2026-03-27T01:45:37,680 Created temporary directory: /tmp/pip-ephem-wheel-cache-al9hzy9_
2026-03-27T01:45:37,682 Created temporary directory: /tmp/pip-build-tracker-mvfz97hh
2026-03-27T01:45:37,683 Initialized build tracking at /tmp/pip-build-tracker-mvfz97hh
2026-03-27T01:45:37,683 Created build tracker: /tmp/pip-build-tracker-mvfz97hh
2026-03-27T01:45:37,684 Entered build tracker: /tmp/pip-build-tracker-mvfz97hh
2026-03-27T01:45:37,685 Created temporary directory: /tmp/pip-wheel-_x9uxtek
2026-03-27T01:45:37,687 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
2026-03-27T01:45:37,690 Created temporary directory: /tmp/pip-ephem-wheel-cache-lykd8nz0
2026-03-27T01:45:37,714 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-03-27T01:45:37,718 2 location(s) to search for versions of scipion-em-tomo3d:
2026-03-27T01:45:37,718 * https://pypi.org/simple/scipion-em-tomo3d/
2026-03-27T01:45:37,718 * https://www.piwheels.org/simple/scipion-em-tomo3d/
2026-03-27T01:45:37,719 Fetching project page and analyzing links: https://pypi.org/simple/scipion-em-tomo3d/
2026-03-27T01:45:37,720 Getting page https://pypi.org/simple/scipion-em-tomo3d/
2026-03-27T01:45:37,721 Found index url https://pypi.org/simple
2026-03-27T01:45:37,945 Fetched page https://pypi.org/simple/scipion-em-tomo3d/ as application/vnd.pypi.simple.v1+json
2026-03-27T01:45:37,949   Found link https://files.pythonhosted.org/packages/6e/7e/a68dc39919161191c35e9bcec3475f69740f49f8f8138499ccfddf0f5f0b/scipion-em-tomo3d-3.1.0.tar.gz (from https://pypi.org/simple/scipion-em-tomo3d/), version: 3.1.0
2026-03-27T01:45:37,950   Skipping link: No binaries permitted for scipion-em-tomo3d: https://files.pythonhosted.org/packages/cb/5b/aac5f9a318fe6bbb63e6ca8afd02528b2982f008a87129feefed6409bc31/scipion_em_tomo3d-3.1.0-py3-none-any.whl (from https://pypi.org/simple/scipion-em-tomo3d/)
2026-03-27T01:45:37,951   Found link https://files.pythonhosted.org/packages/9d/4e/4ed2583cdc9b328f31ce35dac04e8dcf3a7e6c4c28cb5a2b8e3d0de28f66/scipion-em-tomo3d-3.1.1.tar.gz (from https://pypi.org/simple/scipion-em-tomo3d/), version: 3.1.1
2026-03-27T01:45:37,952   Skipping link: No binaries permitted for scipion-em-tomo3d: https://files.pythonhosted.org/packages/f8/4c/c4fe28e7ecff9521fe708df2b9de13ca97d1d03104a77a16b1240fdef7c1/scipion_em_tomo3d-3.1.1-py3-none-any.whl (from https://pypi.org/simple/scipion-em-tomo3d/)
2026-03-27T01:45:37,952   Found link https://files.pythonhosted.org/packages/1b/47/7f33f0e4a4d8afc771f402c102cf3f2ef1f2034825afca65a1dbf940c0c3/scipion-em-tomo3d-3.1.2.tar.gz (from https://pypi.org/simple/scipion-em-tomo3d/), version: 3.1.2
2026-03-27T01:45:37,953   Skipping link: No binaries permitted for scipion-em-tomo3d: https://files.pythonhosted.org/packages/bb/d4/ec3e1c200ae6c204eca1fc45f208fb5d39bcfe64767475c5c33deb595424/scipion_em_tomo3d-3.1.2-py3-none-any.whl (from https://pypi.org/simple/scipion-em-tomo3d/)
2026-03-27T01:45:37,954   Found link https://files.pythonhosted.org/packages/c3/b9/caa468dab576021ee73907b2fefc314818a02a8dc7d7c29c46f88812eb2b/scipion-em-tomo3d-3.1.3.tar.gz (from https://pypi.org/simple/scipion-em-tomo3d/), version: 3.1.3
2026-03-27T01:45:37,954   Skipping link: No binaries permitted for scipion-em-tomo3d: https://files.pythonhosted.org/packages/a1/2d/498a056cfcef0ec4b0c77e469a946d6b622d92e3b50bc21d799d5dc173b7/scipion_em_tomo3d-3.1.3-py3-none-any.whl (from https://pypi.org/simple/scipion-em-tomo3d/)
