2023-11-24T07:11:01,095 Created temporary directory: /tmp/pip-build-tracker-pvegcflv 2023-11-24T07:11:01,096 Initialized build tracking at /tmp/pip-build-tracker-pvegcflv 2023-11-24T07:11:01,097 Created build tracker: /tmp/pip-build-tracker-pvegcflv 2023-11-24T07:11:01,097 Entered build tracker: /tmp/pip-build-tracker-pvegcflv 2023-11-24T07:11:01,098 Created temporary directory: /tmp/pip-wheel-l497aqn0 2023-11-24T07:11:01,101 Created temporary directory: /tmp/pip-ephem-wheel-cache-y_ke2f2b 2023-11-24T07:11:01,123 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-24T07:11:01,127 2 location(s) to search for versions of witch-msa: 2023-11-24T07:11:01,127 * https://pypi.org/simple/witch-msa/ 2023-11-24T07:11:01,127 * https://www.piwheels.org/simple/witch-msa/ 2023-11-24T07:11:01,128 Fetching project page and analyzing links: https://pypi.org/simple/witch-msa/ 2023-11-24T07:11:01,128 Getting page https://pypi.org/simple/witch-msa/ 2023-11-24T07:11:01,130 Found index url https://pypi.org/simple/ 2023-11-24T07:11:01,270 Fetched page https://pypi.org/simple/witch-msa/ as application/vnd.pypi.simple.v1+json 2023-11-24T07:11:01,273 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 2023-11-24T07:11:01,274 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) 2023-11-24T07:11:01,275 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 2023-11-24T07:11:01,276 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) 2023-11-24T07:11:01,277 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 2023-11-24T07:11:01,278 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) 2023-11-24T07:11:01,279 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 2023-11-24T07:11:01,279 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) 2023-11-24T07:11:01,280 Fetching project page and analyzing links: https://www.piwheels.org/simple/witch-msa/ 2023-11-24T07:11:01,281 Getting page https://www.piwheels.org/simple/witch-msa/ 2023-11-24T07:11:01,282 Found index url https://www.piwheels.org/simple/ 2023-11-24T07:11:01,446 Fetched page https://www.piwheels.org/simple/witch-msa/ as text/html 2023-11-24T07:11:01,448 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) 2023-11-24T07:11:01,449 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) 2023-11-24T07:11:01,449 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) 2023-11-24T07:11:01,450 Skipping link: not a file: https://www.piwheels.org/simple/witch-msa/ 2023-11-24T07:11:01,451 Skipping link: not a file: https://pypi.org/simple/witch-msa/ 2023-11-24T07:11:01,479 Given no hashes to check 1 links for project 'witch-msa': discarding no candidates 2023-11-24T07:11:01,507 Collecting witch-msa==1.0.1 2023-11-24T07:11:01,510 Created temporary directory: /tmp/pip-unpack-vsn226ld 2023-11-24T07:11:01,968 Downloading witch-msa-1.0.1.tar.gz (29.0 MB) 2023-11-24T07:11:11,873 Added witch-msa==1.0.1 from https://files.pythonhosted.org/packages/19/e6/150568e28ab0565dd78080eba70d4d2254038ef55327b82919e5915c6101/witch-msa-1.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-pvegcflv' 2023-11-24T07:11:11,877 Created temporary directory: /tmp/pip-build-env-e9w5fx0h 2023-11-24T07:11:11,881 Installing build dependencies: started 2023-11-24T07:11:11,882 Running command pip subprocess to install build dependencies 2023-11-24T07:11:13,097 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-11-24T07:11:13,633 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-24T07:11:15,195 Collecting setuptools 2023-11-24T07:11:15,196 Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/bb/e1/ed2dd0850446b8697ad28d118df885ad04140c64ace06c4bd559f7c8a94f/setuptools-69.0.2-py3-none-any.whl.metadata 2023-11-24T07:11:15,202 Using cached setuptools-69.0.2-py3-none-any.whl.metadata (6.3 kB) 2023-11-24T07:11:15,373 Using cached setuptools-69.0.2-py3-none-any.whl (819 kB) 2023-11-24T07:11:17,831 Installing collected packages: setuptools 2023-11-24T07:11:20,241 Successfully installed setuptools-69.0.2 2023-11-24T07:11:20,728 [notice] A new release of pip is available: 23.2.1 -> 23.3.1 2023-11-24T07:11:20,729 [notice] To update, run: python3 -m pip install --upgrade pip 2023-11-24T07:11:21,021 Installing build dependencies: finished with status 'done' 2023-11-24T07:11:21,026 Getting requirements to build wheel: started 2023-11-24T07:11:21,028 Running command Getting requirements to build wheel 2023-11-24T07:11:22,400 running egg_info 2023-11-24T07:11:22,409 writing witch_msa.egg-info/PKG-INFO 2023-11-24T07:11:22,416 writing dependency_links to witch_msa.egg-info/dependency_links.txt 2023-11-24T07:11:22,419 writing requirements to witch_msa.egg-info/requires.txt 2023-11-24T07:11:22,421 writing top-level names to witch_msa.egg-info/top_level.txt 2023-11-24T07:11:22,450 reading manifest file 'witch_msa.egg-info/SOURCES.txt' 2023-11-24T07:11:22,490 reading manifest template 'MANIFEST.in' 2023-11-24T07:11:22,529 no previously-included directories found matching '*/__pycache__' 2023-11-24T07:11:22,531 warning: no previously-included files matching '*.py[cod]' found anywhere in distribution 2023-11-24T07:11:22,532 adding license file 'LICENSE' 2023-11-24T07:11:22,539 writing manifest file 'witch_msa.egg-info/SOURCES.txt' 2023-11-24T07:11:22,651 Getting requirements to build wheel: finished with status 'done' 2023-11-24T07:11:22,661 Installing backend dependencies: started 2023-11-24T07:11:22,662 Running command pip subprocess to install backend dependencies 2023-11-24T07:11:23,909 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-11-24T07:11:24,410 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-24T07:11:24,926 Collecting wheel 2023-11-24T07:11:24,944 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.3-py3-none-any.whl (65 kB) 2023-11-24T07:11:27,153 Installing collected packages: wheel 2023-11-24T07:11:27,392 Creating /tmp/pip-build-env-e9w5fx0h/normal/local/bin 2023-11-24T07:11:27,395 changing mode of /tmp/pip-build-env-e9w5fx0h/normal/local/bin/wheel to 755 2023-11-24T07:11:27,407 Successfully installed wheel-0.41.3 2023-11-24T07:11:27,675 [notice] A new release of pip is available: 23.2.1 -> 23.3.1 2023-11-24T07:11:27,676 [notice] To update, run: python3 -m pip install --upgrade pip 2023-11-24T07:11:27,902 Installing backend dependencies: finished with status 'done' 2023-11-24T07:11:27,904 Created temporary directory: /tmp/pip-modern-metadata-ptlbo_2q 2023-11-24T07:11:27,906 Preparing metadata (pyproject.toml): started 2023-11-24T07:11:27,907 Running command Preparing metadata (pyproject.toml) 2023-11-24T07:11:28,702 running dist_info 2023-11-24T07:11:28,707 creating /tmp/pip-modern-metadata-ptlbo_2q/witch_msa.egg-info 2023-11-24T07:11:28,711 writing /tmp/pip-modern-metadata-ptlbo_2q/witch_msa.egg-info/PKG-INFO 2023-11-24T07:11:28,715 writing dependency_links to /tmp/pip-modern-metadata-ptlbo_2q/witch_msa.egg-info/dependency_links.txt 2023-11-24T07:11:28,717 writing requirements to /tmp/pip-modern-metadata-ptlbo_2q/witch_msa.egg-info/requires.txt 2023-11-24T07:11:28,718 writing top-level names to /tmp/pip-modern-metadata-ptlbo_2q/witch_msa.egg-info/top_level.txt 2023-11-24T07:11:28,720 writing manifest file '/tmp/pip-modern-metadata-ptlbo_2q/witch_msa.egg-info/SOURCES.txt' 2023-11-24T07:11:28,741 reading manifest file '/tmp/pip-modern-metadata-ptlbo_2q/witch_msa.egg-info/SOURCES.txt' 2023-11-24T07:11:28,743 reading manifest template 'MANIFEST.in' 2023-11-24T07:11:28,776 no previously-included directories found matching '*/__pycache__' 2023-11-24T07:11:28,777 warning: no previously-included files matching '*.py[cod]' found anywhere in distribution 2023-11-24T07:11:28,778 adding license file 'LICENSE' 2023-11-24T07:11:28,784 writing manifest file '/tmp/pip-modern-metadata-ptlbo_2q/witch_msa.egg-info/SOURCES.txt' 2023-11-24T07:11:28,785 creating '/tmp/pip-modern-metadata-ptlbo_2q/witch_msa-1.0.1.dist-info' 2023-11-24T07:11:28,937 Preparing metadata (pyproject.toml): finished with status 'done' 2023-11-24T07:11:28,950 Source in /tmp/pip-wheel-l497aqn0/witch-msa_8f34c789d2c1433d8ad9000b32f03c97 has version 1.0.1, which satisfies requirement witch-msa==1.0.1 from https://files.pythonhosted.org/packages/19/e6/150568e28ab0565dd78080eba70d4d2254038ef55327b82919e5915c6101/witch-msa-1.0.1.tar.gz 2023-11-24T07:11:28,951 Removed witch-msa==1.0.1 from https://files.pythonhosted.org/packages/19/e6/150568e28ab0565dd78080eba70d4d2254038ef55327b82919e5915c6101/witch-msa-1.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-pvegcflv' 2023-11-24T07:11:28,971 Created temporary directory: /tmp/pip-unpack-v2yufmeq 2023-11-24T07:11:28,972 Created temporary directory: /tmp/pip-unpack-ly3gnff2 2023-11-24T07:11:28,997 Building wheels for collected packages: witch-msa 2023-11-24T07:11:29,002 Created temporary directory: /tmp/pip-wheel-nnj0zge3 2023-11-24T07:11:29,002 Destination directory: /tmp/pip-wheel-nnj0zge3 2023-11-24T07:11:29,005 Building wheel for witch-msa (pyproject.toml): started 2023-11-24T07:11:29,006 Running command Building wheel for witch-msa (pyproject.toml) 2023-11-24T07:11:29,752 running bdist_wheel 2023-11-24T07:11:29,768 running build 2023-11-24T07:11:29,769 running build_py 2023-11-24T07:11:29,773 creating build 2023-11-24T07:11:29,774 creating build/lib 2023-11-24T07:11:29,775 creating build/lib/witch_msa 2023-11-24T07:11:29,776 copying witch_msa/__init__.py -> build/lib/witch_msa 2023-11-24T07:11:29,779 copying witch_msa/init_configs.py -> build/lib/witch_msa 2023-11-24T07:11:29,781 copying witch_msa/configs.py -> build/lib/witch_msa 2023-11-24T07:11:29,784 creating build/lib/witch_msa/gcmm 2023-11-24T07:11:29,785 copying witch_msa/gcmm/__init__.py -> build/lib/witch_msa/gcmm 2023-11-24T07:11:29,788 copying witch_msa/gcmm/backbone.py -> build/lib/witch_msa/gcmm 2023-11-24T07:11:29,790 copying witch_msa/gcmm/tree.py -> build/lib/witch_msa/gcmm 2023-11-24T07:11:29,793 copying witch_msa/gcmm/callback.py -> build/lib/witch_msa/gcmm 2023-11-24T07:11:29,795 copying witch_msa/gcmm/results_handler.py -> build/lib/witch_msa/gcmm 2023-11-24T07:11:29,797 copying witch_msa/gcmm/loader.py -> build/lib/witch_msa/gcmm 2023-11-24T07:11:29,800 copying witch_msa/gcmm/aligner.py -> build/lib/witch_msa/gcmm 2023-11-24T07:11:29,802 copying witch_msa/gcmm/merger.py -> build/lib/witch_msa/gcmm 2023-11-24T07:11:29,804 copying witch_msa/gcmm/decompose_tree.py -> build/lib/witch_msa/gcmm 2023-11-24T07:11:29,806 copying witch_msa/gcmm/gcmm.py -> build/lib/witch_msa/gcmm 2023-11-24T07:11:29,808 copying witch_msa/gcmm/algorithm.py -> build/lib/witch_msa/gcmm 2023-11-24T07:11:29,811 copying witch_msa/gcmm/task.py -> build/lib/witch_msa/gcmm 2023-11-24T07:11:29,813 copying witch_msa/gcmm/weighting.py -> build/lib/witch_msa/gcmm 2023-11-24T07:11:29,816 creating build/lib/witch_msa/helpers 2023-11-24T07:11:29,817 copying witch_msa/helpers/__init__.py -> build/lib/witch_msa/helpers 2023-11-24T07:11:29,818 copying witch_msa/helpers/general_tools.py -> build/lib/witch_msa/helpers 2023-11-24T07:11:29,820 copying witch_msa/helpers/pyhmmer_tools.py -> build/lib/witch_msa/helpers 2023-11-24T07:11:29,822 copying witch_msa/helpers/alignment_tools.py -> build/lib/witch_msa/helpers 2023-11-24T07:11:29,825 copying witch_msa/helpers/math_utils.py -> build/lib/witch_msa/helpers 2023-11-24T07:11:29,826 running egg_info 2023-11-24T07:11:29,829 writing witch_msa.egg-info/PKG-INFO 2023-11-24T07:11:29,834 writing dependency_links to witch_msa.egg-info/dependency_links.txt 2023-11-24T07:11:29,835 writing requirements to witch_msa.egg-info/requires.txt 2023-11-24T07:11:29,836 writing top-level names to witch_msa.egg-info/top_level.txt 2023-11-24T07:11:29,846 reading manifest file 'witch_msa.egg-info/SOURCES.txt' 2023-11-24T07:11:29,850 reading manifest template 'MANIFEST.in' 2023-11-24T07:11:29,863 no previously-included directories found matching '*/__pycache__' 2023-11-24T07:11:29,865 warning: no previously-included files matching '*.py[cod]' found anywhere in distribution 2023-11-24T07:11:29,865 adding license file 'LICENSE' 2023-11-24T07:11:29,873 writing manifest file 'witch_msa.egg-info/SOURCES.txt' 2023-11-24T07:11:29,876 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:29,877 !! 2023-11-24T07:11:29,878 ******************************************************************************** 2023-11-24T07:11:29,878 ############################ 2023-11-24T07:11:29,879 # Package would be ignored # 2023-11-24T07:11:29,879 ############################ 2023-11-24T07:11:29,880 Python recognizes 'witch_msa.tools.macOS' as an importable package[^1], 2023-11-24T07:11:29,881 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:29,882 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:29,882 package, please make sure that 'witch_msa.tools.macOS' is explicitly added 2023-11-24T07:11:29,883 to the `packages` configuration field. 