2025-11-04T23:39:05,135 Created temporary directory: /tmp/pip-ephem-wheel-cache-mocgfkqr 2025-11-04T23:39:05,136 Created temporary directory: /tmp/pip-build-tracker-ibozo9pe 2025-11-04T23:39:05,137 Initialized build tracking at /tmp/pip-build-tracker-ibozo9pe 2025-11-04T23:39:05,137 Created build tracker: /tmp/pip-build-tracker-ibozo9pe 2025-11-04T23:39:05,138 Entered build tracker: /tmp/pip-build-tracker-ibozo9pe 2025-11-04T23:39:05,139 Created temporary directory: /tmp/pip-wheel-8zbo150j 2025-11-04T23:39:05,142 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 2025-11-04T23:39:05,144 Created temporary directory: /tmp/pip-ephem-wheel-cache-qv9vprte 2025-11-04T23:39:05,166 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-11-04T23:39:05,169 2 location(s) to search for versions of satellome: 2025-11-04T23:39:05,169 * https://pypi.org/simple/satellome/ 2025-11-04T23:39:05,169 * https://www.piwheels.org/simple/satellome/ 2025-11-04T23:39:05,170 Fetching project page and analyzing links: https://pypi.org/simple/satellome/ 2025-11-04T23:39:05,171 Getting page https://pypi.org/simple/satellome/ 2025-11-04T23:39:05,172 Found index url https://pypi.org/simple 2025-11-04T23:39:05,379 Fetched page https://pypi.org/simple/satellome/ as application/vnd.pypi.simple.v1+json 2025-11-04T23:39:05,382 Skipping link: No binaries permitted for satellome: https://files.pythonhosted.org/packages/56/14/541d7390f45c1e137dfe63ba36a4d0f6ba5a3c274182429f6adf844b79f7/satellome-1.0.0-py3-none-any.whl (from https://pypi.org/simple/satellome/) (requires-python:>=3.6) 2025-11-04T23:39:05,383 Found link https://files.pythonhosted.org/packages/dd/ff/a62902b688812293c147782e060a0d720c161c65385cc933ebd8556244b2/satellome-1.0.0.tar.gz (from https://pypi.org/simple/satellome/) (requires-python:>=3.6), version: 1.0.0 2025-11-04T23:39:05,383 Skipping link: No binaries permitted for satellome: https://files.pythonhosted.org/packages/c0/05/6afb7dd2a76143be0563f69423d99c6e5e4a4d61d18e27dfb80725810182/satellome-1.1.0-py3-none-any.whl (from https://pypi.org/simple/satellome/) (requires-python:>=3.6) 2025-11-04T23:39:05,384 Found link https://files.pythonhosted.org/packages/aa/c1/b56041f7c1b496f518d61b261bc5e8234e91439bcfbe21292d631816d81d/satellome-1.1.0.tar.gz (from https://pypi.org/simple/satellome/) (requires-python:>=3.6), version: 1.1.0 2025-11-04T23:39:05,385 Skipping link: No binaries permitted for satellome: https://files.pythonhosted.org/packages/2b/73/8d2cb0f2bf1a93369f80950bb0b0f7deb522ae974a4cf8cc9e5268691b8b/satellome-1.4.0-py3-none-any.whl (from https://pypi.org/simple/satellome/) (requires-python:>=3.6) 2025-11-04T23:39:05,386 Found link https://files.pythonhosted.org/packages/f2/1b/dfaf33c1e95a45d20d10660ea42d0b97d17e779c37e1200e72a6453118db/satellome-1.4.0.tar.gz (from https://pypi.org/simple/satellome/) (requires-python:>=3.6), version: 1.4.0 2025-11-04T23:39:05,387 Skipping link: No binaries permitted for satellome: https://files.pythonhosted.org/packages/80/b3/1c0ebc1122dae9e14925ccd2021b39b1543396f48c26f81a2c1cd4c2054c/satellome-1.4.1-py3-none-any.whl (from https://pypi.org/simple/satellome/) (requires-python:>=3.6) 2025-11-04T23:39:05,388 Found link https://files.pythonhosted.org/packages/b8/c1/477985e4026bfbe829c1f73a23a4d2b21ec59b5afa9bc9cd1db19b82cd1d/satellome-1.4.1.tar.gz (from https://pypi.org/simple/satellome/) (requires-python:>=3.6), version: 1.4.1 2025-11-04T23:39:05,389 Fetching project page and analyzing links: https://www.piwheels.org/simple/satellome/ 2025-11-04T23:39:05,390 Getting page https://www.piwheels.org/simple/satellome/ 2025-11-04T23:39:05,391 Found index url https://www.piwheels.org/simple 2025-11-04T23:39:05,580 Fetched page https://www.piwheels.org/simple/satellome/ as text/html 2025-11-04T23:39:05,582 Skipping link: No binaries permitted for satellome: https://www.piwheels.org/simple/satellome/satellome-1.4.0-py3-none-any.whl#sha256=05d11035fa4da917d4b9105c447fc715f1e3160458cbc4808be2c44b8942c054 (from https://www.piwheels.org/simple/satellome/) (requires-python:>=3.6) 2025-11-04T23:39:05,583 Skipping link: No binaries permitted for satellome: https://www.piwheels.org/simple/satellome/satellome-1.1.0-py3-none-any.whl#sha256=a703c32811c07247cf558d4a3c285475183bae770a520b080e73d1d8df0d2a35 (from https://www.piwheels.org/simple/satellome/) (requires-python:>=3.6) 2025-11-04T23:39:05,583 Skipping link: No binaries permitted for satellome: https://www.piwheels.org/simple/satellome/satellome-1.0.0-py3-none-any.whl#sha256=eaea8aed0e4d509e821171d996f5eecb178d63fd22d32922809070159b7d9f52 (from https://www.piwheels.org/simple/satellome/) (requires-python:>=3.6) 2025-11-04T23:39:05,584 Skipping link: not a file: https://www.piwheels.org/simple/satellome/ 2025-11-04T23:39:05,584 Skipping link: not a