2025-11-05T02:56:43,875 Created temporary directory: /tmp/pip-ephem-wheel-cache-heyb764u 2025-11-05T02:56:43,877 Created temporary directory: /tmp/pip-build-tracker-7yxiudde 2025-11-05T02:56:43,878 Initialized build tracking at /tmp/pip-build-tracker-7yxiudde 2025-11-05T02:56:43,878 Created build tracker: /tmp/pip-build-tracker-7yxiudde 2025-11-05T02:56:43,879 Entered build tracker: /tmp/pip-build-tracker-7yxiudde 2025-11-05T02:56:43,879 Created temporary directory: /tmp/pip-wheel-q12kq4ep 2025-11-05T02:56:43,882 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 2025-11-05T02:56:43,885 Created temporary directory: /tmp/pip-ephem-wheel-cache-lp413nr0 2025-11-05T02:56:43,908 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-11-05T02:56:43,911 2 location(s) to search for versions of satellome: 2025-11-05T02:56:43,911 * https://pypi.org/simple/satellome/ 2025-11-05T02:56:43,911 * https://www.piwheels.org/simple/satellome/ 2025-11-05T02:56:43,912 Fetching project page and analyzing links: https://pypi.org/simple/satellome/ 2025-11-05T02:56:43,913 Getting page https://pypi.org/simple/satellome/ 2025-11-05T02:56:43,914 Found index url https://pypi.org/simple 2025-11-05T02:56:44,130 Fetched page https://pypi.org/simple/satellome/ as application/vnd.pypi.simple.v1+json 2025-11-05T02:56:44,133 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) 2025-11-05T02:56:44,134 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 2025-11-05T02:56:44,134 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) 2025-11-05T02:56:44,136 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 2025-11-05T02:56:44,136 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) 2025-11-05T02:56:44,137 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 2025-11-05T02:56:44,138 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) 2025-11-05T02:56:44,139 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 2025-11-05T02:56:44,140 Skipping link: No binaries permitted for satellome: https://files.pythonhosted.org/packages/08/9c/3151ff30a4a42f4efe35816d0063d0f4f3f791554fc81e86828cb09b44ce/satellome-1.4.3-py3-none-any.whl (from https://pypi.org/simple/satellome/) (requires-python:>=3.6) 2025-11-05T02:56:44,141 Found link https://files.pythonhosted.org/packages/38/b7/d7c7117fe2ebce8d7f7b1532901b6791161cf9dbde3257eab8eebbf68b56/satellome-1.4.3.tar.gz (from https://pypi.org/simple/satellome/) (requires-python:>=3.6), version: 1.4.3 2025-11-05T02:56:44,142 Fetching project page and analyzing links: https://www.piwheels.org/simple/satellome/ 2025-11-05T02:56:44,142 Getting page https://www.piwheels.org/simple/satellome/ 2025-11-05T02:56:44,144 Found index url https://www.piwheels.org/simple 2025-11-05T02:56:44,307 Fetched page https://www.piwheels.org/simple/satellome/ as text/html 2025-11-05T02:56:44,309 Skipping link: No binaries permitted for satellome: https://www.piwheels.org/simple/satellome/satellome-1.4.1-py3-none-any.whl#sha256=cc09ca7ca07d023d0191a042830f3aa4870c7f0e990e03286a1d5bee949a34ed (from https://www.piwheels.org/simple/satellome/) (requires-python:>=3.6) 2025-11-05T02:56:44,310 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) 2025-11-05T02:56:44,310 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) 2025-11-05T02:56:44,311 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) 2025-11-05T02:56:44,311 Skipping link: not a file: https://www.piwheels.org/simple/satellome/ 2025-11-05T02:56:44,312 Skipping link: not a file: https://pypi.org/simple/satellome/ 2025-11-05T02:56:44,331 Given no hashes to check 1 links for project 'satellome': discarding no candidates 2025-11-05T02:56:44,349 Collecting satellome==1.4.3 2025-11-05T02:56:44,351 Created temporary directory: /tmp/pip-unpack-2ojzpk3_ 2025-11-05T02:56:44,489 Downloading satellome-1.4.3.tar.gz (135 kB) 2025-11-05T02:56:44,745 Added satellome==1.4.3 from https://files.pythonhosted.org/packages/38/b7/d7c7117fe2ebce8d7f7b1532901b6791161cf9dbde3257eab8eebbf68b56/satellome-1.4.3.tar.gz to build tracker '/tmp/pip-build-tracker-7yxiudde' 2025-11-05T02:56:44,752 Created temporary directory: /tmp/pip-build-env-yaacmlzh 2025-11-05T02:56:44,756 Installing build dependencies: started 2025-11-05T02:56:44,758 Running command pip subprocess to install build dependencies 2025-11-05T02:56:45,885 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2025-11-05T02:56:46,487 