2023-11-24T07:11:29,884 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:29,885 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:29,885 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:29,886 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:29,887 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:29,888 If you don't want 'witch_msa.tools.macOS' to be distributed and are 2023-11-24T07:11:29,889 already explicitly excluding 'witch_msa.tools.macOS' via 2023-11-24T07:11:29,889 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:29,890 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:29,891 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:29,891 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:29,892 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:29,893 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:29,894 even if it does not contain any `.py` files. 2023-11-24T07:11:29,894 On the other hand, currently there is no concept of package data 2023-11-24T07:11:29,894 directory, all directories are treated like packages. 2023-11-24T07:11:29,895 ******************************************************************************** 2023-11-24T07:11:29,896 !! 2023-11-24T07:11:29,896 check.warn(importable) 2023-11-24T07:11:29,897 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:29,897 !! 2023-11-24T07:11:29,898 ******************************************************************************** 2023-11-24T07:11:29,898 ############################ 2023-11-24T07:11:29,899 # Package would be ignored # 2023-11-24T07:11:29,899 ############################ 2023-11-24T07:11:29,900 Python recognizes 'witch_msa.tools.magus' as an importable package[^1], 2023-11-24T07:11:29,900 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:29,901 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:29,902 package, please make sure that 'witch_msa.tools.magus' is explicitly added 2023-11-24T07:11:29,902 to the `packages` configuration field. 2023-11-24T07:11:29,903 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:29,904 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:29,904 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:29,905 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:29,906 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:29,907 If you don't want 'witch_msa.tools.magus' to be distributed and are 2023-11-24T07:11:29,908 already explicitly excluding 'witch_msa.tools.magus' via 2023-11-24T07:11:29,909 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:29,909 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:29,910 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:29,911 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:29,912 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:29,914 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:29,919 even if it does not contain any `.py` files. 2023-11-24T07:11:29,919 On the other hand, currently there is no concept of package data 2023-11-24T07:11:29,920 directory, all directories are treated like packages. 2023-11-24T07:11:29,920 ******************************************************************************** 2023-11-24T07:11:29,921 !! 2023-11-24T07:11:29,922 check.warn(importable) 2023-11-24T07:11:29,923 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:29,924 !! 2023-11-24T07:11:29,930 ******************************************************************************** 2023-11-24T07:11:29,932 ############################ 2023-11-24T07:11:29,933 # Package would be ignored # 2023-11-24T07:11:29,934 ############################ 2023-11-24T07:11:29,934 Python recognizes 'witch_msa.tools.magus.align' as an importable package[^1], 2023-11-24T07:11:29,934 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:29,935 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:29,936 package, please make sure that 'witch_msa.tools.magus.align' is explicitly added 2023-11-24T07:11:29,936 to the `packages` configuration field. 2023-11-24T07:11:29,937 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:29,938 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:29,938 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:29,945 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:29,949 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:29,950 If you don't want 'witch_msa.tools.magus.align' to be distributed and are 2023-11-24T07:11:29,950 already explicitly excluding 'witch_msa.tools.magus.align' via 2023-11-24T07:11:29,951 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:29,951 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:29,952 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:29,953 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:29,954 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:29,956 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:29,956 even if it does not contain any `.py` files. 2023-11-24T07:11:29,958 On the other hand, currently there is no concept of package data 2023-11-24T07:11:29,961 directory, all directories are treated like packages. 2023-11-24T07:11:29,964 ******************************************************************************** 2023-11-24T07:11:29,967 !! 2023-11-24T07:11:29,968 check.warn(importable) 2023-11-24T07:11:29,968 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:29,968 !! 2023-11-24T07:11:29,970 ******************************************************************************** 2023-11-24T07:11:29,970 ############################ 2023-11-24T07:11:29,971 # Package would be ignored # 2023-11-24T07:11:29,972 ############################ 2023-11-24T07:11:29,973 Python recognizes 'witch_msa.tools.magus.align.decompose' as an importable package[^1], 2023-11-24T07:11:29,973 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:29,974 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:29,975 package, please make sure that 'witch_msa.tools.magus.align.decompose' is explicitly added 2023-11-24T07:11:29,976 to the `packages` configuration field. 2023-11-24T07:11:29,979 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:29,980 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:29,981 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:29,983 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:29,983 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:29,984 If you don't want 'witch_msa.tools.magus.align.decompose' to be distributed and are 2023-11-24T07:11:29,985 already explicitly excluding 'witch_msa.tools.magus.align.decompose' via 2023-11-24T07:11:29,985 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:29,986 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:29,986 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:29,987 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:29,989 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:29,990 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:29,991 even if it does not contain any `.py` files. 2023-11-24T07:11:29,991 On the other hand, currently there is no concept of package data 2023-11-24T07:11:29,992 directory, all directories are treated like packages. 2023-11-24T07:11:29,992 ******************************************************************************** 2023-11-24T07:11:29,993 !! 2023-11-24T07:11:29,994 check.warn(importable) 2023-11-24T07:11:29,994 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:29,995 !! 2023-11-24T07:11:29,996 ******************************************************************************** 2023-11-24T07:11:29,996 ############################ 2023-11-24T07:11:29,997 # Package would be ignored # 2023-11-24T07:11:29,997 ############################ 2023-11-24T07:11:29,998 Python recognizes 'witch_msa.tools.magus.align.merge' as an importable package[^1], 2023-11-24T07:11:29,998 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:30,000 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:30,000 package, please make sure that 'witch_msa.tools.magus.align.merge' is explicitly added 2023-11-24T07:11:30,001 to the `packages` configuration field. 2023-11-24T07:11:30,002 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:30,002 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:30,003 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:30,004 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:30,005 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:30,006 If you don't want 'witch_msa.tools.magus.align.merge' to be distributed and are 2023-11-24T07:11:30,006 already explicitly excluding 'witch_msa.tools.magus.align.merge' via 2023-11-24T07:11:30,007 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:30,007 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:30,008 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:30,009 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:30,010 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:30,012 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:30,013 even if it does not contain any `.py` files. 2023-11-24T07:11:30,013 On the other hand, currently there is no concept of package data 2023-11-24T07:11:30,014 directory, all directories are treated like packages. 2023-11-24T07:11:30,014 ******************************************************************************** 2023-11-24T07:11:30,015 !! 2023-11-24T07:11:30,016 check.warn(importable) 2023-11-24T07:11:30,016 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:30,017 !! 2023-11-24T07:11:30,018 ******************************************************************************** 2023-11-24T07:11:30,018 ############################ 2023-11-24T07:11:30,019 # Package would be ignored # 2023-11-24T07:11:30,019 ############################ 2023-11-24T07:11:30,020 Python recognizes 'witch_msa.tools.magus.align.merge.graph_build' as an importable package[^1], 2023-11-24T07:11:30,020 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:30,021 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:30,022 package, please make sure that 'witch_msa.tools.magus.align.merge.graph_build' is explicitly added 2023-11-24T07:11:30,022 to the `packages` configuration field. 2023-11-24T07:11:30,023 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:30,024 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:30,024 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:30,025 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:30,026 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:30,027 If you don't want 'witch_msa.tools.magus.align.merge.graph_build' to be distributed and are 2023-11-24T07:11:30,028 already explicitly excluding 'witch_msa.tools.magus.align.merge.graph_build' via 2023-11-24T07:11:30,029 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:30,029 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:30,030 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:30,031 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:30,032 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:30,033 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:30,034 even if it does not contain any `.py` files. 2023-11-24T07:11:30,034 On the other hand, currently there is no concept of package data 2023-11-24T07:11:30,035 directory, all directories are treated like packages. 2023-11-24T07:11:30,035 ******************************************************************************** 2023-11-24T07:11:30,037 !! 2023-11-24T07:11:30,037 check.warn(importable) 2023-11-24T07:11:30,038 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:30,038 !! 2023-11-24T07:11:30,039 ******************************************************************************** 2023-11-24T07:11:30,040 ############################ 2023-11-24T07:11:30,041 # Package would be ignored # 2023-11-24T07:11:30,041 ############################ 2023-11-24T07:11:30,042 Python recognizes 'witch_msa.tools.magus.align.merge.graph_cluster' as an importable package[^1], 2023-11-24T07:11:30,042 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:30,043 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:30,044 package, please make sure that 'witch_msa.tools.magus.align.merge.graph_cluster' is explicitly added 2023-11-24T07:11:30,044 to the `packages` configuration field. 