2026-02-10T07:55:09,313 Created temporary directory: /tmp/pip-ephem-wheel-cache-a8y15dsg 2026-02-10T07:55:09,314 Created temporary directory: /tmp/pip-build-tracker-agj4qs24 2026-02-10T07:55:09,315 Initialized build tracking at /tmp/pip-build-tracker-agj4qs24 2026-02-10T07:55:09,315 Created build tracker: /tmp/pip-build-tracker-agj4qs24 2026-02-10T07:55:09,316 Entered build tracker: /tmp/pip-build-tracker-agj4qs24 2026-02-10T07:55:09,317 Created temporary directory: /tmp/pip-wheel-kngh3vrn 2026-02-10T07:55:09,320 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-10T07:55:09,322 Created temporary directory: /tmp/pip-ephem-wheel-cache-_pm3d4ah 2026-02-10T07:55:09,344 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-10T07:55:09,348 2 location(s) to search for versions of scipion-em-imod: 2026-02-10T07:55:09,348 * https://pypi.org/simple/scipion-em-imod/ 2026-02-10T07:55:09,348 * https://www.piwheels.org/simple/scipion-em-imod/ 2026-02-10T07:55:09,348 Fetching project page and analyzing links: https://pypi.org/simple/scipion-em-imod/ 2026-02-10T07:55:09,349 Getting page https://pypi.org/simple/scipion-em-imod/ 2026-02-10T07:55:09,351 Found index url https://pypi.org/simple 2026-02-10T07:55:09,566 Fetched page https://pypi.org/simple/scipion-em-imod/ as application/vnd.pypi.simple.v1+json 2026-02-10T07:55:09,577 Found link 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2026-02-10T07:55:09,583 Found link https://files.pythonhosted.org/packages/0f/dc/2ea0bcfd6db043860ce47bfac573ea4157dcab12cc09deee7770fdf9b0c6/scipion-em-imod-3.0.4.tar.gz (from https://pypi.org/simple/scipion-em-imod/), version: 3.0.4 2026-02-10T07:55:09,584 Skipping link: No binaries permitted for scipion-em-imod: https://files.pythonhosted.org/packages/1f/92/b700066e6aa01e248abb58b7e3a39e6fd9980467e9ec85e0c1ce8b742299/scipion_em_imod-3.0.4-py3-none-any.whl (from https://pypi.org/simple/scipion-em-imod/) 2026-02-10T07:55:09,584 Found link https://files.pythonhosted.org/packages/0c/71/6814fa30b42dee9e589c36d09316cac10d3350902493138b8135c4e15b3f/scipion-em-imod-3.0.5.tar.gz (from https://pypi.org/simple/scipion-em-imod/), version: 3.0.5 2026-02-10T07:55:09,585 Skipping link: No binaries permitted for scipion-em-imod: https://files.pythonhosted.org/packages/ab/76/3a74a7ea4a87e4bfadcc3313802fc9fe9046e91029434e17adc12ff792a6/scipion_em_imod-3.0.5-py3-none-any.whl (from 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2026-02-10T07:55:09,596 Skipping link: No binaries permitted for scipion-em-imod: https://files.pythonhosted.org/packages/49/8b/db6fd21d1d830e82bf8cac16d549eb640e6afb1a8d2d3e99d6bac9fee136/scipion_em_imod-3.1.4-py3-none-any.whl (from https://pypi.org/simple/scipion-em-imod/) 2026-02-10T07:55:09,596 Found link https://files.pythonhosted.org/packages/c5/92/e5e94a63d0a04d0dd369d47fa3a2be425e7d78a35dd9ce9e79aab305d534/scipion-em-imod-3.1.5.tar.gz (from https://pypi.org/simple/scipion-em-imod/), version: 3.1.5 2026-02-10T07:55:09,597 Skipping link: No binaries permitted for scipion-em-imod: https://files.pythonhosted.org/packages/de/4d/8f0eecc78a9db88c27a16a822f35feb2e1c5b23895050f983908f64615cd/scipion_em_imod-3.1.5-py3-none-any.whl (from https://pypi.org/simple/scipion-em-imod/) 2026-02-10T07:55:09,597 Found link https://files.pythonhosted.org/packages/94/7a/262611e5a847824c55b86146850737d1dc13ae5381e451197344741e6571/scipion-em-imod-3.1.7.tar.gz (from 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2026-02-10T07:55:09,602 Found link https://files.pythonhosted.org/packages/da/7f/e4dacaa50a51d2af9d894d02b94862ac6695c66e0985aa546955881f054f/scipion-em-imod-3.2.0.tar.gz (from https://pypi.org/simple/scipion-em-imod/), version: 3.2.0 2026-02-10T07:55:09,603 Skipping link: No binaries permitted for scipion-em-imod: https://files.pythonhosted.org/packages/07/ea/b53a838afe562c293a03c488a583b129bb07d481adf61e1e20e3d4ab8575/scipion_em_imod-3.2.0-py3-none-any.whl (from https://pypi.org/simple/scipion-em-imod/) 2026-02-10T07:55:09,604 Found link https://files.pythonhosted.org/packages/45/1a/1efffdd9371c3404ace83d11d46be0873bcabb96bb4d870eb86f53a30f15/scipion-em-imod-3.2.1.tar.gz (from https://pypi.org/simple/scipion-em-imod/), version: 3.2.1 2026-02-10T07:55:09,604 Found link https://files.pythonhosted.org/packages/b4/5a/747192de3176ac551f77af04316882add2424c6579caa399fa732f417d00/scipion-em-imod-3.2.2.tar.gz (from https://pypi.org/simple/scipion-em-imod/), version: 3.2.2 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https://pypi.org/simple/scipion-em-imod/) (requires-python:>=3.8) 2026-02-10T07:55:09,613 Found link https://files.pythonhosted.org/packages/d9/de/b6cb2c9f31b5e726980b3222a31c919148d327dfe84901188d3d955d4b69/scipion_em_imod-3.7.0.tar.gz (from https://pypi.org/simple/scipion-em-imod/) (requires-python:>=3.8), version: 3.7.0 2026-02-10T07:55:09,613 Skipping link: No binaries permitted for scipion-em-imod: https://files.pythonhosted.org/packages/4e/42/48c62d90519a37a4809ccdf0be9d3eea863181e49fb4c7b467a55067c303/scipion_em_imod-3.8.1-py3-none-any.whl (from https://pypi.org/simple/scipion-em-imod/) (requires-python:>=3.8) 2026-02-10T07:55:09,614 Found link https://files.pythonhosted.org/packages/28/9a/67eaa9b12925f051d84bd22a313bea6c803e135dbcca1f5d11226295dff9/scipion_em_imod-3.8.1.tar.gz (from https://pypi.org/simple/scipion-em-imod/) (requires-python:>=3.8), version: 3.8.1 2026-02-10T07:55:09,615 Fetching project page and analyzing links: https://www.piwheels.org/simple/scipion-em-imod/ 2026-02-10T07:55:09,616 Getting page https://www.piwheels.org/simple/scipion-em-imod/ 2026-02-10T07:55:09,617 Found index url https://www.piwheels.org/simple 2026-02-10T07:55:10,089 Fetched page https://www.piwheels.org/simple/scipion-em-imod/ as text/html 2026-02-10T07:55:10,094 Skipping link: No binaries permitted for scipion-em-imod: https://archive1.piwheels.org/simple/scipion-em-imod/scipion_em_imod-3.7.0-py3-none-any.whl#sha256=1c8cc0f57d511963c36a27ca0dbd15729afa136b310b7843c8975a9e57b472b6 (from https://www.piwheels.org/simple/scipion-em-imod/) (requires-python:>=3.8) 2026-02-10T07:55:10,094 Skipping link: No binaries permitted for scipion-em-imod: https://archive1.piwheels.org/simple/scipion-em-imod/scipion_em_imod-3.0.10-py3-none-any.whl#sha256=e88296fe992acd54edb0e515051076f9c789a11501ff4ba8094c7693841d5415 (from https://www.piwheels.org/simple/scipion-em-imod/) 2026-02-10T07:55:10,095 Skipping link: No binaries permitted for scipion-em-imod: https://archive1.piwheels.org/simple/scipion-em-imod/scipion_em_imod-3.0.8-py3-none-any.whl#sha256=afb83f78445abc1cb854accac0c3d1570d55429917e3f570cad3d8b13ee3f8f9 (from https://www.piwheels.org/simple/scipion-em-imod/) 2026-02-10T07:55:10,095 Skipping link: No binaries permitted for scipion-em-imod: https://archive1.piwheels.org/simple/scipion-em-imod/scipion_em_imod-3.0.7-py3-none-any.whl#sha256=bb435763046d060aa1c750a7e80be49a757b37b10874cbb9269e07f39d1e69b0 (from https://www.piwheels.org/simple/scipion-em-imod/) 2026-02-10T07:55:10,096 Skipping link: No binaries permitted for scipion-em-imod: https://archive1.piwheels.org/simple/scipion-em-imod/scipion_em_imod-3.0.6-py3-none-any.whl#sha256=6ee85d60b600792f00d6ed7efd0e9fff2a3aefb68d10a081e6cc452cda627069 (from https://www.piwheels.org/simple/scipion-em-imod/) 2026-02-10T07:55:10,096 Skipping link: No binaries permitted for scipion-em-imod: https://archive1.piwheels.org/simple/scipion-em-imod/scipion_em_imod-3.0.5-py3-none-any.whl#sha256=7036f2b9a181e4503906bf5c8f66e4720407f685571c801b5a85d9fa9bd50874 (from https://www.piwheels.org/simple/scipion-em-imod/) 2026-02-10T07:55:10,096 Skipping link: No binaries permitted for scipion-em-imod: https://archive1.piwheels.org/simple/scipion-em-imod/scipion_em_imod-3.0.4-py3-none-any.whl#sha256=a84a83fae0d65c8c8662b02573129285d2e5d6547b610c211df3fe29b5b21e52 (from https://www.piwheels.org/simple/scipion-em-imod/) 2026-02-10T07:55:10,097 Skipping link: No binaries permitted for scipion-em-imod: https://archive1.piwheels.org/simple/scipion-em-imod/scipion_em_imod-3.0.3-py3-none-any.whl#sha256=e5d9d7dcf9f53d9a4d81555633ef3903475af9ccc9b05de4e50157452b49633c (from https://www.piwheels.org/simple/scipion-em-imod/) 2026-02-10T07:55:10,098 Skipping link: No binaries permitted for scipion-em-imod: https://archive1.piwheels.org/simple/scipion-em-imod/scipion_em_imod-3.0.2-py3-none-any.whl#sha256=80d142347a232a52e13798429c5d119f47b79ed91fd9c36261cb1a563d7a559d (from https://www.piwheels.org/simple/scipion-em-imod/) 2026-02-10T07:55:10,098 Skipping link: No binaries permitted for scipion-em-imod: https://archive1.piwheels.org/simple/scipion-em-imod/scipion_em_imod-3.0.1-py3-none-any.whl#sha256=d11fbbe1be8c6803cc87df31d80d8a128a8a08fabc54bb435ad7f4a7ef3c9907 (from https://www.piwheels.org/simple/scipion-em-imod/) 2026-02-10T07:55:10,099 Skipping link: No binaries permitted for scipion-em-imod: https://archive1.piwheels.org/simple/scipion-em-imod/scipion_em_imod-3.0.0-py3-none-any.whl#sha256=fa280b8a7267e0738d2f7600545d93ebdb151637b0f451f64e7293aea68e8b5c (from https://www.piwheels.org/simple/scipion-em-imod/) 2026-02-10T07:55:10,099 Skipping link: No binaries permitted for scipion-em-imod: https://archive1.piwheels.org/simple/scipion-em-imod/scipion_em_imod-0.0.2-py3-none-any.whl#sha256=ac05aa954753dc24cd74ceeb67e9e2a09f68245de68fb0f6382bee984dcb278f (from https://www.piwheels.org/simple/scipion-em-imod/) 2026-02-10T07:55:10,100 Skipping link: No binaries permitted for scipion-em-imod: https://archive1.piwheels.org/simple/scipion-em-imod/scipion_em_imod-0.0.1-py3-none-any.whl#sha256=e640d2126e3ab4529224058f0b44b52c2e9e917451016f414c41d77a968271e3 (from https://www.piwheels.org/simple/scipion-em-imod/) 2026-02-10T07:55:10,101 Skipping link: not a file: https://www.piwheels.org/simple/scipion-em-imod/ 2026-02-10T07:55:10,101 Skipping link: not a file: https://pypi.org/simple/scipion-em-imod/ 2026-02-10T07:55:10,124 Given no hashes to check 1 links for project 'scipion-em-imod': discarding no candidates 2026-02-10T07:55:10,143 Collecting scipion-em-imod==3.8.1 2026-02-10T07:55:10,145 Created temporary directory: /tmp/pip-unpack-di1hs7mm 2026-02-10T07:55:10,317 Downloading scipion_em_imod-3.8.1.tar.gz (131 kB) 2026-02-10T07:55:10,541 Added scipion-em-imod==3.8.1 from https://files.pythonhosted.org/packages/28/9a/67eaa9b12925f051d84bd22a313bea6c803e135dbcca1f5d11226295dff9/scipion_em_imod-3.8.1.tar.gz to build tracker '/tmp/pip-build-tracker-agj4qs24' 2026-02-10T07:55:10,546 Created temporary directory: /tmp/pip-build-env-44jzjghc 2026-02-10T07:55:10,550 Installing build dependencies: started 2026-02-10T07:55:10,552 Running command pip subprocess to install build dependencies 2026-02-10T07:55:11,676 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-02-10T07:55:12,226 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-10T07:55:12,248 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-10T07:55:13,988 Collecting setuptools 2026-02-10T07:55:14,008 Using cached setuptools-82.0.0-py3-none-any.whl (1.0 MB) 2026-02-10T07:55:14,272 Collecting wheel 2026-02-10T07:55:14,287 Using cached https://www.piwheels.org/simple/wheel/wheel-0.46.3-py3-none-any.whl (30 kB) 2026-02-10T07:55:14,471 Collecting packaging>=24.0 2026-02-10T07:55:14,487 Using cached https://www.piwheels.org/simple/packaging/packaging-26.0-py3-none-any.whl (74 kB) 2026-02-10T07:55:17,474 Installing collected packages: setuptools, packaging, wheel 2026-02-10T07:55:20,808 Creating /tmp/pip-build-env-44jzjghc/overlay/local/bin 2026-02-10T07:55:20,810 changing mode of /tmp/pip-build-env-44jzjghc/overlay/local/bin/wheel to 755 2026-02-10T07:55:20,832 Successfully installed packaging-26.0 setuptools-82.0.0 wheel-0.46.3 2026-02-10T07:55:21,109 Installing build dependencies: finished with status 'done' 2026-02-10T07:55:21,115 Getting requirements to build wheel: started 2026-02-10T07:55:21,116 Running command Getting requirements to build wheel 2026-02-10T07:55:21,726 No `packages` or `py_modules` configuration, performing automatic discovery. 2026-02-10T07:55:21,726 `flat-layout` detected -- analysing . 2026-02-10T07:55:21,744 discovered packages -- ['imod', 'imod.convert', 'imod.tests', 'imod.viewers', 'imod.templates', 'imod.protocols'] 2026-02-10T07:55:21,753 /tmp/pip-build-env-44jzjghc/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-02-10T07:55:21,754 !! 2026-02-10T07:55:21,755 ******************************************************************************** 2026-02-10T07:55:21,756 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-02-10T07:55:21,757 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-02-10T07:55:21,758 or your builds will no longer be supported. 2026-02-10T07:55:21,759 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-10T07:55:21,760 ******************************************************************************** 2026-02-10T07:55:21,761 !! 2026-02-10T07:55:21,761 corresp(dist, value, root_dir) 2026-02-10T07:55:21,829 /tmp/pip-build-env-44jzjghc/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-10T07:55:21,830 !! 2026-02-10T07:55:21,831 ******************************************************************************** 2026-02-10T07:55:21,831 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-10T07:55:21,832 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2026-02-10T07:55:21,833 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-10T07:55:21,833 ******************************************************************************** 2026-02-10T07:55:21,834 !! 2026-02-10T07:55:21,835 dist._finalize_license_expression() 2026-02-10T07:55:21,835 /tmp/pip-build-env-44jzjghc/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-10T07:55:21,835 !! 2026-02-10T07:55:21,836 ******************************************************************************** 2026-02-10T07:55:21,837 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-10T07:55:21,838 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2026-02-10T07:55:21,839 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-10T07:55:21,839 ******************************************************************************** 2026-02-10T07:55:21,841 !! 