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 2025-11-05T02:56:46,525 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-11-05T02:56:48,287 Collecting setuptools>=45 2025-11-05T02:56:48,375 Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB) 2025-11-05T02:56:48,644 Collecting wheel 2025-11-05T02:56:48,662 Using cached https://www.piwheels.org/simple/wheel/wheel-0.45.1-py3-none-any.whl (72 kB) 2025-11-05T02:56:48,996 Collecting setuptools_scm[toml]>=6.2 2025-11-05T02:56:49,014 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-9.2.2-py3-none-any.whl (62 kB) 2025-11-05T02:56:49,211 Collecting packaging>=20 2025-11-05T02:56:49,230 Using cached https://www.piwheels.org/simple/packaging/packaging-25.0-py3-none-any.whl (66 kB) 2025-11-05T02:56:52,137 Installing collected packages: wheel, setuptools, packaging, setuptools_scm 2025-11-05T02:56:52,377 Creating /tmp/pip-build-env-yaacmlzh/overlay/local/bin 2025-11-05T02:56:52,379 changing mode of /tmp/pip-build-env-yaacmlzh/overlay/local/bin/wheel to 755 2025-11-05T02:56:56,364 changing mode of /tmp/pip-build-env-yaacmlzh/overlay/local/bin/setuptools-scm to 755 2025-11-05T02:56:56,394 Successfully installed packaging-25.0 setuptools-80.9.0 setuptools_scm-9.2.2 wheel-0.45.1 2025-11-05T02:56:56,686 Installing build dependencies: finished with status 'done' 2025-11-05T02:56:56,692 Getting requirements to build wheel: started 2025-11-05T02:56:56,693 Running command Getting requirements to build wheel 2025-11-05T02:56:57,314 toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section 2025-11-05T02:56:57,390 /tmp/pip-build-env-yaacmlzh/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2025-11-05T02:56:57,391 !! 2025-11-05T02:56:57,392 ******************************************************************************** 2025-11-05T02:56:57,392 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). 2025-11-05T02:56:57,393 By 2026-Feb-18, you need to update your project and remove deprecated calls 2025-11-05T02:56:57,394 or your builds will no longer be supported. 2025-11-05T02:56:57,395 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-11-05T02:56:57,396 ******************************************************************************** 2025-11-05T02:56:57,397 !! 2025-11-05T02:56:57,397 corresp(dist, value, root_dir) 2025-11-05T02:56:57,398 /tmp/pip-build-env-yaacmlzh/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2025-11-05T02:56:57,399 corresp(dist, value, root_dir) 2025-11-05T02:56:57,482 running egg_info 2025-11-05T02:56:57,491 writing src/satellome.egg-info/PKG-INFO 2025-11-05T02:56:57,495 writing dependency_links to src/satellome.egg-info/dependency_links.txt 2025-11-05T02:56:57,496 writing entry points to src/satellome.egg-info/entry_points.txt 2025-11-05T02:56:57,498 writing requirements to src/satellome.egg-info/requires.txt 2025-11-05T02:56:57,499 writing top-level names to src/satellome.egg-info/top_level.txt 2025-11-05T02:56:57,558 listing git files failed - pretending there aren't any 2025-11-05T02:56:57,565 reading manifest file 'src/satellome.egg-info/SOURCES.txt' 2025-11-05T02:56:57,575 reading manifest template 'MANIFEST.in' 2025-11-05T02:56:57,610 warning: no files found matching '*.yml' under directory 'src/satellome' 2025-11-05T02:56:57,627 warning: no previously-included files matching '__pycache__' found under directory '*' 2025-11-05T02:56:57,628 warning: no previously-included files matching '*.py[co]' found under directory '*' 2025-11-05T02:56:57,629 warning: no previously-included files matching '.DS_Store' found under directory '*' 2025-11-05T02:56:57,629 adding license file 'LICENSE' 2025-11-05T02:56:57,635 writing manifest file 'src/satellome.egg-info/SOURCES.txt' 2025-11-05T02:56:57,720 Getting requirements to build wheel: finished with status 'done' 2025-11-05T02:56:57,724 Created temporary directory: /tmp/pip-modern-metadata-nudsplpl 2025-11-05T02:56:57,726 Preparing metadata (pyproject.toml): started 2025-11-05T02:56:57,728 Running command Preparing metadata (pyproject.toml) 2025-11-05T02:56:58,326 toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section 2025-11-05T02:56:58,365 /tmp/pip-build-env-yaacmlzh/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2025-11-05T02:56:58,365 !! 2025-11-05T02:56:58,367 ******************************************************************************** 2025-11-05T02:56:58,367 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). 