2023-12-01T02:59:57,316 Created temporary directory: /tmp/pip-build-tracker-9x2h5zzl 2023-12-01T02:59:57,318 Initialized build tracking at /tmp/pip-build-tracker-9x2h5zzl 2023-12-01T02:59:57,318 Created build tracker: /tmp/pip-build-tracker-9x2h5zzl 2023-12-01T02:59:57,319 Entered build tracker: /tmp/pip-build-tracker-9x2h5zzl 2023-12-01T02:59:57,319 Created temporary directory: /tmp/pip-wheel-ewk4kzol 2023-12-01T02:59:57,323 Created temporary directory: /tmp/pip-ephem-wheel-cache-aie2lrlr 2023-12-01T02:59:57,347 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-12-01T02:59:57,351 2 location(s) to search for versions of witch-msa: 2023-12-01T02:59:57,351 * https://pypi.org/simple/witch-msa/ 2023-12-01T02:59:57,351 * https://www.piwheels.org/simple/witch-msa/ 2023-12-01T02:59:57,351 Fetching project page and analyzing links: https://pypi.org/simple/witch-msa/ 2023-12-01T02:59:57,352 Getting page https://pypi.org/simple/witch-msa/ 2023-12-01T02:59:57,354 Found index url https://pypi.org/simple/ 2023-12-01T02:59:57,570 Fetched page https://pypi.org/simple/witch-msa/ as application/vnd.pypi.simple.v1+json 2023-12-01T02:59:57,574 Found link https://files.pythonhosted.org/packages/9f/57/80dd0c29162c6b84cd017182095b5cb2aa4dc11260bbae056f3ef0351943/witch-msa-1.0.0rc1.tar.gz (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7), version: 1.0.0rc1 2023-12-01T02:59:57,574 Skipping link: No binaries permitted for witch-msa: https://files.pythonhosted.org/packages/43/78/272d4d835763bc77476391081248647987723a7b0226719cd93618a44b8a/witch_msa-1.0.0rc1-py3-none-any.whl (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7) 2023-12-01T02:59:57,575 Found link https://files.pythonhosted.org/packages/04/42/abe66ef86387d93b5b0bc9f23ec71b3660310d62820b56cb6315b13db266/witch-msa-1.0.0rc3.tar.gz (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7), version: 1.0.0rc3 2023-12-01T02:59:57,576 Skipping link: No binaries permitted for witch-msa: https://files.pythonhosted.org/packages/d5/e8/f939cdd95425dcd48632cc7a2fdaa939beabfed6d2004dff600c8afc0be1/witch_msa-1.0.0rc3-py3-none-any.whl (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7) 2023-12-01T02:59:57,577 Found link https://files.pythonhosted.org/packages/18/10/e568ef8fa1a5a231130cc83c420b1bed9bf69ceaf17911f5b45f67496b39/witch-msa-1.0.0rc4.tar.gz (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7), version: 1.0.0rc4 2023-12-01T02:59:57,578 Skipping link: No binaries permitted for witch-msa: https://files.pythonhosted.org/packages/de/20/c1d8c0f03fe35ea092495a73a29d3bca6a94ea55ea917d04b73cc7582215/witch_msa-1.0.0rc4-py3-none-any.whl (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7) 2023-12-01T02:59:57,579 Found link https://files.pythonhosted.org/packages/19/e6/150568e28ab0565dd78080eba70d4d2254038ef55327b82919e5915c6101/witch-msa-1.0.1.tar.gz (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7), version: 1.0.1 2023-12-01T02:59:57,580 Skipping link: No binaries permitted for witch-msa: https://files.pythonhosted.org/packages/6a/bf/e791b97aa9ff2e5592b40328ac11461a5dae4ecd40e175d1349be75cf37a/witch_msa-1.0.1-py3-none-any.whl (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7) 2023-12-01T02:59:57,581 Found link https://files.pythonhosted.org/packages/c6/81/4a0953d4b062ea116c7e89fbeb65f537958b489d02bee8263b6044d3aeb5/witch-msa-1.0.2a1.tar.gz (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7), version: 1.0.2a1 2023-12-01T02:59:57,582 Skipping link: No binaries permitted for witch-msa: https://files.pythonhosted.org/packages/ac/96/5021e8835aef45c1a4f6b35c072002d7b7fd870cb4fe75f87b71b5d163b2/witch_msa-1.0.2a1-py3-none-any.whl (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7) 2023-12-01T02:59:57,583 Fetching project page and analyzing links: https://www.piwheels.org/simple/witch-msa/ 2023-12-01T02:59:57,583 Getting page https://www.piwheels.org/simple/witch-msa/ 2023-12-01T02:59:57,585 Found index url https://www.piwheels.org/simple/ 2023-12-01T02:59:57,749 Fetched page https://www.piwheels.org/simple/witch-msa/ as text/html 2023-12-01T02:59:57,751 Skipping link: No binaries permitted for witch-msa: https://www.piwheels.org/simple/witch-msa/witch_msa-1.0.1-py3-none-any.whl#sha256=9a991d73586803bc132937a46dd0adf27f1c8b87b2e31d0a029497a7b20fd007 (from https://www.piwheels.org/simple/witch-msa/) (requires-python:>=3.7) 2023-12-01T02:59:57,752 Skipping link: No binaries permitted for witch-msa: https://www.piwheels.org/simple/witch-msa/witch_msa-1.0.0rc4-py3-none-any.whl#sha256=2c2a928f16f5a02983f953a35cc22dfab97abebe5984290e665cfb59e940d4e3 (from https://www.piwheels.org/simple/witch-msa/) (requires-python:>=3.7) 2023-12-01T02:59:57,752 Skipping link: No binaries permitted for witch-msa: https://www.piwheels.org/simple/witch-msa/witch_msa-1.0.0rc3-py3-none-any.whl#sha256=c99577c2a6e9a75c03f497d93f5f54ee9a04036357ca0b4cfb53f08df1f8023f (from https://www.piwheels.org/simple/witch-msa/) (requires-python:>=3.7) 2023-12-01T02:59:57,753 Skipping link: No binaries permitted for witch-msa: https://www.piwheels.org/simple/witch-msa/witch_msa-1.0.0rc1-py3-none-any.whl#sha256=7639b8df3d4a6b6fc2a4e2654e2da8d9636881239740deb58f44b604e93074d6 (from https://www.piwheels.org/simple/witch-msa/) (requires-python:>=3.7) 2023-12-01T02:59:57,753 Skipping link: not a file: https://www.piwheels.org/simple/witch-msa/ 2023-12-01T02:59:57,754 Skipping link: not a file: https://pypi.org/simple/witch-msa/ 2023-12-01T02:59:57,774 Given no hashes to check 1 links for project 'witch-msa': discarding no candidates 2023-12-01T02:59:57,793 Collecting witch-msa==1.0.2a1 2023-12-01T02:59:57,796 Created temporary directory: /tmp/pip-unpack-jyd38z62 2023-12-01T02:59:58,012 Downloading witch-msa-1.0.2a1.tar.gz (29.0 MB) 2023-12-01T03:00:07,363 Added witch-msa==1.0.2a1 from https://files.pythonhosted.org/packages/c6/81/4a0953d4b062ea116c7e89fbeb65f537958b489d02bee8263b6044d3aeb5/witch-msa-1.0.2a1.tar.gz to build tracker '/tmp/pip-build-tracker-9x2h5zzl' 2023-12-01T03:00:07,367 Created temporary directory: /tmp/pip-build-env-nfmkf0fz 2023-12-01T03:00:07,372 Installing build dependencies: started 2023-12-01T03:00:07,373 Running command pip subprocess to install build dependencies 2023-12-01T03:00:08,652 Using pip 23.3.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-12-01T03:00:09,224 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-12-01T03:00:10,671 Collecting setuptools 2023-12-01T03:00:10,688 Using cached https://www.piwheels.org/simple/setuptools/setuptools-69.0.2-py3-none-any.whl (819 kB) 2023-12-01T03:00:13,302 Installing collected packages: setuptools 2023-12-01T03:00:15,733 Successfully installed setuptools-69.0.2 2023-12-01T03:00:16,339 Installing build dependencies: finished with status 'done' 2023-12-01T03:00:16,343 Getting requirements to build wheel: started 2023-12-01T03:00:16,344 Running command Getting requirements to build wheel 2023-12-01T03:00:17,160 running egg_info 2023-12-01T03:00:17,165 writing witch_msa.egg-info/PKG-INFO 2023-12-01T03:00:17,171 writing dependency_links to witch_msa.egg-info/dependency_links.txt 2023-12-01T03:00:17,173 writing requirements to witch_msa.egg-info/requires.txt 2023-12-01T03:00:17,175 writing top-level names to witch_msa.egg-info/top_level.txt 2023-12-01T03:00:17,196 reading manifest file 'witch_msa.egg-info/SOURCES.txt' 2023-12-01T03:00:17,219 reading manifest template 'MANIFEST.in' 2023-12-01T03:00:17,240 no previously-included directories found matching '*/__pycache__' 2023-12-01T03:00:17,241 warning: no previously-included files matching '*.py[cod]' found anywhere in distribution 2023-12-01T03:00:17,242 adding license file 'LICENSE' 2023-12-01T03:00:17,250 writing manifest file 'witch_msa.egg-info/SOURCES.txt' 2023-12-01T03:00:17,366 Getting requirements to build wheel: finished with status 'done' 2023-12-01T03:00:17,375 Installing backend dependencies: started 2023-12-01T03:00:17,377 Running command pip subprocess to install backend dependencies 2023-12-01T03:00:18,593 Using pip 23.3.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-12-01T03:00:19,142 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-12-01T03:00:19,641 Collecting wheel 2023-12-01T03:00:19,661 Using cached https://www.piwheels.org/simple/wheel/wheel-0.42.0-py3-none-any.whl (65 kB) 2023-12-01T03:00:21,956 Installing collected packages: wheel 2023-12-01T03:00:22,211 Creating /tmp/pip-build-env-nfmkf0fz/normal/local/bin 2023-12-01T03:00:22,214 changing mode of /tmp/pip-build-env-nfmkf0fz/normal/local/bin/wheel to 755 2023-12-01T03:00:22,227 Successfully installed wheel-0.42.0 2023-12-01T03:00:22,796 Installing backend dependencies: finished with status 'done' 2023-12-01T03:00:22,798 Created temporary directory: /tmp/pip-modern-metadata-i3wz4bp4 2023-12-01T03:00:22,801 Preparing metadata (pyproject.toml): started 2023-12-01T03:00:22,802 Running command Preparing metadata (pyproject.toml) 2023-12-01T03:00:23,658 running dist_info 2023-12-01T03:00:23,663 creating /tmp/pip-modern-metadata-i3wz4bp4/witch_msa.egg-info 2023-12-01T03:00:23,667 writing /tmp/pip-modern-metadata-i3wz4bp4/witch_msa.egg-info/PKG-INFO 2023-12-01T03:00:23,673 writing dependency_links to /tmp/pip-modern-metadata-i3wz4bp4/witch_msa.egg-info/dependency_links.txt 2023-12-01T03:00:23,675 writing requirements to /tmp/pip-modern-metadata-i3wz4bp4/witch_msa.egg-info/requires.txt 2023-12-01T03:00:23,676 writing top-level names to /tmp/pip-modern-metadata-i3wz4bp4/witch_msa.egg-info/top_level.txt 2023-12-01T03:00:23,677 writing manifest file '/tmp/pip-modern-metadata-i3wz4bp4/witch_msa.egg-info/SOURCES.txt' 2023-12-01T03:00:23,700 reading manifest file '/tmp/pip-modern-metadata-i3wz4bp4/witch_msa.egg-info/SOURCES.txt' 2023-12-01T03:00:23,703 reading manifest template 'MANIFEST.in' 2023-12-01T03:00:23,734 no previously-included directories found matching '*/__pycache__' 2023-12-01T03:00:23,735 warning: no previously-included files matching '*.py[cod]' found anywhere in distribution 2023-12-01T03:00:23,736 adding license file 'LICENSE' 2023-12-01T03:00:23,742 writing manifest file '/tmp/pip-modern-metadata-i3wz4bp4/witch_msa.egg-info/SOURCES.txt' 2023-12-01T03:00:23,744 creating '/tmp/pip-modern-metadata-i3wz4bp4/witch_msa-1.0.2a1.dist-info' 2023-12-01T03:00:23,909 Preparing metadata (pyproject.toml): finished with status 'done' 2023-12-01T03:00:23,922 Source in /tmp/pip-wheel-ewk4kzol/witch-msa_f723d08cc5a4475988151bdf223cda99 has version 1.0.2a1, which satisfies requirement witch-msa==1.0.2a1 from https://files.pythonhosted.org/packages/c6/81/4a0953d4b062ea116c7e89fbeb65f537958b489d02bee8263b6044d3aeb5/witch-msa-1.0.2a1.tar.gz 2023-12-01T03:00:23,923 Removed witch-msa==1.0.2a1 from https://files.pythonhosted.org/packages/c6/81/4a0953d4b062ea116c7e89fbeb65f537958b489d02bee8263b6044d3aeb5/witch-msa-1.0.2a1.tar.gz from build tracker '/tmp/pip-build-tracker-9x2h5zzl' 2023-12-01T03:00:23,944 Created temporary directory: /tmp/pip-unpack-wk7pv5l4 2023-12-01T03:00:23,945 Created temporary directory: /tmp/pip-unpack-nqlwnqzs 2023-12-01T03:00:23,970 Building wheels for collected packages: witch-msa 2023-12-01T03:00:23,974 Created temporary directory: /tmp/pip-wheel-s38amxw0 2023-12-01T03:00:23,975 Destination directory: /tmp/pip-wheel-s38amxw0 2023-12-01T03:00:23,977 Building wheel for witch-msa (pyproject.toml): started 2023-12-01T03:00:23,979 Running command Building wheel for witch-msa (pyproject.toml) 2023-12-01T03:00:24,779 running bdist_wheel 2023-12-01T03:00:24,796 running build 2023-12-01T03:00:24,796 running build_py 2023-12-01T03:00:24,801 creating build 2023-12-01T03:00:24,802 creating build/lib 2023-12-01T03:00:24,802 creating build/lib/witch_msa 2023-12-01T03:00:24,804 copying witch_msa/configs.py -> build/lib/witch_msa 2023-12-01T03:00:24,807 copying witch_msa/__init__.py -> build/lib/witch_msa 2023-12-01T03:00:24,810 copying witch_msa/init_configs.py -> build/lib/witch_msa 2023-12-01T03:00:24,813 creating build/lib/witch_msa/gcmm 2023-12-01T03:00:24,814 copying witch_msa/gcmm/results_handler.py -> build/lib/witch_msa/gcmm 2023-12-01T03:00:24,817 copying witch_msa/gcmm/algorithm.py -> build/lib/witch_msa/gcmm 2023-12-01T03:00:24,820 copying witch_msa/gcmm/decompose_tree.py -> build/lib/witch_msa/gcmm 2023-12-01T03:00:24,822 copying witch_msa/gcmm/aligner.py -> build/lib/witch_msa/gcmm 2023-12-01T03:00:24,825 copying witch_msa/gcmm/__init__.py -> build/lib/witch_msa/gcmm 2023-12-01T03:00:24,827 copying witch_msa/gcmm/loader.py -> build/lib/witch_msa/gcmm 2023-12-01T03:00:24,830 copying witch_msa/gcmm/backbone.py -> build/lib/witch_msa/gcmm 2023-12-01T03:00:24,832 copying witch_msa/gcmm/weighting.py -> build/lib/witch_msa/gcmm 2023-12-01T03:00:24,835 copying witch_msa/gcmm/gcmm.py -> build/lib/witch_msa/gcmm 2023-12-01T03:00:24,837 copying witch_msa/gcmm/merger.py -> build/lib/witch_msa/gcmm 2023-12-01T03:00:24,839 copying witch_msa/gcmm/tree.py -> build/lib/witch_msa/gcmm 2023-12-01T03:00:24,842 copying witch_msa/gcmm/task.py -> build/lib/witch_msa/gcmm 2023-12-01T03:00:24,844 copying witch_msa/gcmm/callback.py -> build/lib/witch_msa/gcmm 2023-12-01T03:00:24,847 creating build/lib/witch_msa/helpers 2023-12-01T03:00:24,848 copying witch_msa/helpers/alignment_tools.py -> build/lib/witch_msa/helpers 2023-12-01T03:00:24,851 copying witch_msa/helpers/pyhmmer_tools.py -> build/lib/witch_msa/helpers 2023-12-01T03:00:24,853 copying witch_msa/helpers/__init__.py -> build/lib/witch_msa/helpers 2023-12-01T03:00:24,855 copying witch_msa/helpers/general_tools.py -> build/lib/witch_msa/helpers 2023-12-01T03:00:24,857 copying witch_msa/helpers/math_utils.py -> build/lib/witch_msa/helpers 2023-12-01T03:00:24,858 running egg_info 2023-12-01T03:00:24,862 writing witch_msa.egg-info/PKG-INFO 2023-12-01T03:00:24,867 writing dependency_links to witch_msa.egg-info/dependency_links.txt 2023-12-01T03:00:24,869 writing requirements to witch_msa.egg-info/requires.txt 2023-12-01T03:00:24,870 writing top-level names to witch_msa.egg-info/top_level.txt 2023-12-01T03:00:24,880 reading manifest file 'witch_msa.egg-info/SOURCES.txt' 2023-12-01T03:00:24,885 reading manifest template 'MANIFEST.in' 2023-12-01T03:00:24,900 no previously-included directories found matching '*/__pycache__' 2023-12-01T03:00:24,902 warning: no previously-included files matching '*.py[cod]' found anywhere in distribution 2023-12-01T03:00:24,902 adding license file 'LICENSE' 2023-12-01T03:00:24,910 writing manifest file 'witch_msa.egg-info/SOURCES.txt' 2023-12-01T03:00:24,914 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.macOS' is absent from the `packages` configuration. 