file: https://pypi.org/simple/satellome/ 2025-11-04T23:39:05,603 Given no hashes to check 1 links for project 'satellome': discarding no candidates 2025-11-04T23:39:05,621 Collecting satellome==1.4.1 2025-11-04T23:39:05,623 Created temporary directory: /tmp/pip-unpack-pyxcfts9 2025-11-04T23:39:05,828 Downloading satellome-1.4.1.tar.gz (124 kB) 2025-11-04T23:39:06,087 Added satellome==1.4.1 from https://files.pythonhosted.org/packages/b8/c1/477985e4026bfbe829c1f73a23a4d2b21ec59b5afa9bc9cd1db19b82cd1d/satellome-1.4.1.tar.gz to build tracker '/tmp/pip-build-tracker-ibozo9pe' 2025-11-04T23:39:06,095 Created temporary directory: /tmp/pip-build-env-a914d6pp 2025-11-04T23:39:06,099 Installing build dependencies: started 2025-11-04T23:39:06,100 Running command pip subprocess to install build dependencies 2025-11-04T23:39:07,239 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2025-11-04T23:39:07,855 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 2025-11-04T23:39:07,880 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-11-04T23:39:09,649 Collecting setuptools>=45 2025-11-04T23:39:09,744 Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB) 2025-11-04T23:39:10,021 Collecting wheel 2025-11-04T23:39:10,040 Using cached https://www.piwheels.org/simple/wheel/wheel-0.45.1-py3-none-any.whl (72 kB) 2025-11-04T23:39:10,375 Collecting setuptools_scm[toml]>=6.2 2025-11-04T23:39:10,392 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-9.2.2-py3-none-any.whl (62 kB) 2025-11-04T23:39:10,588 Collecting packaging>=20 2025-11-04T23:39:10,604 Using cached https://www.piwheels.org/simple/packaging/packaging-25.0-py3-none-any.whl (66 kB) 2025-11-04T23:39:13,521 Installing collected packages: wheel, setuptools, packaging, setuptools_scm 2025-11-04T23:39:13,756 Creating /tmp/pip-build-env-a914d6pp/overlay/local/bin 2025-11-04T23:39:13,759 changing mode of /tmp/pip-build-env-a914d6pp/overlay/local/bin/wheel to 755 2025-11-04T23:39:17,823 changing mode of /tmp/pip-build-env-a914d6pp/overlay/local/bin/setuptools-scm to 755 2025-11-04T23:39:17,853 Successfully installed packaging-25.0 setuptools-80.9.0 setuptools_scm-9.2.2 wheel-0.45.1 2025-11-04T23:39:18,144 Installing build dependencies: finished with status 'done' 2025-11-04T23:39:18,151 Getting requirements to build wheel: started 2025-11-04T23:39:18,152 Running command Getting requirements to build wheel 2025-11-04T23:39:18,824 toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section 2025-11-04T23:39:18,862 /tmp/pip-build-env-a914d6pp/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2025-11-04T23:39:18,863 !! 2025-11-04T23:39:18,864 ******************************************************************************** 2025-11-04T23:39:18,864 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). 2025-11-04T23:39:18,865 By 2026-Feb-18, you need to update your project and remove deprecated calls 2025-11-04T23:39:18,865 or your builds will no longer be supported. 2025-11-04T23:39:18,866 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-11-04T23:39:18,867 ******************************************************************************** 2025-11-04T23:39:18,868 !! 2025-11-04T23:39:18,868 corresp(dist, value, root_dir) 2025-11-04T23:39:18,869 /tmp/pip-build-env-a914d6pp/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2025-11-04T23:39:18,869 corresp(dist, value, root_dir) 2025-11-04T23:39:18,962 running egg_info 2025-11-04T23:39:18,971 writing src/satellome.egg-info/PKG-INFO 2025-11-04T23:39:18,976 writing dependency_links to src/satellome.egg-info/dependency_links.txt 2025-11-04T23:39:18,978 writing entry points to src/satellome.egg-info/entry_points.txt 2025-11-04T23:39:18,980 writing requirements to src/satellome.egg-info/requires.txt 2025-11-04T23:39:18,981 writing top-level names to src/satellome.egg-info/top_level.txt 2025-11-04T23:39:19,043 listing git files failed - pretending there aren't any 2025-11-04T23:39:19,051 reading manifest file 'src/satellome.egg-info/SOURCES.txt' 2025-11-04T23:39:19,063 reading manifest template 'MANIFEST.in' 2025-11-04T23:39:19,102 warning: no files found matching '*.yml' under directory 'src/satellome' 2025-11-04T23:39:19,122 warning: no previously-included files matching '__pycache__' found under directory '*' 2025-11-04T23:39:19,123 warning: no previously-included files matching '*.py[co]' found under directory '*' 2025-11-04T23:39:19,124 warning: no previously-included files matching '.DS_Store' found under directory '*' 2025-11-04T23:39:19,125 adding license file 'LICENSE' 2025-11-04T23:39:19,131 writing manifest file 'src/satellome.egg-info/SOURCES.txt' 2025-11-04T23:39:19,217 Getting requirements to build wheel: finished with status 'done' 2025-11-04T23:39:19,220 Created temporary directory: /tmp/pip-modern-metadata-1k8irc8y 2025-11-04T23:39:19,223 Preparing metadata (pyproject.toml): started 2025-11-04T23:39:19,224 Running command Preparing metadata (pyproject.toml) 2025-11-04T23:39:19,847 toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section 2025-11-04T23:39:19,884 /tmp/pip-build-env-a914d6pp/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2025-11-04T23:39:19,885 !! 