2024-01-09T02:48:03,466 Created temporary directory: /tmp/pip-build-tracker-87yb8sky 2024-01-09T02:48:03,467 Initialized build tracking at /tmp/pip-build-tracker-87yb8sky 2024-01-09T02:48:03,467 Created build tracker: /tmp/pip-build-tracker-87yb8sky 2024-01-09T02:48:03,468 Entered build tracker: /tmp/pip-build-tracker-87yb8sky 2024-01-09T02:48:03,469 Created temporary directory: /tmp/pip-wheel-ry2kv_su 2024-01-09T02:48:03,472 Created temporary directory: /tmp/pip-ephem-wheel-cache-xomq2ypa 2024-01-09T02:48:03,494 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-01-09T02:48:03,497 2 location(s) to search for versions of witch-msa: 2024-01-09T02:48:03,497 * https://pypi.org/simple/witch-msa/ 2024-01-09T02:48:03,497 * https://www.piwheels.org/simple/witch-msa/ 2024-01-09T02:48:03,498 Fetching project page and analyzing links: https://pypi.org/simple/witch-msa/ 2024-01-09T02:48:03,499 Getting page https://pypi.org/simple/witch-msa/ 2024-01-09T02:48:03,500 Found index url https://pypi.org/simple/ 2024-01-09T02:48:03,711 Fetched page https://pypi.org/simple/witch-msa/ as application/vnd.pypi.simple.v1+json 2024-01-09T02:48:03,715 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 2024-01-09T02:48:03,716 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) 2024-01-09T02:48:03,716 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 2024-01-09T02:48:03,717 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) 2024-01-09T02:48:03,718 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 2024-01-09T02:48:03,719 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) 2024-01-09T02:48:03,720 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 2024-01-09T02:48:03,720 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) 2024-01-09T02:48:03,721 Found link https://files.pythonhosted.org/packages/c6/81/4a0953d4b062ea116c7e89fbeb65f537958b489d02bee8263b6044d3aeb5/witch-msa-1.0.2a1.tar.gz (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7), version: 1.0.2a1 2024-01-09T02:48:03,722 Skipping link: No binaries permitted for witch-msa: https://files.pythonhosted.org/packages/ac/96/5021e8835aef45c1a4f6b35c072002d7b7fd870cb4fe75f87b71b5d163b2/witch_msa-1.0.2a1-py3-none-any.whl (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7) 2024-01-09T02:48:03,723 Found link https://files.pythonhosted.org/packages/64/5e/5c1c155504577b54c69c77cab4f13b188e09352f4e1f6bdee2cd24fdc79b/witch-msa-1.0.2.tar.gz (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7), version: 1.0.2 2024-01-09T02:48:03,723 Skipping link: No binaries permitted for witch-msa: https://files.pythonhosted.org/packages/20/8a/6d9b66587c199643ee2fa476eca10667d34c5f1b98f0f50a1b67a255d245/witch_msa-1.0.2-py3-none-any.whl (from https://pypi.org/simple/witch-msa/) (requires-python:>=3.7) 2024-01-09T02:48:03,725 Fetching project page and analyzing links: https://www.piwheels.org/simple/witch-msa/ 2024-01-09T02:48:03,725 Getting page https://www.piwheels.org/simple/witch-msa/ 2024-01-09T02:48:03,726 Found index url https://www.piwheels.org/simple/ 2024-01-09T02:48:03,887 Fetched page https://www.piwheels.org/simple/witch-msa/ as text/html 2024-01-09T02:48:03,890 Skipping link: No binaries permitted for witch-msa: https://www.piwheels.org/simple/witch-msa/witch_msa-1.0.2a1-py3-none-any.whl#sha256=4ba431635ab1cb66b533f39a613a0451577fdbf854dace83aad27dbac829afac (from https://www.piwheels.org/simple/witch-msa/) (requires-python:>=3.7) 2024-01-09T02:48:03,891 Skipping link: No binaries permitted for witch-msa: https://www.piwheels.org/simple/witch-msa/witch_msa-1.0.1-py3-none-any.whl#sha256=9a991d73586803bc132937a46dd0adf27f1c8b87b2e31d0a029497a7b20fd007 (from https://www.piwheels.org/simple/witch-msa/) (requires-python:>=3.7) 2024-01-09T02:48:03,891 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) 2024-01-09T02:48:03,892 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) 2024-01-09T02:48:03,892 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) 2024-01-09T02:48:03,893 Skipping link: not a file: https://www.piwheels.org/simple/witch-msa/ 2024-01-09T02:48:03,893 Skipping link: not a file: https://pypi.org/simple/witch-msa/ 2024-01-09T02:48:03,912 Given no hashes to check 1 links for project 'witch-msa': discarding no candidates 2024-01-09T02:48:03,930 Collecting witch-msa==1.0.2 2024-01-09T02:48:03,932 Created temporary directory: /tmp/pip-unpack-lfu4byo1 2024-01-09T02:48:04,155 Downloading witch-msa-1.0.2.tar.gz (29.0 MB) 2024-01-09T02:48:11,744 Added witch-msa==1.0.2 from https://files.pythonhosted.org/packages/64/5e/5c1c155504577b54c69c77cab4f13b188e09352f4e1f6bdee2cd24fdc79b/witch-msa-1.0.2.tar.gz to build tracker '/tmp/pip-build-tracker-87yb8sky' 2024-01-09T02:48:11,747 Created temporary directory: /tmp/pip-build-env-cjgplgdk 2024-01-09T02:48:11,752 Installing build dependencies: started 2024-01-09T02:48:11,753 Running command pip subprocess to install build dependencies 2024-01-09T02:48:12,886 Using pip 23.3.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2024-01-09T02:48:13,385 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-01-09T02:48:14,789 Collecting setuptools 2024-01-09T02:48:14,804 Using cached https://www.piwheels.org/simple/setuptools/setuptools-69.0.3-py3-none-any.whl (819 kB) 2024-01-09T02:48:17,381 Installing collected packages: setuptools 2024-01-09T02:48:19,598 Successfully installed setuptools-69.0.3 2024-01-09T02:48:19,848 [notice] A new release of pip is available: 23.3.1 -> 23.3.2 2024-01-09T02:48:19,848 [notice] To update, run: python3 -m pip install --upgrade pip 2024-01-09T02:48:20,109 Installing build dependencies: finished with status 'done' 2024-01-09T02:48:20,113 Getting requirements to build wheel: started 2024-01-09T02:48:20,114 Running command Getting requirements to build wheel 2024-01-09T02:48:20,867 running egg_info 2024-01-09T02:48:20,871 writing witch_msa.egg-info/PKG-INFO 2024-01-09T02:48:20,876 writing dependency_links to witch_msa.egg-info/dependency_links.txt 2024-01-09T02:48:20,879 writing requirements to witch_msa.egg-info/requires.txt 2024-01-09T02:48:20,880 writing top-level names to witch_msa.egg-info/top_level.txt 2024-01-09T02:48:20,900 reading manifest file 'witch_msa.egg-info/SOURCES.txt' 2024-01-09T02:48:20,921 reading manifest template 'MANIFEST.in' 2024-01-09T02:48:20,940 no previously-included directories found matching '*/__pycache__' 2024-01-09T02:48:20,941 warning: no previously-included files matching '*.py[cod]' found anywhere in distribution 2024-01-09T02:48:20,942 adding license file 'LICENSE' 2024-01-09T02:48:20,949 writing manifest file 'witch_msa.egg-info/SOURCES.txt' 2024-01-09T02:48:21,061 Getting requirements to build wheel: finished with status 'done' 2024-01-09T02:48:21,068 Installing backend dependencies: started 2024-01-09T02:48:21,070 Running command pip subprocess to install backend dependencies 2024-01-09T02:48:22,194 Using pip 23.3.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2024-01-09T02:48:22,691 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-01-09T02:48:23,164 Collecting wheel 2024-01-09T02:48:23,180 Using cached https://www.piwheels.org/simple/wheel/wheel-0.42.0-py3-none-any.whl (65 kB) 2024-01-09T02:48:25,411 Installing collected packages: wheel 2024-01-09T02:48:25,631 Creating /tmp/pip-build-env-cjgplgdk/normal/local/bin 2024-01-09T02:48:25,633 changing mode of /tmp/pip-build-env-cjgplgdk/normal/local/bin/wheel to 755 2024-01-09T02:48:25,644 Successfully installed wheel-0.42.0 2024-01-09T02:48:25,894 [notice] A new release of pip is available: 23.3.1 -> 23.3.2 2024-01-09T02:48:25,895 [notice] To update, run: python3 -m pip install --upgrade pip 2024-01-09T02:48:26,122 Installing backend dependencies: finished with status 'done' 2024-01-09T02:48:26,124 Created temporary directory: /tmp/pip-modern-metadata-m9knpanb 2024-01-09T02:48:26,126 Preparing metadata (pyproject.toml): started 2024-01-09T02:48:26,127 Running command Preparing metadata (pyproject.toml) 2024-01-09T02:48:26,928 running dist_info 2024-01-09T02:48:26,932 creating /tmp/pip-modern-metadata-m9knpanb/witch_msa.egg-info 2024-01-09T02:48:26,936 writing /tmp/pip-modern-metadata-m9knpanb/witch_msa.egg-info/PKG-INFO 2024-01-09T02:48:26,941 writing dependency_links to /tmp/pip-modern-metadata-m9knpanb/witch_msa.egg-info/dependency_links.txt 2024-01-09T02:48:26,943 writing requirements to /tmp/pip-modern-metadata-m9knpanb/witch_msa.egg-info/requires.txt 2024-01-09T02:48:26,944 writing top-level names to /tmp/pip-modern-metadata-m9knpanb/witch_msa.egg-info/top_level.txt 2024-01-09T02:48:26,945 writing manifest file '/tmp/pip-modern-metadata-m9knpanb/witch_msa.egg-info/SOURCES.txt' 2024-01-09T02:48:26,966 reading manifest file '/tmp/pip-modern-metadata-m9knpanb/witch_msa.egg-info/SOURCES.txt' 2024-01-09T02:48:26,968 reading manifest template 'MANIFEST.in' 2024-01-09T02:48:26,996 no previously-included directories found matching '*/__pycache__' 2024-01-09T02:48:26,997 warning: no previously-included files matching '*.py[cod]' found anywhere in distribution 2024-01-09T02:48:26,997 adding license file 'LICENSE' 2024-01-09T02:48:27,003 writing manifest file '/tmp/pip-modern-metadata-m9knpanb/witch_msa.egg-info/SOURCES.txt' 2024-01-09T02:48:27,004 creating '/tmp/pip-modern-metadata-m9knpanb/witch_msa-1.0.2.dist-info' 2024-01-09T02:48:27,160 Preparing metadata (pyproject.toml): finished with status 'done' 2024-01-09T02:48:27,172 Source in /tmp/pip-wheel-ry2kv_su/witch-msa_d80425bca87d4bf190edab85c8bb5aa1 has version 1.0.2, which satisfies requirement witch-msa==1.0.2 from https://files.pythonhosted.org/packages/64/5e/5c1c155504577b54c69c77cab4f13b188e09352f4e1f6bdee2cd24fdc79b/witch-msa-1.0.2.tar.gz 2024-01-09T02:48:27,173 Removed witch-msa==1.0.2 from https://files.pythonhosted.org/packages/64/5e/5c1c155504577b54c69c77cab4f13b188e09352f4e1f6bdee2cd24fdc79b/witch-msa-1.0.2.tar.gz from build tracker '/tmp/pip-build-tracker-87yb8sky' 2024-01-09T02:48:27,193 Created temporary directory: /tmp/pip-unpack-lahstcds 2024-01-09T02:48:27,194 Created temporary directory: /tmp/pip-unpack-4a0a04h4 2024-01-09T02:48:27,222 Building wheels for collected packages: witch-msa 2024-01-09T02:48:27,226 Created temporary directory: /tmp/pip-wheel-mt9b1vzu 2024-01-09T02:48:27,226 Destination directory: /tmp/pip-wheel-mt9b1vzu 2024-01-09T02:48:27,228 Building wheel for witch-msa (pyproject.toml): started 2024-01-09T02:48:27,230 Running command Building wheel for witch-msa (pyproject.toml) 2024-01-09T02:48:27,990 running bdist_wheel 2024-01-09T02:48:28,006 running build 2024-01-09T02:48:28,006 running build_py 2024-01-09T02:48:28,010 creating build 2024-01-09T02:48:28,011 creating build/lib 2024-01-09T02:48:28,012 creating build/lib/witch_msa 