2026-03-27T01:45:37,955   Found link https://files.pythonhosted.org/packages/a0/c8/608d0803be9f03aa5046683e42a3ff77c37441a98fc37cc53b7a8a95c11a/scipion-em-tomo3d-3.1.4.tar.gz (from https://pypi.org/simple/scipion-em-tomo3d/), version: 3.1.4
2026-03-27T01:45:37,956   Skipping link: No binaries permitted for scipion-em-tomo3d: https://files.pythonhosted.org/packages/27/6f/7944b907374c4e7bc37c9e1310f6e29ff25dbec87d5b25b17ca736dc84bb/scipion_em_tomo3d-3.1.4-py3-none-any.whl (from https://pypi.org/simple/scipion-em-tomo3d/)
2026-03-27T01:45:37,956   Found link https://files.pythonhosted.org/packages/ad/69/e5078246d342a97cce6b1e41dcbe1d90ae1fbb9293303423627b753049f3/scipion-em-tomo3d-3.2.0.tar.gz (from https://pypi.org/simple/scipion-em-tomo3d/), version: 3.2.0
2026-03-27T01:45:37,957   Skipping link: No binaries permitted for scipion-em-tomo3d: https://files.pythonhosted.org/packages/6f/d6/4c0d3ff077f11c64c7a24a934201e43dc4fb358d013292e5d130a06383b0/scipion_em_tomo3d-3.2.0-py3-none-any.whl (from https://pypi.org/simple/scipion-em-tomo3d/)
2026-03-27T01:45:37,958   Skipping link: No binaries permitted for scipion-em-tomo3d: https://files.pythonhosted.org/packages/23/ef/e43daebbbe7c4a02b7c647ac2a0dfc1d8eda51ff70872a1afea5e407ffa2/scipion_em_tomo3d-3.3.0-py3-none-any.whl (from https://pypi.org/simple/scipion-em-tomo3d/) (requires-python:>=3.8)
2026-03-27T01:45:37,958   Found link https://files.pythonhosted.org/packages/94/40/985adf1d5512ddbb5e2227665573a80d429206aca6ec0a66cdd9ca917b0c/scipion_em_tomo3d-3.3.0.tar.gz (from https://pypi.org/simple/scipion-em-tomo3d/) (requires-python:>=3.8), version: 3.3.0
2026-03-27T01:45:37,959   Skipping link: No binaries permitted for scipion-em-tomo3d: https://files.pythonhosted.org/packages/53/e7/03839e14214e253c248ba6d8eedd77789a470635c3489ef0acee945cfb9e/scipion_em_tomo3d-3.4.1-py3-none-any.whl (from https://pypi.org/simple/scipion-em-tomo3d/) (requires-python:>=3.8)
2026-03-27T01:45:37,960   Found link https://files.pythonhosted.org/packages/d4/56/31498479859e3af830187df6f657a8e1e0883b9cd914e4f5dac431e6379f/scipion_em_tomo3d-3.4.1.tar.gz (from https://pypi.org/simple/scipion-em-tomo3d/) (requires-python:>=3.8), version: 3.4.1
2026-03-27T01:45:37,961   Skipping link: No binaries permitted for scipion-em-tomo3d: https://files.pythonhosted.org/packages/ed/bf/fc0e223d827b5c8b2ee0bcc2a62d929a516cfe40237750baa139583db2b3/scipion_em_tomo3d-3.4.2-py3-none-any.whl (from https://pypi.org/simple/scipion-em-tomo3d/) (requires-python:>=3.8)
2026-03-27T01:45:37,961   Found link https://files.pythonhosted.org/packages/b2/d8/0e9cda31d4b77e5d894d82d4be22f17b3990a597f7de600b2e9e39ea4636/scipion_em_tomo3d-3.4.2.tar.gz (from https://pypi.org/simple/scipion-em-tomo3d/) (requires-python:>=3.8), version: 3.4.2
2026-03-27T01:45:37,962 Fetching project page and analyzing links: https://www.piwheels.org/simple/scipion-em-tomo3d/
2026-03-27T01:45:37,963 Getting page https://www.piwheels.org/simple/scipion-em-tomo3d/
2026-03-27T01:45:37,964 Found index url https://www.piwheels.org/simple
2026-03-27T01:45:38,140 Fetched page https://www.piwheels.org/simple/scipion-em-tomo3d/ as text/html