2025-11-05T02:56:58,368 By 2026-Feb-18, you need to update your project and remove deprecated calls 2025-11-05T02:56:58,368 or your builds will no longer be supported. 2025-11-05T02:56:58,369 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-11-05T02:56:58,370 ******************************************************************************** 2025-11-05T02:56:58,371 !! 2025-11-05T02:56:58,371 corresp(dist, value, root_dir) 2025-11-05T02:56:58,372 /tmp/pip-build-env-yaacmlzh/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2025-11-05T02:56:58,372 corresp(dist, value, root_dir) 2025-11-05T02:56:58,459 running dist_info 2025-11-05T02:56:58,475 creating /tmp/pip-modern-metadata-nudsplpl/satellome.egg-info 2025-11-05T02:56:58,476 writing /tmp/pip-modern-metadata-nudsplpl/satellome.egg-info/PKG-INFO 2025-11-05T02:56:58,480 writing dependency_links to /tmp/pip-modern-metadata-nudsplpl/satellome.egg-info/dependency_links.txt 2025-11-05T02:56:58,482 writing entry points to /tmp/pip-modern-metadata-nudsplpl/satellome.egg-info/entry_points.txt 2025-11-05T02:56:58,483 writing requirements to /tmp/pip-modern-metadata-nudsplpl/satellome.egg-info/requires.txt 2025-11-05T02:56:58,484 writing top-level names to /tmp/pip-modern-metadata-nudsplpl/satellome.egg-info/top_level.txt 2025-11-05T02:56:58,486 writing manifest file '/tmp/pip-modern-metadata-nudsplpl/satellome.egg-info/SOURCES.txt' 2025-11-05T02:56:58,543 listing git files failed - pretending there aren't any 2025-11-05T02:56:58,549 reading manifest file '/tmp/pip-modern-metadata-nudsplpl/satellome.egg-info/SOURCES.txt' 2025-11-05T02:56:58,552 reading manifest template 'MANIFEST.in' 2025-11-05T02:56:58,595 warning: no files found matching '*.yml' under directory 'src/satellome' 2025-11-05T02:56:58,613 warning: no previously-included files matching '__pycache__' found under directory '*' 2025-11-05T02:56:58,614 warning: no previously-included files matching '*.py[co]' found under directory '*' 2025-11-05T02:56:58,615 warning: no previously-included files matching '.DS_Store' found under directory '*' 2025-11-05T02:56:58,616 adding license file 'LICENSE' 2025-11-05T02:56:58,620 writing manifest file '/tmp/pip-modern-metadata-nudsplpl/satellome.egg-info/SOURCES.txt' 2025-11-05T02:56:58,621 creating '/tmp/pip-modern-metadata-nudsplpl/satellome-1.4.3.dist-info' 2025-11-05T02:56:58,740 Preparing metadata (pyproject.toml): finished with status 'done' 2025-11-05T02:56:58,746 Source in /tmp/pip-wheel-q12kq4ep/satellome_7f50fef5d0f24309ade02fdf212d8e4c has version 1.4.3, which satisfies requirement satellome==1.4.3 from https://files.pythonhosted.org/packages/38/b7/d7c7117fe2ebce8d7f7b1532901b6791161cf9dbde3257eab8eebbf68b56/satellome-1.4.3.tar.gz 2025-11-05T02:56:58,747 Removed satellome==1.4.3 from https://files.pythonhosted.org/packages/38/b7/d7c7117fe2ebce8d7f7b1532901b6791161cf9dbde3257eab8eebbf68b56/satellome-1.4.3.tar.gz from build tracker '/tmp/pip-build-tracker-7yxiudde' 2025-11-05T02:56:58,755 Created temporary directory: /tmp/pip-unpack-hj6yq1fm 2025-11-05T02:56:58,756 Building wheels for collected packages: satellome 2025-11-05T02:56:58,761 Created temporary directory: /tmp/pip-wheel-p680f04b 2025-11-05T02:56:58,761 Destination directory: /tmp/pip-wheel-p680f04b 2025-11-05T02:56:58,764 Building wheel for satellome (pyproject.toml): started 2025-11-05T02:56:58,765 Running command Building wheel for satellome (pyproject.toml) 2025-11-05T02:56:59,339 toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section 2025-11-05T02:56:59,379 /tmp/pip-build-env-yaacmlzh/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2025-11-05T02:56:59,379 !! 2025-11-05T02:56:59,380 ******************************************************************************** 2025-11-05T02:56:59,381 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). 2025-11-05T02:56:59,382 By 2026-Feb-18, you need to update your project and remove deprecated calls 2025-11-05T02:56:59,382 or your builds will no longer be supported. 2025-11-05T02:56:59,383 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-11-05T02:56:59,384 ******************************************************************************** 2025-11-05T02:56:59,385 !! 