2025-11-04T23:39:19,886 ******************************************************************************** 2025-11-04T23:39:19,887 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). 2025-11-04T23:39:19,888 By 2026-Feb-18, you need to update your project and remove deprecated calls 2025-11-04T23:39:19,889 or your builds will no longer be supported. 2025-11-04T23:39:19,890 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-11-04T23:39:19,890 ******************************************************************************** 2025-11-04T23:39:19,892 !! 2025-11-04T23:39:19,893 corresp(dist, value, root_dir) 2025-11-04T23:39:19,893 /tmp/pip-build-env-a914d6pp/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2025-11-04T23:39:19,894 corresp(dist, value, root_dir) 2025-11-04T23:39:19,982 running dist_info 2025-11-04T23:39:19,998 creating /tmp/pip-modern-metadata-1k8irc8y/satellome.egg-info 2025-11-04T23:39:19,999 writing /tmp/pip-modern-metadata-1k8irc8y/satellome.egg-info/PKG-INFO 2025-11-04T23:39:20,005 writing dependency_links to /tmp/pip-modern-metadata-1k8irc8y/satellome.egg-info/dependency_links.txt 2025-11-04T23:39:20,007 writing entry points to /tmp/pip-modern-metadata-1k8irc8y/satellome.egg-info/entry_points.txt 2025-11-04T23:39:20,009 writing requirements to /tmp/pip-modern-metadata-1k8irc8y/satellome.egg-info/requires.txt 2025-11-04T23:39:20,010 writing top-level names to /tmp/pip-modern-metadata-1k8irc8y/satellome.egg-info/top_level.txt 2025-11-04T23:39:20,011 writing manifest file '/tmp/pip-modern-metadata-1k8irc8y/satellome.egg-info/SOURCES.txt' 2025-11-04T23:39:20,068 listing git files failed - pretending there aren't any 2025-11-04T23:39:20,074 reading manifest file '/tmp/pip-modern-metadata-1k8irc8y/satellome.egg-info/SOURCES.txt' 2025-11-04T23:39:20,077 reading manifest template 'MANIFEST.in' 2025-11-04T23:39:20,118 warning: no files found matching '*.yml' under directory 'src/satellome' 2025-11-04T23:39:20,136 warning: no previously-included files matching '__pycache__' found under directory '*' 2025-11-04T23:39:20,137 warning: no previously-included files matching '*.py[co]' found under directory '*' 2025-11-04T23:39:20,138 warning: no previously-included files matching '.DS_Store' found under directory '*' 2025-11-04T23:39:20,138 adding license file 'LICENSE' 2025-11-04T23:39:20,143 writing manifest file '/tmp/pip-modern-metadata-1k8irc8y/satellome.egg-info/SOURCES.txt' 2025-11-04T23:39:20,144 creating '/tmp/pip-modern-metadata-1k8irc8y/satellome-1.4.1.dist-info' 2025-11-04T23:39:20,262 Preparing metadata (pyproject.toml): finished with status 'done' 2025-11-04T23:39:20,268 Source in /tmp/pip-wheel-8zbo150j/satellome_0e1235e6db674adfaad3c4331ee9e90f has version 1.4.1, which satisfies requirement satellome==1.4.1 from https://files.pythonhosted.org/packages/b8/c1/477985e4026bfbe829c1f73a23a4d2b21ec59b5afa9bc9cd1db19b82cd1d/satellome-1.4.1.tar.gz 2025-11-04T23:39:20,269 Removed satellome==1.4.1 from https://files.pythonhosted.org/packages/b8/c1/477985e4026bfbe829c1f73a23a4d2b21ec59b5afa9bc9cd1db19b82cd1d/satellome-1.4.1.tar.gz from build tracker '/tmp/pip-build-tracker-ibozo9pe' 2025-11-04T23:39:20,277 Created temporary directory: /tmp/pip-unpack-1c01ybpr 2025-11-04T23:39:20,277 Building wheels for collected packages: satellome 2025-11-04T23:39:20,282 Created temporary directory: /tmp/pip-wheel-3yi3eu8w 2025-11-04T23:39:20,283 Destination directory: /tmp/pip-wheel-3yi3eu8w 2025-11-04T23:39:20,285 Building wheel for satellome (pyproject.toml): started 2025-11-04T23:39:20,286 Running command Building wheel for satellome (pyproject.toml) 2025-11-04T23:39:20,890 toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section 2025-11-04T23:39:20,925 /tmp/pip-build-env-a914d6pp/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2025-11-04T23:39:20,925 !! 2025-11-04T23:39:20,927 ******************************************************************************** 2025-11-04T23:39:20,927 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). 2025-11-04T23:39:20,928 By 2026-Feb-18, you need to update your project and remove deprecated calls 2025-11-04T23:39:20,929 or your builds will no longer be supported. 2025-11-04T23:39:20,930 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-11-04T23:39:20,931 ******************************************************************************** 2025-11-04T23:39:20,931 !! 