2026-02-10T07:55:21,841 self._finalize_license_expression() 2026-02-10T07:55:21,842 running egg_info 2026-02-10T07:55:21,847 writing scipion_em_imod.egg-info/PKG-INFO 2026-02-10T07:55:21,851 writing dependency_links to scipion_em_imod.egg-info/dependency_links.txt 2026-02-10T07:55:21,853 writing entry points to scipion_em_imod.egg-info/entry_points.txt 2026-02-10T07:55:21,855 writing requirements to scipion_em_imod.egg-info/requires.txt 2026-02-10T07:55:21,856 writing top-level names to scipion_em_imod.egg-info/top_level.txt 2026-02-10T07:55:21,881 reading manifest file 'scipion_em_imod.egg-info/SOURCES.txt' 2026-02-10T07:55:21,886 reading manifest template 'MANIFEST.in' 2026-02-10T07:55:21,889 adding license file 'LICENSE' 2026-02-10T07:55:21,893 writing manifest file 'scipion_em_imod.egg-info/SOURCES.txt' 2026-02-10T07:55:21,990 Getting requirements to build wheel: finished with status 'done' 2026-02-10T07:55:21,993 Created temporary directory: /tmp/pip-modern-metadata-qmsizcdh 2026-02-10T07:55:21,995 Preparing metadata (pyproject.toml): started 2026-02-10T07:55:21,996 Running command Preparing metadata (pyproject.toml) 2026-02-10T07:55:22,807 No `packages` or `py_modules` configuration, performing automatic discovery. 2026-02-10T07:55:22,807 `flat-layout` detected -- analysing . 2026-02-10T07:55:22,823 discovered packages -- ['imod', 'imod.convert', 'imod.tests', 'imod.viewers', 'imod.templates', 'imod.protocols'] 2026-02-10T07:55:22,832 /tmp/pip-build-env-44jzjghc/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-02-10T07:55:22,832 !! 2026-02-10T07:55:22,833 ******************************************************************************** 2026-02-10T07:55:22,834 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-02-10T07:55:22,835 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-02-10T07:55:22,836 or your builds will no longer be supported. 2026-02-10T07:55:22,837 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-10T07:55:22,838 ******************************************************************************** 2026-02-10T07:55:22,839 !! 2026-02-10T07:55:22,839 corresp(dist, value, root_dir) 2026-02-10T07:55:22,904 /tmp/pip-build-env-44jzjghc/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-10T07:55:22,904 !! 2026-02-10T07:55:22,905 ******************************************************************************** 2026-02-10T07:55:22,906 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-10T07:55:22,906 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2026-02-10T07:55:22,907 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-10T07:55:22,908 ******************************************************************************** 2026-02-10T07:55:22,909 !! 2026-02-10T07:55:22,909 dist._finalize_license_expression() 2026-02-10T07:55:22,910 /tmp/pip-build-env-44jzjghc/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-10T07:55:22,910 !! 2026-02-10T07:55:22,911 ******************************************************************************** 2026-02-10T07:55:22,912 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-10T07:55:22,913 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2026-02-10T07:55:22,914 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-10T07:55:22,915 ******************************************************************************** 2026-02-10T07:55:22,916 !! 2026-02-10T07:55:22,917 self._finalize_license_expression() 2026-02-10T07:55:22,917 running dist_info 2026-02-10T07:55:22,925 creating /tmp/pip-modern-metadata-qmsizcdh/scipion_em_imod.egg-info 2026-02-10T07:55:22,926 writing /tmp/pip-modern-metadata-qmsizcdh/scipion_em_imod.egg-info/PKG-INFO 2026-02-10T07:55:22,929 writing dependency_links to /tmp/pip-modern-metadata-qmsizcdh/scipion_em_imod.egg-info/dependency_links.txt 2026-02-10T07:55:22,931 writing entry points to /tmp/pip-modern-metadata-qmsizcdh/scipion_em_imod.egg-info/entry_points.txt 2026-02-10T07:55:22,932 writing requirements to /tmp/pip-modern-metadata-qmsizcdh/scipion_em_imod.egg-info/requires.txt 2026-02-10T07:55:22,933 writing top-level names to /tmp/pip-modern-metadata-qmsizcdh/scipion_em_imod.egg-info/top_level.txt 2026-02-10T07:55:22,935 writing manifest file '/tmp/pip-modern-metadata-qmsizcdh/scipion_em_imod.egg-info/SOURCES.txt' 2026-02-10T07:55:22,958 reading manifest file '/tmp/pip-modern-metadata-qmsizcdh/scipion_em_imod.egg-info/SOURCES.txt' 2026-02-10T07:55:22,960 reading manifest template 'MANIFEST.in' 