2025-11-05T02:56:59,385 corresp(dist, value, root_dir) 2025-11-05T02:56:59,385 /tmp/pip-build-env-yaacmlzh/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2025-11-05T02:56:59,386 corresp(dist, value, root_dir) 2025-11-05T02:56:59,461 running bdist_wheel 2025-11-05T02:56:59,489 running build 2025-11-05T02:56:59,490 running build_py 2025-11-05T02:56:59,499 creating build/lib/satellome 2025-11-05T02:56:59,501 copying src/satellome/redraw.py -> build/lib/satellome 2025-11-05T02:56:59,504 copying src/satellome/trc_set_tr_names_color.py -> build/lib/satellome 2025-11-05T02:56:59,506 copying src/satellome/__init__.py -> build/lib/satellome 2025-11-05T02:56:59,507 copying src/satellome/install_command.py -> build/lib/satellome 2025-11-05T02:56:59,510 copying src/satellome/main.py -> build/lib/satellome 2025-11-05T02:56:59,512 copying src/satellome/constants.py -> build/lib/satellome 2025-11-05T02:56:59,515 creating build/lib/satellome/core_functions 2025-11-05T02:56:59,517 copying src/satellome/core_functions/trf_clusters.py -> build/lib/satellome/core_functions 2025-11-05T02:56:59,520 copying src/satellome/core_functions/__init__.py -> build/lib/satellome/core_functions 2025-11-05T02:56:59,521 copying src/satellome/core_functions/settings.py -> build/lib/satellome/core_functions 2025-11-05T02:56:59,524 copying src/satellome/core_functions/trf_embedings.py -> build/lib/satellome/core_functions 2025-11-05T02:56:59,526 copying src/satellome/core_functions/classification_micro.py -> build/lib/satellome/core_functions 2025-11-05T02:56:59,529 copying src/satellome/core_functions/trf_drawing.py -> build/lib/satellome/core_functions 2025-11-05T02:56:59,532 creating build/lib/satellome/core_functions/io 2025-11-05T02:56:59,533 copying src/satellome/core_functions/io/tr_file.py -> build/lib/satellome/core_functions/io 2025-11-05T02:56:59,535 copying src/satellome/core_functions/io/__init__.py -> build/lib/satellome/core_functions/io 2025-11-05T02:56:59,537 copying src/satellome/core_functions/io/gff_file.py -> build/lib/satellome/core_functions/io 2025-11-05T02:56:59,539 copying src/satellome/core_functions/io/file_system.py -> build/lib/satellome/core_functions/io 2025-11-05T02:56:59,541 copying src/satellome/core_functions/io/trf_file.py -> build/lib/satellome/core_functions/io 2025-11-05T02:56:59,544 copying src/satellome/core_functions/io/tab_file.py -> build/lib/satellome/core_functions/io 2025-11-05T02:56:59,546 copying src/satellome/core_functions/io/fasta_file.py -> build/lib/satellome/core_functions/io 2025-11-05T02:56:59,548 copying src/satellome/core_functions/io/abstract_reader.py -> build/lib/satellome/core_functions/io 2025-11-05T02:56:59,551 copying src/satellome/core_functions/io/block_file.py -> build/lib/satellome/core_functions/io 2025-11-05T02:56:59,554 creating build/lib/satellome/core_functions/models 2025-11-05T02:56:59,555 copying src/satellome/core_functions/models/abstract_model.py -> build/lib/satellome/core_functions/models 2025-11-05T02:56:59,558 copying src/satellome/core_functions/models/__init__.py -> build/lib/satellome/core_functions/models 2025-11-05T02:56:59,559 copying src/satellome/core_functions/models/gff3_model.py -> build/lib/satellome/core_functions/models 2025-11-05T02:56:59,562 copying src/satellome/core_functions/models/trf_model.py -> build/lib/satellome/core_functions/models 2025-11-05T02:56:59,565 creating build/lib/satellome/core_functions/tools 2025-11-05T02:56:59,566 copying src/satellome/core_functions/tools/__init__.py -> build/lib/satellome/core_functions/tools 2025-11-05T02:56:59,568 copying src/satellome/core_functions/tools/reports.py -> build/lib/satellome/core_functions/tools 2025-11-05T02:56:59,570 copying src/satellome/core_functions/tools/ncbi.py -> build/lib/satellome/core_functions/tools 2025-11-05T02:56:59,572 copying src/satellome/core_functions/tools/clusterization.py -> build/lib/satellome/core_functions/tools 2025-11-05T02:56:59,574 copying src/satellome/core_functions/tools/processing.py -> build/lib/satellome/core_functions/tools 2025-11-05T02:56:59,576 copying src/satellome/core_functions/tools/statistics.py -> build/lib/satellome/core_functions/tools 2025-11-05T02:56:59,578 copying src/satellome/core_functions/tools/gene_intersect.py -> build/lib/satellome/core_functions/tools 2025-11-05T02:56:59,580 copying src/satellome/core_functions/tools/distances.py -> build/lib/satellome/core_functions/tools 2025-11-05T02:56:59,582 copying src/satellome/core_functions/tools/parsers.py -> build/lib/satellome/core_functions/tools 2025-11-05T02:56:59,584 copying