2023-12-01T03:00:24,915 !! 2023-12-01T03:00:24,916 ******************************************************************************** 2023-12-01T03:00:24,917 ############################ 2023-12-01T03:00:24,917 # Package would be ignored # 2023-12-01T03:00:24,918 ############################ 2023-12-01T03:00:24,918 Python recognizes 'witch_msa.tools.macOS' as an importable package[^1], 2023-12-01T03:00:24,919 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:24,920 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:24,921 package, please make sure that 'witch_msa.tools.macOS' is explicitly added 2023-12-01T03:00:24,921 to the `packages` configuration field. 2023-12-01T03:00:24,923 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:24,923 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:24,924 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:24,925 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:24,927 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:24,928 If you don't want 'witch_msa.tools.macOS' to be distributed and are 2023-12-01T03:00:24,929 already explicitly excluding 'witch_msa.tools.macOS' via 2023-12-01T03:00:24,929 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:24,929 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:24,930 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:24,931 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:24,932 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:24,933 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:24,933 even if it does not contain any `.py` files. 2023-12-01T03:00:24,934 On the other hand, currently there is no concept of package data 2023-12-01T03:00:24,934 directory, all directories are treated like packages. 2023-12-01T03:00:24,935 ******************************************************************************** 2023-12-01T03:00:24,935 !! 2023-12-01T03:00:24,936 check.warn(importable) 2023-12-01T03:00:24,936 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus' is absent from the `packages` configuration. 2023-12-01T03:00:24,937 !! 2023-12-01T03:00:24,938 ******************************************************************************** 2023-12-01T03:00:24,938 ############################ 2023-12-01T03:00:24,939 # Package would be ignored # 2023-12-01T03:00:24,939 ############################ 2023-12-01T03:00:24,940 Python recognizes 'witch_msa.tools.magus' as an importable package[^1], 2023-12-01T03:00:24,941 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:24,942 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:24,942 package, please make sure that 'witch_msa.tools.magus' is explicitly added 2023-12-01T03:00:24,943 to the `packages` configuration field. 2023-12-01T03:00:24,944 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:24,945 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:24,945 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:24,947 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:24,948 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:24,949 If you don't want 'witch_msa.tools.magus' to be distributed and are 2023-12-01T03:00:24,950 already explicitly excluding 'witch_msa.tools.magus' via 2023-12-01T03:00:24,950 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:24,951 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:24,951 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:24,953 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:24,954 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:24,957 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:24,959 even if it does not contain any `.py` files. 2023-12-01T03:00:24,961 On the other hand, currently there is no concept of package data 2023-12-01T03:00:24,962 directory, all directories are treated like packages. 2023-12-01T03:00:24,963 ******************************************************************************** 2023-12-01T03:00:24,964 !! 2023-12-01T03:00:24,965 check.warn(importable) 2023-12-01T03:00:24,965 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.align' is absent from the `packages` configuration. 2023-12-01T03:00:24,966 !! 2023-12-01T03:00:24,967 ******************************************************************************** 2023-12-01T03:00:24,970 ############################ 2023-12-01T03:00:24,974 # Package would be ignored # 2023-12-01T03:00:24,977 ############################ 2023-12-01T03:00:24,977 Python recognizes 'witch_msa.tools.magus.align' as an importable package[^1], 2023-12-01T03:00:24,978 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:24,979 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:24,979 package, please make sure that 'witch_msa.tools.magus.align' is explicitly added 2023-12-01T03:00:24,980 to the `packages` configuration field. 2023-12-01T03:00:24,981 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:24,982 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:24,982 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:24,990 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:24,994 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:24,995 If you don't want 'witch_msa.tools.magus.align' to be distributed and are 2023-12-01T03:00:24,996 already explicitly excluding 'witch_msa.tools.magus.align' via 2023-12-01T03:00:24,996 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:24,997 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:24,998 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,000 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,006 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,013 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,014 even if it does not contain any `.py` files. 2023-12-01T03:00:25,014 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,016 directory, all directories are treated like packages. 2023-12-01T03:00:25,017 ******************************************************************************** 2023-12-01T03:00:25,019 !! 2023-12-01T03:00:25,019 check.warn(importable) 2023-12-01T03:00:25,020 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.align.decompose' is absent from the `packages` configuration. 2023-12-01T03:00:25,020 !! 2023-12-01T03:00:25,023 ******************************************************************************** 2023-12-01T03:00:25,027 ############################ 2023-12-01T03:00:25,028 # Package would be ignored # 2023-12-01T03:00:25,029 ############################ 2023-12-01T03:00:25,030 Python recognizes 'witch_msa.tools.magus.align.decompose' as an importable package[^1], 2023-12-01T03:00:25,030 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,031 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,032 package, please make sure that 'witch_msa.tools.magus.align.decompose' is explicitly added 2023-12-01T03:00:25,033 to the `packages` configuration field. 2023-12-01T03:00:25,034 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,035 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,035 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,036 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,037 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,038 If you don't want 'witch_msa.tools.magus.align.decompose' to be distributed and are 2023-12-01T03:00:25,039 already explicitly excluding 'witch_msa.tools.magus.align.decompose' via 2023-12-01T03:00:25,039 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,040 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,040 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,041 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,042 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,044 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,044 even if it does not contain any `.py` files. 2023-12-01T03:00:25,045 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,045 directory, all directories are treated like packages. 2023-12-01T03:00:25,045 ******************************************************************************** 2023-12-01T03:00:25,046 !! 2023-12-01T03:00:25,047 check.warn(importable) 2023-12-01T03:00:25,048 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.align.merge' is absent from the `packages` configuration. 2023-12-01T03:00:25,048 !! 2023-12-01T03:00:25,049 ******************************************************************************** 2023-12-01T03:00:25,050 ############################ 2023-12-01T03:00:25,050 # Package would be ignored # 2023-12-01T03:00:25,051 ############################ 2023-12-01T03:00:25,051 Python recognizes 'witch_msa.tools.magus.align.merge' as an importable package[^1], 2023-12-01T03:00:25,052 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,053 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,053 package, please make sure that 'witch_msa.tools.magus.align.merge' is explicitly added 2023-12-01T03:00:25,054 to the `packages` configuration field. 2023-12-01T03:00:25,055 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,055 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,056 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,057 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,058 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,059 If you don't want 'witch_msa.tools.magus.align.merge' to be distributed and are 2023-12-01T03:00:25,060 already explicitly excluding 'witch_msa.tools.magus.align.merge' via 2023-12-01T03:00:25,060 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,061 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,062 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,063 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,064 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,066 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,066 even if it does not contain any `.py` files. 2023-12-01T03:00:25,067 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,067 directory, all directories are treated like packages. 2023-12-01T03:00:25,068 ******************************************************************************** 2023-12-01T03:00:25,069 !! 2023-12-01T03:00:25,069 check.warn(importable) 2023-12-01T03:00:25,070 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.align.merge.graph_build' is absent from the `packages` configuration. 2023-12-01T03:00:25,070 !! 2023-12-01T03:00:25,072 ******************************************************************************** 2023-12-01T03:00:25,072 ############################ 2023-12-01T03:00:25,073 # Package would be ignored # 2023-12-01T03:00:25,073 ############################ 2023-12-01T03:00:25,074 Python recognizes 'witch_msa.tools.magus.align.merge.graph_build' as an importable package[^1], 2023-12-01T03:00:25,074 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,075 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,076 package, please make sure that 'witch_msa.tools.magus.align.merge.graph_build' is explicitly added 2023-12-01T03:00:25,076 to the `packages` configuration field. 2023-12-01T03:00:25,077 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,077 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,078 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,079 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,080 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,081 If you don't want 'witch_msa.tools.magus.align.merge.graph_build' to be distributed and are 2023-12-01T03:00:25,082 already explicitly excluding 'witch_msa.tools.magus.align.merge.graph_build' via 2023-12-01T03:00:25,083 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,083 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,084 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,085 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,086 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,087 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,088 even if it does not contain any `.py` files. 