2025-02-13T09:26:48,944 Created temporary directory: /tmp/pip-build-tracker-s7atz79g 2025-02-13T09:26:48,945 Initialized build tracking at /tmp/pip-build-tracker-s7atz79g 2025-02-13T09:26:48,946 Created build tracker: /tmp/pip-build-tracker-s7atz79g 2025-02-13T09:26:48,946 Entered build tracker: /tmp/pip-build-tracker-s7atz79g 2025-02-13T09:26:48,947 Created temporary directory: /tmp/pip-wheel-kgnm_7j6 2025-02-13T09:26:48,951 Created temporary directory: /tmp/pip-ephem-wheel-cache-gxtc4hqn 2025-02-13T09:26:48,996 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-02-13T09:26:48,998 2 location(s) to search for versions of pyloopsage: 2025-02-13T09:26:48,998 * https://pypi.org/simple/pyloopsage/ 2025-02-13T09:26:48,998 * https://www.piwheels.org/simple/pyloopsage/ 2025-02-13T09:26:48,999 Fetching project page and analyzing links: https://pypi.org/simple/pyloopsage/ 2025-02-13T09:26:49,000 Getting page https://pypi.org/simple/pyloopsage/ 2025-02-13T09:26:49,001 Found index url https://pypi.org/simple/ 2025-02-13T09:26:49,220 Fetched page https://pypi.org/simple/pyloopsage/ as application/vnd.pypi.simple.v1+json 2025-02-13T09:26:49,223 Skipping link: No binaries permitted for pyloopsage: https://files.pythonhosted.org/packages/a2/53/c8f2f823b430a9477e549d8a7e8ab36ac976aacd58fe05f84de97db3bd8e/pyLoopSage-1.0.12-py3-none-any.whl (from https://pypi.org/simple/pyloopsage/) (requires-python:>=3.10) 2025-02-13T09:26:49,224 Found link https://files.pythonhosted.org/packages/06/24/b7f5b33dd6254e6c36949878606f20d09ddb3c1e0291a1cb48e2d8888ea6/pyloopsage-1.0.12.tar.gz (from https://pypi.org/simple/pyloopsage/) (requires-python:>=3.10), version: 1.0.12 2025-02-13T09:26:49,225 Skipping link: No binaries permitted for pyloopsage: https://files.pythonhosted.org/packages/18/43/8d63b472c98e81ae43d778d4ba563c0e0fd875dd77396857390c7cc78e00/pyLoopSage-1.0.14-py3-none-any.whl (from https://pypi.org/simple/pyloopsage/) (requires-python:>=3.10) 2025-02-13T09:26:49,226 Found link https://files.pythonhosted.org/packages/b1/08/a7909cae609d3b17ff3ba9084b3277a9004ec6e5e59cd02f1e87c735bc49/pyloopsage-1.0.14.tar.gz (from https://pypi.org/simple/pyloopsage/) (requires-python:>=3.10), version: 1.0.14 2025-02-13T09:26:49,226 Skipping link: No binaries permitted for pyloopsage: https://files.pythonhosted.org/packages/3d/9f/417d8f08f90cc93cb9b1f9aee56a42ce3d518476b0178cfc03272f1a9ba8/pyLoopSage-1.0.15-py3-none-any.whl (from https://pypi.org/simple/pyloopsage/) (requires-python:>=3.10) 2025-02-13T09:26:49,227 Found link https://files.pythonhosted.org/packages/63/8a/a516f808ee477a6b7493574d4537ad9bd33852feea1f99f13eacfafe120e/pyloopsage-1.0.15.tar.gz (from https://pypi.org/simple/pyloopsage/) (requires-python:>=3.10), version: 1.0.15 2025-02-13T09:26:49,228 Skipping link: No binaries permitted for pyloopsage: https://files.pythonhosted.org/packages/04/b8/dbc24fbda627ea30ed6c02c0b8f839cc14ab3e569ce5217e01ef6b607fef/pyLoopSage-1.0.16-py3-none-any.whl (from https://pypi.org/simple/pyloopsage/) (requires-python:>=3.10) 2025-02-13T09:26:49,229 