2026-03-27T01:45:38,142   Skipping link: No binaries permitted for scipion-em-tomo3d: https://archive1.piwheels.org/simple/scipion-em-tomo3d/scipion_em_tomo3d-3.4.1-py3-none-any.whl#sha256=0ff41484c923c67e077a6a10dd8bb0f138ce128ab64b549bdd801b3d6412e871 (from https://www.piwheels.org/simple/scipion-em-tomo3d/) (requires-python:>=3.8)
2026-03-27T01:45:38,142   Skipping link: No binaries permitted for scipion-em-tomo3d: https://archive1.piwheels.org/simple/scipion-em-tomo3d/scipion_em_tomo3d-3.3.0-py3-none-any.whl#sha256=1cd2384a0f4c240fae0d131391175ee7e53f430ffa9216b4af06ea55b9004798 (from https://www.piwheels.org/simple/scipion-em-tomo3d/) (requires-python:>=3.8)
2026-03-27T01:45:38,143 Skipping link: not a file: https://www.piwheels.org/simple/scipion-em-tomo3d/
2026-03-27T01:45:38,144 Skipping link: not a file: https://pypi.org/simple/scipion-em-tomo3d/
2026-03-27T01:45:38,163 Given no hashes to check 1 links for project 'scipion-em-tomo3d': discarding no candidates
2026-03-27T01:45:38,181 Collecting scipion-em-tomo3d==3.4.2
2026-03-27T01:45:38,183   Created temporary directory: /tmp/pip-unpack-65x9zyaf
2026-03-27T01:45:38,414   Downloading scipion_em_tomo3d-3.4.2.tar.gz (34 kB)
2026-03-27T01:45:38,498   Added scipion-em-tomo3d==3.4.2 from https://files.pythonhosted.org/packages/b2/d8/0e9cda31d4b77e5d894d82d4be22f17b3990a597f7de600b2e9e39ea4636/scipion_em_tomo3d-3.4.2.tar.gz to build tracker '/tmp/pip-build-tracker-mvfz97hh'
2026-03-27T01:45:38,503   Created temporary directory: /tmp/pip-build-env-z0jkw_gt
2026-03-27T01:45:38,508   Installing build dependencies: started
2026-03-27T01:45:38,509   Running command pip subprocess to install build dependencies
2026-03-27T01:45:39,641   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-03-27T01:45:40,088   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
2026-03-27T01:45:40,112   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-03-27T01:45:41,862   Collecting setuptools
2026-03-27T01:45:41,958     Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-03-27T01:45:42,228   Collecting wheel
2026-03-27T01:45:42,243     Using cached https://www.piwheels.org/simple/wheel/wheel-0.46.3-py3-none-any.whl (30 kB)
2026-03-27T01:45:42,429   Collecting packaging>=24.0
2026-03-27T01:45:42,445     Using cached https://www.piwheels.org/simple/packaging/packaging-26.0-py3-none-any.whl (74 kB)
2026-03-27T01:45:45,379   Installing collected packages: setuptools, packaging, wheel
2026-03-27T01:45:48,943     Creating /tmp/pip-build-env-z0jkw_gt/overlay/local/bin
2026-03-27T01:45:48,945     changing mode of /tmp/pip-build-env-z0jkw_gt/overlay/local/bin/wheel to 755
2026-03-27T01:45:48,966   Successfully installed packaging-26.0 setuptools-82.0.1 wheel-0.46.3
2026-03-27T01:45:49,244   Installing build dependencies: finished with status 'done'
2026-03-27T01:45:49,251   Getting requirements to build wheel: started
2026-03-27T01:45:49,252   Running command Getting requirements to build wheel
2026-03-27T01:45:49,864   No `packages` or `py_modules` configuration, performing automatic discovery.
2026-03-27T01:45:49,864   `flat-layout` detected -- analysing .
2026-03-27T01:45:49,880   discovered packages -- ['tomo3d', 'tomo3d.tests', 'tomo3d.protocols']
2026-03-27T01:45:49,886   /tmp/pip-build-env-z0jkw_gt/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2026-03-27T01:45:49,886   !!