2026-02-10T07:55:22,963 adding license file 'LICENSE' 2026-02-10T07:55:22,966 writing manifest file '/tmp/pip-modern-metadata-qmsizcdh/scipion_em_imod.egg-info/SOURCES.txt' 2026-02-10T07:55:22,968 creating '/tmp/pip-modern-metadata-qmsizcdh/scipion_em_imod-3.8.1.dist-info' 2026-02-10T07:55:23,091 Preparing metadata (pyproject.toml): finished with status 'done' 2026-02-10T07:55:23,096 Source in /tmp/pip-wheel-kngh3vrn/scipion-em-imod_a18ba8dd59a6453eb358b6948e89a501 has version 3.8.1, which satisfies requirement scipion-em-imod==3.8.1 from https://files.pythonhosted.org/packages/28/9a/67eaa9b12925f051d84bd22a313bea6c803e135dbcca1f5d11226295dff9/scipion_em_imod-3.8.1.tar.gz 2026-02-10T07:55:23,097 Removed scipion-em-imod==3.8.1 from https://files.pythonhosted.org/packages/28/9a/67eaa9b12925f051d84bd22a313bea6c803e135dbcca1f5d11226295dff9/scipion_em_imod-3.8.1.tar.gz from build tracker '/tmp/pip-build-tracker-agj4qs24' 2026-02-10T07:55:23,102 Created temporary directory: /tmp/pip-unpack-9fovhi_6 2026-02-10T07:55:23,103 Building wheels for collected packages: scipion-em-imod 2026-02-10T07:55:23,107 Created temporary directory: /tmp/pip-wheel-z13otdzu 2026-02-10T07:55:23,108 Destination directory: /tmp/pip-wheel-z13otdzu 2026-02-10T07:55:23,110 Building wheel for scipion-em-imod (pyproject.toml): started 2026-02-10T07:55:23,111 Running command Building wheel for scipion-em-imod (pyproject.toml) 2026-02-10T07:55:23,651 No `packages` or `py_modules` configuration, performing automatic discovery. 2026-02-10T07:55:23,651 `flat-layout` detected -- analysing . 2026-02-10T07:55:23,667 discovered packages -- ['imod', 'imod.convert', 'imod.tests', 'imod.viewers', 'imod.templates', 'imod.protocols'] 2026-02-10T07:55:23,677 /tmp/pip-build-env-44jzjghc/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-02-10T07:55:23,677 !! 2026-02-10T07:55:23,678 ******************************************************************************** 2026-02-10T07:55:23,679 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-02-10T07:55:23,680 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-02-10T07:55:23,680 or your builds will no longer be supported. 2026-02-10T07:55:23,682 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-10T07:55:23,682 ******************************************************************************** 2026-02-10T07:55:23,683 !! 2026-02-10T07:55:23,684 corresp(dist, value, root_dir) 2026-02-10T07:55:23,744 /tmp/pip-build-env-44jzjghc/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-10T07:55:23,744 !! 2026-02-10T07:55:23,745 ******************************************************************************** 2026-02-10T07:55:23,746 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-10T07:55:23,747 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2026-02-10T07:55:23,749 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-10T07:55:23,749 ******************************************************************************** 2026-02-10T07:55:23,750 !! 2026-02-10T07:55:23,751 dist._finalize_license_expression() 2026-02-10T07:55:23,752 /tmp/pip-build-env-44jzjghc/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-10T07:55:23,752 !! 2026-02-10T07:55:23,753 ******************************************************************************** 2026-02-10T07:55:23,754 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-10T07:55:23,755 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2026-02-10T07:55:23,756 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-10T07:55:23,757 ******************************************************************************** 2026-02-10T07:55:23,758 !! 2026-02-10T07:55:23,759 self._finalize_license_expression() 2026-02-10T07:55:23,759 running bdist_wheel 2026-02-10T07:55:23,770 running build 2026-02-10T07:55:23,771 running build_py 2026-02-10T07:55:23,777 creating build/lib/imod 2026-02-10T07:55:23,779 copying imod/utils.py -> build/lib/imod 2026-02-10T07:55:23,782 copying imod/bibtex.py -> build/lib/imod 2026-02-10T07:55:23,784 copying imod/file_handlers.py -> build/lib/imod 2026-02-10T07:55:23,786 copying imod/wizards.py -> build/lib/imod 2026-02-10T07:55:23,788 copying imod/__init__.py -> build/lib/imod 2026-02-10T07:55:23,790 copying imod/constants.py -> build/lib/imod 2026-02-10T07:55:23,792 creating build/lib/imod/convert 2026-02-10T07:55:23,793 copying imod/convert/dataimport.py -> build/lib/imod/convert 2026-02-10T07:55:23,796 copying imod/convert/convert.py -> build/lib/imod/convert 2026-02-10T07:55:23,798 copying imod/convert/__init__.py -> build/lib/imod/convert 2026-02-10T07:55:23,800 creating build/lib/imod/tests 2026-02-10T07:55:23,801 copying