2023-12-01T03:00:25,088 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,089 directory, all directories are treated like packages. 2023-12-01T03:00:25,090 ******************************************************************************** 2023-12-01T03:00:25,091 !! 2023-12-01T03:00:25,091 check.warn(importable) 2023-12-01T03:00:25,092 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.align.merge.graph_cluster' is absent from the `packages` configuration. 2023-12-01T03:00:25,092 !! 2023-12-01T03:00:25,093 ******************************************************************************** 2023-12-01T03:00:25,094 ############################ 2023-12-01T03:00:25,095 # Package would be ignored # 2023-12-01T03:00:25,095 ############################ 2023-12-01T03:00:25,095 Python recognizes 'witch_msa.tools.magus.align.merge.graph_cluster' as an importable package[^1], 2023-12-01T03:00:25,096 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,097 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,097 package, please make sure that 'witch_msa.tools.magus.align.merge.graph_cluster' is explicitly added 2023-12-01T03:00:25,098 to the `packages` configuration field. 2023-12-01T03:00:25,099 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,099 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,099 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,100 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,101 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,102 If you don't want 'witch_msa.tools.magus.align.merge.graph_cluster' to be distributed and are 2023-12-01T03:00:25,103 already explicitly excluding 'witch_msa.tools.magus.align.merge.graph_cluster' via 2023-12-01T03:00:25,103 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,104 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,104 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,105 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,106 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,108 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,108 even if it does not contain any `.py` files. 2023-12-01T03:00:25,109 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,109 directory, all directories are treated like packages. 2023-12-01T03:00:25,110 ******************************************************************************** 2023-12-01T03:00:25,111 !! 2023-12-01T03:00:25,112 check.warn(importable) 2023-12-01T03:00:25,112 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.align.merge.graph_trace' is absent from the `packages` configuration. 2023-12-01T03:00:25,113 !! 2023-12-01T03:00:25,114 ******************************************************************************** 2023-12-01T03:00:25,114 ############################ 2023-12-01T03:00:25,115 # Package would be ignored # 2023-12-01T03:00:25,116 ############################ 2023-12-01T03:00:25,116 Python recognizes 'witch_msa.tools.magus.align.merge.graph_trace' as an importable package[^1], 2023-12-01T03:00:25,117 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,118 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,118 package, please make sure that 'witch_msa.tools.magus.align.merge.graph_trace' is explicitly added 2023-12-01T03:00:25,119 to the `packages` configuration field. 2023-12-01T03:00:25,120 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,121 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,121 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,122 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,123 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,124 If you don't want 'witch_msa.tools.magus.align.merge.graph_trace' to be distributed and are 2023-12-01T03:00:25,124 already explicitly excluding 'witch_msa.tools.magus.align.merge.graph_trace' via 2023-12-01T03:00:25,125 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,125 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,126 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,127 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,128 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,129 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,130 even if it does not contain any `.py` files. 2023-12-01T03:00:25,130 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,130 directory, all directories are treated like packages. 2023-12-01T03:00:25,131 ******************************************************************************** 2023-12-01T03:00:25,132 !! 2023-12-01T03:00:25,133 check.warn(importable) 2023-12-01T03:00:25,133 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.helpers' is absent from the `packages` configuration. 2023-12-01T03:00:25,134 !! 2023-12-01T03:00:25,135 ******************************************************************************** 2023-12-01T03:00:25,135 ############################ 2023-12-01T03:00:25,136 # Package would be ignored # 2023-12-01T03:00:25,136 ############################ 2023-12-01T03:00:25,137 Python recognizes 'witch_msa.tools.magus.helpers' as an importable package[^1], 2023-12-01T03:00:25,137 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,138 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,139 package, please make sure that 'witch_msa.tools.magus.helpers' is explicitly added 2023-12-01T03:00:25,139 to the `packages` configuration field. 2023-12-01T03:00:25,141 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,141 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,142 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,143 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,144 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,145 If you don't want 'witch_msa.tools.magus.helpers' to be distributed and are 2023-12-01T03:00:25,146 already explicitly excluding 'witch_msa.tools.magus.helpers' via 2023-12-01T03:00:25,147 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,147 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,148 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,149 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,150 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,152 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,152 even if it does not contain any `.py` files. 2023-12-01T03:00:25,153 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,154 directory, all directories are treated like packages. 2023-12-01T03:00:25,154 ******************************************************************************** 2023-12-01T03:00:25,155 !! 2023-12-01T03:00:25,156 check.warn(importable) 2023-12-01T03:00:25,156 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tasks' is absent from the `packages` configuration. 2023-12-01T03:00:25,157 !! 2023-12-01T03:00:25,158 ******************************************************************************** 2023-12-01T03:00:25,158 ############################ 2023-12-01T03:00:25,159 # Package would be ignored # 2023-12-01T03:00:25,159 ############################ 2023-12-01T03:00:25,160 Python recognizes 'witch_msa.tools.magus.tasks' as an importable package[^1], 2023-12-01T03:00:25,160 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,162 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,162 package, please make sure that 'witch_msa.tools.magus.tasks' is explicitly added 2023-12-01T03:00:25,163 to the `packages` configuration field. 2023-12-01T03:00:25,164 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,164 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,165 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,166 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,167 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,168 If you don't want 'witch_msa.tools.magus.tasks' to be distributed and are 2023-12-01T03:00:25,168 already explicitly excluding 'witch_msa.tools.magus.tasks' via 2023-12-01T03:00:25,169 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,169 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,170 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,172 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,174 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,176 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,177 even if it does not contain any `.py` files. 2023-12-01T03:00:25,178 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,178 directory, all directories are treated like packages. 2023-12-01T03:00:25,179 ******************************************************************************** 2023-12-01T03:00:25,181 !! 2023-12-01T03:00:25,182 check.warn(importable) 2023-12-01T03:00:25,182 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools' is absent from the `packages` configuration. 2023-12-01T03:00:25,183 !! 2023-12-01T03:00:25,185 ******************************************************************************** 2023-12-01T03:00:25,185 ############################ 2023-12-01T03:00:25,187 # Package would be ignored # 2023-12-01T03:00:25,189 ############################ 2023-12-01T03:00:25,199 Python recognizes 'witch_msa.tools.magus.tools' as an importable package[^1], 2023-12-01T03:00:25,216 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,244 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,247 package, please make sure that 'witch_msa.tools.magus.tools' is explicitly added 2023-12-01T03:00:25,248 to the `packages` configuration field. 2023-12-01T03:00:25,249 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,249 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,253 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,258 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,259 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,260 If you don't want 'witch_msa.tools.magus.tools' to be distributed and are 2023-12-01T03:00:25,261 already explicitly excluding 'witch_msa.tools.magus.tools' via 2023-12-01T03:00:25,263 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,265 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,267 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,268 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,270 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,271 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,271 even if it does not contain any `.py` files. 2023-12-01T03:00:25,272 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,274 directory, all directories are treated like packages. 2023-12-01T03:00:25,275 ******************************************************************************** 2023-12-01T03:00:25,282 !! 2023-12-01T03:00:25,284 check.warn(importable) 2023-12-01T03:00:25,287 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.clustal' is absent from the `packages` configuration. 2023-12-01T03:00:25,290 !! 2023-12-01T03:00:25,292 ******************************************************************************** 2023-12-01T03:00:25,293 ############################ 2023-12-01T03:00:25,294 # Package would be ignored # 2023-12-01T03:00:25,298 ############################ 2023-12-01T03:00:25,307 Python recognizes 'witch_msa.tools.magus.tools.clustal' as an importable package[^1], 2023-12-01T03:00:25,309 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,311 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,311 package, please make sure that 'witch_msa.tools.magus.tools.clustal' is explicitly added 2023-12-01T03:00:25,316 to the `packages` configuration field. 2023-12-01T03:00:25,318 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,323 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,327 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,333 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,335 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,336 If you don't want 'witch_msa.tools.magus.tools.clustal' to be distributed and are 2023-12-01T03:00:25,336 already explicitly excluding 'witch_msa.tools.magus.tools.clustal' via 2023-12-01T03:00:25,337 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,338 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,339 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,340 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,342 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,356 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,366 even if it does not contain any `.py` files. 2023-12-01T03:00:25,368 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,369 directory, all directories are treated like packages. 2023-12-01T03:00:25,370 ******************************************************************************** 2023-12-01T03:00:25,371 !! 2023-12-01T03:00:25,371 check.warn(importable) 2023-12-01T03:00:25,372 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.fasttree' is absent from the `packages` configuration. 