2025-11-04T23:37:26,977 Created temporary directory: /tmp/pip-ephem-wheel-cache-igmkx_1q 2025-11-04T23:37:26,978 Created temporary directory: /tmp/pip-build-tracker-gxre2u52 2025-11-04T23:37:26,979 Initialized build tracking at /tmp/pip-build-tracker-gxre2u52 2025-11-04T23:37:26,979 Created build tracker: /tmp/pip-build-tracker-gxre2u52 2025-11-04T23:37:26,980 Entered build tracker: /tmp/pip-build-tracker-gxre2u52 2025-11-04T23:37:26,981 Created temporary directory: /tmp/pip-wheel-p8ed2ifa 2025-11-04T23:37:26,984 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 2025-11-04T23:37:26,986 Created temporary directory: /tmp/pip-ephem-wheel-cache-do2ie2_6 2025-11-04T23:37:27,007 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-11-04T23:37:27,011 2 location(s) to search for versions of satellome: 2025-11-04T23:37:27,011 * https://pypi.org/simple/satellome/ 2025-11-04T23:37:27,011 * https://www.piwheels.org/simple/satellome/ 2025-11-04T23:37:27,012 Fetching project page and analyzing links: https://pypi.org/simple/satellome/ 2025-11-04T23:37:27,012 Getting page https://pypi.org/simple/satellome/ 2025-11-04T23:37:27,014 Found index url https://pypi.org/simple 2025-11-04T23:37:27,228 Fetched page https://pypi.org/simple/satellome/ as application/vnd.pypi.simple.v1+json 2025-11-04T23:37:27,231 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) 2025-11-04T23:37:27,232 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 2025-11-04T23:37:27,233 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) 2025-11-04T23:37:27,234 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 2025-11-04T23:37:27,235 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) 2025-11-04T23:37:27,236 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 2025-11-04T23:37:27,236 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) 2025-11-04T23:37:27,237 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 2025-11-04T23:37:27,238 Fetching project page and analyzing links: https://www.piwheels.org/simple/satellome/ 2025-11-04T23:37:27,239 Getting page https://www.piwheels.org/simple/satellome/ 2025-11-04T23:37:27,240 Found index url https://www.piwheels.org/simple 2025-11-04T23:37:27,541 Fetched page https://www.piwheels.org/simple/satellome/ as text/html 2025-11-04T23:37:27,543 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) 2025-11-04T23:37:27,544 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) 2025-11-04T23:37:27,545 Skipping link: not a file: https://www.piwheels.org/simple/satellome/ 2025-11-04T23:37:27,545 Skipping link: not a file: https://pypi.org/simple/satellome/ 2025-11-04T23:37:27,565 Given no hashes to check 1 links for project 'satellome': discarding no candidates 2025-11-04T23:37:27,585 Collecting satellome==1.4.0 2025-11-04T23:37:27,587 Created temporary directory: /tmp/pip-unpack-_f52drid 2025-11-04T23:37:27,800 Downloading satellome-1.4.0.tar.gz (124 kB) 2025-11-04T23:37:28,054 Added satellome==1.4.0 from https://files.pythonhosted.org/packages/f2/1b/dfaf33c1e95a45d20d10660ea42d0b97d17e779c37e1200e72a6453118db/satellome-1.4.0.tar.gz to build tracker '/tmp/pip-build-tracker-gxre2u52' 2025-11-04T23:37:28,061 Created temporary directory: /tmp/pip-build-env-d0odga4_ 2025-11-04T23:37:28,065 Installing build dependencies: started 2025-11-04T23:37:28,066 Running command pip subprocess to install build dependencies 2025-11-04T23:37:29,250 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2025-11-04T23:37:29,866 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 2025-11-04T23:37:29,889 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-11-04T23:37:31,649 Collecting setuptools>=45 2025-11-04T23:37:31,740 Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB) 2025-11-04T23:37:32,010 Collecting wheel 2025-11-04T23:37:32,027 Using cached https://www.piwheels.org/simple/wheel/wheel-0.45.1-py3-none-any.whl (72 kB) 2025-11-04T23:37:32,360 Collecting setuptools_scm[toml]>=6.2 2025-11-04T23:37:32,376 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-9.2.2-py3-none-any.whl (62 kB) 2025-11-04T23:37:32,571 Collecting packaging>=20 2025-11-04T23:37:32,587 Using cached https://www.piwheels.org/simple/packaging/packaging-25.0-py3-none-any.whl (66 kB) 2025-11-04T23:37:35,483 Installing collected packages: wheel, setuptools, packaging, setuptools_scm 2025-11-04T23:37:35,728 Creating /tmp/pip-build-env-d0odga4_/overlay/local/bin 2025-11-04T23:37:35,730 changing mode of /tmp/pip-build-env-d0odga4_/overlay/local/bin/wheel to 755 2025-11-04T23:37:39,768 changing mode of /tmp/pip-build-env-d0odga4_/overlay/local/bin/setuptools-scm to 755 2025-11-04T23:37:39,797 Successfully installed packaging-25.0 setuptools-80.9.0 setuptools_scm-9.2.2 wheel-0.45.1 2025-11-04T23:37:40,088 Installing build dependencies: finished with status 'done' 2025-11-04T23:37:40,095 Getting requirements to build wheel: started 2025-11-04T23:37:40,096 Running command Getting requirements to build wheel 2025-11-04T23:37:40,721 toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section 2025-11-04T23:37:40,760 /tmp/pip-build-env-d0odga4_/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2025-11-04T23:37:40,761 !! 