imod/tests/tests_imod_workflows.py -> build/lib/imod/tests 2026-02-10T07:55:23,804 copying imod/tests/__init__.py -> build/lib/imod/tests 2026-02-10T07:55:23,806 copying imod/tests/tests_imod.py -> build/lib/imod/tests 2026-02-10T07:55:23,811 creating build/lib/imod/viewers 2026-02-10T07:55:23,812 copying imod/viewers/__init__.py -> build/lib/imod/viewers 2026-02-10T07:55:23,813 copying imod/viewers/viewers.py -> build/lib/imod/viewers 2026-02-10T07:55:23,816 copying imod/viewers/views_tkinter_tree.py -> build/lib/imod/viewers 2026-02-10T07:55:23,820 creating build/lib/imod/protocols 2026-02-10T07:55:23,821 copying imod/protocols/protocol_xCorrPrealignment.py -> build/lib/imod/protocols 2026-02-10T07:55:23,823 copying imod/protocols/protocol_base_xcorr_fidmodel.py -> build/lib/imod/protocols 2026-02-10T07:55:23,826 copying imod/protocols/protocol_tomoProjection.py -> build/lib/imod/protocols 2026-02-10T07:55:23,828 copying imod/protocols/protocol_xRaysEraser.py -> build/lib/imod/protocols 2026-02-10T07:55:23,830 copying imod/protocols/protocol_base_ts_align.py -> build/lib/imod/protocols 2026-02-10T07:55:23,832 copying imod/protocols/protocol_doseFilter.py -> build/lib/imod/protocols 2026-02-10T07:55:23,835 copying imod/protocols/protocol_fiducial_eraser.py -> build/lib/imod/protocols 2026-02-10T07:55:23,837 copying imod/protocols/protocol_ctfCorrection.py -> build/lib/imod/protocols 2026-02-10T07:55:23,840 copying imod/protocols/protocol_ctfEstimation_manual.py -> build/lib/imod/protocols 2026-02-10T07:55:23,842 copying imod/protocols/protocol_fiducialAlignment.py -> build/lib/imod/protocols 2026-02-10T07:55:23,844 copying imod/protocols/protocol_etomo.py -> build/lib/imod/protocols 2026-02-10T07:55:23,847 copying imod/protocols/protocol_applyTransformationMatrix.py -> build/lib/imod/protocols 2026-02-10T07:55:23,850 copying imod/protocols/protocol_tsPreprocess.py -> build/lib/imod/protocols 2026-02-10T07:55:23,852 copying imod/protocols/protocol_tomoPreprocess.py -> build/lib/imod/protocols 2026-02-10T07:55:23,855 copying imod/protocols/protocol_goldBeadPicker3d.py -> build/lib/imod/protocols 2026-02-10T07:55:23,857 copying imod/protocols/protocol_tomoReconstruction.py -> build/lib/imod/protocols 2026-02-10T07:55:23,860 copying imod/protocols/__init__.py -> build/lib/imod/protocols 2026-02-10T07:55:23,862 copying imod/protocols/protocol_base.py -> build/lib/imod/protocols 2026-02-10T07:55:23,865 copying imod/protocols/protocol_base_preprocess.py -> build/lib/imod/protocols 2026-02-10T07:55:23,867 copying imod/protocols/protocol_batch_run_tomo.py -> build/lib/imod/protocols 2026-02-10T07:55:23,869 copying imod/protocols/protocol_fiducialModel.py -> build/lib/imod/protocols 2026-02-10T07:55:23,872 copying imod/protocols/protocol_excludeViews.py -> build/lib/imod/protocols 2026-02-10T07:55:23,874 copying imod/protocols/protocol_importSetOfTM.py -> build/lib/imod/protocols 2026-02-10T07:55:23,877 copying imod/protocols/protocol_ctfEstimation_automatic.py -> build/lib/imod/protocols 2026-02-10T07:55:23,880 running egg_info 2026-02-10T07:55:23,889 writing scipion_em_imod.egg-info/PKG-INFO 2026-02-10T07:55:23,892 writing dependency_links to scipion_em_imod.egg-info/dependency_links.txt 2026-02-10T07:55:23,894 writing entry points to scipion_em_imod.egg-info/entry_points.txt 2026-02-10T07:55:23,895 writing requirements to scipion_em_imod.egg-info/requires.txt 2026-02-10T07:55:23,896 writing top-level names to scipion_em_imod.egg-info/top_level.txt 2026-02-10T07:55:23,910 reading manifest file 'scipion_em_imod.egg-info/SOURCES.txt' 2026-02-10T07:55:23,914 reading manifest template 'MANIFEST.in' 2026-02-10T07:55:23,917 adding license file 'LICENSE' 2026-02-10T07:55:23,921 writing manifest file 'scipion_em_imod.egg-info/SOURCES.txt' 2026-02-10T07:55:23,927 copying imod/icon.png -> build/lib/imod 2026-02-10T07:55:23,929 copying imod/protocols.conf -> build/lib/imod 2026-02-10T07:55:23,931 creating build/lib/imod/templates 2026-02-10T07:55:23,932 copying imod/templates/automatic_tilt_series_alignment.json.template -> build/lib/imod/templates 2026-02-10T07:55:23,946 installing to build/bdist.linux-armv7l/wheel 2026-02-10T07:55:23,946 running install 2026-02-10T07:55:23,969 running install_lib 2026-02-10T07:55:23,975 creating build/bdist.linux-armv7l/wheel 2026-02-10T07:55:23,977 creating build/bdist.linux-armv7l/wheel/imod 2026-02-10T07:55:23,978 copying build/lib/imod/utils.py -> build/bdist.linux-armv7l/wheel/./imod 2026-02-10T07:55:23,981 creating build/bdist.linux-armv7l/wheel/imod/convert 2026-02-10T07:55:23,982 copying build/lib/imod/convert/dataimport.py -> build/bdist.linux-armv7l/wheel/./imod/convert 