2026-03-27T01:45:49,888           ********************************************************************************
2026-03-27T01:45:49,888           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).

2026-03-27T01:45:49,890           By 2027-Feb-18, you need to update your project and remove deprecated calls
2026-03-27T01:45:49,890           or your builds will no longer be supported.

2026-03-27T01:45:49,892           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-03-27T01:45:49,892           ********************************************************************************

2026-03-27T01:45:49,893   !!
2026-03-27T01:45:49,894     corresp(dist, value, root_dir)
2026-03-27T01:45:49,964   /tmp/pip-build-env-z0jkw_gt/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-03-27T01:45:49,964   !!

2026-03-27T01:45:49,965           ********************************************************************************
2026-03-27T01:45:49,966           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-03-27T01:45:49,968           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2026-03-27T01:45:49,969           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-03-27T01:45:49,970           ********************************************************************************

2026-03-27T01:45:49,971   !!
2026-03-27T01:45:49,971     dist._finalize_license_expression()
2026-03-27T01:45:49,972   /tmp/pip-build-env-z0jkw_gt/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-03-27T01:45:49,972   !!

2026-03-27T01:45:49,973           ********************************************************************************
2026-03-27T01:45:49,974           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-03-27T01:45:49,975           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2026-03-27T01:45:49,976           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-03-27T01:45:49,976           ********************************************************************************

2026-03-27T01:45:49,977   !!
2026-03-27T01:45:49,978     self._finalize_license_expression()
2026-03-27T01:45:49,978   running egg_info
2026-03-27T01:45:49,981   writing scipion_em_tomo3d.egg-info/PKG-INFO
2026-03-27T01:45:49,985   writing dependency_links to scipion_em_tomo3d.egg-info/dependency_links.txt
2026-03-27T01:45:49,986   writing entry points to scipion_em_tomo3d.egg-info/entry_points.txt
2026-03-27T01:45:49,988   writing requirements to scipion_em_tomo3d.egg-info/requires.txt
2026-03-27T01:45:49,989   writing top-level names to scipion_em_tomo3d.egg-info/top_level.txt
2026-03-27T01:45:50,011   reading manifest file 'scipion_em_tomo3d.egg-info/SOURCES.txt'
2026-03-27T01:45:50,014   reading manifest template 'MANIFEST.in'
2026-03-27T01:45:50,015   warning: manifest_maker: MANIFEST.in, line 2: unknown action 'inlcude'

2026-03-27T01:45:50,017   adding license file 'LICENSE'
2026-03-27T01:45:50,019   writing manifest file 'scipion_em_tomo3d.egg-info/SOURCES.txt'
2026-03-27T01:45:50,117   Getting requirements to build wheel: finished with status 'done'
2026-03-27T01:45:50,120   Created temporary directory: /tmp/pip-modern-metadata-sd25dmnn
2026-03-27T01:45:50,123   Preparing metadata (pyproject.toml): started
2026-03-27T01:45:50,124   Running command Preparing metadata (pyproject.toml)
2026-03-27T01:45:50,686   No `packages` or `py_modules` configuration, performing automatic discovery.
2026-03-27T01:45:50,686   `flat-layout` detected -- analysing .
2026-03-27T01:45:50,701   discovered packages -- ['tomo3d', 'tomo3d.tests', 'tomo3d.protocols']
2026-03-27T01:45:50,706   /tmp/pip-build-env-z0jkw_gt/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2026-03-27T01:45:50,707   !!

2026-03-27T01:45:50,708           ********************************************************************************
2026-03-27T01:45:50,709           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).

2026-03-27T01:45:50,710           By 2027-Feb-18, you need to update your project and remove deprecated calls
2026-03-27T01:45:50,711           or your builds will no longer be supported.