2025-11-04T23:39:20,932 corresp(dist, value, root_dir) 2025-11-04T23:39:20,932 /tmp/pip-build-env-a914d6pp/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2025-11-04T23:39:20,933 corresp(dist, value, root_dir) 2025-11-04T23:39:21,006 running bdist_wheel 2025-11-04T23:39:21,035 running build 2025-11-04T23:39:21,035 running build_py 2025-11-04T23:39:21,044 creating build/lib/satellome 2025-11-04T23:39:21,046 copying src/satellome/install_command.py -> build/lib/satellome 2025-11-04T23:39:21,049 copying src/satellome/constants.py -> build/lib/satellome 2025-11-04T23:39:21,051 copying src/satellome/redraw.py -> build/lib/satellome 2025-11-04T23:39:21,054 copying src/satellome/trc_set_tr_names_color.py -> build/lib/satellome 2025-11-04T23:39:21,056 copying src/satellome/__init__.py -> build/lib/satellome 2025-11-04T23:39:21,058 copying src/satellome/main.py -> build/lib/satellome 2025-11-04T23:39:21,061 creating build/lib/satellome/core_functions 2025-11-04T23:39:21,062 copying src/satellome/core_functions/trf_embedings.py -> build/lib/satellome/core_functions 2025-11-04T23:39:21,064 copying src/satellome/core_functions/classification_micro.py -> build/lib/satellome/core_functions 2025-11-04T23:39:21,067 copying src/satellome/core_functions/settings.py -> build/lib/satellome/core_functions 2025-11-04T23:39:21,069 copying src/satellome/core_functions/trf_drawing.py -> build/lib/satellome/core_functions 2025-11-04T23:39:21,071 copying src/satellome/core_functions/__init__.py -> build/lib/satellome/core_functions 2025-11-04T23:39:21,073 copying src/satellome/core_functions/trf_clusters.py -> build/lib/satellome/core_functions 2025-11-04T23:39:21,077 creating build/lib/satellome/core_functions/io 2025-11-04T23:39:21,078 copying src/satellome/core_functions/io/file_system.py -> build/lib/satellome/core_functions/io 2025-11-04T23:39:21,080 copying src/satellome/core_functions/io/abstract_reader.py -> build/lib/satellome/core_functions/io 2025-11-04T23:39:21,083 copying src/satellome/core_functions/io/tab_file.py -> build/lib/satellome/core_functions/io 2025-11-04T23:39:21,086 copying src/satellome/core_functions/io/fasta_file.py -> build/lib/satellome/core_functions/io 2025-11-04T23:39:21,088 copying src/satellome/core_functions/io/tr_file.py -> build/lib/satellome/core_functions/io 2025-11-04T23:39:21,090 copying src/satellome/core_functions/io/block_file.py -> build/lib/satellome/core_functions/io 2025-11-04T23:39:21,092 copying src/satellome/core_functions/io/__init__.py -> build/lib/satellome/core_functions/io 2025-11-04T23:39:21,094 copying src/satellome/core_functions/io/gff_file.py -> build/lib/satellome/core_functions/io 2025-11-04T23:39:21,096 copying src/satellome/core_functions/io/trf_file.py -> build/lib/satellome/core_functions/io 2025-11-04T23:39:21,099 creating build/lib/satellome/core_functions/models 2025-11-04T23:39:21,101 copying src/satellome/core_functions/models/abstract_model.py -> build/lib/satellome/core_functions/models 2025-11-04T23:39:21,103 copying src/satellome/core_functions/models/gff3_model.py -> build/lib/satellome/core_functions/models 2025-11-04T23:39:21,106 copying src/satellome/core_functions/models/__init__.py -> build/lib/satellome/core_functions/models 2025-11-04T23:39:21,107 copying src/satellome/core_functions/models/trf_model.py -> build/lib/satellome/core_functions/models 2025-11-04T23:39:21,111 creating build/lib/satellome/core_functions/tools 2025-11-04T23:39:21,112 copying src/satellome/core_functions/tools/gene_intersect.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:39:21,115 copying src/satellome/core_functions/tools/parsers.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:39:21,117 copying src/satellome/core_functions/tools/processing.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:39:21,119 copying src/satellome/core_functions/tools/ncbi.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:39:21,121 copying src/satellome/core_functions/tools/trf_tools.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:39:21,124 copying src/satellome/core_functions/tools/clusterization.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:39:21,126 copying src/satellome/core_functions/tools/reports.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:39:21,128 copying src/satellome/core_functions/tools/distances.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:39:21,130 copying src/satellome/core_functions/tools/statistics.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:39:21,132 copying src/satellome/core_functions/tools/__init__.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:39:21,133 copying src/satellome/core_functions/tools/kmer_splitting.