2026-02-10T07:55:23,985 copying build/lib/imod/convert/convert.py -> build/bdist.linux-armv7l/wheel/./imod/convert 2026-02-10T07:55:23,987 copying build/lib/imod/convert/__init__.py -> build/bdist.linux-armv7l/wheel/./imod/convert 2026-02-10T07:55:23,989 creating build/bdist.linux-armv7l/wheel/imod/tests 2026-02-10T07:55:23,990 copying build/lib/imod/tests/tests_imod_workflows.py -> build/bdist.linux-armv7l/wheel/./imod/tests 2026-02-10T07:55:23,993 copying build/lib/imod/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./imod/tests 2026-02-10T07:55:23,995 copying build/lib/imod/tests/tests_imod.py -> build/bdist.linux-armv7l/wheel/./imod/tests 2026-02-10T07:55:23,999 copying build/lib/imod/bibtex.py -> build/bdist.linux-armv7l/wheel/./imod 2026-02-10T07:55:24,001 copying build/lib/imod/file_handlers.py -> build/bdist.linux-armv7l/wheel/./imod 2026-02-10T07:55:24,003 creating build/bdist.linux-armv7l/wheel/imod/viewers 2026-02-10T07:55:24,004 copying build/lib/imod/viewers/__init__.py -> build/bdist.linux-armv7l/wheel/./imod/viewers 2026-02-10T07:55:24,006 copying build/lib/imod/viewers/viewers.py -> build/bdist.linux-armv7l/wheel/./imod/viewers 2026-02-10T07:55:24,008 copying build/lib/imod/viewers/views_tkinter_tree.py -> build/bdist.linux-armv7l/wheel/./imod/viewers 2026-02-10T07:55:24,011 copying build/lib/imod/protocols.conf -> build/bdist.linux-armv7l/wheel/./imod 2026-02-10T07:55:24,013 copying build/lib/imod/wizards.py -> build/bdist.linux-armv7l/wheel/./imod 2026-02-10T07:55:24,015 copying build/lib/imod/__init__.py -> build/bdist.linux-armv7l/wheel/./imod 2026-02-10T07:55:24,017 copying build/lib/imod/icon.png -> build/bdist.linux-armv7l/wheel/./imod 2026-02-10T07:55:24,019 copying build/lib/imod/constants.py -> build/bdist.linux-armv7l/wheel/./imod 2026-02-10T07:55:24,021 creating build/bdist.linux-armv7l/wheel/imod/templates 2026-02-10T07:55:24,022 copying build/lib/imod/templates/automatic_tilt_series_alignment.json.template -> build/bdist.linux-armv7l/wheel/./imod/templates 2026-02-10T07:55:24,025 creating build/bdist.linux-armv7l/wheel/imod/protocols 2026-02-10T07:55:24,026 copying build/lib/imod/protocols/protocol_xCorrPrealignment.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,029 copying build/lib/imod/protocols/protocol_base_xcorr_fidmodel.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,031 copying build/lib/imod/protocols/protocol_tomoProjection.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,033 copying build/lib/imod/protocols/protocol_xRaysEraser.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,036 copying build/lib/imod/protocols/protocol_base_ts_align.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,038 copying build/lib/imod/protocols/protocol_doseFilter.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,041 copying build/lib/imod/protocols/protocol_fiducial_eraser.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,043 copying build/lib/imod/protocols/protocol_ctfCorrection.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,045 copying build/lib/imod/protocols/protocol_ctfEstimation_manual.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,047 copying build/lib/imod/protocols/protocol_fiducialAlignment.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,050 copying build/lib/imod/protocols/protocol_etomo.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,053 copying build/lib/imod/protocols/protocol_applyTransformationMatrix.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,055 copying build/lib/imod/protocols/protocol_tsPreprocess.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,057 copying build/lib/imod/protocols/protocol_tomoPreprocess.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,060 copying build/lib/imod/protocols/protocol_goldBeadPicker3d.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,062 copying build/lib/imod/protocols/protocol_tomoReconstruction.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,064 copying build/lib/imod/protocols/__init__.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,066 copying build/lib/imod/protocols/protocol_base.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,069 copying build/lib/imod/protocols/protocol_base_preprocess.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,071 copying build/lib/imod/protocols/protocol_batch_run_tomo.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,073 copying build/lib/imod/protocols/protocol_fiducialModel.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,076 copying build/lib/imod/protocols/protocol_excludeViews.