Found link https://files.pythonhosted.org/packages/f5/bd/50b332151faafc5dc5f8511ada882889b96b13ba9f5047120b2a85ecd4ad/pyloopsage-1.0.16.tar.gz (from https://pypi.org/simple/pyloopsage/) (requires-python:>=3.10), version: 1.0.16 2025-02-13T09:26:49,230 Skipping link: No binaries permitted for pyloopsage: https://files.pythonhosted.org/packages/89/56/0ab1e78ae4cf32b2676de4290ca9a08e996ea817f8f94d2bbf57497e079c/pyLoopSage-1.0.17-py3-none-any.whl (from https://pypi.org/simple/pyloopsage/) (requires-python:>=3.10) 2025-02-13T09:26:49,231 Found link https://files.pythonhosted.org/packages/1c/f1/3270386e220bea717406fafd6ef786871af3932da048bc9a7607e4d4a17b/pyloopsage-1.0.17.tar.gz (from https://pypi.org/simple/pyloopsage/) (requires-python:>=3.10), version: 1.0.17 2025-02-13T09:26:49,231 Skipping link: No binaries permitted for pyloopsage: https://files.pythonhosted.org/packages/67/9c/51659ac07ece62a4f82818803df2f0fcdb99c6c574a5289e35885bf0b99c/pyLoopSage-1.0.18-py3-none-any.whl (from https://pypi.org/simple/pyloopsage/) (requires-python:>=3.10) 2025-02-13T09:26:49,232 Found link https://files.pythonhosted.org/packages/af/89/aeb7dc5a6cfae03c23cb396082954edc36abd34f64787f287fff316c10f3/pyloopsage-1.0.18.tar.gz (from https://pypi.org/simple/pyloopsage/) (requires-python:>=3.10), version: 1.0.18 2025-02-13T09:26:49,233 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyloopsage/ 2025-02-13T09:26:49,234 Getting page https://www.piwheels.org/simple/pyloopsage/ 2025-02-13T09:26:49,235 Found index url https://www.piwheels.org/simple/ 2025-02-13T09:26:49,407 Fetched page https://www.piwheels.org/simple/pyloopsage/ as text/html 2025-02-13T09:26:49,410 Skipping link: No binaries permitted for pyloopsage: https://www.piwheels.org/simple/pyloopsage/pyLoopSage-1.0.17-py3-none-any.whl#sha256=9de4f048ba4072592b866c23a92985ac6c58c21b5cba14d9260369b83f97e3c1 (from https://www.piwheels.org/simple/pyloopsage/) (requires-python:>=3.10) 2025-02-13T09:26:49,410 Skipping link: No binaries permitted for pyloopsage: https://www.piwheels.org/simple/pyloopsage/pyLoopSage-1.0.16-py3-none-any.whl#sha256=b91f8c9389d9958394c84184b1373a01557822f205ad93a5f2220ca7e7ccd215 (from https://www.piwheels.org/simple/pyloopsage/) (requires-python:>=3.10) 2025-02-13T09:26:49,411 Skipping link: No binaries permitted for pyloopsage: https://www.piwheels.org/simple/pyloopsage/pyLoopSage-1.0.15-py3-none-any.whl#sha256=48e01b2501714ecada636b1f533c03ee3ddf55d43bc374416a5c371d222135af (from https://www.piwheels.org/simple/pyloopsage/) (requires-python:>=3.10) 2025-02-13T09:26:49,411 Skipping link: No binaries permitted for pyloopsage: https://www.piwheels.org/simple/pyloopsage/pyLoopSage-1.0.14-py3-none-any.whl#sha256=a549aad40a794a609d2c75529df7d7e2f0499307bd0dca0e6dfbcf75f495ea78 (from https://www.piwheels.org/simple/pyloopsage/) (requires-python:>=3.10) 2025-02-13T09:26:49,412 Skipping link: No binaries permitted for pyloopsage: https://www.piwheels.org/simple/pyloopsage/pyLoopSage-1.0.12-py3-none-any.whl#sha256=fdd655ad8f0fe2be4aac31401ecb52091c64e4de37eeedfa793b309191bba454 (from https://www.piwheels.org/simple/pyloopsage/) (requires-python:>=3.10) 2025-02-13T09:26:49,412 Skipping link: not a file: https://www.piwheels.org/simple/pyloopsage/ 2025-02-13T09:26:49,413 Skipping link: not a file: https://pypi.org/simple/pyloopsage/ 2025-02-13T09:26:49,431 Given no hashes to check 1 links for project 'pyloopsage': discarding no candidates 2025-02-13T09:26:49,433 Collecting pyloopsage==1.0.18 2025-02-13T09:26:49,435 Created temporary directory: /tmp/pip-unpack-fwzvuc8l 2025-02-13T09:26:49,660 Downloading pyloopsage-1.0.18.tar.gz (56 kB) 2025-02-13T09:26:49,752 Added pyloopsage==1.0.18 from https://files.pythonhosted.org/packages/af/89/aeb7dc5a6cfae03c23cb396082954edc36abd34f64787f287fff316c10f3/pyloopsage-1.0.18.tar.gz to build tracker '/tmp/pip-build-tracker-s7atz79g' 2025-02-13T09:26:49,753 Running setup.py (path:/tmp/pip-wheel-kgnm_7j6/pyloopsage_05d1f4ac621a4dcd8ddbe988baf2178d/setup.py) egg_info for package pyloopsage 2025-02-13T09:26:49,754 Created temporary directory: /tmp/pip-pip-egg-info-fl5lxb23 2025-02-13T09:26:49,755 Preparing metadata (setup.py): started 2025-02-13T09:26:49,756 Running command python setup.py egg_info 2025-02-13T09:26:50,806 running egg_info 2025-02-13T09:26:50,834 creating /tmp/pip-pip-egg-info-fl5lxb23/pyLoopSage.egg-info 2025-02-13T09:26:50,836 writing /tmp/pip-pip-egg-info-fl5lxb23/pyLoopSage.egg-info/PKG-INFO 2025-02-13T09:26:50,841 writing dependency_links to /tmp/pip-pip-egg-info-fl5lxb23/pyLoopSage.egg-info/dependency_links.txt 2025-02-13T09:26:50,842 writing entry points to /tmp/pip-pip-egg-info-fl5lxb23/pyLoopSage.egg-info/entry_points.txt 2025-02-13T09:26:50,844 writing requirements to /tmp/pip-pip-egg-info-fl5lxb23/pyLoopSage.egg-info/requires.txt 2025-02-13T09:26:50,845 writing top-level names to /tmp/pip-pip-egg-info-fl5lxb23/pyLoopSage.egg-info/top_level.txt 2025-02-13T09:26:50,847 writing manifest file '/tmp/pip-pip-egg-info-fl5lxb23/pyLoopSage.egg-info/SOURCES.txt' 2025-02-13T09:26:50,935 reading manifest file '/tmp/pip-pip-egg-info-fl5lxb23/pyLoopSage.egg-info/SOURCES.txt' 2025-02-13T09:26:50,937 adding license file 'LICENSE' 2025-02-13T09:26:50,939 writing manifest file '/tmp/pip-pip-egg-info-fl5lxb23/pyLoopSage.egg-info/SOURCES.txt' 2025-02-13T09:26:51,049 Preparing metadata (setup.py): finished with status 'done' 2025-02-13T09:26:51,054 Source in /tmp/pip-wheel-kgnm_7j6/pyloopsage_05d1f4ac621a4dcd8ddbe988baf2178d has version 1.0.18, which satisfies requirement pyloopsage==1.0.18 from https://files.pythonhosted.org/packages/af/89/aeb7dc5a6cfae03c23cb396082954edc36abd34f64787f287fff316c10f3/pyloopsage-1.0.18.tar.gz 2025-02-13T09:26:51,055 Removed pyloopsage==1.0.18 from https://files.pythonhosted.org/packages/af/89/aeb7dc5a6cfae03c23cb396082954edc36abd34f64787f287fff316c10f3/pyloopsage-1.0.18.tar.gz from build tracker '/tmp/pip-build-tracker-s7atz79g' 2025-02-13T09:26:51,065 Created temporary directory: /tmp/pip-unpack-bvm588r3 2025-02-13T09:26:51,066 Created temporary