepoints[self.timepoints <= final_time]) 2025-09-11T10:19:09,438 cdef unsigned N_species = len(species_inds) 2025-09-11T10:19:09,438 cdef double dP = 1./(tend - tstart) 2025-09-11T10:19:09,438 cdef np.ndarray[np.int_t, ndim=1] index_ar = np.zeros(N_species, dtype = np.int_) #index array 2025-09-11T10:19:09,438 ^ 2025-09-11T10:19:09,438 ------------------------------------------------------------ 2025-09-11T10:19:09,438 bioscrape/simulator.pyx:732:27: Invalid type. 2025-09-11T10:19:09,441 Traceback (most recent call last): 2025-09-11T10:19:09,443 File "", line 2, in 2025-09-11T10:19:09,443 exec(compile(''' 2025-09-11T10:19:09,444 ~~~~^^^^^^^^^^^^ 2025-09-11T10:19:09,444 # This is -- a caller that pip uses to run setup.py 2025-09-11T10:19:09,444 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T10:19:09,444 ...<32 lines>... 2025-09-11T10:19:09,444 exec(compile(setup_py_code, filename, "exec")) 2025-09-11T10:19:09,444 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T10:19:09,444 ''' % ('/tmp/pip-wheel-9sjhv7p8/bioscrape_6ac83037eb0e4716a062cbbe0cb83dc0/setup.py',), "", "exec")) 2025-09-11T10:19:09,445 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T10:19:09,445 File "", line 35, in 2025-09-11T10:19:09,445 File "/tmp/pip-wheel-9sjhv7p8/bioscrape_6ac83037eb0e4716a062cbbe0cb83dc0/setup.py", line 94, in 2025-09-11T10:19:09,445 cython_extensions += cythonize(bioscrape_extensions, **cythonize_options) 2025-09-11T10:19:09,445 ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T10:19:09,445 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1154, in cythonize 2025-09-11T10:19:09,446 cythonize_one(*args) 2025-09-11T10:19:09,446 ~~~~~~~~~~~~~^^^^^^^ 2025-09-11T10:19:09,446 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1298, in cythonize_one 2025-09-11T10:19:09,446 raise CompileError(None, pyx_file) 2025-09-11T10:19:09,446 Cython.Compiler.Errors.CompileError: bioscrape/simulator.pyx 2025-09-11T10:19:09,446 Installing Bioscrape... 2025-09-11T10:19:09,447 Compiling bioscrape/random.pyx because it changed. 2025-09-11T10:19:09,447 Compiling bioscrape/types.pyx because it changed. 2025-09-11T10:19:09,447 Compiling bioscrape/simulator.pyx because it changed. 2025-09-11T10:19:09,447 Compiling bioscrape/inference.pyx because it changed. 2025-09-11T10:19:09,447 [1/4] Cythonizing bioscrape/inference.pyx 2025-09-11T10:19:09,447 [2/4] Cythonizing bioscrape/random.pyx 2025-09-11T10:19:09,447 [3/4] Cythonizing bioscrape/simulator.pyx 2025-09-11T10:19:09,448 Error occured during Cython Compilation. Check C++ Compiler and Cython Installation. 2025-09-11T10:19:10,310 ERROR: python setup.py egg_info exited with 1 2025-09-11T10:19:10,324 [bold magenta]full command[/]: [blue]/usr/bin/python3 -c ' 2025-09-11T10:19:10,324 exec(compile('"'"''"'"''"'"' 2025-09-11T10:19:10,324 # This is -- a caller that pip uses to run setup.py 2025-09-11T10:19:10,324 # 2025-09-11T10:19:10,324 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-11T10:19:10,324 # import from `distutils.core` to work with newer packaging standards. 2025-09-11T10:19:10,324 # - It provides a clear error message when setuptools is not installed. 2025-09-11T10:19:10,324 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-11T10:19:10,324 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-11T10:19:10,324 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-11T10:19:10,324 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-11T10:19:10,324 import os, sys, tokenize, traceback 2025-09-11T10:19:10,324 2025-09-11T10:19:10,324 try: 2025-09-11T10:19:10,324 import setuptools 2025-09-11T10:19:10,324 except ImportError: 2025-09-11T10:19:10,324 print( 2025-09-11T10:19:10,324 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-11T10:19:10,324 "the build environment with exception:", 2025-09-11T10:19:10,324 file=sys.stderr, 2025-09-11T10:19:10,324 ) 2025-09-11T10:19:10,324 traceback.print_exc() 2025-09-11T10:19:10,324 sys.exit(1) 2025-09-11T10:19:10,324 