2023-11-24T07:11:30,045 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:30,046 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:30,046 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:30,047 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:30,048 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:30,049 If you don't want 'witch_msa.tools.magus.align.merge.graph_cluster' to be distributed and are 2023-11-24T07:11:30,049 already explicitly excluding 'witch_msa.tools.magus.align.merge.graph_cluster' via 2023-11-24T07:11:30,050 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:30,050 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:30,051 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:30,052 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:30,053 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:30,055 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:30,056 even if it does not contain any `.py` files. 2023-11-24T07:11:30,056 On the other hand, currently there is no concept of package data 2023-11-24T07:11:30,057 directory, all directories are treated like packages. 2023-11-24T07:11:30,057 ******************************************************************************** 2023-11-24T07:11:30,058 !! 2023-11-24T07:11:30,059 check.warn(importable) 2023-11-24T07:11:30,059 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:30,060 !! 2023-11-24T07:11:30,061 ******************************************************************************** 2023-11-24T07:11:30,062 ############################ 2023-11-24T07:11:30,062 # Package would be ignored # 2023-11-24T07:11:30,063 ############################ 2023-11-24T07:11:30,063 Python recognizes 'witch_msa.tools.magus.align.merge.graph_trace' as an importable package[^1], 2023-11-24T07:11:30,064 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:30,065 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:30,066 package, please make sure that 'witch_msa.tools.magus.align.merge.graph_trace' is explicitly added 2023-11-24T07:11:30,066 to the `packages` configuration field. 2023-11-24T07:11:30,067 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:30,068 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:30,068 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:30,069 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:30,070 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:30,071 If you don't want 'witch_msa.tools.magus.align.merge.graph_trace' to be distributed and are 2023-11-24T07:11:30,072 already explicitly excluding 'witch_msa.tools.magus.align.merge.graph_trace' via 2023-11-24T07:11:30,073 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:30,073 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:30,073 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:30,075 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:30,076 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:30,077 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:30,077 even if it does not contain any `.py` files. 2023-11-24T07:11:30,078 On the other hand, currently there is no concept of package data 2023-11-24T07:11:30,078 directory, all directories are treated like packages. 2023-11-24T07:11:30,079 ******************************************************************************** 2023-11-24T07:11:30,080 !! 2023-11-24T07:11:30,080 check.warn(importable) 2023-11-24T07:11:30,081 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:30,081 !! 2023-11-24T07:11:30,082 ******************************************************************************** 2023-11-24T07:11:30,083 ############################ 2023-11-24T07:11:30,083 # Package would be ignored # 2023-11-24T07:11:30,084 ############################ 2023-11-24T07:11:30,084 Python recognizes 'witch_msa.tools.magus.helpers' as an importable package[^1], 2023-11-24T07:11:30,085 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:30,086 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:30,086 package, please make sure that 'witch_msa.tools.magus.helpers' is explicitly added 2023-11-24T07:11:30,087 to the `packages` configuration field. 2023-11-24T07:11:30,088 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:30,088 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:30,089 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:30,090 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:30,091 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:30,092 If you don't want 'witch_msa.tools.magus.helpers' to be distributed and are 2023-11-24T07:11:30,092 already explicitly excluding 'witch_msa.tools.magus.helpers' via 2023-11-24T07:11:30,093 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:30,093 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:30,094 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:30,095 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:30,096 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:30,098 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:30,098 even if it does not contain any `.py` files. 2023-11-24T07:11:30,099 On the other hand, currently there is no concept of package data 2023-11-24T07:11:30,100 directory, all directories are treated like packages. 2023-11-24T07:11:30,100 ******************************************************************************** 2023-11-24T07:11:30,102 !! 2023-11-24T07:11:30,103 check.warn(importable) 2023-11-24T07:11:30,103 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:30,103 !! 2023-11-24T07:11:30,104 ******************************************************************************** 2023-11-24T07:11:30,105 ############################ 2023-11-24T07:11:30,105 # Package would be ignored # 2023-11-24T07:11:30,106 ############################ 2023-11-24T07:11:30,106 Python recognizes 'witch_msa.tools.magus.tasks' as an importable package[^1], 2023-11-24T07:11:30,107 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:30,108 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:30,108 package, please make sure that 'witch_msa.tools.magus.tasks' is explicitly added 2023-11-24T07:11:30,108 to the `packages` configuration field. 2023-11-24T07:11:30,110 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:30,110 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:30,110 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:30,111 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:30,112 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:30,113 If you don't want 'witch_msa.tools.magus.tasks' to be distributed and are 2023-11-24T07:11:30,114 already explicitly excluding 'witch_msa.tools.magus.tasks' via 2023-11-24T07:11:30,115 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:30,115 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:30,116 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:30,117 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:30,122 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:30,128 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:30,134 even if it does not contain any `.py` files. 2023-11-24T07:11:30,142 On the other hand, currently there is no concept of package data 2023-11-24T07:11:30,159 directory, all directories are treated like packages. 2023-11-24T07:11:30,167 ******************************************************************************** 2023-11-24T07:11:30,168 !! 2023-11-24T07:11:30,169 check.warn(importable) 2023-11-24T07:11:30,169 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:30,169 !! 2023-11-24T07:11:30,170 ******************************************************************************** 2023-11-24T07:11:30,171 ############################ 2023-11-24T07:11:30,172 # Package would be ignored # 2023-11-24T07:11:30,172 ############################ 2023-11-24T07:11:30,173 Python recognizes 'witch_msa.tools.magus.tools' as an importable package[^1], 2023-11-24T07:11:30,176 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:30,179 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:30,180 package, please make sure that 'witch_msa.tools.magus.tools' is explicitly added 2023-11-24T07:11:30,181 to the `packages` configuration field. 2023-11-24T07:11:30,182 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:30,182 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:30,183 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:30,185 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:30,188 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:30,189 If you don't want 'witch_msa.tools.magus.tools' to be distributed and are 2023-11-24T07:11:30,190 already explicitly excluding 'witch_msa.tools.magus.tools' via 2023-11-24T07:11:30,191 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:30,191 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:30,192 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:30,193 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:30,194 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:30,195 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:30,195 even if it does not contain any `.py` files. 2023-11-24T07:11:30,196 On the other hand, currently there is no concept of package data 2023-11-24T07:11:30,196 directory, all directories are treated like packages. 2023-11-24T07:11:30,197 ******************************************************************************** 2023-11-24T07:11:30,198 !! 2023-11-24T07:11:30,199 check.warn(importable) 2023-11-24T07:11:30,199 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:30,200 !! 2023-11-24T07:11:30,206 ******************************************************************************** 2023-11-24T07:11:30,208 ############################ 2023-11-24T07:11:30,213 # Package would be ignored # 2023-11-24T07:11:30,213 ############################ 2023-11-24T07:11:30,214 Python recognizes 'witch_msa.tools.magus.tools.clustal' as an importable package[^1], 2023-11-24T07:11:30,215 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:30,216 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:30,216 package, please make sure that 'witch_msa.tools.magus.tools.clustal' is explicitly added 2023-11-24T07:11:30,217 to the `packages` configuration field. 2023-11-24T07:11:30,218 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:30,218 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:30,219 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:30,220 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:30,221 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:30,224 If you don't want 'witch_msa.tools.magus.tools.clustal' to be distributed and are 2023-11-24T07:11:30,229 already explicitly excluding 'witch_msa.tools.magus.tools.clustal' via 2023-11-24T07:11:30,236 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:30,237 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:30,238 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:30,239 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:30,241 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:30,242 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:30,243 even if it does not contain any `.py` files. 2023-11-24T07:11:30,243 On the other hand, currently there is no concept of package data 2023-11-24T07:11:30,244 directory, all directories are treated like packages. 2023-11-24T07:11:30,244 ******************************************************************************** 2023-11-24T07:11:30,245 !! 2023-11-24T07:11:30,245 check.warn(importable) 2023-11-24T07:11:30,246 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:30,246 !! 2023-11-24T07:11:30,249 ******************************************************************************** 2023-11-24T07:11:30,249 ############################ 2023-11-24T07:11:30,250 # Package would be ignored # 2023-11-24T07:11:30,251 ############################ 2023-11-24T07:11:30,257 Python recognizes 'witch_msa.tools.magus.tools.fasttree' as an importable package[^1], 2023-11-24T07:11:30,265 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:30,266 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:30,266 package, please make sure that 'witch_msa.tools.magus.tools.fasttree' is explicitly added 2023-11-24T07:11:30,267 to the `packages` configuration field. 2023-11-24T07:11:30,268 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:30,269 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:30,269 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:30,270 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:30,271 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:30,272 If you don't want 'witch_msa.tools.magus.tools.fasttree' to be distributed and are 2023-11-24T07:11:30,273 already explicitly excluding 'witch_msa.tools.magus.tools.fasttree' via 2023-11-24T07:11:30,273 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:30,274 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:30,275 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:30,277 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:30,278 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:30,279 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:30,280 even if it does not contain any `.py` files. 