2025-11-04T23:37:40,762 ******************************************************************************** 2025-11-04T23:37:40,762 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). 2025-11-04T23:37:40,763 By 2026-Feb-18, you need to update your project and remove deprecated calls 2025-11-04T23:37:40,764 or your builds will no longer be supported. 2025-11-04T23:37:40,765 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-11-04T23:37:40,765 ******************************************************************************** 2025-11-04T23:37:40,766 !! 2025-11-04T23:37:40,767 corresp(dist, value, root_dir) 2025-11-04T23:37:40,767 /tmp/pip-build-env-d0odga4_/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2025-11-04T23:37:40,767 corresp(dist, value, root_dir) 2025-11-04T23:37:40,856 running egg_info 2025-11-04T23:37:40,865 writing src/satellome.egg-info/PKG-INFO 2025-11-04T23:37:40,869 writing dependency_links to src/satellome.egg-info/dependency_links.txt 2025-11-04T23:37:40,871 writing entry points to src/satellome.egg-info/entry_points.txt 2025-11-04T23:37:40,872 writing requirements to src/satellome.egg-info/requires.txt 2025-11-04T23:37:40,874 writing top-level names to src/satellome.egg-info/top_level.txt 2025-11-04T23:37:40,933 listing git files failed - pretending there aren't any 2025-11-04T23:37:40,941 reading manifest file 'src/satellome.egg-info/SOURCES.txt' 2025-11-04T23:37:40,951 reading manifest template 'MANIFEST.in' 2025-11-04T23:37:40,987 warning: no files found matching '*.yml' under directory 'src/satellome' 2025-11-04T23:37:41,007 warning: no previously-included files matching '__pycache__' found under directory '*' 2025-11-04T23:37:41,008 warning: no previously-included files matching '*.py[co]' found under directory '*' 2025-11-04T23:37:41,009 warning: no previously-included files matching '.DS_Store' found under directory '*' 2025-11-04T23:37:41,010 adding license file 'LICENSE' 2025-11-04T23:37:41,016 writing manifest file 'src/satellome.egg-info/SOURCES.txt' 2025-11-04T23:37:41,102 Getting requirements to build wheel: finished with status 'done' 2025-11-04T23:37:41,105 Created temporary directory: /tmp/pip-modern-metadata-22y1kmiz 2025-11-04T23:37:41,108 Preparing metadata (pyproject.toml): started 2025-11-04T23:37:41,109 Running command Preparing metadata (pyproject.toml) 2025-11-04T23:37:41,723 toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section 2025-11-04T23:37:41,760 /tmp/pip-build-env-d0odga4_/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2025-11-04T23:37:41,761 !! 2025-11-04T23:37:41,762 ******************************************************************************** 2025-11-04T23:37:41,762 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). 2025-11-04T23:37:41,764 By 2026-Feb-18, you need to update your project and remove deprecated calls 2025-11-04T23:37:41,764 or your builds will no longer be supported. 2025-11-04T23:37:41,765 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-11-04T23:37:41,766 ******************************************************************************** 2025-11-04T23:37:41,767 !! 2025-11-04T23:37:41,768 corresp(dist, value, root_dir) 2025-11-04T23:37:41,768 /tmp/pip-build-env-d0odga4_/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2025-11-04T23:37:41,769 corresp(dist, value, root_dir) 2025-11-04T23:37:41,857 running dist_info 2025-11-04T23:37:41,874 creating /tmp/pip-modern-metadata-22y1kmiz/satellome.egg-info 2025-11-04T23:37:41,875 writing /tmp/pip-modern-metadata-22y1kmiz/satellome.egg-info/PKG-INFO 2025-11-04T23:37:41,878 writing dependency_links to /tmp/pip-modern-metadata-22y1kmiz/satellome.egg-info/dependency_links.txt 2025-11-04T23:37:41,880 writing entry points to /tmp/pip-modern-metadata-22y1kmiz/satellome.egg-info/entry_points.txt 2025-11-04T23:37:41,881 writing requirements to /tmp/pip-modern-metadata-22y1kmiz/satellome.egg-info/requires.txt 2025-11-04T23:37:41,882 writing top-level names to /tmp/pip-modern-metadata-22y1kmiz/satellome.egg-info/top_level.txt 2025-11-04T23:37:41,884 writing manifest file '/tmp/pip-modern-metadata-22y1kmiz/satellome.egg-info/SOURCES.txt' 2025-11-04T23:37:41,939 listing git files failed - pretending there aren't any 2025-11-04T23:37:41,945 reading manifest file '/tmp/pip-modern-metadata-22y1kmiz/satellome.egg-info/SOURCES.txt' 2025-11-04T23:37:41,948 reading manifest template 'MANIFEST.in' 2025-11-04T23:37:41,985 warning: no files found matching '*.yml' under directory 'src/satellome' 2025-11-04T23:37:42,002 warning: no previously-included files matching '__pycache__' found under directory '*' 2025-11-04T23:37:42,003 warning: no previously-included files matching '*.py[co]' found under directory '*' 2025-11-04T23:37:42,004 warning: no previously-included files matching '.DS_Store' found under directory '*' 2025-11-04T23:37:42,004 adding license file 'LICENSE' 2025-11-04T23:37:42,009 writing manifest file '/tmp/pip-modern-metadata-22y1kmiz/satellome.egg-info/SOURCES.txt' 2025-11-04T23:37:42,011 creating '/tmp/pip-modern-metadata-22y1kmiz/satellome-1.4.0.dist-info' 2025-11-04T23:37:42,127 Preparing metadata (pyproject.toml): finished with status 'done' 2025-11-04T23:37:42,133 Source in /tmp/pip-wheel-p8ed2ifa/satellome_2e98c9dff3a942689638921f8b81958b has version 1.4.0, which satisfies requirement satellome==1.4.0 from https://files.pythonhosted.org/packages/f2/1b/dfaf33c1e95a45d20d10660ea42d0b97d17e779c37e1200e72a6453118db/satellome-1.4.0.tar.gz 2025-11-04T23:37:42,134 Removed satellome==1.4.0 from https://files.pythonhosted.org/packages/f2/1b/dfaf33c1e95a45d20d10660ea42d0b97d17e779c37e1200e72a6453118db/satellome-1.4.0.tar.gz from build tracker '/tmp/pip-build-tracker-gxre2u52' 2025-11-04T23:37:42,142 Created temporary directory: /tmp/pip-unpack-88rykui1 2025-11-04T23:37:42,142 Building wheels for collected packages: satellome 2025-11-04T23:37:42,147 Created temporary directory: /tmp/pip-wheel-8qunazv8 2025-11-04T23:37:42,147 Destination directory: /tmp/pip-wheel-8qunazv8 2025-11-04T23:37:42,149 Building wheel for satellome (pyproject.toml): started 2025-11-04T23:37:42,151 Running command Building wheel for satellome (pyproject.toml) 2025-11-04T23:37:42,714 toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section 2025-11-04T23:37:42,750 /tmp/pip-build-env-d0odga4_/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2025-11-04T23:37:42,750 !! 2025-11-04T23:37:42,752 ******************************************************************************** 2025-11-04T23:37:42,752 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). 2025-11-04T23:37:42,753 By 2026-Feb-18, you need to update your project and remove deprecated calls 2025-11-04T23:37:42,754 or your builds will no longer be supported. 2025-11-04T23:37:42,755 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-11-04T23:37:42,756 ******************************************************************************** 2025-11-04T23:37:42,757 !! 2025-11-04T23:37:42,758 corresp(dist, value, root_dir) 2025-11-04T23:37:42,758 /tmp/pip-build-env-d0odga4_/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2025-11-04T23:37:42,759 corresp(dist, value, root_dir) 2025-11-04T23:37:42,829 running bdist_wheel 2025-11-04T23:37:42,857 running build 2025-11-04T23:37:42,857 running build_py 2025-11-04T23:37:42,866 creating build/lib/satellome 2025-11-04T23:37:42,868 copying src/satellome/install_command.py -> build/lib/satellome 2025-11-04T23:37:42,870 copying src/satellome/__init__.py -> build/lib/satellome 2025-11-04T23:37:42,871 copying src/satellome/constants.py -> build/lib/satellome 2025-11-04T23:37:42,874 copying src/satellome/trc_set_tr_names_color.py -> build/lib/satellome 2025-11-04T23:37:42,875 copying src/satellome/main.py -> build/lib/satellome 2025-11-04T23:37:42,878 copying src/satellome/redraw.py -> build/lib/satellome 2025-11-04T23:37:42,881 creating build/lib/satellome/core_functions 2025-11-04T23:37:42,882 copying src/satellome/core_functions/trf_drawing.py -> build/lib/satellome/core_functions 2025-11-04T23:37:42,884 copying src/satellome/core_functions/trf_embedings.py -> build/lib/satellome/core_functions 2025-11-04T23:37:42,886 copying src/satellome/core_functions/__init__.py -> build/lib/satellome/core_functions 2025-11-04T23:37:42,887 copying src/satellome/core_functions/settings.py -> build/lib/satellome/core_functions 