2024-01-09T02:48:28,013 copying witch_msa/configs.py -> build/lib/witch_msa 2024-01-09T02:48:28,015 copying witch_msa/__init__.py -> build/lib/witch_msa 2024-01-09T02:48:28,017 copying witch_msa/init_configs.py -> build/lib/witch_msa 2024-01-09T02:48:28,020 creating build/lib/witch_msa/gcmm 2024-01-09T02:48:28,021 copying witch_msa/gcmm/backbone.py -> build/lib/witch_msa/gcmm 2024-01-09T02:48:28,024 copying witch_msa/gcmm/weighting.py -> build/lib/witch_msa/gcmm 2024-01-09T02:48:28,026 copying witch_msa/gcmm/loader.py -> build/lib/witch_msa/gcmm 2024-01-09T02:48:28,028 copying witch_msa/gcmm/results_handler.py -> build/lib/witch_msa/gcmm 2024-01-09T02:48:28,030 copying witch_msa/gcmm/callback.py -> build/lib/witch_msa/gcmm 2024-01-09T02:48:28,032 copying witch_msa/gcmm/algorithm.py -> build/lib/witch_msa/gcmm 2024-01-09T02:48:28,034 copying witch_msa/gcmm/gcmm.py -> build/lib/witch_msa/gcmm 2024-01-09T02:48:28,037 copying witch_msa/gcmm/__init__.py -> build/lib/witch_msa/gcmm 2024-01-09T02:48:28,038 copying witch_msa/gcmm/decompose_tree.py -> build/lib/witch_msa/gcmm 2024-01-09T02:48:28,040 copying witch_msa/gcmm/merger.py -> build/lib/witch_msa/gcmm 2024-01-09T02:48:28,042 copying witch_msa/gcmm/aligner.py -> build/lib/witch_msa/gcmm 2024-01-09T02:48:28,045 copying witch_msa/gcmm/task.py -> build/lib/witch_msa/gcmm 2024-01-09T02:48:28,047 copying witch_msa/gcmm/tree.py -> build/lib/witch_msa/gcmm 2024-01-09T02:48:28,050 creating build/lib/witch_msa/helpers 2024-01-09T02:48:28,051 copying witch_msa/helpers/general_tools.py -> build/lib/witch_msa/helpers 2024-01-09T02:48:28,053 copying witch_msa/helpers/pyhmmer_tools.py -> build/lib/witch_msa/helpers 2024-01-09T02:48:28,054 copying witch_msa/helpers/math_utils.py -> build/lib/witch_msa/helpers 2024-01-09T02:48:28,056 copying witch_msa/helpers/__init__.py -> build/lib/witch_msa/helpers 2024-01-09T02:48:28,057 copying witch_msa/helpers/alignment_tools.py -> build/lib/witch_msa/helpers 2024-01-09T02:48:28,060 running egg_info 2024-01-09T02:48:28,063 writing witch_msa.egg-info/PKG-INFO 2024-01-09T02:48:28,068 writing dependency_links to witch_msa.egg-info/dependency_links.txt 2024-01-09T02:48:28,070 writing requirements to witch_msa.egg-info/requires.txt 2024-01-09T02:48:28,071 writing top-level names to witch_msa.egg-info/top_level.txt 2024-01-09T02:48:28,080 reading manifest file 'witch_msa.egg-info/SOURCES.txt' 2024-01-09T02:48:28,085 reading manifest template 'MANIFEST.in' 2024-01-09T02:48:28,097 no previously-included directories found matching '*/__pycache__' 2024-01-09T02:48:28,099 warning: no previously-included files matching '*.py[cod]' found anywhere in distribution 2024-01-09T02:48:28,099 adding license file 'LICENSE' 2024-01-09T02:48:28,107 writing manifest file 'witch_msa.egg-info/SOURCES.txt' 2024-01-09T02:48:28,109 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,110 !! 2024-01-09T02:48:28,111 ******************************************************************************** 2024-01-09T02:48:28,112 ############################ 2024-01-09T02:48:28,113 # Package would be ignored # 2024-01-09T02:48:28,114 ############################ 2024-01-09T02:48:28,114 Python recognizes 'witch_msa.tools.macOS' as an importable package[^1], 2024-01-09T02:48:28,114 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,115 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,116 package, please make sure that 'witch_msa.tools.macOS' is explicitly added 2024-01-09T02:48:28,116 to the `packages` configuration field. 2024-01-09T02:48:28,117 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,117 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,118 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,119 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,120 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,121 If you don't want 'witch_msa.tools.macOS' to be distributed and are 2024-01-09T02:48:28,121 already explicitly excluding 'witch_msa.tools.macOS' via 2024-01-09T02:48:28,122 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,122 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,123 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,124 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,125 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,127 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,132 even if it does not contain any `.py` files. 2024-01-09T02:48:28,132 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,133 directory, all directories are treated like packages. 2024-01-09T02:48:28,133 ******************************************************************************** 2024-01-09T02:48:28,134 !! 2024-01-09T02:48:28,135 check.warn(importable) 2024-01-09T02:48:28,136 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,136 !! 2024-01-09T02:48:28,138 ******************************************************************************** 2024-01-09T02:48:28,138 ############################ 2024-01-09T02:48:28,139 # Package would be ignored # 2024-01-09T02:48:28,139 ############################ 2024-01-09T02:48:28,140 Python recognizes 'witch_msa.tools.magus' as an importable package[^1], 2024-01-09T02:48:28,140 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,141 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,142 package, please make sure that 'witch_msa.tools.magus' is explicitly added 2024-01-09T02:48:28,142 to the `packages` configuration field. 2024-01-09T02:48:28,144 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,144 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,145 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,146 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,147 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,149 If you don't want 'witch_msa.tools.magus' to be distributed and are 2024-01-09T02:48:28,149 already explicitly excluding 'witch_msa.tools.magus' via 2024-01-09T02:48:28,149 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,150 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,150 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,151 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,152 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,154 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,155 even if it does not contain any `.py` files. 2024-01-09T02:48:28,156 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,157 directory, all directories are treated like packages. 2024-01-09T02:48:28,158 ******************************************************************************** 2024-01-09T02:48:28,159 !! 2024-01-09T02:48:28,159 check.warn(importable) 2024-01-09T02:48:28,160 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,161 !! 2024-01-09T02:48:28,162 ******************************************************************************** 2024-01-09T02:48:28,162 ############################ 2024-01-09T02:48:28,163 # Package would be ignored # 2024-01-09T02:48:28,163 ############################ 2024-01-09T02:48:28,164 Python recognizes 'witch_msa.tools.magus.align' as an importable package[^1], 2024-01-09T02:48:28,164 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,166 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,166 package, please make sure that 'witch_msa.tools.magus.align' is explicitly added 2024-01-09T02:48:28,167 to the `packages` configuration field. 2024-01-09T02:48:28,168 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,169 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,169 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,171 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,172 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,173 If you don't want 'witch_msa.tools.magus.align' to be distributed and are 2024-01-09T02:48:28,173 already explicitly excluding 'witch_msa.tools.magus.align' via 2024-01-09T02:48:28,174 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,174 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,175 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,176 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,178 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,179 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,180 even if it does not contain any `.py` files. 2024-01-09T02:48:28,181 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,181 directory, all directories are treated like packages. 2024-01-09T02:48:28,182 ******************************************************************************** 2024-01-09T02:48:28,183 !! 2024-01-09T02:48:28,184 check.warn(importable) 2024-01-09T02:48:28,185 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,185 !! 2024-01-09T02:48:28,186 ******************************************************************************** 2024-01-09T02:48:28,186 ############################ 2024-01-09T02:48:28,187 # Package would be ignored # 2024-01-09T02:48:28,187 ############################ 2024-01-09T02:48:28,187 Python recognizes 'witch_msa.tools.magus.align.decompose' as an importable package[^1], 2024-01-09T02:48:28,188 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,189 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,189 package, please make sure that 'witch_msa.tools.magus.align.decompose' is explicitly added 2024-01-09T02:48:28,189 to the `packages` configuration field. 2024-01-09T02:48:28,190 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,191 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,191 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,192 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,193 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,194 If you don't want 'witch_msa.tools.magus.align.decompose' to be distributed and are 2024-01-09T02:48:28,195 already explicitly excluding 'witch_msa.tools.magus.align.decompose' via 2024-01-09T02:48:28,195 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,196 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,196 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,197 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,199 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,202 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,205 even if it does not contain any `.py` files. 2024-01-09T02:48:28,206 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,207 directory, all directories are treated like packages. 2024-01-09T02:48:28,207 ******************************************************************************** 2024-01-09T02:48:28,208 !! 2024-01-09T02:48:28,209 check.warn(importable) 2024-01-09T02:48:28,209 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,210 !! 