2026-03-27T01:45:50,712           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-03-27T01:45:50,713           ********************************************************************************

2026-03-27T01:45:50,714   !!
2026-03-27T01:45:50,715     corresp(dist, value, root_dir)
2026-03-27T01:45:50,783   /tmp/pip-build-env-z0jkw_gt/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-03-27T01:45:50,784   !!

2026-03-27T01:45:50,786           ********************************************************************************
2026-03-27T01:45:50,786           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-03-27T01:45:50,787           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2026-03-27T01:45:50,788           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-03-27T01:45:50,789           ********************************************************************************

2026-03-27T01:45:50,790   !!
2026-03-27T01:45:50,790     dist._finalize_license_expression()
2026-03-27T01:45:50,791   /tmp/pip-build-env-z0jkw_gt/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-03-27T01:45:50,791   !!

2026-03-27T01:45:50,792           ********************************************************************************
2026-03-27T01:45:50,793           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-03-27T01:45:50,794           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2026-03-27T01:45:50,795           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-03-27T01:45:50,795           ********************************************************************************

2026-03-27T01:45:50,796   !!
2026-03-27T01:45:50,797     self._finalize_license_expression()
2026-03-27T01:45:50,797   running dist_info
2026-03-27T01:45:50,806   creating /tmp/pip-modern-metadata-sd25dmnn/scipion_em_tomo3d.egg-info
2026-03-27T01:45:50,807   writing /tmp/pip-modern-metadata-sd25dmnn/scipion_em_tomo3d.egg-info/PKG-INFO
2026-03-27T01:45:50,811   writing dependency_links to /tmp/pip-modern-metadata-sd25dmnn/scipion_em_tomo3d.egg-info/dependency_links.txt
2026-03-27T01:45:50,812   writing entry points to /tmp/pip-modern-metadata-sd25dmnn/scipion_em_tomo3d.egg-info/entry_points.txt
2026-03-27T01:45:50,814   writing requirements to /tmp/pip-modern-metadata-sd25dmnn/scipion_em_tomo3d.egg-info/requires.txt
2026-03-27T01:45:50,815   writing top-level names to /tmp/pip-modern-metadata-sd25dmnn/scipion_em_tomo3d.egg-info/top_level.txt
2026-03-27T01:45:50,816   writing manifest file '/tmp/pip-modern-metadata-sd25dmnn/scipion_em_tomo3d.egg-info/SOURCES.txt'
2026-03-27T01:45:50,836   reading manifest file '/tmp/pip-modern-metadata-sd25dmnn/scipion_em_tomo3d.egg-info/SOURCES.txt'
2026-03-27T01:45:50,838   reading manifest template 'MANIFEST.in'
2026-03-27T01:45:50,839   warning: manifest_maker: MANIFEST.in, line 2: unknown action 'inlcude'

2026-03-27T01:45:50,840   adding license file 'LICENSE'
2026-03-27T01:45:50,843   writing manifest file '/tmp/pip-modern-metadata-sd25dmnn/scipion_em_tomo3d.egg-info/SOURCES.txt'
2026-03-27T01:45:50,844   creating '/tmp/pip-modern-metadata-sd25dmnn/scipion_em_tomo3d-3.4.2.dist-info'
2026-03-27T01:45:50,978   Preparing metadata (pyproject.toml): finished with status 'done'
2026-03-27T01:45:50,983   Source in /tmp/pip-wheel-_x9uxtek/scipion-em-tomo3d_69f21d60b4fd43a1ae783896b9446986 has version 3.4.2, which satisfies requirement scipion-em-tomo3d==3.4.2 from https://files.pythonhosted.org/packages/b2/d8/0e9cda31d4b77e5d894d82d4be22f17b3990a597f7de600b2e9e39ea4636/scipion_em_tomo3d-3.4.2.tar.gz
2026-03-27T01:45:50,984   Removed scipion-em-tomo3d==3.4.2 from https://files.pythonhosted.org/packages/b2/d8/0e9cda31d4b77e5d894d82d4be22f17b3990a597f7de600b2e9e39ea4636/scipion_em_tomo3d-3.4.2.tar.gz from build tracker '/tmp/pip-build-tracker-mvfz97hh'
2026-03-27T01:45:50,990 Created temporary directory: /tmp/pip-unpack-3_53wuos
2026-03-27T01:45:50,991 Building wheels for collected packages: scipion-em-tomo3d
2026-03-27T01:45:50,995   Created temporary directory: /tmp/pip-wheel-0v5izb7w
2026-03-27T01:45:50,996   Destination directory: /tmp/pip-wheel-0v5izb7w
2026-03-27T01:45:50,998   Building wheel for scipion-em-tomo3d (pyproject.toml): started
2026-03-27T01:45:50,999   Running command Building wheel for scipion-em-tomo3d (pyproject.toml)
2026-03-27T01:45:51,570   No `packages` or `py_modules` configuration, performing automatic discovery.
2026-03-27T01:45:51,570   `flat-layout` detected -- analysing .
2026-03-27T01:45:51,585   discovered packages -- ['tomo3d', 'tomo3d.tests', 'tomo3d.protocols']
2026-03-27T01:45:51,590   /tmp/pip-build-env-z0jkw_gt/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2026-03-27T01:45:51,591   !!