2023-12-01T03:00:25,372 !! 2023-12-01T03:00:25,373 ******************************************************************************** 2023-12-01T03:00:25,374 ############################ 2023-12-01T03:00:25,374 # Package would be ignored # 2023-12-01T03:00:25,375 ############################ 2023-12-01T03:00:25,375 Python recognizes 'witch_msa.tools.magus.tools.fasttree' as an importable package[^1], 2023-12-01T03:00:25,376 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,377 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,379 package, please make sure that 'witch_msa.tools.magus.tools.fasttree' is explicitly added 2023-12-01T03:00:25,380 to the `packages` configuration field. 2023-12-01T03:00:25,381 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,381 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,382 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,383 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,385 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,387 If you don't want 'witch_msa.tools.magus.tools.fasttree' to be distributed and are 2023-12-01T03:00:25,388 already explicitly excluding 'witch_msa.tools.magus.tools.fasttree' via 2023-12-01T03:00:25,392 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,396 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,402 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,405 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,407 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,409 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,410 even if it does not contain any `.py` files. 2023-12-01T03:00:25,410 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,411 directory, all directories are treated like packages. 2023-12-01T03:00:25,415 ******************************************************************************** 2023-12-01T03:00:25,422 !! 2023-12-01T03:00:25,423 check.warn(importable) 2023-12-01T03:00:25,423 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.hmmer' is absent from the `packages` configuration. 2023-12-01T03:00:25,424 !! 2023-12-01T03:00:25,425 ******************************************************************************** 2023-12-01T03:00:25,428 ############################ 2023-12-01T03:00:25,431 # Package would be ignored # 2023-12-01T03:00:25,437 ############################ 2023-12-01T03:00:25,438 Python recognizes 'witch_msa.tools.magus.tools.hmmer' as an importable package[^1], 2023-12-01T03:00:25,439 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,440 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,440 package, please make sure that 'witch_msa.tools.magus.tools.hmmer' is explicitly added 2023-12-01T03:00:25,441 to the `packages` configuration field. 2023-12-01T03:00:25,442 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,443 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,443 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,445 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,446 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,447 If you don't want 'witch_msa.tools.magus.tools.hmmer' to be distributed and are 2023-12-01T03:00:25,448 already explicitly excluding 'witch_msa.tools.magus.tools.hmmer' via 2023-12-01T03:00:25,448 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,449 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,450 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,451 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,453 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,455 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,456 even if it does not contain any `.py` files. 2023-12-01T03:00:25,456 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,457 directory, all directories are treated like packages. 2023-12-01T03:00:25,458 ******************************************************************************** 2023-12-01T03:00:25,467 !! 2023-12-01T03:00:25,473 check.warn(importable) 2023-12-01T03:00:25,476 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.mafft' is absent from the `packages` configuration. 2023-12-01T03:00:25,486 !! 2023-12-01T03:00:25,503 ******************************************************************************** 2023-12-01T03:00:25,505 ############################ 2023-12-01T03:00:25,508 # Package would be ignored # 2023-12-01T03:00:25,509 ############################ 2023-12-01T03:00:25,512 Python recognizes 'witch_msa.tools.magus.tools.mafft' as an importable package[^1], 2023-12-01T03:00:25,513 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,516 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,519 package, please make sure that 'witch_msa.tools.magus.tools.mafft' is explicitly added 2023-12-01T03:00:25,522 to the `packages` configuration field. 2023-12-01T03:00:25,524 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,526 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,531 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,533 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,534 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,535 If you don't want 'witch_msa.tools.magus.tools.mafft' to be distributed and are 2023-12-01T03:00:25,535 already explicitly excluding 'witch_msa.tools.magus.tools.mafft' via 2023-12-01T03:00:25,536 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,537 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,537 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,539 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,543 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,553 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,553 even if it does not contain any `.py` files. 2023-12-01T03:00:25,554 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,555 directory, all directories are treated like packages. 2023-12-01T03:00:25,555 ******************************************************************************** 2023-12-01T03:00:25,556 !! 2023-12-01T03:00:25,557 check.warn(importable) 2023-12-01T03:00:25,557 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' is absent from the `packages` configuration. 2023-12-01T03:00:25,558 !! 2023-12-01T03:00:25,560 ******************************************************************************** 2023-12-01T03:00:25,562 ############################ 2023-12-01T03:00:25,563 # Package would be ignored # 2023-12-01T03:00:25,565 ############################ 2023-12-01T03:00:25,571 Python recognizes 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' as an importable package[^1], 2023-12-01T03:00:25,572 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,573 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,574 package, please make sure that 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' is explicitly added 2023-12-01T03:00:25,574 to the `packages` configuration field. 2023-12-01T03:00:25,576 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,577 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,578 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,582 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,590 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,592 If you don't want 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' to be distributed and are 2023-12-01T03:00:25,593 already explicitly excluding 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' via 2023-12-01T03:00:25,593 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,594 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,595 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,597 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,606 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,615 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,616 even if it does not contain any `.py` files. 2023-12-01T03:00:25,617 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,618 directory, all directories are treated like packages. 2023-12-01T03:00:25,618 ******************************************************************************** 2023-12-01T03:00:25,619 !! 2023-12-01T03:00:25,620 check.warn(importable) 2023-12-01T03:00:25,620 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' is absent from the `packages` configuration. 2023-12-01T03:00:25,621 !! 2023-12-01T03:00:25,623 ******************************************************************************** 2023-12-01T03:00:25,624 ############################ 2023-12-01T03:00:25,627 # Package would be ignored # 2023-12-01T03:00:25,631 ############################ 2023-12-01T03:00:25,632 Python recognizes 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' as an importable package[^1], 2023-12-01T03:00:25,632 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,633 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,634 package, please make sure that 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' is explicitly added 2023-12-01T03:00:25,635 to the `packages` configuration field. 2023-12-01T03:00:25,636 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,637 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,637 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,642 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,646 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,655 If you don't want 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' to be distributed and are 2023-12-01T03:00:25,656 already explicitly excluding 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' via 2023-12-01T03:00:25,656 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,657 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,658 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,660 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,664 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,669 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,670 even if it does not contain any `.py` files. 2023-12-01T03:00:25,671 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,671 directory, all directories are treated like packages. 2023-12-01T03:00:25,672 ******************************************************************************** 2023-12-01T03:00:25,673 !! 2023-12-01T03:00:25,674 check.warn(importable) 2023-12-01T03:00:25,675 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.mcl.bin' is absent from the `packages` configuration. 2023-12-01T03:00:25,675 !! 2023-12-01T03:00:25,680 ******************************************************************************** 2023-12-01T03:00:25,681 ############################ 2023-12-01T03:00:25,684 # Package would be ignored # 2023-12-01T03:00:25,686 ############################ 2023-12-01T03:00:25,688 Python recognizes 'witch_msa.tools.magus.tools.mcl.bin' as an importable package[^1], 2023-12-01T03:00:25,690 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,691 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,692 package, please make sure that 'witch_msa.tools.magus.tools.mcl.bin' is explicitly added 2023-12-01T03:00:25,693 to the `packages` configuration field. 2023-12-01T03:00:25,694 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,695 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,700 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,707 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,716 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,717 If you don't want 'witch_msa.tools.magus.tools.mcl.bin' to be distributed and are 2023-12-01T03:00:25,718 already explicitly excluding 'witch_msa.tools.magus.tools.mcl.bin' via 2023-12-01T03:00:25,719 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,720 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,720 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,722 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,723 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,725 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,726 even if it does not contain any `.py` files. 2023-12-01T03:00:25,726 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,727 directory, all directories are treated like packages. 2023-12-01T03:00:25,728 ******************************************************************************** 2023-12-01T03:00:25,729 !! 2023-12-01T03:00:25,732 check.warn(importable) 2023-12-01T03:00:25,734 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.mlrmcl' is absent from the `packages` configuration. 2023-12-01T03:00:25,737 !! 2023-12-01T03:00:25,738 ******************************************************************************** 2023-12-01T03:00:25,739 ############################ 2023-12-01T03:00:25,739 # Package would be ignored # 2023-12-01T03:00:25,740 ############################ 2023-12-01T03:00:25,741 Python recognizes 'witch_msa.tools.magus.tools.mlrmcl' as an importable package[^1], 2023-12-01T03:00:25,741 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,743 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,744 package, please make sure that 'witch_msa.tools.magus.tools.mlrmcl' is explicitly added 2023-12-01T03:00:25,748 to the `packages` configuration field. 