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:39:21,136 creating build/lib/satellome/steps 2025-11-04T23:39:21,137 copying src/satellome/steps/trf_parse_raw.py -> build/lib/satellome/steps 2025-11-04T23:39:21,139 copying src/satellome/steps/__init__.py -> build/lib/satellome/steps 2025-11-04T23:39:21,141 copying src/satellome/steps/trf_draw.py -> build/lib/satellome/steps 2025-11-04T23:39:21,143 copying src/satellome/steps/trf_classify.py -> build/lib/satellome/steps 2025-11-04T23:39:21,145 copying src/satellome/steps/trf_search.py -> build/lib/satellome/steps 2025-11-04T23:39:21,147 running egg_info 2025-11-04T23:39:21,162 writing src/satellome.egg-info/PKG-INFO 2025-11-04T23:39:21,166 writing dependency_links to src/satellome.egg-info/dependency_links.txt 2025-11-04T23:39:21,167 writing entry points to src/satellome.egg-info/entry_points.txt 2025-11-04T23:39:21,168 writing requirements to src/satellome.egg-info/requires.txt 2025-11-04T23:39:21,169 writing top-level names to src/satellome.egg-info/top_level.txt 2025-11-04T23:39:21,210 listing git files failed - pretending there aren't any 2025-11-04T23:39:21,216 reading manifest file 'src/satellome.egg-info/SOURCES.txt' 2025-11-04T23:39:21,223 reading manifest template 'MANIFEST.in' 2025-11-04T23:39:21,264 warning: no files found matching '*.yml' under directory 'src/satellome' 2025-11-04T23:39:21,282 warning: no previously-included files matching '__pycache__' found under directory '*' 2025-11-04T23:39:21,283 warning: no previously-included files matching '*.py[co]' found under directory '*' 2025-11-04T23:39:21,284 warning: no previously-included files matching '.DS_Store' found under directory '*' 2025-11-04T23:39:21,285 adding license file 'LICENSE' 2025-11-04T23:39:21,290 writing manifest file 'src/satellome.egg-info/SOURCES.txt' 2025-11-04T23:39:21,293 /tmp/pip-build-env-a914d6pp/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'satellome.installers' is absent from the `packages` configuration. 2025-11-04T23:39:21,294 !! 2025-11-04T23:39:21,295 ******************************************************************************** 2025-11-04T23:39:21,296 ############################ 2025-11-04T23:39:21,296 # Package would be ignored # 2025-11-04T23:39:21,297 ############################ 2025-11-04T23:39:21,298 Python recognizes 'satellome.installers' as an importable package[^1], 2025-11-04T23:39:21,298 but it is absent from setuptools' `packages` configuration. 2025-11-04T23:39:21,299 This leads to an ambiguous overall configuration. If you want to distribute this 2025-11-04T23:39:21,300 package, please make sure that 'satellome.installers' is explicitly added 2025-11-04T23:39:21,300 to the `packages` configuration field. 2025-11-04T23:39:21,302 Alternatively, you can also rely on setuptools' discovery methods 2025-11-04T23:39:21,302 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-11-04T23:39:21,302 instead of `find_packages(...)`/`find:`). 2025-11-04T23:39:21,303 You can read more about "package discovery" on setuptools documentation page: 2025-11-04T23:39:21,304 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-11-04T23:39:21,305 If you don't want 'satellome.installers' to be distributed and are 2025-11-04T23:39:21,305 already explicitly excluding 'satellome.installers' via 2025-11-04T23:39:21,306 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-11-04T23:39:21,306 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-11-04T23:39:21,307 combination with a more fine grained `package-data` configuration. 2025-11-04T23:39:21,308 You can read more about "package data files" on setuptools documentation page: 2025-11-04T23:39:21,309 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-11-04T23:39:21,310 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-11-04T23:39:21,311 even if it does not contain any `.py` files. 2025-11-04T23:39:21,311 On the other hand, currently there is no concept of package data 2025-11-04T23:39:21,312 directory, all directories are treated like packages. 2025-11-04T23:39:21,312 ******************************************************************************** 2025-11-04T23:39:21,313 !! 2025-11-04T23:39:21,314 check.warn(importable) 2025-11-04T23:39:21,314 copying src/satellome/settings.yaml -> build/lib/satellome 2025-11-04T23:39:21,315 creating build/lib/satellome/installers 2025-11-04T23:39:21,315 copying src/satellome/installers/__init__.py -> build/lib/satellome/installers 2025-11-04T23:39:21,316 copying src/satellome/installers/base.py -> build/lib/satellome/installers 2025-11-04T23:39:21,316 copying src/satellome/installers/fastan.py -> build/lib/satellome/installers 2025-11-04T23:39:21,317 copying src/satellome/installers/tanbed.py -> build/lib/satellome/installers 2025-11-04T23:39:21,317 copying src/satellome/installers/trf_large.py -> build/lib/satellome/installers 2025-11-04T23:39:21,330 installing to build/bdist.linux-armv7l/wheel 2025-11-04T23:39:21,331 running install 2025-11-04T23:39:21,354 running install_lib 2025-11-04T23:39:21,362 creating build/bdist.linux-armv7l/wheel 2025-11-04T23:39:21,365 creating build/bdist.linux-armv7l/wheel/satellome 2025-11-04T23:39:21,366 copying build/lib/satellome/install_command.