2026-03-27T01:45:51,592           ********************************************************************************
2026-03-27T01:45:51,592           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).

2026-03-27T01:45:51,593           By 2027-Feb-18, you need to update your project and remove deprecated calls
2026-03-27T01:45:51,594           or your builds will no longer be supported.

2026-03-27T01:45:51,595           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-03-27T01:45:51,595           ********************************************************************************

2026-03-27T01:45:51,596   !!
2026-03-27T01:45:51,596     corresp(dist, value, root_dir)
2026-03-27T01:45:51,658   /tmp/pip-build-env-z0jkw_gt/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-03-27T01:45:51,659   !!

2026-03-27T01:45:51,660           ********************************************************************************
2026-03-27T01:45:51,661           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-03-27T01:45:51,662           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2026-03-27T01:45:51,663           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-03-27T01:45:51,663           ********************************************************************************

2026-03-27T01:45:51,664   !!
2026-03-27T01:45:51,665     dist._finalize_license_expression()
2026-03-27T01:45:51,666   /tmp/pip-build-env-z0jkw_gt/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-03-27T01:45:51,666   !!

2026-03-27T01:45:51,668           ********************************************************************************
2026-03-27T01:45:51,668           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-03-27T01:45:51,669           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2026-03-27T01:45:51,671           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-03-27T01:45:51,671           ********************************************************************************

2026-03-27T01:45:51,672   !!
2026-03-27T01:45:51,673     self._finalize_license_expression()
2026-03-27T01:45:51,673   running bdist_wheel
2026-03-27T01:45:51,687   running build
2026-03-27T01:45:51,687   running build_py
2026-03-27T01:45:51,694   creating build/lib/tomo3d
2026-03-27T01:45:51,696   copying tomo3d/constants.py -> build/lib/tomo3d
2026-03-27T01:45:51,698   copying tomo3d/bibtex.py -> build/lib/tomo3d
2026-03-27T01:45:51,700   copying tomo3d/__init__.py -> build/lib/tomo3d
2026-03-27T01:45:51,702   creating build/lib/tomo3d/tests
2026-03-27T01:45:51,704   copying tomo3d/tests/test_protocol_reconstruct_tomogram.py -> build/lib/tomo3d/tests
2026-03-27T01:45:51,706   copying tomo3d/tests/test_protocol_denoise_tomogram.py -> build/lib/tomo3d/tests
2026-03-27T01:45:51,708   copying tomo3d/tests/_test_protocol_alignts.py -> build/lib/tomo3d/tests
2026-03-27T01:45:51,711   copying tomo3d/tests/__init__.py -> build/lib/tomo3d/tests
2026-03-27T01:45:51,713   creating build/lib/tomo3d/protocols
2026-03-27T01:45:51,714   copying tomo3d/protocols/protocol_reconstruct_tomogram.py -> build/lib/tomo3d/protocols
2026-03-27T01:45:51,717   copying tomo3d/protocols/protocol_base.py -> build/lib/tomo3d/protocols
2026-03-27T01:45:51,719   copying tomo3d/protocols/protocol_denoise_tomogram.py -> build/lib/tomo3d/protocols
2026-03-27T01:45:51,722   copying tomo3d/protocols/protocol_align_ts.py -> build/lib/tomo3d/protocols
2026-03-27T01:45:51,724   copying tomo3d/protocols/protocol_motion_compensation.py -> build/lib/tomo3d/protocols
2026-03-27T01:45:51,726   copying tomo3d/protocols/__init__.py -> build/lib/tomo3d/protocols
2026-03-27T01:45:51,728   running egg_info
2026-03-27T01:45:51,737   writing scipion_em_tomo3d.egg-info/PKG-INFO
2026-03-27T01:45:51,740   writing dependency_links to scipion_em_tomo3d.egg-info/dependency_links.txt
2026-03-27T01:45:51,741   writing entry points to scipion_em_tomo3d.egg-info/entry_points.txt
2026-03-27T01:45:51,743   writing requirements to scipion_em_tomo3d.egg-info/requires.txt
2026-03-27T01:45:51,744   writing top-level names to scipion_em_tomo3d.egg-info/top_level.txt
2026-03-27T01:45:51,754   reading manifest file 'scipion_em_tomo3d.egg-info/SOURCES.txt'
2026-03-27T01:45:51,757   reading manifest template 'MANIFEST.in'
2026-03-27T01:45:51,759   warning: manifest_maker: MANIFEST.in, line 2: unknown action 'inlcude'