src/satellome/core_functions/tools/trf_tools.py -> build/lib/satellome/core_functions/tools 2025-11-05T02:56:59,587 copying src/satellome/core_functions/tools/kmer_splitting.py -> build/lib/satellome/core_functions/tools 2025-11-05T02:56:59,590 creating build/lib/satellome/steps 2025-11-05T02:56:59,591 copying src/satellome/steps/__init__.py -> build/lib/satellome/steps 2025-11-05T02:56:59,593 copying src/satellome/steps/trf_classify.py -> build/lib/satellome/steps 2025-11-05T02:56:59,595 copying src/satellome/steps/trf_search.py -> build/lib/satellome/steps 2025-11-05T02:56:59,597 copying src/satellome/steps/trf_draw.py -> build/lib/satellome/steps 2025-11-05T02:56:59,599 copying src/satellome/steps/trf_parse_raw.py -> build/lib/satellome/steps 2025-11-05T02:56:59,602 creating build/lib/satellome/installers 2025-11-05T02:56:59,603 copying src/satellome/installers/fastan.py -> build/lib/satellome/installers 2025-11-05T02:56:59,605 copying src/satellome/installers/__init__.py -> build/lib/satellome/installers 2025-11-05T02:56:59,607 copying src/satellome/installers/trf_standard.py -> build/lib/satellome/installers 2025-11-05T02:56:59,609 copying src/satellome/installers/trf_large.py -> build/lib/satellome/installers 2025-11-05T02:56:59,611 copying src/satellome/installers/tanbed.py -> build/lib/satellome/installers 2025-11-05T02:56:59,614 copying src/satellome/installers/base.py -> build/lib/satellome/installers 2025-11-05T02:56:59,616 running egg_info 2025-11-05T02:56:59,631 writing src/satellome.egg-info/PKG-INFO 2025-11-05T02:56:59,635 writing dependency_links to src/satellome.egg-info/dependency_links.txt 2025-11-05T02:56:59,636 writing entry points to src/satellome.egg-info/entry_points.txt 2025-11-05T02:56:59,637 writing requirements to src/satellome.egg-info/requires.txt 2025-11-05T02:56:59,639 writing top-level names to src/satellome.egg-info/top_level.txt 2025-11-05T02:56:59,682 listing git files failed - pretending there aren't any 2025-11-05T02:56:59,688 reading manifest file 'src/satellome.egg-info/SOURCES.txt' 2025-11-05T02:56:59,695 reading manifest template 'MANIFEST.in' 2025-11-05T02:56:59,733 warning: no files found matching '*.yml' under directory 'src/satellome' 2025-11-05T02:56:59,753 warning: no previously-included files matching '__pycache__' found under directory '*' 2025-11-05T02:56:59,754 warning: no previously-included files matching '*.py[co]' found under directory '*' 2025-11-05T02:56:59,755 warning: no previously-included files matching '.DS_Store' found under directory '*' 2025-11-05T02:56:59,755 adding license file 'LICENSE' 2025-11-05T02:56:59,761 writing manifest file 'src/satellome.egg-info/SOURCES.txt' 2025-11-05T02:56:59,769 copying src/satellome/settings.yaml -> build/lib/satellome 2025-11-05T02:56:59,782 installing to build/bdist.linux-armv7l/wheel 2025-11-05T02:56:59,783 running install 2025-11-05T02:56:59,807 running install_lib 2025-11-05T02:56:59,815 creating build/bdist.linux-armv7l/wheel 2025-11-05T02:56:59,817 creating build/bdist.linux-armv7l/wheel/satellome 2025-11-05T02:56:59,818 copying build/lib/satellome/redraw.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-05T02:56:59,821 copying build/lib/satellome/trc_set_tr_names_color.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-05T02:56:59,823 copying build/lib/satellome/settings.yaml -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-05T02:56:59,825 copying build/lib/satellome/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-05T02:56:59,826 copying build/lib/satellome/install_command.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-05T02:56:59,829 creating build/bdist.linux-armv7l/wheel/satellome/core_functions 2025-11-05T02:56:59,830 copying build/lib/satellome/core_functions/trf_clusters.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-05T02:56:59,834 copying build/lib/satellome/core_functions/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-05T02:56:59,837 creating build/bdist.linux-armv7l/wheel/satellome/core_functions/io 2025-11-05T02:56:59,838 copying build/lib/satellome/core_functions/io/tr_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-05T02:56:59,841 copying build/lib/satellome/core_functions/io/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-05T02:56:59,843 copying build/lib/satellome/core_functions/io/gff_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-05T02:56:59,844 copying build/lib/satellome/core_functions/io/file_system.