2025-11-04T23:37:42,889 copying src/satellome/core_functions/classification_micro.py -> build/lib/satellome/core_functions 2025-11-04T23:37:42,891 copying src/satellome/core_functions/trf_clusters.py -> build/lib/satellome/core_functions 2025-11-04T23:37:42,895 creating build/lib/satellome/core_functions/io 2025-11-04T23:37:42,896 copying src/satellome/core_functions/io/file_system.py -> build/lib/satellome/core_functions/io 2025-11-04T23:37:42,898 copying src/satellome/core_functions/io/trf_file.py -> build/lib/satellome/core_functions/io 2025-11-04T23:37:42,901 copying src/satellome/core_functions/io/tab_file.py -> build/lib/satellome/core_functions/io 2025-11-04T23:37:42,903 copying src/satellome/core_functions/io/fasta_file.py -> build/lib/satellome/core_functions/io 2025-11-04T23:37:42,905 copying src/satellome/core_functions/io/__init__.py -> build/lib/satellome/core_functions/io 2025-11-04T23:37:42,906 copying src/satellome/core_functions/io/gff_file.py -> build/lib/satellome/core_functions/io 2025-11-04T23:37:42,908 copying src/satellome/core_functions/io/tr_file.py -> build/lib/satellome/core_functions/io 2025-11-04T23:37:42,910 copying src/satellome/core_functions/io/block_file.py -> build/lib/satellome/core_functions/io 2025-11-04T23:37:42,912 copying src/satellome/core_functions/io/abstract_reader.py -> build/lib/satellome/core_functions/io 2025-11-04T23:37:42,916 creating build/lib/satellome/core_functions/models 2025-11-04T23:37:42,917 copying src/satellome/core_functions/models/trf_model.py -> build/lib/satellome/core_functions/models 2025-11-04T23:37:42,919 copying src/satellome/core_functions/models/abstract_model.py -> build/lib/satellome/core_functions/models 2025-11-04T23:37:42,921 copying src/satellome/core_functions/models/__init__.py -> build/lib/satellome/core_functions/models 2025-11-04T23:37:42,923 copying src/satellome/core_functions/models/gff3_model.py -> build/lib/satellome/core_functions/models 2025-11-04T23:37:42,926 creating build/lib/satellome/core_functions/tools 2025-11-04T23:37:42,927 copying src/satellome/core_functions/tools/gene_intersect.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:37:42,929 copying src/satellome/core_functions/tools/trf_tools.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:37:42,932 copying src/satellome/core_functions/tools/ncbi.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:37:42,934 copying src/satellome/core_functions/tools/__init__.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:37:42,935 copying src/satellome/core_functions/tools/parsers.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:37:42,938 copying src/satellome/core_functions/tools/distances.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:37:42,939 copying src/satellome/core_functions/tools/reports.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:37:42,941 copying src/satellome/core_functions/tools/clusterization.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:37:42,943 copying src/satellome/core_functions/tools/processing.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:37:42,945 copying src/satellome/core_functions/tools/kmer_splitting.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:37:42,947 copying src/satellome/core_functions/tools/statistics.py -> build/lib/satellome/core_functions/tools 2025-11-04T23:37:42,949 creating build/lib/satellome/steps 2025-11-04T23:37:42,950 copying src/satellome/steps/trf_classify.py -> build/lib/satellome/steps 2025-11-04T23:37:42,952 copying src/satellome/steps/__init__.py -> build/lib/satellome/steps 2025-11-04T23:37:42,954 copying src/satellome/steps/trf_search.py -> build/lib/satellome/steps 2025-11-04T23:37:42,956 copying src/satellome/steps/trf_parse_raw.py -> build/lib/satellome/steps 2025-11-04T23:37:42,958 copying src/satellome/steps/trf_draw.py -> build/lib/satellome/steps 2025-11-04T23:37:42,959 running egg_info 2025-11-04T23:37:42,974 writing src/satellome.egg-info/PKG-INFO 2025-11-04T23:37:42,978 writing dependency_links to src/satellome.egg-info/dependency_links.txt 2025-11-04T23:37:42,979 writing entry points to src/satellome.egg-info/entry_points.txt 2025-11-04T23:37:42,980 writing requirements to src/satellome.egg-info/requires.txt 2025-11-04T23:37:42,981 writing top-level names to src/satellome.egg-info/top_level.txt 2025-11-04T23:37:43,022 listing git files failed - pretending there aren't any 2025-11-04T23:37:43,028 reading manifest file 'src/satellome.egg-info/SOURCES.txt' 2025-11-04T23:37:43,034 reading