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-04T23:39:21,368 copying build/lib/satellome/constants.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-04T23:39:21,371 copying build/lib/satellome/redraw.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-04T23:39:21,373 copying build/lib/satellome/trc_set_tr_names_color.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-04T23:39:21,376 creating build/bdist.linux-armv7l/wheel/satellome/steps 2025-11-04T23:39:21,377 copying build/lib/satellome/steps/trf_parse_raw.py -> build/bdist.linux-armv7l/wheel/./satellome/steps 2025-11-04T23:39:21,379 copying build/lib/satellome/steps/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/steps 2025-11-04T23:39:21,380 copying build/lib/satellome/steps/trf_draw.py -> build/bdist.linux-armv7l/wheel/./satellome/steps 2025-11-04T23:39:21,382 copying build/lib/satellome/steps/trf_classify.py -> build/bdist.linux-armv7l/wheel/./satellome/steps 2025-11-04T23:39:21,385 copying build/lib/satellome/steps/trf_search.py -> build/bdist.linux-armv7l/wheel/./satellome/steps 2025-11-04T23:39:21,387 copying build/lib/satellome/settings.yaml -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-04T23:39:21,389 creating build/bdist.linux-armv7l/wheel/satellome/core_functions 2025-11-04T23:39:21,391 creating build/bdist.linux-armv7l/wheel/satellome/core_functions/models 2025-11-04T23:39:21,392 copying build/lib/satellome/core_functions/models/abstract_model.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/models 2025-11-04T23:39:21,394 copying build/lib/satellome/core_functions/models/gff3_model.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/models 2025-11-04T23:39:21,397 copying build/lib/satellome/core_functions/models/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/models 2025-11-04T23:39:21,398 copying build/lib/satellome/core_functions/models/trf_model.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/models 2025-11-04T23:39:21,401 copying build/lib/satellome/core_functions/trf_embedings.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-04T23:39:21,403 creating build/bdist.linux-armv7l/wheel/satellome/core_functions/io 2025-11-04T23:39:21,404 copying build/lib/satellome/core_functions/io/file_system.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:39:21,406 copying build/lib/satellome/core_functions/io/abstract_reader.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:39:21,409 copying build/lib/satellome/core_functions/io/tab_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:39:21,412 copying build/lib/satellome/core_functions/io/fasta_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:39:21,414 copying build/lib/satellome/core_functions/io/tr_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:39:21,417 copying build/lib/satellome/core_functions/io/block_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:39:21,419 copying build/lib/satellome/core_functions/io/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:39:21,421 copying build/lib/satellome/core_functions/io/gff_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:39:21,423 copying build/lib/satellome/core_functions/io/trf_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:39:21,426 copying build/lib/satellome/core_functions/classification_micro.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-04T23:39:21,429 copying build/lib/satellome/core_functions/settings.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-04T23:39:21,432 creating build/bdist.linux-armv7l/wheel/satellome/core_functions/tools 2025-11-04T23:39:21,433 copying build/lib/satellome/core_functions/tools/gene_intersect.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:39:21,435 copying build/lib/satellome/core_functions/tools/parsers.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:39:21,437 copying build/lib/satellome/core_functions/tools/processing.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:39:21,439 copying build/lib/satellome/core_functions/tools/ncbi.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:39:21,441 copying build/lib/satellome/core_functions/tools/trf_tools.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:39:21,444 copying build/lib/satellome/core_functions/tools/clusterization.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:39:21,446 copying build/lib/satellome/core_functions/tools/reports.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:39:21,448 copying build/lib/satellome/core_functions/tools/distances.