2024-01-09T02:48:28,211 ******************************************************************************** 2024-01-09T02:48:28,211 ############################ 2024-01-09T02:48:28,212 # Package would be ignored # 2024-01-09T02:48:28,213 ############################ 2024-01-09T02:48:28,213 Python recognizes 'witch_msa.tools.magus.align.merge' as an importable package[^1], 2024-01-09T02:48:28,217 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,225 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,227 package, please make sure that 'witch_msa.tools.magus.align.merge' is explicitly added 2024-01-09T02:48:28,228 to the `packages` configuration field. 2024-01-09T02:48:28,229 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,229 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,230 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,231 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,232 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,237 If you don't want 'witch_msa.tools.magus.align.merge' to be distributed and are 2024-01-09T02:48:28,240 already explicitly excluding 'witch_msa.tools.magus.align.merge' via 2024-01-09T02:48:28,240 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,241 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,241 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,242 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,243 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,245 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,245 even if it does not contain any `.py` files. 2024-01-09T02:48:28,246 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,246 directory, all directories are treated like packages. 2024-01-09T02:48:28,246 ******************************************************************************** 2024-01-09T02:48:28,247 !! 2024-01-09T02:48:28,248 check.warn(importable) 2024-01-09T02:48:28,248 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,249 !! 2024-01-09T02:48:28,250 ******************************************************************************** 2024-01-09T02:48:28,250 ############################ 2024-01-09T02:48:28,251 # Package would be ignored # 2024-01-09T02:48:28,251 ############################ 2024-01-09T02:48:28,252 Python recognizes 'witch_msa.tools.magus.align.merge.graph_build' as an importable package[^1], 2024-01-09T02:48:28,252 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,253 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,254 package, please make sure that 'witch_msa.tools.magus.align.merge.graph_build' is explicitly added 2024-01-09T02:48:28,254 to the `packages` configuration field. 2024-01-09T02:48:28,255 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,256 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,256 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,257 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,258 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,259 If you don't want 'witch_msa.tools.magus.align.merge.graph_build' to be distributed and are 2024-01-09T02:48:28,260 already explicitly excluding 'witch_msa.tools.magus.align.merge.graph_build' via 2024-01-09T02:48:28,260 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,261 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,261 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,262 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,263 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,265 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,265 even if it does not contain any `.py` files. 2024-01-09T02:48:28,266 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,266 directory, all directories are treated like packages. 2024-01-09T02:48:28,267 ******************************************************************************** 2024-01-09T02:48:28,267 !! 2024-01-09T02:48:28,268 check.warn(importable) 2024-01-09T02:48:28,268 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,269 !! 2024-01-09T02:48:28,270 ******************************************************************************** 2024-01-09T02:48:28,270 ############################ 2024-01-09T02:48:28,270 # Package would be ignored # 2024-01-09T02:48:28,271 ############################ 2024-01-09T02:48:28,271 Python recognizes 'witch_msa.tools.magus.align.merge.graph_cluster' as an importable package[^1], 2024-01-09T02:48:28,272 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,273 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,273 package, please make sure that 'witch_msa.tools.magus.align.merge.graph_cluster' is explicitly added 2024-01-09T02:48:28,274 to the `packages` configuration field. 2024-01-09T02:48:28,275 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,275 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,276 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,277 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,278 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,279 If you don't want 'witch_msa.tools.magus.align.merge.graph_cluster' to be distributed and are 2024-01-09T02:48:28,279 already explicitly excluding 'witch_msa.tools.magus.align.merge.graph_cluster' via 2024-01-09T02:48:28,280 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,280 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,281 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,282 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,283 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,285 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,285 even if it does not contain any `.py` files. 2024-01-09T02:48:28,286 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,286 directory, all directories are treated like packages. 2024-01-09T02:48:28,287 ******************************************************************************** 2024-01-09T02:48:28,288 !! 2024-01-09T02:48:28,288 check.warn(importable) 2024-01-09T02:48:28,289 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,289 !! 2024-01-09T02:48:28,290 ******************************************************************************** 2024-01-09T02:48:28,291 ############################ 2024-01-09T02:48:28,291 # Package would be ignored # 2024-01-09T02:48:28,292 ############################ 2024-01-09T02:48:28,292 Python recognizes 'witch_msa.tools.magus.align.merge.graph_trace' as an importable package[^1], 2024-01-09T02:48:28,293 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,294 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,294 package, please make sure that 'witch_msa.tools.magus.align.merge.graph_trace' is explicitly added 2024-01-09T02:48:28,294 to the `packages` configuration field. 2024-01-09T02:48:28,295 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,296 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,296 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,297 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,298 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,299 If you don't want 'witch_msa.tools.magus.align.merge.graph_trace' to be distributed and are 2024-01-09T02:48:28,299 already explicitly excluding 'witch_msa.tools.magus.align.merge.graph_trace' via 2024-01-09T02:48:28,300 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,300 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,301 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,302 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,303 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,305 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,305 even if it does not contain any `.py` files. 2024-01-09T02:48:28,306 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,306 directory, all directories are treated like packages. 2024-01-09T02:48:28,307 ******************************************************************************** 2024-01-09T02:48:28,308 !! 2024-01-09T02:48:28,308 check.warn(importable) 2024-01-09T02:48:28,309 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,309 !! 2024-01-09T02:48:28,311 ******************************************************************************** 2024-01-09T02:48:28,311 ############################ 2024-01-09T02:48:28,312 # Package would be ignored # 2024-01-09T02:48:28,312 ############################ 2024-01-09T02:48:28,313 Python recognizes 'witch_msa.tools.magus.helpers' as an importable package[^1], 2024-01-09T02:48:28,313 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,315 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,316 package, please make sure that 'witch_msa.tools.magus.helpers' is explicitly added 2024-01-09T02:48:28,316 to the `packages` configuration field. 2024-01-09T02:48:28,317 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,318 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,318 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,319 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,321 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,322 If you don't want 'witch_msa.tools.magus.helpers' to be distributed and are 2024-01-09T02:48:28,322 already explicitly excluding 'witch_msa.tools.magus.helpers' via 2024-01-09T02:48:28,322 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,323 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,323 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,324 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,325 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,326 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,327 even if it does not contain any `.py` files. 2024-01-09T02:48:28,327 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,328 directory, all directories are treated like packages. 2024-01-09T02:48:28,328 ******************************************************************************** 2024-01-09T02:48:28,329 !! 2024-01-09T02:48:28,329 check.warn(importable) 2024-01-09T02:48:28,330 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,331 !! 2024-01-09T02:48:28,331 ******************************************************************************** 2024-01-09T02:48:28,332 ############################ 2024-01-09T02:48:28,332 # Package would be ignored # 2024-01-09T02:48:28,333 ############################ 2024-01-09T02:48:28,334 Python recognizes 'witch_msa.tools.magus.tasks' as an importable package[^1], 2024-01-09T02:48:28,334 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,335 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,336 package, please make sure that 'witch_msa.tools.magus.tasks' is explicitly added 2024-01-09T02:48:28,336 to the `packages` configuration field. 