manifest template 'MANIFEST.in' 2025-11-04T23:37:43,070 warning: no files found matching '*.yml' under directory 'src/satellome' 2025-11-04T23:37:43,086 warning: no previously-included files matching '__pycache__' found under directory '*' 2025-11-04T23:37:43,087 warning: no previously-included files matching '*.py[co]' found under directory '*' 2025-11-04T23:37:43,088 warning: no previously-included files matching '.DS_Store' found under directory '*' 2025-11-04T23:37:43,089 adding license file 'LICENSE' 2025-11-04T23:37:43,095 writing manifest file 'src/satellome.egg-info/SOURCES.txt' 2025-11-04T23:37:43,097 /tmp/pip-build-env-d0odga4_/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'satellome.installers' is absent from the `packages` configuration. 2025-11-04T23:37:43,098 !! 2025-11-04T23:37:43,099 ******************************************************************************** 2025-11-04T23:37:43,100 ############################ 2025-11-04T23:37:43,100 # Package would be ignored # 2025-11-04T23:37:43,101 ############################ 2025-11-04T23:37:43,101 Python recognizes 'satellome.installers' as an importable package[^1], 2025-11-04T23:37:43,102 but it is absent from setuptools' `packages` configuration. 2025-11-04T23:37:43,103 This leads to an ambiguous overall configuration. If you want to distribute this 2025-11-04T23:37:43,103 package, please make sure that 'satellome.installers' is explicitly added 2025-11-04T23:37:43,104 to the `packages` configuration field. 2025-11-04T23:37:43,105 Alternatively, you can also rely on setuptools' discovery methods 2025-11-04T23:37:43,106 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-11-04T23:37:43,106 instead of `find_packages(...)`/`find:`). 2025-11-04T23:37:43,107 You can read more about "package discovery" on setuptools documentation page: 2025-11-04T23:37:43,108 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-11-04T23:37:43,109 If you don't want 'satellome.installers' to be distributed and are 2025-11-04T23:37:43,109 already explicitly excluding 'satellome.installers' via 2025-11-04T23:37:43,110 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-11-04T23:37:43,110 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-11-04T23:37:43,110 combination with a more fine grained `package-data` configuration. 2025-11-04T23:37:43,111 You can read more about "package data files" on setuptools documentation page: 2025-11-04T23:37:43,112 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-11-04T23:37:43,114 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-11-04T23:37:43,114 even if it does not contain any `.py` files. 2025-11-04T23:37:43,115 On the other hand, currently there is no concept of package data 2025-11-04T23:37:43,115 directory, all directories are treated like packages. 2025-11-04T23:37:43,115 ******************************************************************************** 2025-11-04T23:37:43,116 !! 2025-11-04T23:37:43,117 check.warn(importable) 2025-11-04T23:37:43,117 copying src/satellome/settings.yaml -> build/lib/satellome 2025-11-04T23:37:43,118 creating build/lib/satellome/installers 2025-11-04T23:37:43,118 copying src/satellome/installers/__init__.py -> build/lib/satellome/installers 2025-11-04T23:37:43,119 copying src/satellome/installers/base.py -> build/lib/satellome/installers 2025-11-04T23:37:43,119 copying src/satellome/installers/fastan.py -> build/lib/satellome/installers 2025-11-04T23:37:43,120 copying src/satellome/installers/tanbed.py -> build/lib/satellome/installers 2025-11-04T23:37:43,120 copying src/satellome/installers/trf_large.py -> build/lib/satellome/installers 2025-11-04T23:37:43,133 installing to build/bdist.linux-armv7l/wheel 2025-11-04T23:37:43,134 running install 2025-11-04T23:37:43,157 running install_lib 2025-11-04T23:37:43,165 creating build/bdist.linux-armv7l/wheel 2025-11-04T23:37:43,167 creating build/bdist.linux-armv7l/wheel/satellome 2025-11-04T23:37:43,169 creating build/bdist.linux-armv7l/wheel/satellome/core_functions 2025-11-04T23:37:43,170 copying build/lib/satellome/core_functions/trf_drawing.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-04T23:37:43,172 copying build/lib/satellome/core_functions/trf_embedings.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-04T23:37:43,175 creating build/bdist.linux-armv7l/wheel/satellome/core_functions/io 2025-11-04T23:37:43,176 copying build/lib/satellome/core_functions/io/file_system.