2023-11-24T07:11:30,280 On the other hand, currently there is no concept of package data 2023-11-24T07:11:30,281 directory, all directories are treated like packages. 2023-11-24T07:11:30,281 ******************************************************************************** 2023-11-24T07:11:30,282 !! 2023-11-24T07:11:30,283 check.warn(importable) 2023-11-24T07:11:30,284 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:30,287 !! 2023-11-24T07:11:30,300 ******************************************************************************** 2023-11-24T07:11:30,301 ############################ 2023-11-24T07:11:30,302 # Package would be ignored # 2023-11-24T07:11:30,303 ############################ 2023-11-24T07:11:30,304 Python recognizes 'witch_msa.tools.magus.tools.hmmer' as an importable package[^1], 2023-11-24T07:11:30,309 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:30,314 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:30,316 package, please make sure that 'witch_msa.tools.magus.tools.hmmer' is explicitly added 2023-11-24T07:11:30,319 to the `packages` configuration field. 2023-11-24T07:11:30,321 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:30,321 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:30,321 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:30,322 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:30,323 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:30,324 If you don't want 'witch_msa.tools.magus.tools.hmmer' to be distributed and are 2023-11-24T07:11:30,325 already explicitly excluding 'witch_msa.tools.magus.tools.hmmer' via 2023-11-24T07:11:30,325 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:30,330 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:30,332 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:30,334 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:30,335 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:30,341 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:30,342 even if it does not contain any `.py` files. 2023-11-24T07:11:30,342 On the other hand, currently there is no concept of package data 2023-11-24T07:11:30,343 directory, all directories are treated like packages. 2023-11-24T07:11:30,344 ******************************************************************************** 2023-11-24T07:11:30,345 !! 2023-11-24T07:11:30,346 check.warn(importable) 2023-11-24T07:11:30,346 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:30,347 !! 2023-11-24T07:11:30,348 ******************************************************************************** 2023-11-24T07:11:30,349 ############################ 2023-11-24T07:11:30,349 # Package would be ignored # 2023-11-24T07:11:30,350 ############################ 2023-11-24T07:11:30,350 Python recognizes 'witch_msa.tools.magus.tools.mafft' as an importable package[^1], 2023-11-24T07:11:30,351 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:30,352 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:30,353 package, please make sure that 'witch_msa.tools.magus.tools.mafft' is explicitly added 2023-11-24T07:11:30,353 to the `packages` configuration field. 2023-11-24T07:11:30,354 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:30,355 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:30,355 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:30,357 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:30,358 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:30,359 If you don't want 'witch_msa.tools.magus.tools.mafft' to be distributed and are 2023-11-24T07:11:30,360 already explicitly excluding 'witch_msa.tools.magus.tools.mafft' via 2023-11-24T07:11:30,360 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:30,361 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:30,361 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:30,362 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:30,363 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:30,364 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:30,365 even if it does not contain any `.py` files. 2023-11-24T07:11:30,365 On the other hand, currently there is no concept of package data 2023-11-24T07:11:30,366 directory, all directories are treated like packages. 2023-11-24T07:11:30,366 ******************************************************************************** 2023-11-24T07:11:30,367 !! 2023-11-24T07:11:30,373 check.warn(importable) 2023-11-24T07:11:30,384 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:30,407 !! 2023-11-24T07:11:30,413 ******************************************************************************** 2023-11-24T07:11:30,414 ############################ 2023-11-24T07:11:30,414 # Package would be ignored # 2023-11-24T07:11:30,415 ############################ 2023-11-24T07:11:30,415 Python recognizes 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' as an importable package[^1], 2023-11-24T07:11:30,416 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:30,416 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:30,417 package, please make sure that 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' is explicitly added 2023-11-24T07:11:30,417 to the `packages` configuration field. 2023-11-24T07:11:30,419 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:30,419 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:30,420 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:30,421 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:30,423 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:30,426 If you don't want 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' to be distributed and are 2023-11-24T07:11:30,429 already explicitly excluding 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' via 2023-11-24T07:11:30,436 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:30,437 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:30,438 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:30,439 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:30,440 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:30,442 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:30,443 even if it does not contain any `.py` files. 2023-11-24T07:11:30,447 On the other hand, currently there is no concept of package data 2023-11-24T07:11:30,450 directory, all directories are treated like packages. 2023-11-24T07:11:30,453 ******************************************************************************** 2023-11-24T07:11:30,455 !! 2023-11-24T07:11:30,456 check.warn(importable) 2023-11-24T07:11:30,456 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:30,457 !! 2023-11-24T07:11:30,458 ******************************************************************************** 2023-11-24T07:11:30,458 ############################ 2023-11-24T07:11:30,462 # Package would be ignored # 2023-11-24T07:11:30,463 ############################ 2023-11-24T07:11:30,467 Python recognizes 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' as an importable package[^1], 2023-11-24T07:11:30,471 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:30,473 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:30,473 package, please make sure that 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' is explicitly added 2023-11-24T07:11:30,474 to the `packages` configuration field. 2023-11-24T07:11:30,475 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:30,475 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:30,476 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:30,477 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:30,478 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:30,479 If you don't want 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' to be distributed and are 2023-11-24T07:11:30,485 already explicitly excluding 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' via 2023-11-24T07:11:30,489 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:30,489 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:30,490 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:30,491 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:30,499 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:30,507 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:30,510 even if it does not contain any `.py` files. 2023-11-24T07:11:30,513 On the other hand, currently there is no concept of package data 2023-11-24T07:11:30,514 directory, all directories are treated like packages. 2023-11-24T07:11:30,514 ******************************************************************************** 2023-11-24T07:11:30,515 !! 2023-11-24T07:11:30,516 check.warn(importable) 2023-11-24T07:11:30,516 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:30,517 !! 2023-11-24T07:11:30,518 ******************************************************************************** 2023-11-24T07:11:30,518 ############################ 2023-11-24T07:11:30,519 # Package would be ignored # 2023-11-24T07:11:30,519 ############################ 2023-11-24T07:11:30,520 Python recognizes 'witch_msa.tools.magus.tools.mcl.bin' as an importable package[^1], 2023-11-24T07:11:30,521 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:30,522 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:30,523 package, please make sure that 'witch_msa.tools.magus.tools.mcl.bin' is explicitly added 2023-11-24T07:11:30,527 to the `packages` configuration field. 2023-11-24T07:11:30,534 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:30,534 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:30,535 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:30,536 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:30,537 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:30,538 If you don't want 'witch_msa.tools.magus.tools.mcl.bin' to be distributed and are 2023-11-24T07:11:30,538 already explicitly excluding 'witch_msa.tools.magus.tools.mcl.bin' via 2023-11-24T07:11:30,539 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:30,539 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:30,540 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:30,541 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:30,552 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:30,558 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:30,558 even if it does not contain any `.py` files. 2023-11-24T07:11:30,559 On the other hand, currently there is no concept of package data 2023-11-24T07:11:30,559 directory, all directories are treated like packages. 2023-11-24T07:11:30,560 ******************************************************************************** 2023-11-24T07:11:30,562 !! 2023-11-24T07:11:30,563 check.warn(importable) 2023-11-24T07:11:30,564 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:30,565 !! 2023-11-24T07:11:30,567 ******************************************************************************** 2023-11-24T07:11:30,569 ############################ 2023-11-24T07:11:30,571 # Package would be ignored # 2023-11-24T07:11:30,571 ############################ 2023-11-24T07:11:30,572 Python recognizes 'witch_msa.tools.magus.tools.mlrmcl' as an importable package[^1], 2023-11-24T07:11:30,572 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:30,574 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:30,574 package, please make sure that 'witch_msa.tools.magus.tools.mlrmcl' is explicitly added 2023-11-24T07:11:30,575 to the `packages` configuration field. 2023-11-24T07:11:30,576 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:30,577 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:30,577 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:30,581 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:30,585 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:30,591 If you don't want 'witch_msa.tools.magus.tools.mlrmcl' to be distributed and are 2023-11-24T07:11:30,591 already explicitly excluding 'witch_msa.tools.magus.tools.mlrmcl' via 2023-11-24T07:11:30,592 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:30,592 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:30,593 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:30,594 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:30,595 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:30,596 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:30,596 even if it does not contain any `.py` files. 