2024-01-09T02:48:28,337 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,338 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,338 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,339 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,340 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,341 If you don't want 'witch_msa.tools.magus.tasks' to be distributed and are 2024-01-09T02:48:28,342 already explicitly excluding 'witch_msa.tools.magus.tasks' via 2024-01-09T02:48:28,342 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,343 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,343 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,344 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,345 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,347 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,347 even if it does not contain any `.py` files. 2024-01-09T02:48:28,348 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,348 directory, all directories are treated like packages. 2024-01-09T02:48:28,349 ******************************************************************************** 2024-01-09T02:48:28,350 !! 2024-01-09T02:48:28,351 check.warn(importable) 2024-01-09T02:48:28,351 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,352 !! 2024-01-09T02:48:28,352 ******************************************************************************** 2024-01-09T02:48:28,353 ############################ 2024-01-09T02:48:28,353 # Package would be ignored # 2024-01-09T02:48:28,354 ############################ 2024-01-09T02:48:28,354 Python recognizes 'witch_msa.tools.magus.tools' as an importable package[^1], 2024-01-09T02:48:28,355 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,356 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,356 package, please make sure that 'witch_msa.tools.magus.tools' is explicitly added 2024-01-09T02:48:28,357 to the `packages` configuration field. 2024-01-09T02:48:28,357 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,358 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,358 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,359 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,360 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,362 If you don't want 'witch_msa.tools.magus.tools' to be distributed and are 2024-01-09T02:48:28,362 already explicitly excluding 'witch_msa.tools.magus.tools' via 2024-01-09T02:48:28,363 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,364 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,364 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,365 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,367 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,369 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,369 even if it does not contain any `.py` files. 2024-01-09T02:48:28,370 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,371 directory, all directories are treated like packages. 2024-01-09T02:48:28,371 ******************************************************************************** 2024-01-09T02:48:28,372 !! 2024-01-09T02:48:28,373 check.warn(importable) 2024-01-09T02:48:28,373 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,374 !! 2024-01-09T02:48:28,375 ******************************************************************************** 2024-01-09T02:48:28,376 ############################ 2024-01-09T02:48:28,376 # Package would be ignored # 2024-01-09T02:48:28,377 ############################ 2024-01-09T02:48:28,378 Python recognizes 'witch_msa.tools.magus.tools.clustal' as an importable package[^1], 2024-01-09T02:48:28,378 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,383 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,396 package, please make sure that 'witch_msa.tools.magus.tools.clustal' is explicitly added 2024-01-09T02:48:28,434 to the `packages` configuration field. 2024-01-09T02:48:28,441 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,441 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,442 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,442 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,443 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,444 If you don't want 'witch_msa.tools.magus.tools.clustal' to be distributed and are 2024-01-09T02:48:28,445 already explicitly excluding 'witch_msa.tools.magus.tools.clustal' via 2024-01-09T02:48:28,445 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,446 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,446 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,447 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,449 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,453 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,454 even if it does not contain any `.py` files. 2024-01-09T02:48:28,457 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,457 directory, all directories are treated like packages. 2024-01-09T02:48:28,458 ******************************************************************************** 2024-01-09T02:48:28,459 !! 2024-01-09T02:48:28,460 check.warn(importable) 2024-01-09T02:48:28,461 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,463 !! 2024-01-09T02:48:28,467 ******************************************************************************** 2024-01-09T02:48:28,468 ############################ 2024-01-09T02:48:28,468 # Package would be ignored # 2024-01-09T02:48:28,469 ############################ 2024-01-09T02:48:28,470 Python recognizes 'witch_msa.tools.magus.tools.fasttree' as an importable package[^1], 2024-01-09T02:48:28,476 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,478 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,479 package, please make sure that 'witch_msa.tools.magus.tools.fasttree' is explicitly added 2024-01-09T02:48:28,484 to the `packages` configuration field. 2024-01-09T02:48:28,488 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,491 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,492 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,501 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,504 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,512 If you don't want 'witch_msa.tools.magus.tools.fasttree' to be distributed and are 2024-01-09T02:48:28,515 already explicitly excluding 'witch_msa.tools.magus.tools.fasttree' via 2024-01-09T02:48:28,516 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,517 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,517 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,518 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,519 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,521 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,521 even if it does not contain any `.py` files. 2024-01-09T02:48:28,521 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,522 directory, all directories are treated like packages. 2024-01-09T02:48:28,522 ******************************************************************************** 2024-01-09T02:48:28,523 !! 2024-01-09T02:48:28,524 check.warn(importable) 2024-01-09T02:48:28,524 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,524 !! 2024-01-09T02:48:28,542 ******************************************************************************** 2024-01-09T02:48:28,546 ############################ 2024-01-09T02:48:28,547 # Package would be ignored # 2024-01-09T02:48:28,548 ############################ 2024-01-09T02:48:28,548 Python recognizes 'witch_msa.tools.magus.tools.hmmer' as an importable package[^1], 2024-01-09T02:48:28,549 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,550 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,551 package, please make sure that 'witch_msa.tools.magus.tools.hmmer' is explicitly added 2024-01-09T02:48:28,551 to the `packages` configuration field. 2024-01-09T02:48:28,552 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,553 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,554 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,555 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,556 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,558 If you don't want 'witch_msa.tools.magus.tools.hmmer' to be distributed and are 2024-01-09T02:48:28,559 already explicitly excluding 'witch_msa.tools.magus.tools.hmmer' via 2024-01-09T02:48:28,560 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,560 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,561 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,562 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,564 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,572 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,574 even if it does not contain any `.py` files. 2024-01-09T02:48:28,579 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,585 directory, all directories are treated like packages. 2024-01-09T02:48:28,586 ******************************************************************************** 2024-01-09T02:48:28,587 !! 2024-01-09T02:48:28,588 check.warn(importable) 2024-01-09T02:48:28,589 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,589 !! 2024-01-09T02:48:28,591 ******************************************************************************** 2024-01-09T02:48:28,592 ############################ 2024-01-09T02:48:28,592 # Package would be ignored # 2024-01-09T02:48:28,593 ############################ 2024-01-09T02:48:28,594 Python recognizes 'witch_msa.tools.magus.tools.mafft' as an importable package[^1], 2024-01-09T02:48:28,597 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,603 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,604 package, please make sure that 'witch_msa.tools.magus.tools.mafft' is explicitly added 2024-01-09T02:48:28,604 to the `packages` configuration field. 2024-01-09T02:48:28,611 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,613 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,615 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,616 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,617 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,618 If you don't want 'witch_msa.tools.magus.tools.mafft' to be distributed and are 2024-01-09T02:48:28,618 already explicitly excluding 'witch_msa.tools.magus.tools.mafft' via 2024-01-09T02:48:28,619 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,619 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,620 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,621 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,622 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,623 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,624 even if it does not contain any `.py` files. 2024-01-09T02:48:28,624 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,625 directory, all directories are treated like packages. 2024-01-09T02:48:28,626 ******************************************************************************** 2024-01-09T02:48:28,627 !! 