2023-12-01T03:00:25,758 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,758 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,760 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,762 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,763 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,764 If you don't want 'witch_msa.tools.magus.tools.mlrmcl' to be distributed and are 2023-12-01T03:00:25,765 already explicitly excluding 'witch_msa.tools.magus.tools.mlrmcl' via 2023-12-01T03:00:25,765 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,766 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,767 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,768 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,770 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,774 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,777 even if it does not contain any `.py` files. 2023-12-01T03:00:25,782 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,783 directory, all directories are treated like packages. 2023-12-01T03:00:25,783 ******************************************************************************** 2023-12-01T03:00:25,784 !! 2023-12-01T03:00:25,785 check.warn(importable) 2023-12-01T03:00:25,788 /tmp/pip-build-env-nfmkf0fz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'witch_msa.tools.magus.tools.raxmlng' is absent from the `packages` configuration. 2023-12-01T03:00:25,788 !! 2023-12-01T03:00:25,790 ******************************************************************************** 2023-12-01T03:00:25,792 ############################ 2023-12-01T03:00:25,794 # Package would be ignored # 2023-12-01T03:00:25,796 ############################ 2023-12-01T03:00:25,799 Python recognizes 'witch_msa.tools.magus.tools.raxmlng' as an importable package[^1], 2023-12-01T03:00:25,801 but it is absent from setuptools' `packages` configuration. 2023-12-01T03:00:25,803 This leads to an ambiguous overall configuration. If you want to distribute this 2023-12-01T03:00:25,803 package, please make sure that 'witch_msa.tools.magus.tools.raxmlng' is explicitly added 2023-12-01T03:00:25,804 to the `packages` configuration field. 2023-12-01T03:00:25,805 Alternatively, you can also rely on setuptools' discovery methods 2023-12-01T03:00:25,806 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-12-01T03:00:25,807 instead of `find_packages(...)`/`find:`). 2023-12-01T03:00:25,808 You can read more about "package discovery" on setuptools documentation page: 2023-12-01T03:00:25,816 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-12-01T03:00:25,824 If you don't want 'witch_msa.tools.magus.tools.raxmlng' to be distributed and are 2023-12-01T03:00:25,825 already explicitly excluding 'witch_msa.tools.magus.tools.raxmlng' via 2023-12-01T03:00:25,825 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-12-01T03:00:25,826 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-12-01T03:00:25,827 combination with a more fine grained `package-data` configuration. 2023-12-01T03:00:25,828 You can read more about "package data files" on setuptools documentation page: 2023-12-01T03:00:25,830 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-12-01T03:00:25,836 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-12-01T03:00:25,846 even if it does not contain any `.py` files. 2023-12-01T03:00:25,848 On the other hand, currently there is no concept of package data 2023-12-01T03:00:25,849 directory, all directories are treated like packages. 2023-12-01T03:00:25,850 ******************************************************************************** 2023-12-01T03:00:25,852 !! 2023-12-01T03:00:25,853 check.warn(importable) 2023-12-01T03:00:25,854 copying witch_msa/default.config -> build/lib/witch_msa 2023-12-01T03:00:25,858 creating build/lib/witch_msa/tools 2023-12-01T03:00:25,860 creating build/lib/witch_msa/tools/macOS 2023-12-01T03:00:25,861 copying witch_msa/tools/macOS/FastTreeMP -> build/lib/witch_msa/tools/macOS 2023-12-01T03:00:25,863 copying witch_msa/tools/macOS/hmmalign -> build/lib/witch_msa/tools/macOS 2023-12-01T03:00:25,864 copying witch_msa/tools/macOS/hmmbuild -> build/lib/witch_msa/tools/macOS 2023-12-01T03:00:25,865 copying witch_msa/tools/macOS/hmmsearch -> build/lib/witch_msa/tools/macOS 2023-12-01T03:00:25,867 copying witch_msa/tools/macOS/mafft -> build/lib/witch_msa/tools/macOS 2023-12-01T03:00:25,869 copying witch_msa/tools/macOS/mcl -> build/lib/witch_msa/tools/macOS 2023-12-01T03:00:25,870 creating build/lib/witch_msa/tools/magus 2023-12-01T03:00:25,870 copying witch_msa/tools/magus/README.md -> build/lib/witch_msa/tools/magus 2023-12-01T03:00:25,871 copying witch_msa/tools/magus/configuration.py -> build/lib/witch_msa/tools/magus 2023-12-01T03:00:25,871 copying witch_msa/tools/magus/magus.py -> build/lib/witch_msa/tools/magus 2023-12-01T03:00:25,872 creating build/lib/witch_msa/tools/magus/align 2023-12-01T03:00:25,872 copying witch_msa/tools/magus/align/__init__.py -> build/lib/witch_msa/tools/magus/align 2023-12-01T03:00:25,878 copying witch_msa/tools/magus/align/aligner.py -> build/lib/witch_msa/tools/magus/align 2023-12-01T03:00:25,882 copying witch_msa/tools/magus/align/alignment_context.py -> build/lib/witch_msa/tools/magus/align 2023-12-01T03:00:25,888 creating build/lib/witch_msa/tools/magus/align/decompose 2023-12-01T03:00:25,889 copying witch_msa/tools/magus/align/decompose/__init__.py -> build/lib/witch_msa/tools/magus/align/decompose 2023-12-01T03:00:25,889 copying witch_msa/tools/magus/align/decompose/decomposer.py -> build/lib/witch_msa/tools/magus/align/decompose 2023-12-01T03:00:25,890 copying witch_msa/tools/magus/align/decompose/initial_tree.py -> build/lib/witch_msa/tools/magus/align/decompose 2023-12-01T03:00:25,890 copying witch_msa/tools/magus/align/decompose/kmh.py -> build/lib/witch_msa/tools/magus/align/decompose 2023-12-01T03:00:25,891 creating build/lib/witch_msa/tools/magus/align/merge 2023-12-01T03:00:25,892 copying witch_msa/tools/magus/align/merge/__init__.py -> build/lib/witch_msa/tools/magus/align/merge 2023-12-01T03:00:25,893 copying witch_msa/tools/magus/align/merge/alignment_graph.py -> build/lib/witch_msa/tools/magus/align/merge 2023-12-01T03:00:25,893 copying witch_msa/tools/magus/align/merge/alignment_writer.py -> build/lib/witch_msa/tools/magus/align/merge 2023-12-01T03:00:25,894 copying witch_msa/tools/magus/align/merge/merger.py -> build/lib/witch_msa/tools/magus/align/merge 2023-12-01T03:00:25,902 copying witch_msa/tools/magus/align/merge/optimizer.py -> build/lib/witch_msa/tools/magus/align/merge 2023-12-01T03:00:25,908 creating build/lib/witch_msa/tools/magus/align/merge/graph_build 2023-12-01T03:00:25,910 copying witch_msa/tools/magus/align/merge/graph_build/__init__.py -> build/lib/witch_msa/tools/magus/align/merge/graph_build 2023-12-01T03:00:25,911 copying witch_msa/tools/magus/align/merge/graph_build/graph_builder.py -> build/lib/witch_msa/tools/magus/align/merge/graph_build 2023-12-01T03:00:25,911 creating build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-12-01T03:00:25,912 copying witch_msa/tools/magus/align/merge/graph_cluster/__init__.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-12-01T03:00:25,912 copying witch_msa/tools/magus/align/merge/graph_cluster/clean_clusters.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-12-01T03:00:25,913 copying witch_msa/tools/magus/align/merge/graph_cluster/clusterer.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-12-01T03:00:25,914 copying witch_msa/tools/magus/align/merge/graph_cluster/mcl.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-12-01T03:00:25,915 copying witch_msa/tools/magus/align/merge/graph_cluster/mlr_mcl.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-12-01T03:00:25,919 copying witch_msa/tools/magus/align/merge/graph_cluster/rg.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-12-01T03:00:25,920 creating build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:25,922 copying witch_msa/tools/magus/align/merge/graph_trace/__init__.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:25,923 copying witch_msa/tools/magus/align/merge/graph_trace/fm.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:25,924 copying witch_msa/tools/magus/align/merge/graph_trace/min_clusters.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:25,927 copying witch_msa/tools/magus/align/merge/graph_trace/mwt_search.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:25,928 copying witch_msa/tools/magus/align/merge/graph_trace/naive.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:25,928 copying witch_msa/tools/magus/align/merge/graph_trace/rg_fast_search.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:25,929 copying witch_msa/tools/magus/align/merge/graph_trace/rg_search.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:25,929 copying witch_msa/tools/magus/align/merge/graph_trace/tracer.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:25,930 creating build/lib/witch_msa/tools/magus/helpers 2023-12-01T03:00:25,932 copying witch_msa/tools/magus/helpers/__init__.py -> build/lib/witch_msa/tools/magus/helpers 2023-12-01T03:00:25,932 copying witch_msa/tools/magus/helpers/hmmutils.py -> build/lib/witch_msa/tools/magus/helpers 2023-12-01T03:00:25,933 copying witch_msa/tools/magus/helpers/sequenceutils.py -> build/lib/witch_msa/tools/magus/helpers 2023-12-01T03:00:25,934 copying witch_msa/tools/magus/helpers/treeutils.py -> build/lib/witch_msa/tools/magus/helpers 2023-12-01T03:00:25,938 creating build/lib/witch_msa/tools/magus/tasks 2023-12-01T03:00:25,944 copying witch_msa/tools/magus/tasks/__init__.py -> build/lib/witch_msa/tools/magus/tasks 2023-12-01T03:00:25,945 copying witch_msa/tools/magus/tasks/controller.py -> build/lib/witch_msa/tools/magus/tasks 2023-12-01T03:00:25,946 copying witch_msa/tools/magus/tasks/files.py -> build/lib/witch_msa/tools/magus/tasks 2023-12-01T03:00:25,947 copying witch_msa/tools/magus/tasks/manager.py -> build/lib/witch_msa/tools/magus/tasks 2023-12-01T03:00:25,947 copying witch_msa/tools/magus/tasks/task.py -> build/lib/witch_msa/tools/magus/tasks 2023-12-01T03:00:25,948 creating build/lib/witch_msa/tools/magus/tools 2023-12-01T03:00:25,949 copying witch_msa/tools/magus/tools/__init__.py -> build/lib/witch_msa/tools/magus/tools 2023-12-01T03:00:25,950 copying witch_msa/tools/magus/tools/external_tools.py -> build/lib/witch_msa/tools/magus/tools 2023-12-01T03:00:25,951 creating build/lib/witch_msa/tools/magus/tools/clustal 2023-12-01T03:00:25,951 copying witch_msa/tools/magus/tools/clustal/clustalo -> build/lib/witch_msa/tools/magus/tools/clustal 2023-12-01T03:00:25,952 creating build/lib/witch_msa/tools/magus/tools/fasttree 2023-12-01T03:00:25,953 copying witch_msa/tools/magus/tools/fasttree/FastTree -> build/lib/witch_msa/tools/magus/tools/fasttree 2023-12-01T03:00:25,956 copying witch_msa/tools/magus/tools/fasttree/FastTreeMP -> build/lib/witch_msa/tools/magus/tools/fasttree 2023-12-01T03:00:25,958 creating build/lib/witch_msa/tools/magus/tools/hmmer 2023-12-01T03:00:25,960 copying witch_msa/tools/magus/tools/hmmer/hmmalign -> build/lib/witch_msa/tools/magus/tools/hmmer 2023-12-01T03:00:25,963 copying witch_msa/tools/magus/tools/hmmer/hmmbuild -> build/lib/witch_msa/tools/magus/tools/hmmer 2023-12-01T03:00:25,964 copying witch_msa/tools/magus/tools/hmmer/hmmsearch -> build/lib/witch_msa/tools/magus/tools/hmmer 2023-12-01T03:00:25,964 creating build/lib/witch_msa/tools/magus/tools/mafft 2023-12-01T03:00:25,965 copying witch_msa/tools/magus/tools/mafft/mafft -> build/lib/witch_msa/tools/magus/tools/mafft 2023-12-01T03:00:25,966 creating build/lib/witch_msa/tools/magus/tools/mafft/mafftdir 2023-12-01T03:00:25,966 creating build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/bin 2023-12-01T03:00:25,967 copying witch_msa/tools/magus/tools/mafft/mafftdir/bin/mafft -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/bin 2023-12-01T03:00:25,967 creating build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,968 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/addsingle -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,968 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/contrafoldwrap -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,969 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/countlen -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,970 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dash_client -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,970 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/disttbfast -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,971 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndblast -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,973 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndfast7 -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,974 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndpre -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,975 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dvtditr -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,976 