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:37:43,177 copying build/lib/satellome/core_functions/io/trf_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:37:43,180 copying build/lib/satellome/core_functions/io/tab_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:37:43,182 copying build/lib/satellome/core_functions/io/fasta_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:37:43,184 copying build/lib/satellome/core_functions/io/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:37:43,185 copying build/lib/satellome/core_functions/io/gff_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:37:43,187 copying build/lib/satellome/core_functions/io/tr_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:37:43,189 copying build/lib/satellome/core_functions/io/block_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:37:43,191 copying build/lib/satellome/core_functions/io/abstract_reader.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-04T23:37:43,193 copying build/lib/satellome/core_functions/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-04T23:37:43,195 copying build/lib/satellome/core_functions/settings.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-04T23:37:43,197 creating build/bdist.linux-armv7l/wheel/satellome/core_functions/tools 2025-11-04T23:37:43,198 copying build/lib/satellome/core_functions/tools/gene_intersect.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:37:43,200 copying build/lib/satellome/core_functions/tools/trf_tools.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:37:43,203 copying build/lib/satellome/core_functions/tools/ncbi.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:37:43,205 copying build/lib/satellome/core_functions/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:37:43,206 copying build/lib/satellome/core_functions/tools/parsers.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:37:43,208 copying build/lib/satellome/core_functions/tools/distances.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:37:43,210 copying build/lib/satellome/core_functions/tools/reports.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:37:43,212 copying build/lib/satellome/core_functions/tools/clusterization.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:37:43,214 copying build/lib/satellome/core_functions/tools/processing.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:37:43,216 copying build/lib/satellome/core_functions/tools/kmer_splitting.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:37:43,218 copying build/lib/satellome/core_functions/tools/statistics.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-04T23:37:43,220 creating build/bdist.linux-armv7l/wheel/satellome/core_functions/models 2025-11-04T23:37:43,221 copying build/lib/satellome/core_functions/models/trf_model.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/models 2025-11-04T23:37:43,224 copying build/lib/satellome/core_functions/models/abstract_model.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/models 2025-11-04T23:37:43,226 copying build/lib/satellome/core_functions/models/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/models 2025-11-04T23:37:43,228 copying build/lib/satellome/core_functions/models/gff3_model.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/models 2025-11-04T23:37:43,230 copying build/lib/satellome/core_functions/classification_micro.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-04T23:37:43,232 copying build/lib/satellome/core_functions/trf_clusters.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-04T23:37:43,235 copying build/lib/satellome/install_command.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-04T23:37:43,237 copying build/lib/satellome/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-04T23:37:43,239 copying build/lib/satellome/constants.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-04T23:37:43,241 copying build/lib/satellome/trc_set_tr_names_color.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-04T23:37:43,243 creating build/bdist.linux-armv7l/wheel/satellome/steps 2025-11-04T23:37:43,244 copying build/lib/satellome/steps/trf_classify.py -> build/bdist.linux-armv7l/wheel/./satellome/steps 2025-11-04T23:37:43,247 copying build/lib/satellome/steps/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/steps 2025-11-04T23:37:43,248 copying build/lib/satellome/steps/trf_search.py -> build/bdist.linux-armv7l/wheel/./satellome/steps 2025-11-04T23:37:43,250 copying build/lib/satellome/steps/trf_parse_raw.py -> build/bdist.linux-armv7l/wheel/./satellome/steps 2025-11-04T23:37:43,251 copying build/lib/satellome/steps/trf_draw.py -> build/bdist.linux-armv7l/wheel/./satellome/steps 2025-11-04T23:37:43,253 copying build/lib/satellome/main.