2024-01-09T02:48:28,627 check.warn(importable) 2024-01-09T02:48:28,628 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,628 !! 2024-01-09T02:48:28,630 ******************************************************************************** 2024-01-09T02:48:28,630 ############################ 2024-01-09T02:48:28,631 # Package would be ignored # 2024-01-09T02:48:28,631 ############################ 2024-01-09T02:48:28,632 Python recognizes 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' as an importable package[^1], 2024-01-09T02:48:28,632 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,633 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,634 package, please make sure that 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' is explicitly added 2024-01-09T02:48:28,635 to the `packages` configuration field. 2024-01-09T02:48:28,636 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,637 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,644 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,680 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,681 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,682 If you don't want 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' to be distributed and are 2024-01-09T02:48:28,682 already explicitly excluding 'witch_msa.tools.magus.tools.mafft.mafftdir.bin' via 2024-01-09T02:48:28,683 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,683 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,683 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,684 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,685 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,686 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,687 even if it does not contain any `.py` files. 2024-01-09T02:48:28,687 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,688 directory, all directories are treated like packages. 2024-01-09T02:48:28,688 ******************************************************************************** 2024-01-09T02:48:28,689 !! 2024-01-09T02:48:28,689 check.warn(importable) 2024-01-09T02:48:28,690 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,691 !! 2024-01-09T02:48:28,702 ******************************************************************************** 2024-01-09T02:48:28,742 ############################ 2024-01-09T02:48:28,743 # Package would be ignored # 2024-01-09T02:48:28,743 ############################ 2024-01-09T02:48:28,744 Python recognizes 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' as an importable package[^1], 2024-01-09T02:48:28,744 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,746 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,746 package, please make sure that 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' is explicitly added 2024-01-09T02:48:28,747 to the `packages` configuration field. 2024-01-09T02:48:28,748 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,751 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,756 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,759 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,760 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,761 If you don't want 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' to be distributed and are 2024-01-09T02:48:28,762 already explicitly excluding 'witch_msa.tools.magus.tools.mafft.mafftdir.libexec' via 2024-01-09T02:48:28,763 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,763 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,764 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,765 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,775 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,778 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,778 even if it does not contain any `.py` files. 2024-01-09T02:48:28,780 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,780 directory, all directories are treated like packages. 2024-01-09T02:48:28,781 ******************************************************************************** 2024-01-09T02:48:28,782 !! 2024-01-09T02:48:28,782 check.warn(importable) 2024-01-09T02:48:28,783 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,783 !! 2024-01-09T02:48:28,784 ******************************************************************************** 2024-01-09T02:48:28,784 ############################ 2024-01-09T02:48:28,785 # Package would be ignored # 2024-01-09T02:48:28,786 ############################ 2024-01-09T02:48:28,787 Python recognizes 'witch_msa.tools.magus.tools.mcl.bin' as an importable package[^1], 2024-01-09T02:48:28,790 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,796 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,796 package, please make sure that 'witch_msa.tools.magus.tools.mcl.bin' is explicitly added 2024-01-09T02:48:28,797 to the `packages` configuration field. 2024-01-09T02:48:28,797 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,798 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,798 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,800 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,801 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,802 If you don't want 'witch_msa.tools.magus.tools.mcl.bin' to be distributed and are 2024-01-09T02:48:28,803 already explicitly excluding 'witch_msa.tools.magus.tools.mcl.bin' via 2024-01-09T02:48:28,803 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,808 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,810 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,821 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,822 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,824 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,824 even if it does not contain any `.py` files. 2024-01-09T02:48:28,825 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,825 directory, all directories are treated like packages. 2024-01-09T02:48:28,826 ******************************************************************************** 2024-01-09T02:48:28,830 !! 2024-01-09T02:48:28,835 check.warn(importable) 2024-01-09T02:48:28,837 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,837 !! 2024-01-09T02:48:28,838 ******************************************************************************** 2024-01-09T02:48:28,839 ############################ 2024-01-09T02:48:28,840 # Package would be ignored # 2024-01-09T02:48:28,840 ############################ 2024-01-09T02:48:28,841 Python recognizes 'witch_msa.tools.magus.tools.mlrmcl' as an importable package[^1], 2024-01-09T02:48:28,842 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,843 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,844 package, please make sure that 'witch_msa.tools.magus.tools.mlrmcl' is explicitly added 2024-01-09T02:48:28,844 to the `packages` configuration field. 2024-01-09T02:48:28,845 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,846 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,849 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,858 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,859 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,860 If you don't want 'witch_msa.tools.magus.tools.mlrmcl' to be distributed and are 2024-01-09T02:48:28,861 already explicitly excluding 'witch_msa.tools.magus.tools.mlrmcl' via 2024-01-09T02:48:28,861 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,861 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,862 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,863 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,864 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,866 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,867 even if it does not contain any `.py` files. 2024-01-09T02:48:28,868 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,871 directory, all directories are treated like packages. 2024-01-09T02:48:28,872 ******************************************************************************** 2024-01-09T02:48:28,873 !! 2024-01-09T02:48:28,873 check.warn(importable) 2024-01-09T02:48:28,874 /tmp/pip-build-env-cjgplgdk/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. 2024-01-09T02:48:28,875 !! 2024-01-09T02:48:28,876 ******************************************************************************** 2024-01-09T02:48:28,876 ############################ 2024-01-09T02:48:28,877 # Package would be ignored # 2024-01-09T02:48:28,878 ############################ 2024-01-09T02:48:28,878 Python recognizes 'witch_msa.tools.magus.tools.raxmlng' as an importable package[^1], 2024-01-09T02:48:28,880 but it is absent from setuptools' `packages` configuration. 2024-01-09T02:48:28,888 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-09T02:48:28,892 package, please make sure that 'witch_msa.tools.magus.tools.raxmlng' is explicitly added 2024-01-09T02:48:28,892 to the `packages` configuration field. 2024-01-09T02:48:28,893 Alternatively, you can also rely on setuptools' discovery methods 2024-01-09T02:48:28,894 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-09T02:48:28,894 instead of `find_packages(...)`/`find:`). 2024-01-09T02:48:28,895 You can read more about "package discovery" on setuptools documentation page: 2024-01-09T02:48:28,896 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-09T02:48:28,897 If you don't want 'witch_msa.tools.magus.tools.raxmlng' to be distributed and are 2024-01-09T02:48:28,898 already explicitly excluding 'witch_msa.tools.magus.tools.raxmlng' via 2024-01-09T02:48:28,899 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-09T02:48:28,900 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-09T02:48:28,900 combination with a more fine grained `package-data` configuration. 2024-01-09T02:48:28,901 You can read more about "package data files" on setuptools documentation page: 2024-01-09T02:48:28,902 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-09T02:48:28,910 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-09T02:48:28,914 even if it does not contain any `.py` files. 2024-01-09T02:48:28,915 On the other hand, currently there is no concept of package data 2024-01-09T02:48:28,915 directory, all directories are treated like packages. 2024-01-09T02:48:28,916 ******************************************************************************** 2024-01-09T02:48:28,918 !! 