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-05T02:56:59,846 copying build/lib/satellome/core_functions/io/trf_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-05T02:56:59,849 copying build/lib/satellome/core_functions/io/tab_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-05T02:56:59,851 copying build/lib/satellome/core_functions/io/fasta_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-05T02:56:59,853 copying build/lib/satellome/core_functions/io/abstract_reader.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-05T02:56:59,856 copying build/lib/satellome/core_functions/io/block_file.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/io 2025-11-05T02:56:59,859 copying build/lib/satellome/core_functions/settings.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-05T02:56:59,861 creating build/bdist.linux-armv7l/wheel/satellome/core_functions/tools 2025-11-05T02:56:59,862 copying build/lib/satellome/core_functions/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-05T02:56:59,864 copying build/lib/satellome/core_functions/tools/reports.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-05T02:56:59,866 copying build/lib/satellome/core_functions/tools/ncbi.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-05T02:56:59,868 copying build/lib/satellome/core_functions/tools/clusterization.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-05T02:56:59,870 copying build/lib/satellome/core_functions/tools/processing.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-05T02:56:59,872 copying build/lib/satellome/core_functions/tools/statistics.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-05T02:56:59,874 copying build/lib/satellome/core_functions/tools/gene_intersect.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-05T02:56:59,876 copying build/lib/satellome/core_functions/tools/distances.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-05T02:56:59,878 copying build/lib/satellome/core_functions/tools/parsers.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-05T02:56:59,881 copying build/lib/satellome/core_functions/tools/trf_tools.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-05T02:56:59,884 copying build/lib/satellome/core_functions/tools/kmer_splitting.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/tools 2025-11-05T02:56:59,886 copying build/lib/satellome/core_functions/trf_embedings.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-05T02:56:59,888 copying build/lib/satellome/core_functions/classification_micro.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-05T02:56:59,892 creating build/bdist.linux-armv7l/wheel/satellome/core_functions/models 2025-11-05T02:56:59,893 copying build/lib/satellome/core_functions/models/abstract_model.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/models 2025-11-05T02:56:59,895 copying build/lib/satellome/core_functions/models/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/models 2025-11-05T02:56:59,897 copying build/lib/satellome/core_functions/models/gff3_model.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/models 2025-11-05T02:56:59,899 copying build/lib/satellome/core_functions/models/trf_model.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions/models 2025-11-05T02:56:59,902 copying build/lib/satellome/core_functions/trf_drawing.py -> build/bdist.linux-armv7l/wheel/./satellome/core_functions 2025-11-05T02:56:59,905 creating build/bdist.linux-armv7l/wheel/satellome/installers 2025-11-05T02:56:59,906 copying build/lib/satellome/installers/fastan.py -> build/bdist.linux-armv7l/wheel/./satellome/installers 2025-11-05T02:56:59,908 copying build/lib/satellome/installers/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/installers 2025-11-05T02:56:59,910 copying build/lib/satellome/installers/trf_standard.py -> build/bdist.linux-armv7l/wheel/./satellome/installers 2025-11-05T02:56:59,912 copying build/lib/satellome/installers/trf_large.py -> build/bdist.linux-armv7l/wheel/./satellome/installers 2025-11-05T02:56:59,915 copying build/lib/satellome/installers/tanbed.py -> build/bdist.linux-armv7l/wheel/./satellome/installers 2025-11-05T02:56:59,917 copying build/lib/satellome/installers/base.py -> build/bdist.linux-armv7l/wheel/./satellome/installers 2025-11-05T02:56:59,920 copying build/lib/satellome/main.