directory: /tmp/pip-unpack-a6p2z9_v 2025-02-13T09:26:51,066 Building wheels for collected packages: pyloopsage 2025-02-13T09:26:51,070 Created temporary directory: /tmp/pip-wheel-b1_5b_dn 2025-02-13T09:26:51,071 Building wheel for pyloopsage (setup.py): started 2025-02-13T09:26:51,072 Destination directory: /tmp/pip-wheel-b1_5b_dn 2025-02-13T09:26:51,072 Running command python setup.py bdist_wheel 2025-02-13T09:26:52,142 running bdist_wheel 2025-02-13T09:26:52,346 running build 2025-02-13T09:26:52,347 running build_py 2025-02-13T09:26:52,381 creating build/lib/loopsage 2025-02-13T09:26:52,384 copying loopsage/initial_structures.py -> build/lib/loopsage 2025-02-13T09:26:52,387 copying loopsage/vizualization_tools.py -> build/lib/loopsage 2025-02-13T09:26:52,390 copying loopsage/preproc.py -> build/lib/loopsage 2025-02-13T09:26:52,393 copying loopsage/md.py -> build/lib/loopsage 2025-02-13T09:26:52,396 copying loopsage/args_definition.py -> build/lib/loopsage 2025-02-13T09:26:52,399 copying loopsage/plots.py -> build/lib/loopsage 2025-02-13T09:26:52,402 copying loopsage/stochastic_simulation.py -> build/lib/loopsage 2025-02-13T09:26:52,406 copying loopsage/em.py -> build/lib/loopsage 2025-02-13T09:26:52,410 copying loopsage/utils.py -> build/lib/loopsage 2025-02-13T09:26:52,413 copying loopsage/__init__.py -> build/lib/loopsage 2025-02-13T09:26:52,415 copying loopsage/run.py -> build/lib/loopsage 2025-02-13T09:26:52,417 running egg_info 2025-02-13T09:26:52,450 writing pyLoopSage.egg-info/PKG-INFO 2025-02-13T09:26:52,494 writing dependency_links to pyLoopSage.egg-info/dependency_links.txt 2025-02-13T09:26:52,497 writing entry points to pyLoopSage.egg-info/entry_points.txt 2025-02-13T09:26:52,498 writing requirements to pyLoopSage.egg-info/requires.txt 2025-02-13T09:26:52,502 writing top-level names to pyLoopSage.egg-info/top_level.txt 2025-02-13T09:26:52,555 reading manifest file 'pyLoopSage.egg-info/SOURCES.txt' 2025-02-13T09:26:52,558 adding license file 'LICENSE' 2025-02-13T09:26:52,561 writing manifest file 'pyLoopSage.egg-info/SOURCES.txt' 2025-02-13T09:26:52,563 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'loopsage.forcefields' is absent from the `packages` configuration. 2025-02-13T09:26:52,564 !! 2025-02-13T09:26:52,565 ******************************************************************************** 2025-02-13T09:26:52,566 ############################ 2025-02-13T09:26:52,566 # Package would be ignored # 2025-02-13T09:26:52,567 ############################ 2025-02-13T09:26:52,568 Python recognizes 'loopsage.forcefields' as an importable package[^1], 2025-02-13T09:26:52,568 but it is absent from setuptools' `packages` configuration. 2025-02-13T09:26:52,569 This leads to an ambiguous overall configuration. If you want to distribute this 2025-02-13T09:26:52,570 package, please make sure that 'loopsage.forcefields' is explicitly added 2025-02-13T09:26:52,571 to the `packages` configuration field. 