2024-01-09T02:48:28,918 check.warn(importable) 2024-01-09T02:48:28,919 copying witch_msa/default.config -> build/lib/witch_msa 2024-01-09T02:48:28,919 creating build/lib/witch_msa/tools 2024-01-09T02:48:28,920 creating build/lib/witch_msa/tools/macOS 2024-01-09T02:48:28,920 copying witch_msa/tools/macOS/FastTreeMP -> build/lib/witch_msa/tools/macOS 2024-01-09T02:48:28,921 copying witch_msa/tools/macOS/hmmalign -> build/lib/witch_msa/tools/macOS 2024-01-09T02:48:28,921 copying witch_msa/tools/macOS/hmmbuild -> build/lib/witch_msa/tools/macOS 2024-01-09T02:48:28,922 copying witch_msa/tools/macOS/hmmsearch -> build/lib/witch_msa/tools/macOS 2024-01-09T02:48:28,926 copying witch_msa/tools/macOS/mafft -> build/lib/witch_msa/tools/macOS 2024-01-09T02:48:28,927 copying witch_msa/tools/macOS/mcl -> build/lib/witch_msa/tools/macOS 2024-01-09T02:48:28,929 creating build/lib/witch_msa/tools/magus 2024-01-09T02:48:28,931 copying witch_msa/tools/magus/README.md -> build/lib/witch_msa/tools/magus 2024-01-09T02:48:28,932 copying witch_msa/tools/magus/configuration.py -> build/lib/witch_msa/tools/magus 2024-01-09T02:48:28,932 copying witch_msa/tools/magus/magus.py -> build/lib/witch_msa/tools/magus 2024-01-09T02:48:28,933 creating build/lib/witch_msa/tools/magus/align 2024-01-09T02:48:28,933 copying witch_msa/tools/magus/align/__init__.py -> build/lib/witch_msa/tools/magus/align 2024-01-09T02:48:28,933 copying witch_msa/tools/magus/align/aligner.py -> build/lib/witch_msa/tools/magus/align 2024-01-09T02:48:28,934 copying witch_msa/tools/magus/align/alignment_context.py -> build/lib/witch_msa/tools/magus/align 2024-01-09T02:48:28,935 creating build/lib/witch_msa/tools/magus/align/decompose 2024-01-09T02:48:28,935 copying witch_msa/tools/magus/align/decompose/__init__.py -> build/lib/witch_msa/tools/magus/align/decompose 2024-01-09T02:48:28,936 copying witch_msa/tools/magus/align/decompose/decomposer.py -> build/lib/witch_msa/tools/magus/align/decompose 2024-01-09T02:48:28,937 copying witch_msa/tools/magus/align/decompose/initial_tree.py -> build/lib/witch_msa/tools/magus/align/decompose 2024-01-09T02:48:28,937 copying witch_msa/tools/magus/align/decompose/kmh.py -> build/lib/witch_msa/tools/magus/align/decompose 2024-01-09T02:48:28,938 creating build/lib/witch_msa/tools/magus/align/merge 2024-01-09T02:48:28,938 copying witch_msa/tools/magus/align/merge/__init__.py -> build/lib/witch_msa/tools/magus/align/merge 2024-01-09T02:48:28,941 copying witch_msa/tools/magus/align/merge/alignment_graph.py -> build/lib/witch_msa/tools/magus/align/merge 2024-01-09T02:48:28,946 copying witch_msa/tools/magus/align/merge/alignment_writer.py -> build/lib/witch_msa/tools/magus/align/merge 2024-01-09T02:48:28,951 copying witch_msa/tools/magus/align/merge/merger.py -> build/lib/witch_msa/tools/magus/align/merge 2024-01-09T02:48:28,952 copying witch_msa/tools/magus/align/merge/optimizer.py -> build/lib/witch_msa/tools/magus/align/merge 2024-01-09T02:48:28,953 creating build/lib/witch_msa/tools/magus/align/merge/graph_build 2024-01-09T02:48:28,954 copying witch_msa/tools/magus/align/merge/graph_build/__init__.py -> build/lib/witch_msa/tools/magus/align/merge/graph_build 2024-01-09T02:48:28,954 copying witch_msa/tools/magus/align/merge/graph_build/graph_builder.py -> build/lib/witch_msa/tools/magus/align/merge/graph_build 2024-01-09T02:48:28,955 creating build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2024-01-09T02:48:28,955 copying witch_msa/tools/magus/align/merge/graph_cluster/__init__.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2024-01-09T02:48:28,959 copying witch_msa/tools/magus/align/merge/graph_cluster/clean_clusters.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2024-01-09T02:48:28,960 copying witch_msa/tools/magus/align/merge/graph_cluster/clusterer.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2024-01-09T02:48:28,961 copying witch_msa/tools/magus/align/merge/graph_cluster/mcl.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2024-01-09T02:48:28,963 copying witch_msa/tools/magus/align/merge/graph_cluster/mlr_mcl.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2024-01-09T02:48:28,966 copying witch_msa/tools/magus/align/merge/graph_cluster/rg.py -> build/lib/witch_msa/tools/magus/align/merge/graph_cluster 2024-01-09T02:48:28,970 creating build/lib/witch_msa/tools/magus/align/merge/graph_trace 2024-01-09T02:48:28,970 copying witch_msa/tools/magus/align/merge/graph_trace/__init__.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2024-01-09T02:48:28,971 copying witch_msa/tools/magus/align/merge/graph_trace/fm.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2024-01-09T02:48:28,971 copying witch_msa/tools/magus/align/merge/graph_trace/min_clusters.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2024-01-09T02:48:28,972 copying witch_msa/tools/magus/align/merge/graph_trace/mwt_search.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2024-01-09T02:48:28,972 copying witch_msa/tools/magus/align/merge/graph_trace/naive.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2024-01-09T02:48:28,973 copying witch_msa/tools/magus/align/merge/graph_trace/rg_fast_search.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2024-01-09T02:48:28,973 copying witch_msa/tools/magus/align/merge/graph_trace/rg_search.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2024-01-09T02:48:28,974 copying witch_msa/tools/magus/align/merge/graph_trace/tracer.py -> build/lib/witch_msa/tools/magus/align/merge/graph_trace 2024-01-09T02:48:28,975 creating build/lib/witch_msa/tools/magus/helpers 2024-01-09T02:48:28,975 copying witch_msa/tools/magus/helpers/__init__.py -> build/lib/witch_msa/tools/magus/helpers 2024-01-09T02:48:28,976 copying witch_msa/tools/magus/helpers/hmmutils.py -> build/lib/witch_msa/tools/magus/helpers 2024-01-09T02:48:28,976 copying witch_msa/tools/magus/helpers/sequenceutils.py -> build/lib/witch_msa/tools/magus/helpers 2024-01-09T02:48:28,977 copying witch_msa/tools/magus/helpers/treeutils.py -> build/lib/witch_msa/tools/magus/helpers 2024-01-09T02:48:28,977 creating build/lib/witch_msa/tools/magus/tasks 2024-01-09T02:48:28,978 copying witch_msa/tools/magus/tasks/__init__.py -> build/lib/witch_msa/tools/magus/tasks 2024-01-09T02:48:28,978 copying witch_msa/tools/magus/tasks/controller.py -> build/lib/witch_msa/tools/magus/tasks 2024-01-09T02:48:28,979 copying witch_msa/tools/magus/tasks/files.py -> build/lib/witch_msa/tools/magus/tasks 2024-01-09T02:48:28,980 copying witch_msa/tools/magus/tasks/manager.py -> build/lib/witch_msa/tools/magus/tasks 2024-01-09T02:48:28,980 copying witch_msa/tools/magus/tasks/task.py -> build/lib/witch_msa/tools/magus/tasks 2024-01-09T02:48:28,981 creating build/lib/witch_msa/tools/magus/tools 2024-01-09T02:48:28,982 copying witch_msa/tools/magus/tools/__init__.py -> build/lib/witch_msa/tools/magus/tools 2024-01-09T02:48:28,982 copying witch_msa/tools/magus/tools/external_tools.py -> build/lib/witch_msa/tools/magus/tools 2024-01-09T02:48:28,983 creating build/lib/witch_msa/tools/magus/tools/clustal 2024-01-09T02:48:28,984 copying witch_msa/tools/magus/tools/clustal/clustalo -> build/lib/witch_msa/tools/magus/tools/clustal 2024-01-09T02:48:28,984 creating build/lib/witch_msa/tools/magus/tools/fasttree 2024-01-09T02:48:28,984 copying witch_msa/tools/magus/tools/fasttree/FastTree -> build/lib/witch_msa/tools/magus/tools/fasttree 2024-01-09T02:48:28,985 copying witch_msa/tools/magus/tools/fasttree/FastTreeMP -> build/lib/witch_msa/tools/magus/tools/fasttree 2024-01-09T02:48:28,985 creating build/lib/witch_msa/tools/magus/tools/hmmer 2024-01-09T02:48:28,986 copying witch_msa/tools/magus/tools/hmmer/hmmalign -> build/lib/witch_msa/tools/magus/tools/hmmer 2024-01-09T02:48:28,986 copying witch_msa/tools/magus/tools/hmmer/hmmbuild -> build/lib/witch_msa/tools/magus/tools/hmmer 2024-01-09T02:48:28,986 copying witch_msa/tools/magus/tools/hmmer/hmmsearch -> build/lib/witch_msa/tools/magus/tools/hmmer 2024-01-09T02:48:28,987 creating build/lib/witch_msa/tools/magus/tools/mafft 2024-01-09T02:48:28,987 copying witch_msa/tools/magus/tools/mafft/mafft -> build/lib/witch_msa/tools/magus/tools/mafft 2024-01-09T02:48:28,988 creating build/lib/witch_msa/tools/magus/tools/mafft/mafftdir 2024-01-09T02:48:28,988 creating build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/bin 2024-01-09T02:48:28,989 copying witch_msa/tools/magus/tools/mafft/mafftdir/bin/mafft -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/bin 2024-01-09T02:48:28,992 creating build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:28,994 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/addsingle -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:28,996 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/contrafoldwrap -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:28,997 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/countlen -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:28,998 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dash_client -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:28,999 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/disttbfast -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:28,999 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndblast -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,000 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndfast7 -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,000 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndpre -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,001 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dvtditr -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,001 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/f2cl -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,002 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/getlag -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,003 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/hex2maffttext -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,003 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-distance -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,004 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-homologs.1 -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,004 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-profile -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,005 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft.1 -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,006 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafftash_premafft.pl -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,006 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/maffttext2hex -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,007 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/makedirectionlist -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,007 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mccaskillwrap -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,008 