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-04T23:37:43,256 copying build/lib/satellome/redraw.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-04T23:37:43,258 copying build/lib/satellome/settings.yaml -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-04T23:37:43,260 creating build/bdist.linux-armv7l/wheel/satellome/installers 2025-11-04T23:37:43,261 copying build/lib/satellome/installers/trf_large.py -> build/bdist.linux-armv7l/wheel/./satellome/installers 2025-11-04T23:37:43,263 copying build/lib/satellome/installers/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/installers 2025-11-04T23:37:43,265 copying build/lib/satellome/installers/base.py -> build/bdist.linux-armv7l/wheel/./satellome/installers 2025-11-04T23:37:43,267 copying build/lib/satellome/installers/tanbed.py -> build/bdist.linux-armv7l/wheel/./satellome/installers 2025-11-04T23:37:43,269 copying build/lib/satellome/installers/fastan.py -> build/bdist.linux-armv7l/wheel/./satellome/installers 2025-11-04T23:37:43,271 running install_egg_info 2025-11-04T23:37:43,278 Copying src/satellome.egg-info to build/bdist.linux-armv7l/wheel/./satellome-1.4.0-py3.11.egg-info 2025-11-04T23:37:43,290 running install_scripts 2025-11-04T23:37:43,291 ============================================================ 2025-11-04T23:37:43,292 Satellome post-installation: Installing external tools... 2025-11-04T23:37:43,292 ============================================================ 2025-11-04T23:37:43,293 This will attempt to compile and install: 2025-11-04T23:37:43,294 • FasTAN (alternative tandem repeat finder) 2025-11-04T23:37:43,294 • tanbed (BED format converter) 2025-11-04T23:37:43,295 • trf-large (modified TRF for large genomes) 2025-11-04T23:37:43,296 Note: Installation may fail on some platforms (especially macOS). 2025-11-04T23:37:43,296 Satellome will work fine even if these tools fail to install. 2025-11-04T23:37:43,297 You can install them later with: satellome --install-all 2025-11-04T23:37:43,298 To skip this step next time, set: SATELLOME_SKIP_AUTO_INSTALL=1 2025-11-04T23:37:43,299 ============================================================ 2025-11-04T23:37:43,317 [1/3] Installing FasTAN... 2025-11-04T23:37:43,318 Starting FasTAN installation... 2025-11-04T23:37:43,323 Cloning FasTAN repository from https://github.com/thegenemyers/FASTAN.git... 2025-11-04T23:37:43,388 Failed to clone FasTAN repository: 2025-11-04T23:37:43,389 Cloning into '/tmp/fastan_build_m85c83q2/FASTAN'... 2025-11-04T23:37:43,389 fatal: transport 'https' not allowed 2025-11-04T23:37:43,390 ✗ FasTAN installation failed 2025-11-04T23:37:43,391 [2/3] Installing tanbed... 2025-11-04T23:37:43,392 Starting tanbed installation... 2025-11-04T23:37:43,393 Cloning alntools repository from https://github.com/richarddurbin/alntools.git... 2025-11-04T23:37:43,436 Failed to clone alntools repository: 2025-11-04T23:37:43,437 Cloning into '/tmp/tanbed_build_itf_92u8/alntools'... 2025-11-04T23:37:43,438 fatal: transport 'https' not allowed 2025-11-04T23:37:43,439 ✗ tanbed installation failed 2025-11-04T23:37:43,440 [3/3] Installing modified TRF (for large genomes)... 2025-11-04T23:37:43,440 Starting modified TRF (for large genomes) installation... 2025-11-04T23:37:43,441 Cloning modified TRF repository from https://github.com/aglabx/trf.git... 2025-11-04T23:37:43,486 Failed to clone modified TRF repository: 2025-11-04T23:37:43,487 Cloning into '/tmp/trf_large_build_ofbk8p0w/trf'... 2025-11-04T23:37:43,487 fatal: transport 'https' not allowed 2025-11-04T23:37:43,488 ✗ Modified TRF installation failed 2025-11-04T23:37:43,489 ============================================================ 2025-11-04T23:37:43,489 Satellome installation summary: 2025-11-04T23:37:43,490 Successfully installed: 0/3 tools 2025-11-04T23:37:43,490 Failed: FasTAN, tanbed, trf-large 2025-11-04T23:37:43,491 To retry installation: 2025-11-04T23:37:43,492 satellome --install-all 2025-11-04T23:37:43,493 Or install individually: 2025-11-04T23:37:43,493 satellome --install-fastan 2025-11-04T23:37:43,493 satellome --install-tanbed 2025-11-04T23:37:43,494 satellome --install-trf-large 2025-11-04T23:37:43,495 ============================================================ 2025-11-04T23:37:43,501 creating build/bdist.linux-armv7l/wheel/satellome-1.4.0.dist-info/WHEEL 2025-11-04T23:37:43,504 creating '/tmp/pip-wheel-8qunazv8/.tmp-o82vpamv/satellome-1.4.