2025-02-13T09:26:52,572 Alternatively, you can also rely on setuptools' discovery methods 2025-02-13T09:26:52,572 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-02-13T09:26:52,573 instead of `find_packages(...)`/`find:`). 2025-02-13T09:26:52,574 You can read more about "package discovery" on setuptools documentation page: 2025-02-13T09:26:52,575 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-02-13T09:26:52,577 If you don't want 'loopsage.forcefields' to be distributed and are 2025-02-13T09:26:52,577 already explicitly excluding 'loopsage.forcefields' via 2025-02-13T09:26:52,578 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-02-13T09:26:52,578 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-02-13T09:26:52,579 combination with a more fine grained `package-data` configuration. 2025-02-13T09:26:52,580 You can read more about "package data files" on setuptools documentation page: 2025-02-13T09:26:52,581 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-02-13T09:26:52,583 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-02-13T09:26:52,583 even if it does not contain any `.py` files. 2025-02-13T09:26:52,584 On the other hand, currently there is no concept of package data 2025-02-13T09:26:52,585 directory, all directories are treated like packages. 2025-02-13T09:26:52,585 ******************************************************************************** 2025-02-13T09:26:52,587 !! 2025-02-13T09:26:52,588 check.warn(importable) 2025-02-13T09:26:52,588 creating build/lib/loopsage/forcefields 2025-02-13T09:26:52,589 copying loopsage/forcefields/classic_sm_ff.xml -> build/lib/loopsage/forcefields 2025-02-13T09:26:52,604 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-02-13T09:26:52,604 !! 2025-02-13T09:26:52,606 ******************************************************************************** 2025-02-13T09:26:52,606 Please avoid running ``setup.py`` directly. 2025-02-13T09:26:52,607 Instead, use pypa/build, pypa/installer or other 2025-02-13T09:26:52,608 standards-based tools. 2025-02-13T09:26:52,609 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-02-13T09:26:52,609 ******************************************************************************** 2025-02-13T09:26:52,611 !! 2025-02-13T09:26:52,611 self.initialize_options() 2025-02-13T09:26:52,633 installing to build/bdist.linux-armv7l/wheel 2025-02-13T09:26:52,634 running install 2025-02-13T09:26:52,659 running install_lib 2025-02-13T09:26:52,690 creating build/bdist.linux-armv7l/wheel 2025-02-13T09:26:52,694 creating build/bdist.linux-armv7l/wheel/loopsage 2025-02-13T09:26:52,697 creating build/bdist.linux-armv7l/wheel/loopsage/forcefields 2025-02-13T09:26:52,700 copying build/lib/loopsage/forcefields/classic_sm_ff.xml -> build/bdist.linux-armv7l/wheel/./loopsage/forcefields 2025-02-13T09:26:52,703 copying build/lib/loopsage/initial_structures.py -> build/bdist.linux-armv7l/wheel/./loopsage 2025-02-13T09:26:52,708 copying build/lib/loopsage/vizualization_tools.py -> build/bdist.linux-armv7l/wheel/./loopsage 2025-02-13T09:26:52,714 copying build/lib/loopsage/preproc.py -> build/bdist.linux-armv7l/wheel/./loopsage 