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/multi2hat3s -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,008 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/nodepair -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,029 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairash -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,050 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairlocalalign -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,075 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/regtable2seq -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,089 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/replaceu -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,105 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/restoreu -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,122 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/score -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,138 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seekquencer_premafft.pl -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,141 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seq2regtable -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,152 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setcore -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,171 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setdirection -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,188 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/sextet5 -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,206 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/splittbfast -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,228 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/tbfast -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,249 copying witch_msa/tools/magus/tools/mafft/mafftdir/libexec/version -> build/lib/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:29,264 creating build/lib/witch_msa/tools/magus/tools/mcl 2024-01-09T02:48:29,265 creating build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,266 copying witch_msa/tools/magus/tools/mcl/bin/clm -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,297 copying witch_msa/tools/magus/tools/mcl/bin/clmformat -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,317 copying witch_msa/tools/magus/tools/mcl/bin/clxdo -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,319 copying witch_msa/tools/magus/tools/mcl/bin/mcl -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,339 copying witch_msa/tools/magus/tools/mcl/bin/mclblastline -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,342 copying witch_msa/tools/magus/tools/mcl/bin/mclcm -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,363 copying witch_msa/tools/magus/tools/mcl/bin/mclpipeline -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,366 copying witch_msa/tools/magus/tools/mcl/bin/mcx -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,393 copying witch_msa/tools/magus/tools/mcl/bin/mcxarray -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,416 copying witch_msa/tools/magus/tools/mcl/bin/mcxassemble -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,436 copying witch_msa/tools/magus/tools/mcl/bin/mcxdeblast -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,439 copying witch_msa/tools/magus/tools/mcl/bin/mcxdump -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,459 copying witch_msa/tools/magus/tools/mcl/bin/mcxi -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,481 copying witch_msa/tools/magus/tools/mcl/bin/mcxload -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,501 copying witch_msa/tools/magus/tools/mcl/bin/mcxmap -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,513 copying witch_msa/tools/magus/tools/mcl/bin/mcxrand -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,525 copying witch_msa/tools/magus/tools/mcl/bin/mcxsubs -> build/lib/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,546 creating build/lib/witch_msa/tools/magus/tools/mlrmcl 2024-01-09T02:48:29,547 copying witch_msa/tools/magus/tools/mlrmcl/README -> build/lib/witch_msa/tools/magus/tools/mlrmcl 2024-01-09T02:48:29,549 copying witch_msa/tools/magus/tools/mlrmcl/mlrmcl -> build/lib/witch_msa/tools/magus/tools/mlrmcl 2024-01-09T02:48:29,554 copying witch_msa/tools/magus/tools/mlrmcl/ncut -> build/lib/witch_msa/tools/magus/tools/mlrmcl 2024-01-09T02:48:29,558 creating build/lib/witch_msa/tools/magus/tools/raxmlng 2024-01-09T02:48:29,558 copying witch_msa/tools/magus/tools/raxmlng/raxml-ng -> build/lib/witch_msa/tools/magus/tools/raxmlng 2024-01-09T02:48:29,657 running build_scripts 2024-01-09T02:48:29,658 creating build/scripts-3.11 2024-01-09T02:48:29,659 copying and adjusting bin/witch-msa -> build/scripts-3.11 2024-01-09T02:48:29,661 copying and adjusting witch.py -> build/scripts-3.11 2024-01-09T02:48:29,662 changing mode of build/scripts-3.11/witch-msa from 644 to 755 2024-01-09T02:48:29,663 changing mode of build/scripts-3.11/witch.py from 644 to 755 2024-01-09T02:48:29,670 installing to build/bdist.linux-armv7l/wheel 2024-01-09T02:48:29,671 running install 2024-01-09T02:48:29,695 running install_lib 2024-01-09T02:48:29,700 creating build/bdist.linux-armv7l 2024-01-09T02:48:29,700 creating build/bdist.linux-armv7l/wheel 2024-01-09T02:48:29,702 creating build/bdist.linux-armv7l/wheel/witch_msa 2024-01-09T02:48:29,704 creating build/bdist.linux-armv7l/wheel/witch_msa/tools 2024-01-09T02:48:29,706 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus 2024-01-09T02:48:29,708 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools 2024-01-09T02:48:29,709 copying build/lib/witch_msa/tools/magus/tools/external_tools.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools 2024-01-09T02:48:29,712 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/raxmlng 2024-01-09T02:48:29,714 copying build/lib/witch_msa/tools/magus/tools/raxmlng/raxml-ng -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/raxmlng 2024-01-09T02:48:29,812 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mlrmcl 2024-01-09T02:48:29,813 copying build/lib/witch_msa/tools/magus/tools/mlrmcl/README -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mlrmcl 2024-01-09T02:48:29,816 copying build/lib/witch_msa/tools/magus/tools/mlrmcl/mlrmcl -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mlrmcl 2024-01-09T02:48:29,820 copying build/lib/witch_msa/tools/magus/tools/mlrmcl/ncut -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mlrmcl 2024-01-09T02:48:29,824 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl 2024-01-09T02:48:29,825 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,826 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mclpipeline -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,829 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/clmformat -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,863 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxdeblast -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,866 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcx -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,890 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxarray -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,910 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxsubs -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,930 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxassemble -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,951 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcl -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,971 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxmap -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:29,985 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxload -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:30,003 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxdump -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:30,022 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxrand -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:30,035 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mclblastline -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:30,037 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/clxdo -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:30,040 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/clm -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:30,063 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mclcm -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:30,083 copying build/lib/witch_msa/tools/magus/tools/mcl/bin/mcxi -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mcl/bin 2024-01-09T02:48:30,105 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/fasttree 2024-01-09T02:48:30,106 copying build/lib/witch_msa/tools/magus/tools/fasttree/FastTreeMP -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/fasttree 2024-01-09T02:48:30,114 copying build/lib/witch_msa/tools/magus/tools/fasttree/FastTree -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/fasttree 2024-01-09T02:48:30,122 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft 2024-01-09T02:48:30,124 copying build/lib/witch_msa/tools/magus/tools/mafft/mafft -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft 2024-01-09T02:48:30,126 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir 2024-01-09T02:48:30,128 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/libexec 2024-01-09T02:48:30,130 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 2024-01-09T02:48:30,141 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 2024-01-09T02:48:30,162 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 2024-01-09T02:48:30,172 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 2024-01-09T02:48:30,194 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 2024-01-09T02:48:30,273 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 2024-01-09T02:48:30,289 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 2024-01-09T02:48:30,311 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 2024-01-09T02:48:30,325 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 2024-01-09T02:48:30,362 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 2024-01-09T02:48:30,376 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 2024-01-09T02:48:30,395 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 2024-01-09T02:48:30,397 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 2024-01-09T02:48:30,412 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 2024-01-09T02:48:30,427 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 