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-05T02:56:59,923 copying build/lib/satellome/constants.py -> build/bdist.linux-armv7l/wheel/./satellome 2025-11-05T02:56:59,926 creating build/bdist.linux-armv7l/wheel/satellome/steps 2025-11-05T02:56:59,927 copying build/lib/satellome/steps/__init__.py -> build/bdist.linux-armv7l/wheel/./satellome/steps 2025-11-05T02:56:59,928 copying build/lib/satellome/steps/trf_classify.py -> build/bdist.linux-armv7l/wheel/./satellome/steps 2025-11-05T02:56:59,931 copying build/lib/satellome/steps/trf_search.py -> build/bdist.linux-armv7l/wheel/./satellome/steps 2025-11-05T02:56:59,933 copying build/lib/satellome/steps/trf_draw.py -> build/bdist.linux-armv7l/wheel/./satellome/steps 2025-11-05T02:56:59,935 copying build/lib/satellome/steps/trf_parse_raw.py -> build/bdist.linux-armv7l/wheel/./satellome/steps 2025-11-05T02:56:59,937 running install_egg_info 2025-11-05T02:56:59,944 Copying src/satellome.egg-info to build/bdist.linux-armv7l/wheel/./satellome-1.4.3-py3.11.egg-info 2025-11-05T02:56:59,957 running install_scripts 2025-11-05T02:56:59,958 six package will be installed from dependencies 2025-11-05T02:56:59,959 ============================================================ 2025-11-05T02:56:59,959 Satellome post-installation: Installing external tools... 2025-11-05T02:56:59,960 ============================================================ 2025-11-05T02:56:59,961 This will attempt to compile and install: 2025-11-05T02:56:59,961 • FasTAN (alternative tandem repeat finder) 2025-11-05T02:56:59,962 • tanbed (BED format converter) 2025-11-05T02:56:59,962 • trf-large (modified TRF for large genomes) 2025-11-05T02:56:59,963 Note: Installation may fail on some platforms (especially macOS). 2025-11-05T02:56:59,963 Satellome will work fine even if these tools fail to install. 2025-11-05T02:56:59,964 You can install them later with: satellome --install-all 2025-11-05T02:56:59,965 To skip this step next time, set: SATELLOME_SKIP_AUTO_INSTALL=1 2025-11-05T02:56:59,965 ============================================================ 2025-11-05T02:56:59,989 [1/3] Installing FasTAN... 2025-11-05T02:56:59,990 Starting FasTAN installation... 2025-11-05T02:56:59,995 Cloning FasTAN repository from https://github.com/ad3002/FASTAN.git... 2025-11-05T02:57:00,050 Failed to clone FasTAN repository: 2025-11-05T02:57:00,050 Cloning into '/tmp/fastan_build_vkrrs09r/FASTAN'... 2025-11-05T02:57:00,051 fatal: transport 'https' not allowed 2025-11-05T02:57:00,052 ✗ FasTAN installation failed 2025-11-05T02:57:00,053 [2/3] Installing tanbed... 2025-11-05T02:57:00,053 Starting tanbed installation... 2025-11-05T02:57:00,054 Cloning alntools repository from https://github.com/richarddurbin/alntools.git... 2025-11-05T02:57:00,106 Failed to clone alntools repository: 2025-11-05T02:57:00,107 Cloning into '/tmp/tanbed_build_yhudyn_2/alntools'... 2025-11-05T02:57:00,107 fatal: transport 'https' not allowed 2025-11-05T02:57:00,109 ✗ tanbed installation failed 2025-11-05T02:57:00,110 [3/3] Installing modified TRF (for large genomes)... 2025-11-05T02:57:00,110 Starting modified TRF (for large genomes) installation... 2025-11-05T02:57:00,111 Cloning modified TRF repository from https://github.com/aglabx/trf.git... 2025-11-05T02:57:00,161 Failed to clone modified TRF repository: 2025-11-05T02:57:00,162 Cloning into '/tmp/trf_large_build_jpi5o9o0/trf'... 2025-11-05T02:57:00,162 fatal: transport 'https' not allowed 2025-11-05T02:57:00,164 ✗ Modified TRF installation failed 2025-11-05T02:57:00,165 ============================================================ 2025-11-05T02:57:00,165 Satellome installation summary: 2025-11-05T02:57:00,166 Successfully installed: 0/3 tools 2025-11-05T02:57:00,166 Failed: FasTAN, tanbed, trf-large 2025-11-05T02:57:00,167 To retry installation: 2025-11-05T02:57:00,168 satellome --install-all 2025-11-05T02:57:00,169 Or install individually: 2025-11-05T02:57:00,169 satellome --install-fastan 2025-11-05T02:57:00,170 satellome --install-tanbed 2025-11-05T02:57:00,170 satellome --install-trf-large 2025-11-05T02:57:00,171 ============================================================ 2025-11-05T02:57:00,179 creating build/bdist.linux-armv7l/wheel/satellome-1.4.3.dist-info/WHEEL 2025-11-05T02:57:00,182 creating '/tmp/pip-wheel-p680f04b/.tmp-xbwa7alm/satellome-1.4.3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-11-05T02:57:00,184 adding 