2023-11-24T07:11:30,597 On the other hand, currently there is no concept of package data 2023-11-24T07:11:30,597 directory, all directories are treated like packages. 2023-11-24T07:11:30,597 ******************************************************************************** 2023-11-24T07:11:30,598 !! 2023-11-24T07:11:30,599 check.warn(importable) 2023-11-24T07:11:30,599 /tmp/pip-build-env-e9w5fx0h/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. 2023-11-24T07:11:30,600 !! 2023-11-24T07:11:30,601 ******************************************************************************** 2023-11-24T07:11:30,608 ############################ 2023-11-24T07:11:30,616 # Package would be ignored # 2023-11-24T07:11:30,617 ############################ 2023-11-24T07:11:30,617 Python recognizes 'witch_msa.tools.magus.tools.raxmlng' as an importable package[^1], 2023-11-24T07:11:30,618 but it is absent from setuptools' `packages` configuration. 2023-11-24T07:11:30,619 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-24T07:11:30,620 package, please make sure that 'witch_msa.tools.magus.tools.raxmlng' is explicitly added 2023-11-24T07:11:30,620 to the `packages` configuration field. 2023-11-24T07:11:30,621 Alternatively, you can also rely on setuptools' discovery methods 2023-11-24T07:11:30,622 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-24T07:11:30,622 instead of `find_packages(...)`/`find:`). 2023-11-24T07:11:30,623 You can read more about "package discovery" on setuptools documentation page: 2023-11-24T07:11:30,624 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-24T07:11:30,626 If you don't want 'witch_msa.tools.magus.tools.raxmlng' to be distributed and are 2023-11-24T07:11:30,626 already explicitly excluding 'witch_msa.tools.magus.tools.raxmlng' via 2023-11-24T07:11:30,627 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-24T07:11:30,628 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-24T07:11:30,630 combination with a more fine grained `package-data` configuration. 2023-11-24T07:11:30,635 You can read more about "package data files" on setuptools documentation page: 2023-11-24T07:11:30,636 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-24T07:11:30,638 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-24T07:11:30,638 even if it does not contain any `.py` files. 2023-11-24T07:11:30,639 On the other hand, currently there is no concept of package data 2023-11-24T07:11:30,640 directory, all directories are treated like packages. 2023-11-24T07:11:30,640 ******************************************************************************** 2023-11-24T07:11:30,641 !! 2023-11-24T07:11:30,642 check.warn(importable) 2023-11-24T07:11:30,643 copying witch_msa/default.config -> build/lib/witch_msa 2023-11-24T07:11:30,643 creating build/lib/witch_msa/tools 2023-11-24T07:11:30,644 creating build/lib/witch_msa/tools/macOS 2023-11-24T07:11:30,645 copying witch_msa/tools/macOS/FastTreeMP -> build/lib/witch_msa/tools/macOS 2023-11-24T07:11:30,647 copying witch_msa/tools/macOS/hmmalign -> build/lib/witch_msa/tools/macOS 2023-11-24T07:11:30,649 copying witch_msa/tools/macOS/hmmbuild -> build/lib/witch_msa/tools/macOS 2023-11-24T07:11:30,651 copying witch_msa/tools/macOS/hmmsearch -> build/lib/witch_msa/tools/macOS 2023-11-24T07:11:30,656 copying witch_msa/tools/macOS/mafft -> build/lib/witch_msa/tools/macOS 2023-11-24T07:11:30,656 copying witch_msa/tools/macOS/mcl -> build/lib/witch_msa/tools/macOS 2023-11-24T07:11:30,657 creating build/lib/witch_msa/tools/magus 2023-11-24T07:11:30,657 copying witch_msa/tools/magus/README.md -> build/lib/witch_msa/tools/magus 2023-11-24T07:11:30,658 copying witch_msa/tools/magus/configuration.py -> build/lib/witch_msa/tools/magus 2023-11-24T07:11:30,658 copying witch_msa/tools/magus/magus.py -> build/lib/witch_msa/tools/magus 2023-11-24T07:11:30,659 creating build/lib/witch_msa/tools/magus/align 2023-11-24T07:11:30,662 copying witch_msa/tools/magus/align/__init__.py -> build/lib/witch_msa/tools/magus/align 2023-11-24T07:11:30,663 copying witch_msa/tools/magus/align/aligner.py -> build/lib/witch_msa/tools/magus/align 2023-11-24T07:11:30,663 copying witch_msa/tools/magus/align/alignment_context.py -> build/lib/witch_msa/tools/magus/align 2023-11-24T07:11:30,664 creating build/lib/witch_msa/tools/magus/align/decompose 2023-11-24T07:11:30,665 copying witch_msa/tools/magus/align/decompose/__init__.py -> build/lib/witch_msa/tools/magus/align/decompose 2023-11-24T07:11:30,666 copying witch_msa/tools/magus/align/decompose/decomposer.py -> build/lib/witch_msa/tools/magus/align/decompose 2023-11-24T07:11:30,668 copying witch_msa/tools/magus/align/decompose/initial_tree.py -> build/lib/witch_msa/tools/magus/align/decompose 2023-11-24T07:11:30,669 copying witch_msa/tools/magus/align/decompose/kmh.py -> build/lib/witch_msa/tools/magus/align/decompose 2023-11-24T07:11:30,670 creating build/lib/witch_msa/tools/magus/align/merge 2023-11-24T07:11:30,673 copying witch_msa/tools/magus/align/merge/__init__.py -> build/lib/witch_msa/tools/magus/align/merge 2023-11-24T07:11:30,674 copying witch_msa/tools/magus/align/merge/alignment_graph.py -> build/lib/witch_msa/tools/magus/align/merge 2023-11-24T07:11:30,674 copying witch_msa/tools/magus/align/merge/alignment_writer.py -> build/lib/witch_msa/tools/magus/align/merge 2023-11-24T07:11:30,675 copying witch_msa/tools/magus/align/merge/merger.py -> build/lib/witch_msa/tools/magus/align/merge 2023-11-24T07:11:30,676 copying witch_msa/tools/magus/align/merge/optimizer.py -> build/lib/witch_msa/tools/magus/align/merge 2023-11-24T07:11:30,680 creating build/lib/witch_msa/tools/magus/align/merge/graph_build 2023-11-24T07:11:30,681 copying witch_msa/tools/magus/align/merge/graph_build/__init__.py -> build/lib/witch_msa/tools/magus/align/merge/graph_build 2023-11-24T07:11:30,685 copying witch_msa/tools/magus/align/merge/graph_build/graph_builder.py -> build/lib/witch_msa/tools/magus/align/merge/graph_build 2023-11-24T07:11:30,691 creating build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:11:30,692 copying witch_msa/tools/magus/align/merge/graph_cluster/__init__.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:11:30,692 copying witch_msa/tools/magus/align/merge/graph_cluster/clean_clusters.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:11:30,693 copying witch_msa/tools/magus/align/merge/graph_cluster/clusterer.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:11:30,693 copying witch_msa/tools/magus/align/merge/graph_cluster/mcl.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:11:30,694 copying witch_msa/tools/magus/align/merge/graph_cluster/mlr_mcl.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:11:30,695 copying witch_msa/tools/magus/align/merge/graph_cluster/rg.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:11:30,695 creating build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:30,696 copying witch_msa/tools/magus/align/merge/graph_trace/__init__.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:30,696 copying witch_msa/tools/magus/align/merge/graph_trace/fm.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:30,697 copying witch_msa/tools/magus/align/merge/graph_trace/min_clusters.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:30,697 copying witch_msa/tools/magus/align/merge/graph_trace/mwt_search.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:30,698 copying witch_msa/tools/magus/align/merge/graph_trace/naive.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:30,698 copying witch_msa/tools/magus/align/merge/graph_trace/rg_fast_search.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:30,699 copying witch_msa/tools/magus/align/merge/graph_trace/rg_search.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:30,699 copying witch_msa/tools/magus/align/merge/graph_trace/tracer.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:30,700 creating build/lib/witch_msa/tools/magus/helpers 2023-11-24T07:11:30,700 copying witch_msa/tools/magus/helpers/__init__.py -> build/lib/witch_msa/tools/magus/helpers 2023-11-24T07:11:30,701 copying witch_msa/tools/magus/helpers/hmmutils.py -> build/lib/witch_msa/tools/magus/helpers 2023-11-24T07:11:30,703 copying witch_msa/tools/magus/helpers/sequenceutils.py -> build/lib/witch_msa/tools/magus/helpers 2023-11-24T07:11:30,704 copying witch_msa/tools/magus/helpers/treeutils.py -> build/lib/witch_msa/tools/magus/helpers 2023-11-24T07:11:30,707 creating build/lib/witch_msa/tools/magus/tasks 2023-11-24T07:11:30,714 copying witch_msa/tools/magus/tasks/__init__.py -> build/lib/witch_msa/tools/magus/tasks 2023-11-24T07:11:30,718 copying witch_msa/tools/magus/tasks/controller.py -> build/lib/witch_msa/tools/magus/tasks 2023-11-24T07:11:30,718 copying witch_msa/tools/magus/tasks/files.py -> build/lib/witch_msa/tools/magus/tasks 2023-11-24T07:11:30,719 copying witch_msa/tools/magus/tasks/manager.py -> build/lib/witch_msa/tools/magus/tasks 2023-11-24T07:11:30,719 copying witch_msa/tools/magus/tasks/task.py -> build/lib/witch_msa/tools/magus/tasks 2023-11-24T07:11:30,720 creating build/lib/witch_msa/tools/magus/tools 2023-11-24T07:11:30,720 copying witch_msa/tools/magus/tools/__init__.py -> build/lib/witch_msa/tools/magus/tools 2023-11-24T07:11:30,721 copying witch_msa/tools/magus/tools/external_tools.py -> build/lib/witch_msa/tools/magus/tools 2023-11-24T07:11:30,722 creating build/lib/witch_msa/tools/magus/tools/clustal 2023-11-24T07:11:30,722 copying witch_msa/tools/magus/tools/clustal/clustalo -> build/lib/witch_msa/tools/magus/tools/clustal 2023-11-24T07:11:30,723 creating build/lib/witch_msa/tools/magus/tools/fasttree 2023-11-24T07:11:30,723 copying witch_msa/tools/magus/tools/fasttree/FastTree -> build/lib/witch_msa/tools/magus/tools/fasttree 2023-11-24T07:11:30,724 copying witch_msa/tools/magus/tools/fasttree/FastTreeMP -> build/lib/witch_msa/tools/magus/tools/fasttree 2023-11-24T07:11:30,724 creating build/lib/witch_msa/tools/magus/tools/hmmer 2023-11-24T07:11:30,725 copying witch_msa/tools/magus/tools/hmmer/hmmalign -> build/lib/witch_msa/tools/magus/tools/hmmer 2023-11-24T07:11:30,725 copying witch_msa/tools/magus/tools/hmmer/hmmbuild -> build/lib/witch_msa/tools/magus/tools/hmmer 2023-11-24T07:11:30,727 copying witch_msa/tools/magus/tools/hmmer/hmmsearch -> build/lib/witch_msa/tools/magus/tools/hmmer 2023-11-24T07:11:30,730 creating build/lib/witch_msa/tools/magus/tools/mafft 2023-11-24T07:11:30,738 copying witch_msa/tools/magus/tools/mafft/mafft -> build/lib/witch_msa/tools/magus/tools/mafft 2023-11-24T07:11:30,742 creating build/lib/witch_msa/tools/magus/tools/mafft/mafftdir 2023-11-24T07:11:30,743 creating build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/bin 2023-11-24T07:11:30,744 copying witch_msa/tools/magus/tools/mafft/mafftdir/bin/mafft -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/bin 2023-11-24T07:11:30,744 creating build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,744 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/addsingle -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,745 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/contrafoldwrap -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,745 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/countlen -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,746 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dash_client -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,746 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/disttbfast -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,747 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndblast -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,747 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndfast7 -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,747 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndpre -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,748 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dvtditr -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,749 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/f2cl -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,749 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/getlag -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,750 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/hex2maffttext -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,751 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-distance -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,753 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-homologs.1 -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,757 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-profile -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,758 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft.1 -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,759 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafftash_premafft.pl -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,760 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/maffttext2hex -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,762 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/makedirectionlist -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,765 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mccaskillwrap -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,766 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/multi2hat3s -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,767 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/nodepair -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,767 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairash -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,768 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairlocalalign -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,769 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/regtable2seq -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,784 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/replaceu -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,803 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/restoreu -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,817 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/score -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,834 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seekquencer_premafft.pl -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,836 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seq2regtable -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,856 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setcore -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,877 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setdirection -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,892 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/sextet5 -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,907 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/splittbfast -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,931 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/tbfast -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,956 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/version -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:30,966 creating build/lib/witch_msa/tools/magus/tools/mcl 2023-11-24T07:11:30,967 creating build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:30,968 copying witch_msa/tools/magus/tools/mcl/bin/clm -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:30,993 copying witch_msa/tools/magus/tools/mcl/bin/clmformat -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,014 copying witch_msa/tools/magus/tools/mcl/bin/clxdo -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,016 copying witch_msa/tools/magus/tools/mcl/bin/mcl -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,038 copying witch_msa/tools/magus/tools/mcl/bin/mclblastline -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,040 copying witch_msa/tools/magus/tools/mcl/bin/mclcm -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,060 copying witch_msa/tools/magus/tools/mcl/bin/mclpipeline -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,063 copying witch_msa/tools/magus/tools/mcl/bin/mcx -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,087 copying witch_msa/tools/magus/tools/mcl/bin/mcxarray -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,108 copying witch_msa/tools/magus/tools/mcl/bin/mcxassemble -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,129 copying witch_msa/tools/magus/tools/mcl/bin/mcxdeblast -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,132 copying witch_msa/tools/magus/tools/mcl/bin/mcxdump -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,155 copying witch_msa/tools/magus/tools/mcl/bin/mcxi -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,178 copying witch_msa/tools/magus/tools/mcl/bin/mcxload -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,197 copying witch_msa/tools/magus/tools/mcl/bin/mcxmap -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,212 copying witch_msa/tools/magus/tools/mcl/bin/mcxrand -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,225 copying witch_msa/tools/magus/tools/mcl/bin/mcxsubs -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,246 creating build/lib/witch_msa/tools/magus/tools/mlrmcl 2023-11-24T07:11:31,247 copying witch_msa/tools/magus/tools/mlrmcl/README -> build/lib/witch_msa/tools/magus/tools/mlrmcl 2023-11-24T07:11:31,250 copying witch_msa/tools/magus/tools/mlrmcl/mlrmcl -> build/lib/witch_msa/tools/magus/tools/mlrmcl 2023-11-24T07:11:31,254 copying witch_msa/tools/magus/tools/mlrmcl/ncut -> build/lib/witch_msa/tools/magus/tools/mlrmcl 2023-11-24T07:11:31,258 creating build/lib/witch_msa/tools/magus/tools/raxmlng 2023-11-24T07:11:31,259 copying witch_msa/tools/magus/tools/raxmlng/raxml-ng -> build/lib/witch_msa/tools/magus/tools/raxmlng 2023-11-24T07:11:31,363 running build_scripts 2023-11-24T07:11:31,364 creating build/scripts-3.11 2023-11-24T07:11:31,365 copying and adjusting bin/witch-msa -> build/scripts-3.11 2023-11-24T07:11:31,367 copying and adjusting witch.py -> build/scripts-3.11 2023-11-24T07:11:31,368 changing mode of build/scripts-3.11/witch-msa from 644 to 755 2023-11-24T07:11:31,368 changing mode of build/scripts-3.11/witch.py from 644 to 755 2023-11-24T07:11:31,375 installing to build/bdist.linux-armv7l/wheel 2023-11-24T07:11:31,375 running install 2023-11-24T07:11:31,398 running install_lib 2023-11-24T07:11:31,403 creating build/bdist.linux-armv7l 2023-11-24T07:11:31,403 creating build/bdist.linux-armv7l/wheel 2023-11-24T07:11:31,405 creating build/bdist.linux-armv7l/wheel/witch_msa 2023-11-24T07:11:31,406 copying build/lib/witch_msa/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa 2023-11-24T07:11:31,409 creating build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:11:31,410 copying build/lib/witch_msa/gcmm/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:11:31,412 copying build/lib/witch_msa/gcmm/backbone.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:11:31,415 copying build/lib/witch_msa/gcmm/tree.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:11:31,417 copying build/lib/witch_msa/gcmm/callback.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:11:31,419 copying build/lib/witch_msa/gcmm/results_handler.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:11:31,422 copying build/lib/witch_msa/gcmm/loader.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:11:31,424 copying build/lib/witch_msa/gcmm/aligner.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:11:31,427 copying build/lib/witch_msa/gcmm/merger.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:11:31,429 copying build/lib/witch_msa/gcmm/decompose_tree.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:11:31,431 copying build/lib/witch_msa/gcmm/gcmm.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:11:31,434 copying build/lib/witch_msa/gcmm/algorithm.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:11:31,436 copying build/lib/witch_msa/gcmm/task.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:11:31,439 copying build/lib/witch_msa/gcmm/weighting.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2023-11-24T07:11:31,441 copying build/lib/witch_msa/init_configs.py -> build/bdist.linux-armv7l/wheel/witch_msa 2023-11-24T07:11:31,444 creating build/bdist.linux-armv7l/wheel/witch_msa/tools 2023-11-24T07:11:31,445 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2023-11-24T07:11:31,446 copying build/lib/witch_msa/tools/macOS/hmmbuild -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2023-11-24T07:11:31,463 copying build/lib/witch_msa/tools/macOS/FastTreeMP -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2023-11-24T07:11:31,470 copying build/lib/witch_msa/tools/macOS/mcl -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2023-11-24T07:11:31,477 copying build/lib/witch_msa/tools/macOS/mafft -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2023-11-24T07:11:31,483 copying build/lib/witch_msa/tools/macOS/hmmsearch -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2023-11-24T07:11:31,502 copying build/lib/witch_msa/tools/macOS/hmmalign -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2023-11-24T07:11:31,517 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus 2023-11-24T07:11:31,518 copying build/lib/witch_msa/tools/magus/configuration.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus 2023-11-24T07:11:31,521 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align 2023-11-24T07:11:31,521 copying build/lib/witch_msa/tools/magus/align/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align 2023-11-24T07:11:31,524 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2023-11-24T07:11:31,525 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:11:31,526 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:11:31,528 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/clusterer.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:11:31,530 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/mcl.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:11:31,531 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/clean_clusters.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:11:31,533 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/mlr_mcl.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:11:31,535 copying build/lib/witch_msa/tools/magus/align/merge/graph_cluster/rg.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2023-11-24T07:11:31,537 copying build/lib/witch_msa/tools/magus/align/merge/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2023-11-24T07:11:31,539 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_build 2023-11-24T07:11:31,540 copying build/lib/witch_msa/tools/magus/align/merge/graph_build/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_build 2023-11-24T07:11:31,542 copying build/lib/witch_msa/tools/magus/align/merge/graph_build/graph_builder.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_build 2023-11-24T07:11:31,544 copying build/lib/witch_msa/tools/magus/align/merge/alignment_graph.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2023-11-24T07:11:31,546 copying build/lib/witch_msa/tools/magus/align/merge/optimizer.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2023-11-24T07:11:31,549 copying build/lib/witch_msa/tools/magus/align/merge/merger.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2023-11-24T07:11:31,551 copying build/lib/witch_msa/tools/magus/align/merge/alignment_writer.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2023-11-24T07:11:31,555 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:31,556 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:31,558 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/tracer.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:31,560 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/mwt_search.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:31,562 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/rg_search.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:31,565 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/fm.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:31,567 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/naive.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:31,569 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/rg_fast_search.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:31,571 copying build/lib/witch_msa/tools/magus/align/merge/graph_trace/min_clusters.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2023-11-24T07:11:31,573 copying build/lib/witch_msa/tools/magus/align/aligner.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align 2023-11-24T07:11:31,575 copying build/lib/witch_msa/tools/magus/align/alignment_context.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align 2023-11-24T07:11:31,578 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/decompose 2023-11-24T07:11:31,579 copying build/lib/witch_msa/tools/magus/align/decompose/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/decompose 2023-11-24T07:11:31,580 copying build/lib/witch_msa/tools/magus/align/decompose/kmh.