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/f2cl -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,978 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/getlag -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,980 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/hex2maffttext -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,984 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-distance -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,986 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-homologs.1 -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,987 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-profile -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,987 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft.1 -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,988 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafftash_premafft.pl -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,992 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/maffttext2hex -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,994 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/makedirectionlist -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:25,996 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mccaskillwrap -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,002 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/multi2hat3s -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,004 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/nodepair -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,005 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairash -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,005 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairlocalalign -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,006 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/regtable2seq -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,006 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/replaceu -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,007 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/restoreu -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,007 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/score -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,008 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seekquencer_premafft.pl -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,009 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seq2regtable -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,009 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setcore -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,010 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setdirection -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,011 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/sextet5 -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,024 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/splittbfast -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,047 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/tbfast -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,070 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/version -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:26,081 creating build/lib/witch_msa/tools/magus/tools/mcl 2023-12-01T03:00:26,082 creating build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,083 copying witch_msa/tools/magus/tools/mcl/bin/clm -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,112 copying witch_msa/tools/magus/tools/mcl/bin/clmformat -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,136 copying witch_msa/tools/magus/tools/mcl/bin/clxdo -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,139 copying witch_msa/tools/magus/tools/mcl/bin/mcl -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,162 copying witch_msa/tools/magus/tools/mcl/bin/mclblastline -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,164 copying witch_msa/tools/magus/tools/mcl/bin/mclcm -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,188 copying witch_msa/tools/magus/tools/mcl/bin/mclpipeline -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,191 copying witch_msa/tools/magus/tools/mcl/bin/mcx -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,224 copying witch_msa/tools/magus/tools/mcl/bin/mcxarray -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,248 copying witch_msa/tools/magus/tools/mcl/bin/mcxassemble -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,269 copying witch_msa/tools/magus/tools/mcl/bin/mcxdeblast -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,272 copying witch_msa/tools/magus/tools/mcl/bin/mcxdump -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,294 copying witch_msa/tools/magus/tools/mcl/bin/mcxi -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,321 copying witch_msa/tools/magus/tools/mcl/bin/mcxload -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,345 copying witch_msa/tools/magus/tools/mcl/bin/mcxmap -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,359 copying witch_msa/tools/magus/tools/mcl/bin/mcxrand -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,373 copying witch_msa/tools/magus/tools/mcl/bin/mcxsubs -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:26,395 creating build/lib/witch_msa/tools/magus/tools/mlrmcl 2023-12-01T03:00:26,396 copying witch_msa/tools/magus/tools/mlrmcl/README -> build/lib/witch_msa/tools/magus/tools/mlrmcl 2023-12-01T03:00:26,400 copying witch_msa/tools/magus/tools/mlrmcl/mlrmcl -> build/lib/witch_msa/tools/magus/tools/mlrmcl 2023-12-01T03:00:26,404 copying witch_msa/tools/magus/tools/mlrmcl/ncut -> build/lib/witch_msa/tools/magus/tools/mlrmcl 2023-12-01T03:00:26,409 creating build/lib/witch_msa/tools/magus/tools/raxmlng 2023-12-01T03:00:26,410 copying witch_msa/tools/magus/tools/raxmlng/raxml-ng -> build/lib/witch_msa/tools/magus/tools/raxmlng 2023-12-01T03:00:26,528 running build_scripts 2023-12-01T03:00:26,529 creating build/scripts-3.11 2023-12-01T03:00:26,530 copying and adjusting bin/witch-msa -> build/scripts-3.11 2023-12-01T03:00:26,532 copying and adjusting witch.py -> build/scripts-3.11 2023-12-01T03:00:26,533 changing mode of build/scripts-3.11/witch-msa from 644 to 755 2023-12-01T03:00:26,534 changing mode of build/scripts-3.11/witch.py from 644 to 755 2023-12-01T03:00:26,541 installing to build/bdist.linux-aarch64/wheel 2023-12-01T03:00:26,541 running install 2023-12-01T03:00:26,565 running install_lib 2023-12-01T03:00:26,570 creating build/bdist.linux-aarch64 2023-12-01T03:00:26,571 creating build/bdist.linux-aarch64/wheel 2023-12-01T03:00:26,573 creating build/bdist.linux-aarch64/wheel/witch_msa 2023-12-01T03:00:26,574 copying build/lib/witch_msa/configs.py -> build/bdist.linux-aarch64/wheel/witch_msa 2023-12-01T03:00:26,577 copying build/lib/witch_msa/__init__.py -> build/bdist.linux-aarch64/wheel/witch_msa 2023-12-01T03:00:26,579 copying build/lib/witch_msa/default.config -> build/bdist.linux-aarch64/wheel/witch_msa 2023-12-01T03:00:26,582 creating build/bdist.linux-aarch64/wheel/witch_msa/gcmm 2023-12-01T03:00:26,583 copying build/lib/witch_msa/gcmm/results_handler.py -> build/bdist.linux-aarch64/wheel/witch_msa/gcmm 2023-12-01T03:00:26,586 copying build/lib/witch_msa/gcmm/algorithm.py -> build/bdist.linux-aarch64/wheel/witch_msa/gcmm 2023-12-01T03:00:26,589 copying build/lib/witch_msa/gcmm/decompose_tree.py -> build/bdist.linux-aarch64/wheel/witch_msa/gcmm 2023-12-01T03:00:26,591 copying build/lib/witch_msa/gcmm/aligner.py -> build/bdist.linux-aarch64/wheel/witch_msa/gcmm 2023-12-01T03:00:26,594 copying build/lib/witch_msa/gcmm/__init__.py -> build/bdist.linux-aarch64/wheel/witch_msa/gcmm 2023-12-01T03:00:26,596 copying build/lib/witch_msa/gcmm/loader.py -> build/bdist.linux-aarch64/wheel/witch_msa/gcmm 2023-12-01T03:00:26,599 copying build/lib/witch_msa/gcmm/backbone.py -> build/bdist.linux-aarch64/wheel/witch_msa/gcmm 2023-12-01T03:00:26,602 copying build/lib/witch_msa/gcmm/weighting.py -> build/bdist.linux-aarch64/wheel/witch_msa/gcmm 2023-12-01T03:00:26,605 copying build/lib/witch_msa/gcmm/gcmm.py -> build/bdist.linux-aarch64/wheel/witch_msa/gcmm 2023-12-01T03:00:26,608 copying build/lib/witch_msa/gcmm/merger.py -> build/bdist.linux-aarch64/wheel/witch_msa/gcmm 2023-12-01T03:00:26,610 copying build/lib/witch_msa/gcmm/tree.py -> build/bdist.linux-aarch64/wheel/witch_msa/gcmm 2023-12-01T03:00:26,614 copying build/lib/witch_msa/gcmm/task.py -> build/bdist.linux-aarch64/wheel/witch_msa/gcmm 2023-12-01T03:00:26,616 copying build/lib/witch_msa/gcmm/callback.py -> build/bdist.linux-aarch64/wheel/witch_msa/gcmm 2023-12-01T03:00:26,618 creating build/bdist.linux-aarch64/wheel/witch_msa/helpers 2023-12-01T03:00:26,619 copying build/lib/witch_msa/helpers/alignment_tools.py -> build/bdist.linux-aarch64/wheel/witch_msa/helpers 2023-12-01T03:00:26,623 copying build/lib/witch_msa/helpers/pyhmmer_tools.py -> build/bdist.linux-aarch64/wheel/witch_msa/helpers 2023-12-01T03:00:26,625 copying build/lib/witch_msa/helpers/__init__.py -> build/bdist.linux-aarch64/wheel/witch_msa/helpers 2023-12-01T03:00:26,627 copying build/lib/witch_msa/helpers/general_tools.py -> build/bdist.linux-aarch64/wheel/witch_msa/helpers 2023-12-01T03:00:26,629 copying build/lib/witch_msa/helpers/math_utils.py -> build/bdist.linux-aarch64/wheel/witch_msa/helpers 2023-12-01T03:00:26,631 creating build/bdist.linux-aarch64/wheel/witch_msa/tools 2023-12-01T03:00:26,633 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/macOS 2023-12-01T03:00:26,634 copying build/lib/witch_msa/tools/macOS/hmmbuild -> build/bdist.linux-aarch64/wheel/witch_msa/tools/macOS 2023-12-01T03:00:26,651 copying build/lib/witch_msa/tools/macOS/hmmalign -> build/bdist.linux-aarch64/wheel/witch_msa/tools/macOS 2023-12-01T03:00:26,668 copying build/lib/witch_msa/tools/macOS/mafft -> build/bdist.linux-aarch64/wheel/witch_msa/tools/macOS 2023-12-01T03:00:26,673 copying build/lib/witch_msa/tools/macOS/FastTreeMP -> build/bdist.linux-aarch64/wheel/witch_msa/tools/macOS 2023-12-01T03:00:26,682 copying build/lib/witch_msa/tools/macOS/hmmsearch -> build/bdist.linux-aarch64/wheel/witch_msa/tools/macOS 2023-12-01T03:00:26,699 copying build/lib/witch_msa/tools/macOS/mcl -> build/bdist.linux-aarch64/wheel/witch_msa/tools/macOS 2023-12-01T03:00:26,709 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus 2023-12-01T03:00:26,710 copying build/lib/witch_msa/tools/magus/magus.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus 2023-12-01T03:00:26,713 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align 2023-12-01T03:00:26,714 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge 2023-12-01T03:00:26,715 copying build/lib/witch_msa/tools/magus/align/merge/alignment_writer.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge 2023-12-01T03:00:26,719 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-12-01T03:00:26,720 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/rg.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-12-01T03:00:26,722 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/clean_clusters.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-12-01T03:00:26,725 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/__init__.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-12-01T03:00:26,727 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/clusterer.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-12-01T03:00:26,729 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/mlr_mcl.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-12-01T03:00:26,731 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/mcl.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-12-01T03:00:26,733 copying build/lib/witch_msa/tools/magus/align/merge/__init__.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge 2023-12-01T03:00:26,735 copying build/lib/witch_msa/tools/magus/align/merge/alignment_graph.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge 2023-12-01T03:00:26,737 copying build/lib/witch_msa/tools/magus/align/merge/optimizer.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge 2023-12-01T03:00:26,740 copying build/lib/witch_msa/tools/magus/align/merge/merger.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge 2023-12-01T03:00:26,743 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_build 2023-12-01T03:00:26,744 copying build/lib/witch_msa/tools/magus/align/merge/graph_build/__init__.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_build 2023-12-01T03:00:26,746 copying build/lib/witch_msa/tools/magus/align/merge/graph_build/graph_builder.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_build 2023-12-01T03:00:26,749 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:26,750 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/mwt_search.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:26,752 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/rg_fast_search.