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:39:21,450 copying build/lib/satellome/core_functions/tools/statistics.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:39:21,452 copying build/lib/satellome/core_functions/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:39:21,454 copying build/lib/satellome/core_functions/tools/kmer_splitting.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:39:21,456 copying build/lib/satellome/core_functions/trf_drawing.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-04T23:39:21,459 copying build/lib/satellome/core_functions/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-04T23:39:21,460 copying build/lib/satellome/core_functions/trf_clusters.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-04T23:39:21,463 copying build/lib/satellome/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-04T23:39:21,466 creating build/bdist.linux-armv7l/wheel/satellome/installers 2025-11-04T23:39:21,467 copying build/lib/satellome/installers/fastan.py -> build/bdist.linux-armv7l/wheel/./satellome/installers 2025-11-04T23:39:21,469 copying build/lib/satellome/installers/tanbed.py -> build/bdist.linux-armv7l/wheel/./satellome/installers 2025-11-04T23:39:21,471 copying build/lib/satellome/installers/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/installers 2025-11-04T23:39:21,473 copying build/lib/satellome/installers/trf_large.py -> build/bdist.linux-armv7l/wheel/./satellome/installers 2025-11-04T23:39:21,475 copying build/lib/satellome/installers/base.py -> build/bdist.linux-armv7l/wheel/./satellome/installers 2025-11-04T23:39:21,478 copying build/lib/satellome/main.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-04T23:39:21,480 running install_egg_info 2025-11-04T23:39:21,488 Copying src/satellome.egg-info to build/bdist.linux-armv7l/wheel/./satellome-1.4.1-py3.11.egg-info 2025-11-04T23:39:21,500 running install_scripts 2025-11-04T23:39:21,501 ============================================================ 2025-11-04T23:39:21,502 Satellome post-installation: Installing external tools... 2025-11-04T23:39:21,502 ============================================================ 2025-11-04T23:39:21,503 This will attempt to compile and install: 2025-11-04T23:39:21,504 • FasTAN (alternative tandem repeat finder) 2025-11-04T23:39:21,505 • tanbed (BED format converter) 2025-11-04T23:39:21,505 • trf-large (modified TRF for large genomes) 2025-11-04T23:39:21,506 Note: Installation may fail on some platforms (especially macOS). 2025-11-04T23:39:21,506 Satellome will work fine even if these tools fail to install. 2025-11-04T23:39:21,507 You can install them later with: satellome --install-all 2025-11-04T23:39:21,508 To skip this step next time, set: SATELLOME_SKIP_AUTO_INSTALL=1 2025-11-04T23:39:21,509 ============================================================ 2025-11-04T23:39:21,527 [1/3] Installing FasTAN... 2025-11-04T23:39:21,527 Starting FasTAN installation... 2025-11-04T23:39:21,533 Cloning FasTAN repository from https://github.com/thegenemyers/FASTAN.git... 2025-11-04T23:39:21,607 Failed to clone FasTAN repository: 2025-11-04T23:39:21,607 Cloning into '/tmp/fastan_build_sg8zvj_q/FASTAN'... 2025-11-04T23:39:21,608 fatal: transport 'https' not allowed 2025-11-04T23:39:21,609 ✗ FasTAN installation failed 2025-11-04T23:39:21,610 [2/3] Installing tanbed... 2025-11-04T23:39:21,611 Starting tanbed installation... 2025-11-04T23:39:21,611 Cloning alntools repository from https://github.com/richarddurbin/alntools.git... 2025-11-04T23:39:21,661 Failed to clone alntools repository: 2025-11-04T23:39:21,662 Cloning into '/tmp/tanbed_build_790sq9uu/alntools'... 2025-11-04T23:39:21,663 fatal: transport 'https' not allowed 2025-11-04T23:39:21,664 ✗ tanbed installation failed 2025-11-04T23:39:21,665 [3/3] Installing modified TRF (for large genomes)... 2025-11-04T23:39:21,666 Starting modified TRF (for large genomes) installation... 2025-11-04T23:39:21,666 Cloning modified TRF repository from https://github.com/aglabx/trf.git... 2025-11-04T23:39:21,720 Failed to clone modified TRF repository: 2025-11-04T23:39:21,721 Cloning into '/tmp/trf_large_build_tmdwzv9t/trf'... 2025-11-04T23:39:21,721 fatal: transport 'https' not allowed 2025-11-04T23:39:21,722 ✗ Modified TRF installation failed 2025-11-04T23:39:21,723 ============================================================ 2025-11-04T23:39:21,723 Satellome installation summary: 2025-11-04T23:39:21,724 Successfully installed: 0/3 tools 2025-11-04T23:39:21,724 Failed: FasTAN, tanbed, trf-large 2025-11-04T23:39:21,725 To retry installation: 2025-11-04T23:39:21,726 satellome --install-all 2025-11-04T23:39:21,727 Or install individually: 2025-11-04T23:39:21,727 satellome --install-fastan 2025-11-04T23:39:21,728 satellome --install-tanbed 2025-11-04T23:39:21,728 satellome --install-trf-large 2025-11-04T23:39:21,729 ============================================================ 2025-11-04T23:39:21,736 creating build/bdist.linux-armv7l/wheel/satellome-1.4.1.dist-info/WHEEL 2025-11-04T23:39:21,739 creating '/tmp/pip-wheel-3yi3eu8w/.tmp-royzi4xz/satellome-1.4.