2026-03-27T01:45:51,760   adding license file 'LICENSE'
2026-03-27T01:45:51,763   writing manifest file 'scipion_em_tomo3d.egg-info/SOURCES.txt'
2026-03-27T01:45:51,766   copying tomo3d/protocols.conf -> build/lib/tomo3d
2026-03-27T01:45:51,778   installing to build/bdist.linux-armv7l/wheel
2026-03-27T01:45:51,779   running install
2026-03-27T01:45:51,802   running install_lib
2026-03-27T01:45:51,808   creating build/bdist.linux-armv7l/wheel
2026-03-27T01:45:51,810   creating build/bdist.linux-armv7l/wheel/tomo3d
2026-03-27T01:45:51,811   copying build/lib/tomo3d/protocols.conf -> build/bdist.linux-armv7l/wheel/./tomo3d
2026-03-27T01:45:51,813   copying build/lib/tomo3d/constants.py -> build/bdist.linux-armv7l/wheel/./tomo3d
2026-03-27T01:45:51,815   creating build/bdist.linux-armv7l/wheel/tomo3d/tests
2026-03-27T01:45:51,816   copying build/lib/tomo3d/tests/test_protocol_reconstruct_tomogram.py -> build/bdist.linux-armv7l/wheel/./tomo3d/tests
2026-03-27T01:45:51,819   copying build/lib/tomo3d/tests/test_protocol_denoise_tomogram.py -> build/bdist.linux-armv7l/wheel/./tomo3d/tests
2026-03-27T01:45:51,821   copying build/lib/tomo3d/tests/_test_protocol_alignts.py -> build/bdist.linux-armv7l/wheel/./tomo3d/tests
2026-03-27T01:45:51,823   copying build/lib/tomo3d/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tomo3d/tests
2026-03-27T01:45:51,825   creating build/bdist.linux-armv7l/wheel/tomo3d/protocols
2026-03-27T01:45:51,826   copying build/lib/tomo3d/protocols/protocol_reconstruct_tomogram.py -> build/bdist.linux-armv7l/wheel/./tomo3d/protocols
2026-03-27T01:45:51,829   copying build/lib/tomo3d/protocols/protocol_base.py -> build/bdist.linux-armv7l/wheel/./tomo3d/protocols
2026-03-27T01:45:51,831   copying build/lib/tomo3d/protocols/protocol_denoise_tomogram.py -> build/bdist.linux-armv7l/wheel/./tomo3d/protocols
2026-03-27T01:45:51,834   copying build/lib/tomo3d/protocols/protocol_align_ts.py -> build/bdist.linux-armv7l/wheel/./tomo3d/protocols
2026-03-27T01:45:51,836   copying build/lib/tomo3d/protocols/protocol_motion_compensation.py -> build/bdist.linux-armv7l/wheel/./tomo3d/protocols
2026-03-27T01:45:51,838   copying build/lib/tomo3d/protocols/__init__.py -> build/bdist.linux-armv7l/wheel/./tomo3d/protocols
2026-03-27T01:45:51,840   copying build/lib/tomo3d/bibtex.py -> build/bdist.linux-armv7l/wheel/./tomo3d
2026-03-27T01:45:51,842   copying build/lib/tomo3d/__init__.py -> build/bdist.linux-armv7l/wheel/./tomo3d
2026-03-27T01:45:51,844   running install_egg_info