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-11-04T23:37:43,506 adding 'satellome/__init__.py' 2025-11-04T23:37:43,508 adding 'satellome/constants.py' 2025-11-04T23:37:43,510 adding 'satellome/install_command.py' 2025-11-04T23:37:43,513 adding 'satellome/main.py' 2025-11-04T23:37:43,515 adding 'satellome/redraw.py' 2025-11-04T23:37:43,516 adding 'satellome/settings.yaml' 2025-11-04T23:37:43,517 adding 'satellome/trc_set_tr_names_color.py' 2025-11-04T23:37:43,519 adding 'satellome/core_functions/__init__.py' 2025-11-04T23:37:43,522 adding 'satellome/core_functions/classification_micro.py' 2025-11-04T23:37:43,523 adding 'satellome/core_functions/settings.py' 2025-11-04T23:37:43,527 adding 'satellome/core_functions/trf_clusters.py' 2025-11-04T23:37:43,528 adding 'satellome/core_functions/trf_drawing.py' 2025-11-04T23:37:43,530 adding 'satellome/core_functions/trf_embedings.py' 2025-11-04T23:37:43,531 adding 'satellome/core_functions/io/__init__.py' 2025-11-04T23:37:43,533 adding 'satellome/core_functions/io/abstract_reader.py' 2025-11-04T23:37:43,535 adding 'satellome/core_functions/io/block_file.py' 2025-11-04T23:37:43,536 adding 'satellome/core_functions/io/fasta_file.py' 2025-11-04T23:37:43,537 adding 'satellome/core_functions/io/file_system.py' 2025-11-04T23:37:43,538 adding 'satellome/core_functions/io/gff_file.py' 2025-11-04T23:37:43,540 adding 'satellome/core_functions/io/tab_file.py' 2025-11-04T23:37:43,541 adding 'satellome/core_functions/io/tr_file.py' 2025-11-04T23:37:43,544 adding 'satellome/core_functions/io/trf_file.py' 2025-11-04T23:37:43,545 adding 'satellome/core_functions/models/__init__.py' 2025-11-04T23:37:43,547 adding 'satellome/core_functions/models/abstract_model.py' 2025-11-04T23:37:43,548 adding 'satellome/core_functions/models/gff3_model.py' 2025-11-04T23:37:43,550 adding 'satellome/core_functions/models/trf_model.py' 2025-11-04T23:37:43,552 adding 'satellome/core_functions/tools/__init__.py' 2025-11-04T23:37:43,553 adding 'satellome/core_functions/tools/clusterization.py' 2025-11-04T23:37:43,555 adding 'satellome/core_functions/tools/distances.py' 2025-11-04T23:37:43,556 adding 'satellome/core_functions/tools/gene_intersect.py' 2025-11-04T23:37:43,558 adding 'satellome/core_functions/tools/kmer_splitting.py' 2025-11-04T23:37:43,560 adding 'satellome/core_functions/tools/ncbi.py' 2025-11-04T23:37:43,561 adding 'satellome/core_functions/tools/parsers.py' 2025-11-04T23:37:43,563 adding 'satellome/core_functions/tools/processing.py' 2025-11-04T23:37:43,564 adding 'satellome/core_functions/tools/reports.py' 2025-11-04T23:37:43,565 adding 'satellome/core_functions/tools/statistics.py' 2025-11-04T23:37:43,568 adding 'satellome/core_functions/tools/trf_tools.py' 2025-11-04T23:37:43,570 adding 'satellome/installers/__init__.py' 2025-11-04T23:37:43,572 adding 'satellome/installers/base.py' 2025-11-04T23:37:43,573 adding 'satellome/installers/fastan.py' 2025-11-04T23:37:43,575 adding 'satellome/installers/tanbed.py' 2025-11-04T23:37:43,577 adding 'satellome/installers/trf_large.py' 2025-11-04T23:37:43,578 adding 'satellome/steps/__init__.py' 2025-11-04T23:37:43,580 adding 'satellome/steps/trf_classify.py' 2025-11-04T23:37:43,581 adding 'satellome/steps/trf_draw.py' 2025-11-04T23:37:43,582 adding 'satellome/steps/trf_parse_raw.py' 2025-11-04T23:37:43,583 adding 'satellome/steps/trf_search.py' 2025-11-04T23:37:43,586 adding 'satellome-1.4.0.dist-info/licenses/LICENSE' 2025-11-04T23:37:43,588 adding 'satellome-1.4.0.dist-info/METADATA' 2025-11-04T23:37:43,589 adding 'satellome-1.4.0.dist-info/WHEEL' 2025-11-04T23:37:43,590 adding 'satellome-1.4.0.dist-info/entry_points.txt' 2025-11-04T23:37:43,591 adding 'satellome-1.4.0.dist-info/top_level.txt' 2025-11-04T23:37:43,592 adding 'satellome-1.4.0.dist-info/RECORD' 2025-11-04T23:37:43,595 removing build/bdist.linux-armv7l/wheel 2025-11-04T23:37:43,695 Building wheel for satellome (pyproject.toml): finished with status 'done' 2025-11-04T23:37:43,701 Created wheel for satellome: filename=satellome-1.4.0-py3-none-any.whl size=93629 sha256=05d11035fa4da917d4b9105c447fc715f1e3160458cbc4808be2c44b8942c054 2025-11-04T23:37:43,702 Stored in directory: /tmp/pip-ephem-wheel-cache-do2ie2_6/wheels/94/0c/f3/580b0858124b24bc68da8efa0a92798e2a15fea09973c496a8 2025-11-04T23:37:43,719 Successfully built satellome 2025-11-04T23:37:43,725 Removed build tracker: '/tmp/pip-build-tracker-gxre2u52'