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-11-04T23:39:21,741 adding 'satellome/__init__.py' 2025-11-04T23:39:21,742 adding 'satellome/constants.py' 2025-11-04T23:39:21,744 adding 'satellome/install_command.py' 2025-11-04T23:39:21,747 adding 'satellome/main.py' 2025-11-04T23:39:21,749 adding 'satellome/redraw.py' 2025-11-04T23:39:21,750 adding 'satellome/settings.yaml' 2025-11-04T23:39:21,751 adding 'satellome/trc_set_tr_names_color.py' 2025-11-04T23:39:21,753 adding 'satellome/core_functions/__init__.py' 2025-11-04T23:39:21,755 adding 'satellome/core_functions/classification_micro.py' 2025-11-04T23:39:21,757 adding 'satellome/core_functions/settings.py' 2025-11-04T23:39:21,760 adding 'satellome/core_functions/trf_clusters.py' 2025-11-04T23:39:21,762 adding 'satellome/core_functions/trf_drawing.py' 2025-11-04T23:39:21,764 adding 'satellome/core_functions/trf_embedings.py' 2025-11-04T23:39:21,765 adding 'satellome/core_functions/io/__init__.py' 2025-11-04T23:39:21,767 adding 'satellome/core_functions/io/abstract_reader.py' 2025-11-04T23:39:21,769 adding 'satellome/core_functions/io/block_file.py' 2025-11-04T23:39:21,771 adding 'satellome/core_functions/io/fasta_file.py' 2025-11-04T23:39:21,772 adding 'satellome/core_functions/io/file_system.py' 2025-11-04T23:39:21,773 adding 'satellome/core_functions/io/gff_file.py' 2025-11-04T23:39:21,775 adding 'satellome/core_functions/io/tab_file.py' 2025-11-04T23:39:21,776 adding 'satellome/core_functions/io/tr_file.py' 2025-11-04T23:39:21,778 adding 'satellome/core_functions/io/trf_file.py' 2025-11-04T23:39:21,780 adding 'satellome/core_functions/models/__init__.py' 2025-11-04T23:39:21,781 adding 'satellome/core_functions/models/abstract_model.py' 2025-11-04T23:39:21,783 adding 'satellome/core_functions/models/gff3_model.py' 2025-11-04T23:39:21,785 adding 'satellome/core_functions/models/trf_model.py' 2025-11-04T23:39:21,788 adding 'satellome/core_functions/tools/__init__.py' 2025-11-04T23:39:21,789 adding 'satellome/core_functions/tools/clusterization.py' 2025-11-04T23:39:21,791 adding 'satellome/core_functions/tools/distances.py' 2025-11-04T23:39:21,793 adding 'satellome/core_functions/tools/gene_intersect.py' 2025-11-04T23:39:21,796 adding 'satellome/core_functions/tools/kmer_splitting.py' 2025-11-04T23:39:21,798 adding 'satellome/core_functions/tools/ncbi.py' 2025-11-04T23:39:21,800 adding 'satellome/core_functions/tools/parsers.py' 2025-11-04T23:39:21,802 adding 'satellome/core_functions/tools/processing.py' 2025-11-04T23:39:21,803 adding 'satellome/core_functions/tools/reports.py' 2025-11-04T23:39:21,805 adding 'satellome/core_functions/tools/statistics.py' 2025-11-04T23:39:21,810 adding 'satellome/core_functions/tools/trf_tools.py' 2025-11-04T23:39:21,812 adding 'satellome/installers/__init__.py' 2025-11-04T23:39:21,814 adding 'satellome/installers/base.py' 2025-11-04T23:39:21,816 adding 'satellome/installers/fastan.py' 2025-11-04T23:39:21,818 adding 'satellome/installers/tanbed.py' 2025-11-04T23:39:21,820 adding 'satellome/installers/trf_large.py' 2025-11-04T23:39:21,822 adding 'satellome/steps/__init__.py' 2025-11-04T23:39:21,824 adding 'satellome/steps/trf_classify.py' 2025-11-04T23:39:21,826 adding 'satellome/steps/trf_draw.py' 2025-11-04T23:39:21,827 adding 'satellome/steps/trf_parse_raw.py' 2025-11-04T23:39:21,829 adding 'satellome/steps/trf_search.py' 2025-11-04T23:39:21,833 adding 'satellome-1.4.1.dist-info/licenses/LICENSE' 2025-11-04T23:39:21,836 adding 'satellome-1.4.1.dist-info/METADATA' 2025-11-04T23:39:21,838 adding 'satellome-1.4.1.dist-info/WHEEL' 2025-11-04T23:39:21,839 adding 'satellome-1.4.1.dist-info/entry_points.txt' 2025-11-04T23:39:21,840 adding 'satellome-1.4.1.dist-info/top_level.txt' 2025-11-04T23:39:21,841 adding 'satellome-1.4.1.dist-info/RECORD' 2025-11-04T23:39:21,845 removing build/bdist.linux-armv7l/wheel 2025-11-04T23:39:21,955 Building wheel for satellome (pyproject.toml): finished with status 'done' 2025-11-04T23:39:21,977 Created wheel for satellome: filename=satellome-1.4.1-py3-none-any.whl size=93524 sha256=cc09ca7ca07d023d0191a042830f3aa4870c7f0e990e03286a1d5bee949a34ed 2025-11-04T23:39:21,979 Stored in directory: /tmp/pip-ephem-wheel-cache-qv9vprte/wheels/24/a3/dc/d4ceea140d9ecb1b0e23f4319f527af405df228705bf1f7c39 2025-11-04T23:39:21,995 Successfully built satellome 2025-11-04T23:39:22,001 Removed build tracker: '/tmp/pip-build-tracker-ibozo9pe'