2026-03-27T01:45:51,849   Copying scipion_em_tomo3d.egg-info to build/bdist.linux-armv7l/wheel/./scipion_em_tomo3d-3.4.2-py3.11.egg-info
2026-03-27T01:45:51,859   running install_scripts
2026-03-27T01:45:51,872   creating build/bdist.linux-armv7l/wheel/scipion_em_tomo3d-3.4.2.dist-info/WHEEL
2026-03-27T01:45:51,874   creating '/tmp/pip-wheel-0v5izb7w/.tmp-fmxphfv5/scipion_em_tomo3d-3.4.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-03-27T01:45:51,882   adding 'scipion_em_tomo3d-3.4.2.dist-info/licenses/LICENSE'
2026-03-27T01:45:51,885   adding 'tomo3d/__init__.py'
2026-03-27T01:45:51,886   adding 'tomo3d/bibtex.py'
2026-03-27T01:45:51,887   adding 'tomo3d/constants.py'
2026-03-27T01:45:51,889   adding 'tomo3d/protocols.conf'
2026-03-27T01:45:51,890   adding 'tomo3d/protocols/__init__.py'
2026-03-27T01:45:51,892   adding 'tomo3d/protocols/protocol_align_ts.py'
2026-03-27T01:45:51,894   adding 'tomo3d/protocols/protocol_base.py'
2026-03-27T01:45:51,897   adding 'tomo3d/protocols/protocol_denoise_tomogram.py'
2026-03-27T01:45:51,898   adding 'tomo3d/protocols/protocol_motion_compensation.py'
2026-03-27T01:45:51,901   adding 'tomo3d/protocols/protocol_reconstruct_tomogram.py'
2026-03-27T01:45:51,903   adding 'tomo3d/tests/__init__.py'
2026-03-27T01:45:51,904   adding 'tomo3d/tests/_test_protocol_alignts.py'
2026-03-27T01:45:51,906   adding 'tomo3d/tests/test_protocol_denoise_tomogram.py'
2026-03-27T01:45:51,907   adding 'tomo3d/tests/test_protocol_reconstruct_tomogram.py'
2026-03-27T01:45:51,909   adding 'scipion_em_tomo3d-3.4.2.dist-info/METADATA'
2026-03-27T01:45:51,910   adding 'scipion_em_tomo3d-3.4.2.dist-info/WHEEL'
2026-03-27T01:45:51,910   adding 'scipion_em_tomo3d-3.4.2.dist-info/entry_points.txt'
2026-03-27T01:45:51,911   adding 'scipion_em_tomo3d-3.4.2.dist-info/top_level.txt'
2026-03-27T01:45:51,912   adding 'scipion_em_tomo3d-3.4.2.dist-info/RECORD'
2026-03-27T01:45:51,914   removing build/bdist.linux-armv7l/wheel
2026-03-27T01:45:52,018   Building wheel for scipion-em-tomo3d (pyproject.toml): finished with status 'done'
2026-03-27T01:45:52,024   Created wheel for scipion-em-tomo3d: filename=scipion_em_tomo3d-3.4.2-py3-none-any.whl size=46276 sha256=61a6fe5af36403904b15f20b5eaeb5b29a0e6b59be8c418b310ab80aa037fd47
2026-03-27T01:45:52,025   Stored in directory: /tmp/pip-ephem-wheel-cache-lykd8nz0/wheels/f5/46/29/b2324163bf9d3bd8530197c4ee8dfa6a45d8fd0d8a37cb9b37
2026-03-27T01:45:52,037 Successfully built scipion-em-tomo3d
2026-03-27T01:45:52,041 Removed build tracker: '/tmp/pip-build-tracker-mvfz97hh'