2025-02-13T09:26:52,717 copying build/lib/loopsage/md.py -> build/bdist.linux-armv7l/wheel/./loopsage 2025-02-13T09:26:52,723 copying build/lib/loopsage/args_definition.py -> build/bdist.linux-armv7l/wheel/./loopsage 2025-02-13T09:26:52,731 copying build/lib/loopsage/plots.py -> build/bdist.linux-armv7l/wheel/./loopsage 2025-02-13T09:26:52,734 copying build/lib/loopsage/stochastic_simulation.py -> build/bdist.linux-armv7l/wheel/./loopsage 2025-02-13T09:26:52,738 copying build/lib/loopsage/em.py -> build/bdist.linux-armv7l/wheel/./loopsage 2025-02-13T09:26:52,740 copying build/lib/loopsage/utils.py -> build/bdist.linux-armv7l/wheel/./loopsage 2025-02-13T09:26:52,742 copying build/lib/loopsage/__init__.py -> build/bdist.linux-armv7l/wheel/./loopsage 2025-02-13T09:26:52,744 copying build/lib/loopsage/run.py -> build/bdist.linux-armv7l/wheel/./loopsage 2025-02-13T09:26:52,746 running install_egg_info 2025-02-13T09:26:52,987 Copying pyLoopSage.egg-info to build/bdist.linux-armv7l/wheel/./pyLoopSage-1.0.18-py3.11.egg-info 2025-02-13T09:26:53,004 running install_scripts 2025-02-13T09:26:53,027 creating build/bdist.linux-armv7l/wheel/pyLoopSage-1.0.18.dist-info/WHEEL 2025-02-13T09:26:53,029 creating '/tmp/pip-wheel-b1_5b_dn/pyLoopSage-1.0.18-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-02-13T09:26:53,032 adding 'loopsage/__init__.py' 2025-02-13T09:26:53,034 adding 'loopsage/args_definition.py' 2025-02-13T09:26:53,036 adding 'loopsage/em.py' 2025-02-13T09:26:53,038 adding 'loopsage/initial_structures.py' 2025-02-13T09:26:53,040 adding 'loopsage/md.py' 2025-02-13T09:26:53,041 adding 'loopsage/plots.py' 2025-02-13T09:26:53,043 adding 'loopsage/preproc.py' 2025-02-13T09:26:53,045 adding 'loopsage/run.py' 2025-02-13T09:26:53,047 adding 'loopsage/stochastic_simulation.py' 2025-02-13T09:26:53,050 adding 'loopsage/utils.py' 2025-02-13T09:26:53,052 adding 'loopsage/vizualization_tools.py' 2025-02-13T09:26:53,053 adding 'loopsage/forcefields/classic_sm_ff.xml' 2025-02-13T09:26:53,061 adding 'pyLoopSage-1.0.18.dist-info/LICENSE' 2025-02-13T09:26:53,064 adding 'pyLoopSage-1.0.18.dist-info/METADATA' 2025-02-13T09:26:53,066 adding 'pyLoopSage-1.0.18.dist-info/WHEEL' 2025-02-13T09:26:53,066 adding 'pyLoopSage-1.0.18.dist-info/entry_points.txt' 2025-02-13T09:26:53,067 adding 'pyLoopSage-1.0.18.dist-info/top_level.txt' 2025-02-13T09:26:53,068 adding 'pyLoopSage-1.0.18.dist-info/RECORD' 2025-02-13T09:26:53,070 removing build/bdist.linux-armv7l/wheel 2025-02-13T09:26:53,222 Building wheel for pyloopsage (setup.py): finished with status 'done' 2025-02-13T09:26:53,226 Created wheel for pyloopsage: filename=pyLoopSage-1.0.18-py3-none-any.whl size=53007 sha256=f8cc8e09161a63c2448892c15bffae0b97304c9aa979bc80ce464d78e1a3c7de 2025-02-13T09:26:53,227 Stored in directory: /tmp/pip-ephem-wheel-cache-gxtc4hqn/wheels/3e/24/22/bf66252c0dc5d43b8beded560d6755bbefc18f7015b67fc741 2025-02-13T09:26:53,242 Successfully built pyloopsage 2025-02-13T09:26:53,247 Removed build tracker: '/tmp/pip-build-tracker-s7atz79g'