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,078 copying build/lib/imod/protocols/protocol_importSetOfTM.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,081 copying build/lib/imod/protocols/protocol_ctfEstimation_automatic.py -> build/bdist.linux-armv7l/wheel/./imod/protocols 2026-02-10T07:55:24,083 running install_egg_info 2026-02-10T07:55:24,088 Copying scipion_em_imod.egg-info to build/bdist.linux-armv7l/wheel/./scipion_em_imod-3.8.1-py3.11.egg-info 2026-02-10T07:55:24,100 running install_scripts 2026-02-10T07:55:24,112 creating build/bdist.linux-armv7l/wheel/scipion_em_imod-3.8.1.dist-info/WHEEL 2026-02-10T07:55:24,115 creating '/tmp/pip-wheel-z13otdzu/.tmp-znngf1vv/scipion_em_imod-3.8.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-02-10T07:55:24,118 adding 'imod/__init__.py' 2026-02-10T07:55:24,119 adding 'imod/bibtex.py' 2026-02-10T07:55:24,121 adding 'imod/constants.py' 2026-02-10T07:55:24,122 adding 'imod/file_handlers.py' 2026-02-10T07:55:24,124 adding 'imod/icon.png' 2026-02-10T07:55:24,125 adding 'imod/protocols.conf' 2026-02-10T07:55:24,127 adding 'imod/utils.py' 2026-02-10T07:55:24,129 adding 'imod/wizards.py' 2026-02-10T07:55:24,131 adding 'imod/convert/__init__.py' 2026-02-10T07:55:24,132 adding 'imod/convert/convert.py' 2026-02-10T07:55:24,134 adding 'imod/convert/dataimport.py' 2026-02-10T07:55:24,136 adding 'imod/protocols/__init__.py' 2026-02-10T07:55:24,139 adding 'imod/protocols/protocol_applyTransformationMatrix.py' 2026-02-10T07:55:24,142 adding 'imod/protocols/protocol_base.py' 2026-02-10T07:55:24,145 adding 'imod/protocols/protocol_base_preprocess.py' 2026-02-10T07:55:24,146 adding 'imod/protocols/protocol_base_ts_align.py' 2026-02-10T07:55:24,148 adding 'imod/protocols/protocol_base_xcorr_fidmodel.py' 2026-02-10T07:55:24,150 adding 'imod/protocols/protocol_batch_run_tomo.py' 2026-02-10T07:55:24,153 adding 'imod/protocols/protocol_ctfCorrection.py' 2026-02-10T07:55:24,155 adding 'imod/protocols/protocol_ctfEstimation_automatic.py' 2026-02-10T07:55:24,157 adding 'imod/protocols/protocol_ctfEstimation_manual.py' 2026-02-10T07:55:24,159 adding 'imod/protocols/protocol_doseFilter.py' 2026-02-10T07:55:24,163 adding 'imod/protocols/protocol_etomo.py' 2026-02-10T07:55:24,165 adding 'imod/protocols/protocol_excludeViews.py' 2026-02-10T07:55:24,168 adding 'imod/protocols/protocol_fiducialAlignment.py' 2026-02-10T07:55:24,172 adding 'imod/protocols/protocol_fiducialModel.py' 2026-02-10T07:55:24,174 adding 'imod/protocols/protocol_fiducial_eraser.py' 2026-02-10T07:55:24,176 adding 'imod/protocols/protocol_goldBeadPicker3d.py' 2026-02-10T07:55:24,178 adding 'imod/protocols/protocol_importSetOfTM.py' 2026-02-10T07:55:24,180 adding 'imod/protocols/protocol_tomoPreprocess.py' 2026-02-10T07:55:24,182 adding 'imod/protocols/protocol_tomoProjection.py' 2026-02-10T07:55:24,185 adding 'imod/protocols/protocol_tomoReconstruction.py' 2026-02-10T07:55:24,187 adding 'imod/protocols/protocol_tsPreprocess.py' 2026-02-10T07:55:24,189 adding 'imod/protocols/protocol_xCorrPrealignment.py' 2026-02-10T07:55:24,191 adding 'imod/protocols/protocol_xRaysEraser.py' 2026-02-10T07:55:24,193 adding 'imod/templates/automatic_tilt_series_alignment.json.template' 2026-02-10T07:55:24,194 adding 'imod/tests/__init__.py' 2026-02-10T07:55:24,201 adding 'imod/tests/tests_imod.py' 2026-02-10T07:55:24,204 adding 'imod/tests/tests_imod_workflows.py' 2026-02-10T07:55:24,206 adding 'imod/viewers/__init__.py' 2026-02-10T07:55:24,208 adding 'imod/viewers/viewers.py' 2026-02-10T07:55:24,211 adding 'imod/viewers/views_tkinter_tree.py' 2026-02-10T07:55:24,218 adding 'scipion_em_imod-3.8.1.dist-info/licenses/LICENSE' 2026-02-10T07:55:24,220 adding 'scipion_em_imod-3.8.1.dist-info/METADATA' 2026-02-10T07:55:24,221 adding 'scipion_em_imod-3.8.1.dist-info/WHEEL' 2026-02-10T07:55:24,222 adding 'scipion_em_imod-3.8.1.dist-info/entry_points.txt' 2026-02-10T07:55:24,223 adding 'scipion_em_imod-3.8.1.dist-info/top_level.txt' 2026-02-10T07:55:24,224 adding 'scipion_em_imod-3.8.1.dist-info/RECORD' 2026-02-10T07:55:24,228 removing build/bdist.linux-armv7l/wheel 2026-02-10T07:55:24,337 Building wheel for scipion-em-imod (pyproject.toml): finished with status 'done' 2026-02-10T07:55:24,346 Created wheel for scipion-em-imod: filename=scipion_em_imod-3.8.1-py3-none-any.whl size=172728 sha256=3a6087eb5f7c7919fefb1b1440cb6d535812e61f8c3c17242a773e79c3001bab 2026-02-10T07:55:24,347 Stored in directory: /tmp/pip-ephem-wheel-cache-_pm3d4ah/wheels/a7/47/2b/907ba11cbd5ce49ddf4f1916c5f9815da0c1b3321c75de96cd 2026-02-10T07:55:24,360 Successfully built scipion-em-imod 2026-02-10T07:55:24,369 Removed build tracker: '/tmp/pip-build-tracker-agj4qs24'