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/decompose 2023-11-24T07:11:31,582 copying build/lib/witch_msa/tools/magus/align/decompose/decomposer.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/decompose 2023-11-24T07:11:31,585 copying build/lib/witch_msa/tools/magus/align/decompose/initial_tree.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/decompose 2023-11-24T07:11:31,587 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools 2023-11-24T07:11:31,588 copying build/lib/witch_msa/tools/magus/tools/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools 2023-11-24T07:11:31,590 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mlrmcl 2023-11-24T07:11:31,591 copying build/lib/witch_msa/tools/magus/tools/mlrmcl/ncut -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mlrmcl 2023-11-24T07:11:31,595 copying build/lib/witch_msa/tools/magus/tools/mlrmcl/mlrmcl -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mlrmcl 2023-11-24T07:11:31,599 copying build/lib/witch_msa/tools/magus/tools/mlrmcl/README -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mlrmcl 2023-11-24T07:11:31,602 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/raxmlng 2023-11-24T07:11:31,603 copying build/lib/witch_msa/tools/magus/tools/raxmlng/raxml-ng -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/raxmlng 2023-11-24T07:11:31,734 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl 2023-11-24T07:11:31,736 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,738 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcl -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,768 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxarray -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,789 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxload -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,810 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxassemble -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,838 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/clmformat -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,859 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxmap -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,871 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxsubs -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,892 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mclblastline -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,895 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mclcm -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,922 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcx -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,946 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxi -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,966 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxrand -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:31,980 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxdump -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:32,004 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mclpipeline -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:32,007 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/clm -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:32,031 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxdeblast -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:32,034 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/clxdo -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2023-11-24T07:11:32,037 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft 2023-11-24T07:11:32,038 copying build/lib/witch_msa/tools/magus/tools/mafft/mafft -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft 2023-11-24T07:11:32,040 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir 2023-11-24T07:11:32,041 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/bin 2023-11-24T07:11:32,042 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/bin/mafft -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/bin 2023-11-24T07:11:32,047 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,048 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/replaceu -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,064 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/makedirectionlist -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,087 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setdirection -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,103 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafftash_premafft.pl -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,105 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dash_client -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,182 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/countlen -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,193 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndfast7 -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,209 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seekquencer_premafft.pl -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,211 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/regtable2seq -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,226 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/restoreu -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,240 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dvtditr -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,259 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/version -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,270 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-profile -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,288 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/f2cl -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,301 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/score -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,317 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairlocalalign -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,338 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/disttbfast -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,361 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/multi2hat3s -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,379 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/tbfast -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,400 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/sextet5 -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,417 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndblast -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,433 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/maffttext2hex -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,444 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/splittbfast -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,468 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/contrafoldwrap -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,483 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairash -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,507 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-distance -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,525 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/hex2maffttext -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,536 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/getlag -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,559 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-homologs.1 -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,562 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/nodepair -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,585 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mccaskillwrap -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,599 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seq2regtable -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,610 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft.1 -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,613 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setcore -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,633 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndpre -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,649 copying build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec/addsingle -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2023-11-24T07:11:32,675 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/clustal 2023-11-24T07:11:32,676 copying build/lib/witch_msa/tools/magus/tools/clustal/clustalo -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/clustal 2023-11-24T07:11:32,752 copying build/lib/witch_msa/tools/magus/tools/external_tools.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools 2023-11-24T07:11:32,755 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/hmmer 2023-11-24T07:11:32,756 copying build/lib/witch_msa/tools/magus/tools/hmmer/hmmbuild -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/hmmer 2023-11-24T07:11:32,786 copying build/lib/witch_msa/tools/magus/tools/hmmer/hmmsearch -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/hmmer 2023-11-24T07:11:32,810 copying build/lib/witch_msa/tools/magus/tools/hmmer/hmmalign -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/hmmer 2023-11-24T07:11:32,833 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/fasttree 2023-11-24T07:11:32,834 copying build/lib/witch_msa/tools/magus/tools/fasttree/FastTreeMP -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/fasttree 2023-11-24T07:11:32,846 copying build/lib/witch_msa/tools/magus/tools/fasttree/FastTree -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/fasttree 2023-11-24T07:11:32,853 copying build/lib/witch_msa/tools/magus/README.md -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus 2023-11-24T07:11:32,855 copying build/lib/witch_msa/tools/magus/magus.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus 2023-11-24T07:11:32,858 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/helpers 2023-11-24T07:11:32,859 copying build/lib/witch_msa/tools/magus/helpers/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/helpers 2023-11-24T07:11:32,861 copying build/lib/witch_msa/tools/magus/helpers/treeutils.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/helpers 2023-11-24T07:11:32,863 copying build/lib/witch_msa/tools/magus/helpers/hmmutils.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/helpers 2023-11-24T07:11:32,865 copying build/lib/witch_msa/tools/magus/helpers/sequenceutils.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/helpers 2023-11-24T07:11:32,868 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2023-11-24T07:11:32,869 copying build/lib/witch_msa/tools/magus/tasks/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2023-11-24T07:11:32,871 copying build/lib/witch_msa/tools/magus/tasks/controller.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2023-11-24T07:11:32,872 copying build/lib/witch_msa/tools/magus/tasks/task.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2023-11-24T07:11:32,874 copying build/lib/witch_msa/tools/magus/tasks/manager.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2023-11-24T07:11:32,876 copying build/lib/witch_msa/tools/magus/tasks/files.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2023-11-24T07:11:32,878 copying build/lib/witch_msa/default.config -> build/bdist.linux-armv7l/wheel/witch_msa 2023-11-24T07:11:32,880 creating build/bdist.linux-armv7l/wheel/witch_msa/helpers 2023-11-24T07:11:32,881 copying build/lib/witch_msa/helpers/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/helpers 2023-11-24T07:11:32,883 copying build/lib/witch_msa/helpers/general_tools.py -> build/bdist.linux-armv7l/wheel/witch_msa/helpers 2023-11-24T07:11:32,884 copying build/lib/witch_msa/helpers/pyhmmer_tools.py -> build/bdist.linux-armv7l/wheel/witch_msa/helpers 2023-11-24T07:11:32,886 copying build/lib/witch_msa/helpers/alignment_tools.py -> build/bdist.linux-armv7l/wheel/witch_msa/helpers 2023-11-24T07:11:32,889 copying build/lib/witch_msa/helpers/math_utils.py -> build/bdist.linux-armv7l/wheel/witch_msa/helpers 2023-11-24T07:11:32,891 copying build/lib/witch_msa/configs.py -> build/bdist.linux-armv7l/wheel/witch_msa 2023-11-24T07:11:32,893 running install_egg_info 2023-11-24T07:11:32,897 Copying witch_msa.egg-info to build/bdist.linux-armv7l/wheel/witch_msa-1.0.1-py3.11.egg-info 2023-11-24T07:11:32,908 running install_scripts 2023-11-24T07:11:32,909 creating build/bdist.linux-armv7l/wheel/witch_msa-1.0.1.data 2023-11-24T07:11:32,909 creating build/bdist.linux-armv7l/wheel/witch_msa-1.0.1.data/scripts 2023-11-24T07:11:32,910 copying build/scripts-3.11/witch.py -> build/bdist.linux-armv7l/wheel/witch_msa-1.0.1.data/scripts 2023-11-24T07:11:32,912 copying build/scripts-3.11/witch-msa -> build/bdist.linux-armv7l/wheel/witch_msa-1.0.1.data/scripts 2023-11-24T07:11:32,914 changing mode of build/bdist.linux-armv7l/wheel/witch_msa-1.0.1.data/scripts/witch.py to 755 2023-11-24T07:11:32,914 changing mode of build/bdist.linux-armv7l/wheel/witch_msa-1.0.1.data/scripts/witch-msa to 755 2023-11-24T07:11:32,936 creating build/bdist.linux-armv7l/wheel/witch_msa-1.0.1.dist-info/WHEEL 2023-11-24T07:11:32,938 creating '/tmp/pip-wheel-nnj0zge3/.tmp-hcal77zn/witch_msa-1.0.