2025-09-11T10:19:10,324 __file__ = %r 2025-09-11T10:19:10,324 sys.argv[0] = __file__ 2025-09-11T10:19:10,324 2025-09-11T10:19:10,324 if os.path.exists(__file__): 2025-09-11T10:19:10,324 filename = __file__ 2025-09-11T10:19:10,324 with tokenize.open(__file__) as f: 2025-09-11T10:19:10,324 setup_py_code = f.read() 2025-09-11T10:19:10,324 else: 2025-09-11T10:19:10,324 filename = "" 2025-09-11T10:19:10,324 setup_py_code = "from setuptools import setup; setup()" 2025-09-11T10:19:10,324 2025-09-11T10:19:10,324 exec(compile(setup_py_code, filename, "exec")) 2025-09-11T10:19:10,324 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-9sjhv7p8/bioscrape_6ac83037eb0e4716a062cbbe0cb83dc0/setup.py'"'"',), "", "exec"))' egg_info --egg-base /tmp/pip-pip-egg-info-m81cx46a[/] 2025-09-11T10:19:10,325 [bold magenta]cwd[/]: /tmp/pip-wheel-9sjhv7p8/bioscrape_6ac83037eb0e4716a062cbbe0cb83dc0/ 2025-09-11T10:19:10,325 Preparing metadata (setup.py): finished with status 'error' 2025-09-11T10:19:10,326 ERROR: metadata generation failed 2025-09-11T10:19:10,333 Exception information: 2025-09-11T10:19:10,333 Traceback (most recent call last): 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 63, in generate_metadata 2025-09-11T10:19:10,333 call_subprocess( 2025-09-11T10:19:10,333 ~~~~~~~~~~~~~~~^ 2025-09-11T10:19:10,333 args, 2025-09-11T10:19:10,333 ^^^^^ 2025-09-11T10:19:10,333 ...<2 lines>... 2025-09-11T10:19:10,333 spinner=spinner, 2025-09-11T10:19:10,333 ^^^^^^^^^^^^^^^^ 2025-09-11T10:19:10,333 ) 2025-09-11T10:19:10,333 ^ 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/utils/subprocess.py", line 209, in call_subprocess 2025-09-11T10:19:10,333 raise error 2025-09-11T10:19:10,333 pip._internal.exceptions.InstallationSubprocessError: python setup.py egg_info exited with 1 2025-09-11T10:19:10,333 2025-09-11T10:19:10,333 The above exception was the direct cause of the following exception: 2025-09-11T10:19:10,333 2025-09-11T10:19:10,333 Traceback (most recent call last): 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-11T10:19:10,333 status = _inner_run() 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-11T10:19:10,333 return self.run(options, args) 2025-09-11T10:19:10,333 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-11T10:19:10,333 return func(self, options, args) 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 147, in run 2025-09-11T10:19:10,333 requirement_set = resolver.resolve(reqs, check_supported_wheels=True) 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 96, in resolve 2025-09-11T10:19:10,333 result = self._result = resolver.resolve( 2025-09-11T10:19:10,333 ~~~~~~~~~~~~~~~~^ 2025-09-11T10:19:10,333 collected.requirements, max_rounds=limit_how_complex_resolution_can_be 2025-09-11T10:19:10,333 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T10:19:10,333 ) 2025-09-11T10:19:10,333 ^ 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 515, in resolve 2025-09-11T10:19:10,333 state = resolution.resolve(requirements, max_rounds=max_rounds) 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 388, in resolve 2025-09-11T10:19:10,333 self._add_to_criteria(self.state.criteria, r, parent=None) 2025-09-11T10:19:10,333 ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 141, in _add_to_criteria 2025-09-11T10:19:10,333 if not criterion.candidates: 2025-09-11T10:19:10,333 ^^^^^^^^^^^^^^^^^^^^ 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/structs.py", line 194, in __bool__ 2025-09-11T10:19:10,333 return bool(self._sequence) 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 163, in __bool__ 2025-09-11T10:19:10,333 self._bool = any(self) 2025-09-11T10:19:10,333 ~~~^^^^^^ 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 147, in 2025-09-11T10:19:10,333 return (c for c in iterator if id(c) not in self._incompatible_ids) 2025-09-11T10:19:10,333 ^^^^^^^^ 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 37, in _iter_built 2025-09-11T10:19:10,333 candidate = func() 