'satellome/__init__.py' 2025-11-05T02:57:00,186 adding 'satellome/constants.py' 2025-11-05T02:57:00,188 adding 'satellome/install_command.py' 2025-11-05T02:57:00,192 adding 'satellome/main.py' 2025-11-05T02:57:00,193 adding 'satellome/redraw.py' 2025-11-05T02:57:00,195 adding 'satellome/settings.yaml' 2025-11-05T02:57:00,196 adding 'satellome/trc_set_tr_names_color.py' 2025-11-05T02:57:00,198 adding 'satellome/core_functions/__init__.py' 2025-11-05T02:57:00,200 adding 'satellome/core_functions/classification_micro.py' 2025-11-05T02:57:00,201 adding 'satellome/core_functions/settings.py' 2025-11-05T02:57:00,206 adding 'satellome/core_functions/trf_clusters.py' 2025-11-05T02:57:00,208 adding 'satellome/core_functions/trf_drawing.py' 2025-11-05T02:57:00,210 adding 'satellome/core_functions/trf_embedings.py' 2025-11-05T02:57:00,211 adding 'satellome/core_functions/io/__init__.py' 2025-11-05T02:57:00,213 adding 'satellome/core_functions/io/abstract_reader.py' 2025-11-05T02:57:00,215 adding 'satellome/core_functions/io/block_file.py' 2025-11-05T02:57:00,216 adding 'satellome/core_functions/io/fasta_file.py' 2025-11-05T02:57:00,217 adding 'satellome/core_functions/io/file_system.py' 2025-11-05T02:57:00,218 adding 'satellome/core_functions/io/gff_file.py' 2025-11-05T02:57:00,220 adding 'satellome/core_functions/io/tab_file.py' 2025-11-05T02:57:00,221 adding 'satellome/core_functions/io/tr_file.py' 2025-11-05T02:57:00,223 adding 'satellome/core_functions/io/trf_file.py' 2025-11-05T02:57:00,225 adding 'satellome/core_functions/models/__init__.py' 2025-11-05T02:57:00,226 adding 'satellome/core_functions/models/abstract_model.py' 2025-11-05T02:57:00,228 adding 'satellome/core_functions/models/gff3_model.py' 2025-11-05T02:57:00,230 adding 'satellome/core_functions/models/trf_model.py' 2025-11-05T02:57:00,232 adding 'satellome/core_functions/tools/__init__.py' 2025-11-05T02:57:00,233 adding 'satellome/core_functions/tools/clusterization.py' 2025-11-05T02:57:00,234 adding 'satellome/core_functions/tools/distances.py' 2025-11-05T02:57:00,236 adding 'satellome/core_functions/tools/gene_intersect.py' 2025-11-05T02:57:00,238 adding 'satellome/core_functions/tools/kmer_splitting.py' 2025-11-05T02:57:00,239 adding 'satellome/core_functions/tools/ncbi.py' 2025-11-05T02:57:00,241 adding 'satellome/core_functions/tools/parsers.py' 2025-11-05T02:57:00,242 adding 'satellome/core_functions/tools/processing.py' 2025-11-05T02:57:00,243 adding 'satellome/core_functions/tools/reports.py' 2025-11-05T02:57:00,245 adding 'satellome/core_functions/tools/statistics.py' 2025-11-05T02:57:00,248 adding 'satellome/core_functions/tools/trf_tools.py' 2025-11-05T02:57:00,250 adding 'satellome/installers/__init__.py' 2025-11-05T02:57:00,251 adding 'satellome/installers/base.py' 2025-11-05T02:57:00,253 adding 'satellome/installers/fastan.py' 2025-11-05T02:57:00,254 adding 'satellome/installers/tanbed.py' 2025-11-05T02:57:00,256 adding 'satellome/installers/trf_large.py' 2025-11-05T02:57:00,257 adding 'satellome/installers/trf_standard.py' 2025-11-05T02:57:00,259 adding 'satellome/steps/__init__.py' 2025-11-05T02:57:00,260 adding 'satellome/steps/trf_classify.py' 2025-11-05T02:57:00,261 adding 'satellome/steps/trf_draw.py' 2025-11-05T02:57:00,263 adding 'satellome/steps/trf_parse_raw.py' 2025-11-05T02:57:00,264 adding 'satellome/steps/trf_search.py' 2025-11-05T02:57:00,267 adding 'satellome-1.4.3.dist-info/licenses/LICENSE' 2025-11-05T02:57:00,269 adding 'satellome-1.4.3.dist-info/METADATA' 2025-11-05T02:57:00,270 adding 'satellome-1.4.3.dist-info/WHEEL' 2025-11-05T02:57:00,271 adding 'satellome-1.4.3.dist-info/entry_points.txt' 2025-11-05T02:57:00,272 adding 'satellome-1.4.3.dist-info/top_level.txt' 2025-11-05T02:57:00,273 adding 'satellome-1.4.3.dist-info/RECORD' 2025-11-05T02:57:00,276 removing build/bdist.linux-armv7l/wheel 2025-11-05T02:57:00,376 Building wheel for satellome (pyproject.toml): finished with status 'done' 2025-11-05T02:57:00,382 Created wheel for satellome: filename=satellome-1.4.3-py3-none-any.whl size=101985 sha256=395f3ee21ad9ad49d764a9097be74166ff9fa899b3316c698911d1d7272d0a96 2025-11-05T02:57:00,384 Stored in directory: /tmp/pip-ephem-wheel-cache-lp413nr0/wheels/a8/79/7b/da0a09cc80e8c80770c73809fc38602a0da2787ce14795b297 2025-11-05T02:57:00,399 Successfully built satellome 2025-11-05T02:57:00,408 Removed build tracker: '/tmp/pip-build-tracker-7yxiudde'