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-11-24T07:11:32,941 adding 'witch_msa/__init__.py' 2023-11-24T07:11:32,943 adding 'witch_msa/configs.py' 2023-11-24T07:11:32,945 adding 'witch_msa/default.config' 2023-11-24T07:11:32,946 adding 'witch_msa/init_configs.py' 2023-11-24T07:11:32,948 adding 'witch_msa/gcmm/__init__.py' 2023-11-24T07:11:32,951 adding 'witch_msa/gcmm/algorithm.py' 2023-11-24T07:11:32,954 adding 'witch_msa/gcmm/aligner.py' 2023-11-24T07:11:32,957 adding 'witch_msa/gcmm/backbone.py' 2023-11-24T07:11:32,958 adding 'witch_msa/gcmm/callback.py' 2023-11-24T07:11:32,959 adding 'witch_msa/gcmm/decompose_tree.py' 2023-11-24T07:11:32,961 adding 'witch_msa/gcmm/gcmm.py' 2023-11-24T07:11:32,964 adding 'witch_msa/gcmm/loader.py' 2023-11-24T07:11:32,965 adding 'witch_msa/gcmm/merger.py' 2023-11-24T07:11:32,967 adding 'witch_msa/gcmm/results_handler.py' 2023-11-24T07:11:32,969 adding 'witch_msa/gcmm/task.py' 2023-11-24T07:11:32,971 adding 'witch_msa/gcmm/tree.py' 2023-11-24T07:11:32,973 adding 'witch_msa/gcmm/weighting.py' 2023-11-24T07:11:32,974 adding 'witch_msa/helpers/__init__.py' 2023-11-24T07:11:32,981 adding 'witch_msa/helpers/alignment_tools.py' 2023-11-24T07:11:32,982 adding 'witch_msa/helpers/general_tools.py' 2023-11-24T07:11:32,984 adding 'witch_msa/helpers/math_utils.py' 2023-11-24T07:11:32,985 adding 'witch_msa/helpers/pyhmmer_tools.py' 2023-11-24T07:11:33,042 adding 'witch_msa/tools/macOS/FastTreeMP' 2023-11-24T07:11:33,192 adding 'witch_msa/tools/macOS/hmmalign' 2023-11-24T07:11:33,361 adding 'witch_msa/tools/macOS/hmmbuild' 2023-11-24T07:11:33,539 adding 'witch_msa/tools/macOS/hmmsearch' 2023-11-24T07:11:33,556 adding 'witch_msa/tools/macOS/mafft' 2023-11-24T07:11:33,625 adding 'witch_msa/tools/macOS/mcl' 2023-11-24T07:11:33,630 adding 'witch_msa/tools/magus/README.md' 2023-11-24T07:11:33,632 adding 'witch_msa/tools/magus/configuration.py' 2023-11-24T07:11:33,633 adding 'witch_msa/tools/magus/magus.py' 2023-11-24T07:11:33,635 adding 'witch_msa/tools/magus/align/__init__.py' 2023-11-24T07:11:33,636 adding 'witch_msa/tools/magus/align/aligner.py' 2023-11-24T07:11:33,637 adding 'witch_msa/tools/magus/align/alignment_context.py' 2023-11-24T07:11:33,639 adding 'witch_msa/tools/magus/align/decompose/__init__.py' 2023-11-24T07:11:33,640 adding 'witch_msa/tools/magus/align/decompose/decomposer.py' 2023-11-24T07:11:33,642 adding 'witch_msa/tools/magus/align/decompose/initial_tree.py' 2023-11-24T07:11:33,643 adding 'witch_msa/tools/magus/align/decompose/kmh.py' 2023-11-24T07:11:33,644 adding 'witch_msa/tools/magus/align/merge/__init__.py' 2023-11-24T07:11:33,646 adding 'witch_msa/tools/magus/align/merge/alignment_graph.py' 2023-11-24T07:11:33,648 adding 'witch_msa/tools/magus/align/merge/alignment_writer.py' 2023-11-24T07:11:33,649 adding 'witch_msa/tools/magus/align/merge/merger.py' 2023-11-24T07:11:33,652 adding 'witch_msa/tools/magus/align/merge/optimizer.py' 2023-11-24T07:11:33,653 adding 'witch_msa/tools/magus/align/merge/graph_build/__init__.py' 2023-11-24T07:11:33,655 adding 'witch_msa/tools/magus/align/merge/graph_build/graph_builder.py' 2023-11-24T07:11:33,657 adding 'witch_msa/tools/magus/align/merge/graph_cluster/__init__.py' 2023-11-24T07:11:33,658 adding 'witch_msa/tools/magus/align/merge/graph_cluster/clean_clusters.py' 2023-11-24T07:11:33,659 adding 'witch_msa/tools/magus/align/merge/graph_cluster/clusterer.py' 2023-11-24T07:11:33,660 adding 'witch_msa/tools/magus/align/merge/graph_cluster/mcl.py' 2023-11-24T07:11:33,661 adding 'witch_msa/tools/magus/align/merge/graph_cluster/mlr_mcl.py' 2023-11-24T07:11:33,662 adding 'witch_msa/tools/magus/align/merge/graph_cluster/rg.py' 2023-11-24T07:11:33,664 adding 'witch_msa/tools/magus/align/merge/graph_trace/__init__.py' 2023-11-24T07:11:33,666 adding 'witch_msa/tools/magus/align/merge/graph_trace/fm.py' 2023-11-24T07:11:33,668 adding 'witch_msa/tools/magus/align/merge/graph_trace/min_clusters.py' 2023-11-24T07:11:33,670 adding 'witch_msa/tools/magus/align/merge/graph_trace/mwt_search.py' 2023-11-24T07:11:33,671 adding 'witch_msa/tools/magus/align/merge/graph_trace/naive.py' 2023-11-24T07:11:33,673 adding 'witch_msa/tools/magus/align/merge/graph_trace/rg_fast_search.py' 2023-11-24T07:11:33,675 adding 'witch_msa/tools/magus/align/merge/graph_trace/rg_search.py' 2023-11-24T07:11:33,676 adding 'witch_msa/tools/magus/align/merge/graph_trace/tracer.py' 2023-11-24T07:11:33,678 adding 'witch_msa/tools/magus/helpers/__init__.py' 2023-11-24T07:11:33,679 adding 'witch_msa/tools/magus/helpers/hmmutils.py' 2023-11-24T07:11:33,681 adding 'witch_msa/tools/magus/helpers/sequenceutils.py' 2023-11-24T07:11:33,682 adding 'witch_msa/tools/magus/helpers/treeutils.py' 2023-11-24T07:11:33,684 adding 'witch_msa/tools/magus/tasks/__init__.py' 2023-11-24T07:11:33,685 adding 'witch_msa/tools/magus/tasks/controller.py' 2023-11-24T07:11:33,687 adding 'witch_msa/tools/magus/tasks/files.py' 2023-11-24T07:11:33,688 adding 'witch_msa/tools/magus/tasks/manager.py' 2023-11-24T07:11:33,690 adding 'witch_msa/tools/magus/tasks/task.py' 2023-11-24T07:11:33,691 adding 'witch_msa/tools/magus/tools/__init__.py' 2023-11-24T07:11:33,693 adding 'witch_msa/tools/magus/tools/external_tools.py' 2023-11-24T07:11:34,508 adding 'witch_msa/tools/magus/tools/clustal/clustalo' 2023-11-24T07:11:34,615 adding 'witch_msa/tools/magus/tools/fasttree/FastTree' 2023-11-24T07:11:34,687 adding 'witch_msa/tools/magus/tools/fasttree/FastTreeMP' 2023-11-24T07:11:34,896 adding 'witch_msa/tools/magus/tools/hmmer/hmmalign' 2023-11-24T07:11:35,121 adding 'witch_msa/tools/magus/tools/hmmer/hmmbuild' 2023-11-24T07:11:35,368 adding 'witch_msa/tools/magus/tools/hmmer/hmmsearch' 2023-11-24T07:11:35,381 adding 'witch_msa/tools/magus/tools/mafft/mafft' 2023-11-24T07:11:35,392 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/bin/mafft' 2023-11-24T07:11:35,649 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/addsingle' 2023-11-24T07:11:35,830 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/contrafoldwrap' 2023-11-24T07:11:35,956 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/countlen' 2023-11-24T07:11:36,777 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dash_client' 2023-11-24T07:11:37,065 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/disttbfast' 2023-11-24T07:11:37,248 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndblast' 2023-11-24T07:11:37,429 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndfast7' 2023-11-24T07:11:37,607 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndpre' 2023-11-24T07:11:37,860 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dvtditr' 2023-11-24T07:11:38,007 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/f2cl' 2023-11-24T07:11:38,243 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/getlag' 2023-11-24T07:11:38,356 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/hex2maffttext' 2023-11-24T07:11:38,534 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-distance' 2023-11-24T07:11:38,543 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-homologs.1' 2023-11-24T07:11:38,773 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-profile' 2023-11-24T07:11:38,785 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft.1' 2023-11-24T07:11:38,787 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafftash_premafft.pl' 2023-11-24T07:11:38,891 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/maffttext2hex' 2023-11-24T07:11:39,133 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/makedirectionlist' 2023-11-24T07:11:39,316 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mccaskillwrap' 2023-11-24T07:11:39,507 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/multi2hat3s' 2023-11-24T07:11:39,757 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/nodepair' 2023-11-24T07:11:39,999 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairash' 2023-11-24T07:11:40,246 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairlocalalign' 2023-11-24T07:11:40,422 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/regtable2seq' 2023-11-24T07:11:40,591 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/replaceu' 2023-11-24T07:11:40,760 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/restoreu' 2023-11-24T07:11:40,939 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/score' 2023-11-24T07:11:40,948 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seekquencer_premafft.pl' 2023-11-24T07:11:41,068 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seq2regtable' 2023-11-24T07:11:41,312 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setcore' 2023-11-24T07:11:41,476 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setdirection' 2023-11-24T07:11:41,660 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/sextet5' 2023-11-24T07:11:41,902 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/splittbfast' 2023-11-24T07:11:42,163 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/tbfast' 2023-11-24T07:11:42,277 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/version' 2023-11-24T07:11:42,537 adding 'witch_msa/tools/magus/tools/mcl/bin/clm' 2023-11-24T07:11:42,776 adding 'witch_msa/tools/magus/tools/mcl/bin/clmformat' 2023-11-24T07:11:42,788 adding 'witch_msa/tools/magus/tools/mcl/bin/clxdo' 2023-11-24T07:11:42,992 adding 'witch_msa/tools/magus/tools/mcl/bin/mcl' 2023-11-24T07:11:43,003 adding 'witch_msa/tools/magus/tools/mcl/bin/mclblastline' 2023-11-24T07:11:43,216 adding 'witch_msa/tools/magus/tools/mcl/bin/mclcm' 2023-11-24T07:11:43,229 adding 'witch_msa/tools/magus/tools/mcl/bin/mclpipeline' 2023-11-24T07:11:43,485 adding 'witch_msa/tools/magus/tools/mcl/bin/mcx' 2023-11-24T07:11:43,715 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxarray' 2023-11-24T07:11:43,933 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxassemble' 2023-11-24T07:11:43,946 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxdeblast' 2023-11-24T07:11:44,154 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxdump' 2023-11-24T07:11:44,391 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxi' 2023-11-24T07:11:44,609 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxload' 2023-11-24T07:11:44,743 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxmap' 2023-11-24T07:11:44,876 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxrand' 2023-11-24T07:11:45,107 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxsubs' 2023-11-24T07:11:45,120 adding 'witch_msa/tools/magus/tools/mlrmcl/README' 2023-11-24T07:11:45,142 adding 'witch_msa/tools/magus/tools/mlrmcl/mlrmcl' 2023-11-24T07:11:45,164 adding 'witch_msa/tools/magus/tools/mlrmcl/ncut' 2023-11-24T07:11:46,364 adding 'witch_msa/tools/magus/tools/raxmlng/raxml-ng' 2023-11-24T07:11:46,420 adding 'witch_msa-1.0.1.data/scripts/witch-msa' 2023-11-24T07:11:46,421 adding 'witch_msa-1.0.1.data/scripts/witch.py' 2023-11-24T07:11:46,428 adding 'witch_msa-1.0.1.dist-info/LICENSE' 2023-11-24T07:11:46,437 adding 'witch_msa-1.0.1.dist-info/METADATA' 2023-11-24T07:11:46,438 adding 'witch_msa-1.0.1.dist-info/WHEEL' 2023-11-24T07:11:46,440 adding 'witch_msa-1.0.1.dist-info/top_level.txt' 2023-11-24T07:11:46,442 adding 'witch_msa-1.0.1.dist-info/RECORD' 2023-11-24T07:11:46,762 removing build/bdist.linux-armv7l/wheel 2023-11-24T07:11:46,949 Building wheel for witch-msa (pyproject.toml): finished with status 'done' 2023-11-24T07:11:47,614 Created wheel for witch-msa: filename=witch_msa-1.0.1-py3-none-any.whl size=29116039 sha256=9a991d73586803bc132937a46dd0adf27f1c8b87b2e31d0a029497a7b20fd007 2023-11-24T07:11:47,615 Stored in directory: /tmp/pip-ephem-wheel-cache-y_ke2f2b/wheels/d9/fe/66/64d04a7b82545210f8c1cc7778ed719f3cad1b3147d228ec59 2023-11-24T07:11:47,661 Successfully built witch-msa 2023-11-24T07:11:48,340 Removed build tracker: '/tmp/pip-build-tracker-pvegcflv'