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 187, in _make_candidate_from_link 2025-09-11T10:19:10,333 base: Optional[BaseCandidate] = self._make_base_candidate_from_link( 2025-09-11T10:19:10,333 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-11T10:19:10,333 link, template, name, version 2025-09-11T10:19:10,333 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T10:19:10,333 ) 2025-09-11T10:19:10,333 ^ 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 233, in _make_base_candidate_from_link 2025-09-11T10:19:10,333 self._link_candidate_cache[link] = LinkCandidate( 2025-09-11T10:19:10,333 ~~~~~~~~~~~~~^ 2025-09-11T10:19:10,333 link, 2025-09-11T10:19:10,333 ^^^^^ 2025-09-11T10:19:10,333 ...<3 lines>... 2025-09-11T10:19:10,333 version=version, 2025-09-11T10:19:10,333 ^^^^^^^^^^^^^^^^ 2025-09-11T10:19:10,333 ) 2025-09-11T10:19:10,333 ^ 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 306, in __init__ 2025-09-11T10:19:10,333 super().__init__( 2025-09-11T10:19:10,333 ~~~~~~~~~~~~~~~~^ 2025-09-11T10:19:10,333 link=link, 2025-09-11T10:19:10,333 ^^^^^^^^^^ 2025-09-11T10:19:10,333 ...<4 lines>... 2025-09-11T10:19:10,333 version=version, 2025-09-11T10:19:10,333 ^^^^^^^^^^^^^^^^ 2025-09-11T10:19:10,333 ) 2025-09-11T10:19:10,333 ^ 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 159, in __init__ 2025-09-11T10:19:10,333 self.dist = self._prepare() 2025-09-11T10:19:10,333 ~~~~~~~~~~~~~^^ 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 236, in _prepare 2025-09-11T10:19:10,333 dist = self._prepare_distribution() 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 317, in _prepare_distribution 2025-09-11T10:19:10,333 return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) 2025-09-11T10:19:10,333 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 532, in prepare_linked_requirement 2025-09-11T10:19:10,333 return self._prepare_linked_requirement(req, parallel_builds) 2025-09-11T10:19:10,333 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 647, in _prepare_linked_requirement 2025-09-11T10:19:10,333 dist = _get_prepared_distribution( 2025-09-11T10:19:10,333 req, 2025-09-11T10:19:10,333 ...<3 lines>... 2025-09-11T10:19:10,333 self.check_build_deps, 2025-09-11T10:19:10,333 ) 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution 2025-09-11T10:19:10,333 abstract_dist.prepare_distribution_metadata( 2025-09-11T10:19:10,333 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-11T10:19:10,333 finder, build_isolation, check_build_deps 2025-09-11T10:19:10,333 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T10:19:10,333 ) 2025-09-11T10:19:10,333 ^ 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/distributions/sdist.py", line 69, in prepare_distribution_metadata 2025-09-11T10:19:10,333 self.req.prepare_metadata() 2025-09-11T10:19:10,333 ~~~~~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/req/req_install.py", line 581, in prepare_metadata 2025-09-11T10:19:10,333 self.metadata_directory = generate_metadata_legacy( 2025-09-11T10:19:10,333 ~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-11T10:19:10,333 build_env=self.build_env, 2025-09-11T10:19:10,333 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T10:19:10,333 ...<3 lines>... 2025-09-11T10:19:10,333 details=details, 2025-09-11T10:19:10,333 ^^^^^^^^^^^^^^^^ 2025-09-11T10:19:10,333 ) 2025-09-11T10:19:10,333 ^ 2025-09-11T10:19:10,333 File "/usr/lib/python3/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 70, in generate_metadata 2025-09-11T10:19:10,333 raise MetadataGenerationFailed(package_details=details) from error 2025-09-11T10:19:10,333 pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed 2025-09-11T10:19:10,356 Removed bioscrape==1.1.0 from https://files.pythonhosted.org/packages/bf/97/3d059aed33d22fb9ade1007310649b0c53335f76a5db010155c97d06c438/bioscrape-1.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-g_in6l9f' 2025-09-11T10:19:10,356 Removed build tracker: '/tmp/pip-build-tracker-g_in6l9f'