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:26,755 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/rg_search.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:26,758 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/fm.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:26,760 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/__init__.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:26,762 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/naive.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:26,764 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/min_clusters.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:26,766 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/tracer.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-12-01T03:00:26,769 copying build/lib/witch_msa/tools/magus/align/aligner.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align 2023-12-01T03:00:26,771 copying build/lib/witch_msa/tools/magus/align/__init__.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align 2023-12-01T03:00:26,773 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/decompose 2023-12-01T03:00:26,774 copying build/lib/witch_msa/tools/magus/align/decompose/__init__.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/decompose 2023-12-01T03:00:26,776 copying build/lib/witch_msa/tools/magus/align/decompose/initial_tree.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/decompose 2023-12-01T03:00:26,778 copying build/lib/witch_msa/tools/magus/align/decompose/decomposer.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/decompose 2023-12-01T03:00:26,781 copying build/lib/witch_msa/tools/magus/align/decompose/kmh.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align/decompose 2023-12-01T03:00:26,784 copying build/lib/witch_msa/tools/magus/align/alignment_context.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/align 2023-12-01T03:00:26,786 copying build/lib/witch_msa/tools/magus/README.md -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus 2023-12-01T03:00:26,789 copying build/lib/witch_msa/tools/magus/configuration.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus 2023-12-01T03:00:26,792 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/helpers 2023-12-01T03:00:26,793 copying build/lib/witch_msa/tools/magus/helpers/hmmutils.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/helpers 2023-12-01T03:00:26,795 copying build/lib/witch_msa/tools/magus/helpers/__init__.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/helpers 2023-12-01T03:00:26,797 copying build/lib/witch_msa/tools/magus/helpers/sequenceutils.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/helpers 2023-12-01T03:00:26,799 copying build/lib/witch_msa/tools/magus/helpers/treeutils.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/helpers 2023-12-01T03:00:26,803 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tasks 2023-12-01T03:00:26,804 copying build/lib/witch_msa/tools/magus/tasks/controller.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tasks 2023-12-01T03:00:26,806 copying build/lib/witch_msa/tools/magus/tasks/files.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tasks 2023-12-01T03:00:26,808 copying build/lib/witch_msa/tools/magus/tasks/__init__.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tasks 2023-12-01T03:00:26,810 copying build/lib/witch_msa/tools/magus/tasks/manager.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tasks 2023-12-01T03:00:26,812 copying build/lib/witch_msa/tools/magus/tasks/task.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tasks 2023-12-01T03:00:26,815 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools 2023-12-01T03:00:26,816 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/hmmer 2023-12-01T03:00:26,817 copying build/lib/witch_msa/tools/magus/tools/hmmer/hmmbuild -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/hmmer 2023-12-01T03:00:26,844 copying build/lib/witch_msa/tools/magus/tools/hmmer/hmmalign -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/hmmer 2023-12-01T03:00:26,877 copying build/lib/witch_msa/tools/magus/tools/hmmer/hmmsearch -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/hmmer 2023-12-01T03:00:26,906 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/fasttree 2023-12-01T03:00:26,907 copying build/lib/witch_msa/tools/magus/tools/fasttree/FastTreeMP -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/fasttree 2023-12-01T03:00:26,916 copying build/lib/witch_msa/tools/magus/tools/fasttree/FastTree -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/fasttree 2023-12-01T03:00:26,924 copying build/lib/witch_msa/tools/magus/tools/external_tools.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools 2023-12-01T03:00:26,927 copying build/lib/witch_msa/tools/magus/tools/__init__.py -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools 2023-12-01T03:00:26,929 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/raxmlng 2023-12-01T03:00:26,930 copying build/lib/witch_msa/tools/magus/tools/raxmlng/raxml-ng -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/raxmlng 2023-12-01T03:00:27,027 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mlrmcl 2023-12-01T03:00:27,028 copying build/lib/witch_msa/tools/magus/tools/mlrmcl/ncut -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mlrmcl 2023-12-01T03:00:27,033 copying build/lib/witch_msa/tools/magus/tools/mlrmcl/README -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mlrmcl 2023-12-01T03:00:27,036 copying build/lib/witch_msa/tools/magus/tools/mlrmcl/mlrmcl -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mlrmcl 2023-12-01T03:00:27,041 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/clustal 2023-12-01T03:00:27,042 copying build/lib/witch_msa/tools/magus/tools/clustal/clustalo -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/clustal 2023-12-01T03:00:27,129 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft 2023-12-01T03:00:27,131 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir 2023-12-01T03:00:27,133 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/bin 2023-12-01T03:00:27,135 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/bin/mafft -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/bin 2023-12-01T03:00:27,141 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,142 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setcore -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,167 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft.1 -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,170 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairlocalalign -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,193 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndfast7 -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,211 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/sextet5 -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,229 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mccaskillwrap -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,250 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-homologs.1 -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,253 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairash -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,273 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/f2cl -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,288 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/version -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,299 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seq2regtable -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,311 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/replaceu -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,327 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/countlen -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,341 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seekquencer_premafft.pl -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,344 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/multi2hat3s -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,362 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/maffttext2hex -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,374 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/contrafoldwrap -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,391 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/hex2maffttext -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,405 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/getlag -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,427 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/disttbfast -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,457 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-profile -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,478 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/splittbfast -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,504 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-distance -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,526 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/tbfast -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,551 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dash_client -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,632 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dvtditr -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,655 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafftash_premafft.pl -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,658 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/regtable2seq -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,675 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/restoreu -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,693 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndpre -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,721 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndblast -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,740 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/nodepair -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,763 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setdirection -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,781 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/score -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,799 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/makedirectionlist -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,822 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/addsingle -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-12-01T03:00:27,851 copying build/lib/witch_msa/tools/magus/tools/mafft/mafft -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mafft 2023-12-01T03:00:27,854 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl 2023-12-01T03:00:27,856 creating build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:27,857 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxdump -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:27,881 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/clm -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:27,904 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mclpipeline -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:27,907 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxassemble -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:27,930 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxmap -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:27,947 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/clxdo -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:27,950 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcx -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:27,976 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxsubs -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:27,998 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxload -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:28,020 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mclcm -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:28,040 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxdeblast -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:28,043 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxrand -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:28,057 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxi -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:28,086 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcl -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:28,110 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxarray -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:28,134 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mclblastline -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:28,137 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/clmformat -> build/bdist.linux-aarch64/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-12-01T03:00:28,163 copying build/lib/witch_msa/init_configs.py -> build/bdist.linux-aarch64/wheel/witch_msa 2023-12-01T03:00:28,166 running install_egg_info 2023-12-01T03:00:28,170 Copying witch_msa.egg-info to build/bdist.linux-aarch64/wheel/witch_msa-1.0.2a1-py3.11.egg-info 2023-12-01T03:00:28,183 running install_scripts 2023-12-01T03:00:28,184 creating build/bdist.linux-aarch64/wheel/witch_msa-1.0.2a1.data 2023-12-01T03:00:28,184 creating build/bdist.linux-aarch64/wheel/witch_msa-1.0.2a1.data/scripts 2023-12-01T03:00:28,186 copying build/scripts-3.11/witch.py -> build/bdist.linux-aarch64/wheel/witch_msa-1.0.2a1.data/scripts 2023-12-01T03:00:28,188 copying build/scripts-3.11/witch-msa -> build/bdist.linux-aarch64/wheel/witch_msa-1.0.2a1.data/scripts 2023-12-01T03:00:28,190 changing mode of build/bdist.linux-aarch64/wheel/witch_msa-1.0.2a1.data/scripts/witch.py to 755 2023-12-01T03:00:28,191 changing mode of build/bdist.linux-aarch64/wheel/witch_msa-1.0.2a1.data/scripts/witch-msa to 755 2023-12-01T03:00:28,214 creating build/bdist.linux-aarch64/wheel/witch_msa-1.0.2a1.dist-info/WHEEL 2023-12-01T03:00:28,216 creating '/tmp/pip-wheel-s38amxw0/.tmp-_cnu572b/witch_msa-1.0.2a1-py3-none-any.whl' and adding 'build/bdist.linux-aarch64/wheel' to it 2023-12-01T03:00:28,220 adding 'witch_msa/__init__.py' 2023-12-01T03:00:28,222 adding 'witch_msa/configs.py' 2023-12-01T03:00:28,223 adding 'witch_msa/default.config' 2023-12-01T03:00:28,225 adding 'witch_msa/init_configs.py' 2023-12-01T03:00:28,227 adding 'witch_msa/gcmm/__init__.py' 2023-12-01T03:00:28,230 adding 'witch_msa/gcmm/algorithm.py' 2023-12-01T03:00:28,234 adding 'witch_msa/gcmm/aligner.py' 2023-12-01T03:00:28,236 adding 'witch_msa/gcmm/backbone.py' 2023-12-01T03:00:28,238 adding 'witch_msa/gcmm/callback.py' 2023-12-01T03:00:28,240 adding 'witch_msa/gcmm/decompose_tree.py' 2023-12-01T03:00:28,242 adding 'witch_msa/gcmm/gcmm.py' 2023-12-01T03:00:28,245 adding 'witch_msa/gcmm/loader.py' 2023-12-01T03:00:28,246 adding 'witch_msa/gcmm/merger.py' 2023-12-01T03:00:28,249 adding 'witch_msa/gcmm/results_handler.py' 2023-12-01T03:00:28,250 adding 'witch_msa/gcmm/task.py' 2023-12-01T03:00:28,253 adding 'witch_msa/gcmm/tree.py' 2023-12-01T03:00:28,255 adding 'witch_msa/gcmm/weighting.py' 2023-12-01T03:00:28,257 adding 'witch_msa/helpers/__init__.py' 2023-12-01T03:00:28,263 adding 'witch_msa/helpers/alignment_tools.py' 2023-12-01T03:00:28,265 adding 'witch_msa/helpers/general_tools.py' 2023-12-01T03:00:28,267 adding 'witch_msa/helpers/math_utils.py' 2023-12-01T03:00:28,268 adding 'witch_msa/helpers/pyhmmer_tools.py' 2023-12-01T03:00:28,325 adding 'witch_msa/tools/macOS/FastTreeMP' 2023-12-01T03:00:28,469 adding 'witch_msa/tools/macOS/hmmalign' 2023-12-01T03:00:28,635 adding 'witch_msa/tools/macOS/hmmbuild' 2023-12-01T03:00:28,810 adding 'witch_msa/tools/macOS/hmmsearch' 2023-12-01T03:00:28,827 adding 'witch_msa/tools/macOS/mafft' 2023-12-01T03:00:28,896 adding 'witch_msa/tools/macOS/mcl' 2023-12-01T03:00:28,901 adding 'witch_msa/tools/magus/README.md' 2023-12-01T03:00:28,903 adding 'witch_msa/tools/magus/configuration.py' 2023-12-01T03:00:28,905 adding 'witch_msa/tools/magus/magus.py' 2023-12-01T03:00:28,907 adding 'witch_msa/tools/magus/align/__init__.py' 2023-12-01T03:00:28,909 adding 'witch_msa/tools/magus/align/aligner.py' 2023-12-01T03:00:28,911 adding 'witch_msa/tools/magus/align/alignment_context.py' 2023-12-01T03:00:28,913 adding 'witch_msa/tools/magus/align/decompose/__init__.py' 2023-12-01T03:00:28,914 adding 'witch_msa/tools/magus/align/decompose/decomposer.py' 2023-12-01T03:00:28,917 adding 'witch_msa/tools/magus/align/decompose/initial_tree.py' 2023-12-01T03:00:28,918 adding 'witch_msa/tools/magus/align/decompose/kmh.py' 2023-12-01T03:00:28,920 adding 'witch_msa/tools/magus/align/merge/__init__.py' 2023-12-01T03:00:28,922 adding 'witch_msa/tools/magus/align/merge/alignment_graph.py' 2023-12-01T03:00:28,924 adding 'witch_msa/tools/magus/align/merge/alignment_writer.py' 2023-12-01T03:00:28,926 adding 'witch_msa/tools/magus/align/merge/merger.py' 2023-12-01T03:00:28,928 adding 'witch_msa/tools/magus/align/merge/optimizer.py' 2023-12-01T03:00:28,930 adding 'witch_msa/tools/magus/align/merge/graph_build/__init__.py' 2023-12-01T03:00:28,933 adding 'witch_msa/tools/magus/align/merge/graph_build/graph_builder.py' 2023-12-01T03:00:28,935 adding 'witch_msa/tools/magus/align/merge/graph_cluster/__init__.py' 2023-12-01T03:00:28,937 adding 'witch_msa/tools/magus/align/merge/graph_cluster/clean_clusters.py' 2023-12-01T03:00:28,938 adding 'witch_msa/tools/magus/align/merge/graph_cluster/clusterer.py' 2023-12-01T03:00:28,940 adding 'witch_msa/tools/magus/align/merge/graph_cluster/mcl.py' 2023-12-01T03:00:28,941 adding 'witch_msa/tools/magus/align/merge/graph_cluster/mlr_mcl.py' 2023-12-01T03:00:28,942 adding 'witch_msa/tools/magus/align/merge/graph_cluster/rg.py' 2023-12-01T03:00:28,944 adding 'witch_msa/tools/magus/align/merge/graph_trace/__init__.py' 2023-12-01T03:00:28,946 adding 'witch_msa/tools/magus/align/merge/graph_trace/fm.py' 2023-12-01T03:00:28,949 adding 'witch_msa/tools/magus/align/merge/graph_trace/min_clusters.py' 2023-12-01T03:00:28,952 adding 'witch_msa/tools/magus/align/merge/graph_trace/mwt_search.py' 2023-12-01T03:00:28,954 adding 'witch_msa/tools/magus/align/merge/graph_trace/naive.py' 2023-12-01T03:00:28,956 adding 'witch_msa/tools/magus/align/merge/graph_trace/rg_fast_search.py' 2023-12-01T03:00:28,958 adding 'witch_msa/tools/magus/align/merge/graph_trace/rg_search.py' 2023-12-01T03:00:28,960 adding 'witch_msa/tools/magus/align/merge/graph_trace/tracer.py' 2023-12-01T03:00:28,962 adding 'witch_msa/tools/magus/helpers/__init__.py' 2023-12-01T03:00:28,964 adding 'witch_msa/tools/magus/helpers/hmmutils.py' 2023-12-01T03:00:28,965 adding 'witch_msa/tools/magus/helpers/sequenceutils.py' 2023-12-01T03:00:28,967 adding 'witch_msa/tools/magus/helpers/treeutils.py' 2023-12-01T03:00:28,969 adding 'witch_msa/tools/magus/tasks/__init__.py' 2023-12-01T03:00:28,971 adding 'witch_msa/tools/magus/tasks/controller.py' 2023-12-01T03:00:28,972 adding 'witch_msa/tools/magus/tasks/files.py' 2023-12-01T03:00:28,974 adding 'witch_msa/tools/magus/tasks/manager.py' 2023-12-01T03:00:28,976 adding 'witch_msa/tools/magus/tasks/task.py' 2023-12-01T03:00:28,977 adding 'witch_msa/tools/magus/tools/__init__.py' 2023-12-01T03:00:28,979 adding 'witch_msa/tools/magus/tools/external_tools.py' 2023-12-01T03:00:29,783 adding 'witch_msa/tools/magus/tools/clustal/clustalo' 2023-12-01T03:00:29,882 adding 'witch_msa/tools/magus/tools/fasttree/FastTree' 2023-12-01T03:00:29,954 adding 'witch_msa/tools/magus/tools/fasttree/FastTreeMP' 2023-12-01T03:00:30,165 adding 'witch_msa/tools/magus/tools/hmmer/hmmalign' 2023-12-01T03:00:30,386 adding 'witch_msa/tools/magus/tools/hmmer/hmmbuild' 2023-12-01T03:00:30,627 adding 'witch_msa/tools/magus/tools/hmmer/hmmsearch' 2023-12-01T03:00:30,639 adding 'witch_msa/tools/magus/tools/mafft/mafft' 2023-12-01T03:00:30,650 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/bin/mafft' 2023-12-01T03:00:30,901 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/addsingle' 2023-12-01T03:00:31,089 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/contrafoldwrap' 2023-12-01T03:00:31,212 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/countlen' 2023-12-01T03:00:32,015 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dash_client' 2023-12-01T03:00:32,294 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/disttbfast' 2023-12-01T03:00:32,474 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndblast' 2023-12-01T03:00:32,651 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndfast7' 2023-12-01T03:00:32,827 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndpre' 2023-12-01T03:00:33,074 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dvtditr' 2023-12-01T03:00:33,214 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/f2cl' 2023-12-01T03:00:33,446 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/getlag' 2023-12-01T03:00:33,557 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/hex2maffttext' 2023-12-01T03:00:33,732 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-distance' 2023-12-01T03:00:33,740 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-homologs.1' 2023-12-01T03:00:33,967 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-profile' 2023-12-01T03:00:33,977 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft.1' 2023-12-01T03:00:33,980 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafftash_premafft.pl' 2023-12-01T03:00:34,083 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/maffttext2hex' 2023-12-01T03:00:34,318 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/makedirectionlist' 2023-12-01T03:00:34,494 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mccaskillwrap' 2023-12-01T03:00:34,682 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/multi2hat3s' 2023-12-01T03:00:34,927 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/nodepair' 2023-12-01T03:00:35,165 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairash' 2023-12-01T03:00:35,406 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairlocalalign' 2023-12-01T03:00:35,574 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/regtable2seq' 2023-12-01T03:00:35,740 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/replaceu' 2023-12-01T03:00:35,907 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/restoreu' 2023-12-01T03:00:36,081 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/score' 2023-12-01T03:00:36,090 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seekquencer_premafft.pl' 2023-12-01T03:00:36,208 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seq2regtable' 2023-12-01T03:00:36,443 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setcore' 2023-12-01T03:00:36,608 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setdirection' 2023-12-01T03:00:36,785 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/sextet5' 2023-12-01T03:00:37,024 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/splittbfast' 2023-12-01T03:00:37,280 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/tbfast' 2023-12-01T03:00:37,395 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/version' 2023-12-01T03:00:37,648 adding 'witch_msa/tools/magus/tools/mcl/bin/clm' 2023-12-01T03:00:37,877 adding 'witch_msa/tools/magus/tools/mcl/bin/clmformat' 2023-12-01T03:00:37,887 adding 'witch_msa/tools/magus/tools/mcl/bin/clxdo' 2023-12-01T03:00:38,089 adding 'witch_msa/tools/magus/tools/mcl/bin/mcl' 2023-12-01T03:00:38,099 adding 'witch_msa/tools/magus/tools/mcl/bin/mclblastline' 2023-12-01T03:00:38,312 adding 'witch_msa/tools/magus/tools/mcl/bin/mclcm' 2023-12-01T03:00:38,323 adding 'witch_msa/tools/magus/tools/mcl/bin/mclpipeline' 2023-12-01T03:00:38,576 adding 'witch_msa/tools/magus/tools/mcl/bin/mcx' 2023-12-01T03:00:38,800 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxarray' 2023-12-01T03:00:39,010 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxassemble' 2023-12-01T03:00:39,020 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxdeblast' 2023-12-01T03:00:39,224 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxdump' 2023-12-01T03:00:39,456 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxi' 2023-12-01T03:00:39,685 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxload' 2023-12-01T03:00:39,814 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxmap' 2023-12-01T03:00:39,946 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxrand' 2023-12-01T03:00:40,170 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxsubs' 2023-12-01T03:00:40,180 adding 'witch_msa/tools/magus/tools/mlrmcl/README' 2023-12-01T03:00:40,209 adding 'witch_msa/tools/magus/tools/mlrmcl/mlrmcl' 2023-12-01T03:00:40,232 adding 'witch_msa/tools/magus/tools/mlrmcl/ncut' 2023-12-01T03:00:41,417 adding 'witch_msa/tools/magus/tools/raxmlng/raxml-ng' 2023-12-01T03:00:41,463 adding 'witch_msa-1.0.2a1.data/scripts/witch-msa' 2023-12-01T03:00:41,464 adding 'witch_msa-1.0.2a1.data/scripts/witch.py' 2023-12-01T03:00:41,472 adding 'witch_msa-1.0.2a1.dist-info/LICENSE' 2023-12-01T03:00:41,480 adding 'witch_msa-1.0.2a1.dist-info/METADATA' 2023-12-01T03:00:41,482 adding 'witch_msa-1.0.2a1.dist-info/WHEEL' 2023-12-01T03:00:41,483 adding 'witch_msa-1.0.2a1.dist-info/top_level.txt' 2023-12-01T03:00:41,485 adding 'witch_msa-1.0.2a1.dist-info/RECORD' 2023-12-01T03:00:41,935 removing build/bdist.linux-aarch64/wheel 2023-12-01T03:00:42,154 Building wheel for witch-msa (pyproject.toml): finished with status 'done' 2023-12-01T03:00:42,750 Created wheel for witch-msa: filename=witch_msa-1.0.2a1-py3-none-any.whl size=29116702 sha256=4ba431635ab1cb66b533f39a613a0451577fdbf854dace83aad27dbac829afac 2023-12-01T03:00:42,752 Stored in directory: /tmp/pip-ephem-wheel-cache-aie2lrlr/wheels/89/de/cb/5bb8392dc1083d0f73b1f1a3930f2b8ab77b1c3088ddf2f1ba 2023-12-01T03:00:42,804 Successfully built witch-msa 2023-12-01T03:00:43,501 Removed build tracker: '/tmp/pip-build-tracker-9x2h5zzl'