2024-01-09T02:48:30,437 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 2024-01-09T02:48:30,454 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 2024-01-09T02:48:30,466 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 2024-01-09T02:48:30,469 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 2024-01-09T02:48:30,484 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 2024-01-09T02:48:30,498 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 2024-01-09T02:48:30,522 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 2024-01-09T02:48:30,544 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 2024-01-09T02:48:30,566 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 2024-01-09T02:48:30,583 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 2024-01-09T02:48:30,599 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 2024-01-09T02:48:30,615 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 2024-01-09T02:48:30,642 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 2024-01-09T02:48:30,658 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 2024-01-09T02:48:30,682 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 2024-01-09T02:48:30,704 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 2024-01-09T02:48:30,719 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 2024-01-09T02:48:30,733 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 2024-01-09T02:48:30,752 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 2024-01-09T02:48:30,754 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 2024-01-09T02:48:30,775 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 2024-01-09T02:48:30,778 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/mafft/mafftdir/bin 2024-01-09T02:48:30,779 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 2024-01-09T02:48:30,784 copying build/lib/witch_msa/tools/magus/tools/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools 2024-01-09T02:48:30,786 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/clustal 2024-01-09T02:48:30,787 copying build/lib/witch_msa/tools/magus/tools/clustal/clustalo -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/clustal 2024-01-09T02:48:30,863 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/hmmer 2024-01-09T02:48:30,864 copying build/lib/witch_msa/tools/magus/tools/hmmer/hmmsearch -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/hmmer 2024-01-09T02:48:30,889 copying build/lib/witch_msa/tools/magus/tools/hmmer/hmmalign -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/hmmer 2024-01-09T02:48:30,911 copying build/lib/witch_msa/tools/magus/tools/hmmer/hmmbuild -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tools/hmmer 2024-01-09T02:48:30,933 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2024-01-09T02:48:30,934 copying build/lib/witch_msa/tools/magus/tasks/files.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2024-01-09T02:48:30,936 copying build/lib/witch_msa/tools/magus/tasks/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2024-01-09T02:48:30,937 copying build/lib/witch_msa/tools/magus/tasks/task.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2024-01-09T02:48:30,939 copying build/lib/witch_msa/tools/magus/tasks/controller.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2024-01-09T02:48:30,941 copying build/lib/witch_msa/tools/magus/tasks/manager.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/tasks 2024-01-09T02:48:30,943 copying build/lib/witch_msa/tools/magus/README.md -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus 2024-01-09T02:48:30,946 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/helpers 2024-01-09T02:48:30,947 copying build/lib/witch_msa/tools/magus/helpers/sequenceutils.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/helpers 2024-01-09T02:48:30,949 copying build/lib/witch_msa/tools/magus/helpers/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/helpers 2024-01-09T02:48:30,951 copying build/lib/witch_msa/tools/magus/helpers/treeutils.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/helpers 2024-01-09T02:48:30,953 copying build/lib/witch_msa/tools/magus/helpers/hmmutils.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/helpers 2024-01-09T02:48:30,955 copying build/lib/witch_msa/tools/magus/magus.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus 2024-01-09T02:48:30,957 copying build/lib/witch_msa/tools/magus/configuration.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus 2024-01-09T02:48:30,960 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align 2024-01-09T02:48:30,961 copying build/lib/witch_msa/tools/magus/align/alignment_context.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align 2024-01-09T02:48:30,963 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/decompose 2024-01-09T02:48:30,964 copying build/lib/witch_msa/tools/magus/align/decompose/decomposer.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/decompose 2024-01-09T02:48:30,966 copying build/lib/witch_msa/tools/magus/align/decompose/initial_tree.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/decompose 2024-01-09T02:48:30,969 copying build/lib/witch_msa/tools/magus/align/decompose/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/decompose 2024-01-09T02:48:30,970 copying build/lib/witch_msa/tools/magus/align/decompose/kmh.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/decompose 2024-01-09T02:48:30,972 copying build/lib/witch_msa/tools/magus/align/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align 2024-01-09T02:48:30,974 copying build/lib/witch_msa/tools/magus/align/aligner.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align 2024-01-09T02:48:30,977 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2024-01-09T02:48:30,978 copying build/lib/witch_msa/tools/magus/align/merge/alignment_graph.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2024-01-09T02:48:30,980 copying build/lib/witch_msa/tools/magus/align/merge/optimizer.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2024-01-09T02:48:30,983 copying build/lib/witch_msa/tools/magus/align/merge/alignment_writer.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2024-01-09T02:48:30,986 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_trace 2024-01-09T02:48:30,987 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 2024-01-09T02:48:30,989 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 2024-01-09T02:48:30,992 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 2024-01-09T02:48:30,994 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 2024-01-09T02:48:30,996 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 2024-01-09T02:48:30,998 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 2024-01-09T02:48:31,000 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 2024-01-09T02:48:31,002 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 2024-01-09T02:48:31,004 copying build/lib/witch_msa/tools/magus/align/merge/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2024-01-09T02:48:31,005 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_cluster 2024-01-09T02:48:31,006 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 2024-01-09T02:48:31,008 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 2024-01-09T02:48:31,010 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 2024-01-09T02:48:31,012 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 2024-01-09T02:48:31,013 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 2024-01-09T02:48:31,015 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 2024-01-09T02:48:31,017 copying build/lib/witch_msa/tools/magus/align/merge/merger.py -> build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge 2024-01-09T02:48:31,019 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/magus/align/merge/graph_build 2024-01-09T02:48:31,020 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 2024-01-09T02:48:31,022 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 2024-01-09T02:48:31,025 creating build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2024-01-09T02:48:31,026 copying build/lib/witch_msa/tools/macOS/mcl -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2024-01-09T02:48:31,033 copying build/lib/witch_msa/tools/macOS/mafft -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2024-01-09T02:48:31,037 copying build/lib/witch_msa/tools/macOS/FastTreeMP -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2024-01-09T02:48:31,047 copying build/lib/witch_msa/tools/macOS/hmmsearch -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2024-01-09T02:48:31,064 copying build/lib/witch_msa/tools/macOS/hmmalign -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2024-01-09T02:48:31,078 copying build/lib/witch_msa/tools/macOS/hmmbuild -> build/bdist.linux-armv7l/wheel/witch_msa/tools/macOS 2024-01-09T02:48:31,100 creating build/bdist.linux-armv7l/wheel/witch_msa/helpers 2024-01-09T02:48:31,101 copying build/lib/witch_msa/helpers/general_tools.py -> build/bdist.linux-armv7l/wheel/witch_msa/helpers 2024-01-09T02:48:31,102 copying build/lib/witch_msa/helpers/pyhmmer_tools.py -> build/bdist.linux-armv7l/wheel/witch_msa/helpers 2024-01-09T02:48:31,104 copying build/lib/witch_msa/helpers/math_utils.py -> build/bdist.linux-armv7l/wheel/witch_msa/helpers 2024-01-09T02:48:31,106 copying build/lib/witch_msa/helpers/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/helpers 2024-01-09T02:48:31,107 copying build/lib/witch_msa/helpers/alignment_tools.py -> build/bdist.linux-armv7l/wheel/witch_msa/helpers 2024-01-09T02:48:31,110 copying build/lib/witch_msa/configs.py -> build/bdist.linux-armv7l/wheel/witch_msa 2024-01-09T02:48:31,112 creating build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2024-01-09T02:48:31,113 copying build/lib/witch_msa/gcmm/backbone.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2024-01-09T02:48:31,116 copying build/lib/witch_msa/gcmm/weighting.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2024-01-09T02:48:31,118 copying build/lib/witch_msa/gcmm/loader.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2024-01-09T02:48:31,120 copying build/lib/witch_msa/gcmm/results_handler.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2024-01-09T02:48:31,123 copying build/lib/witch_msa/gcmm/callback.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2024-01-09T02:48:31,124 copying build/lib/witch_msa/gcmm/algorithm.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2024-01-09T02:48:31,127 copying build/lib/witch_msa/gcmm/gcmm.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2024-01-09T02:48:31,129 copying build/lib/witch_msa/gcmm/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2024-01-09T02:48:31,131 copying build/lib/witch_msa/gcmm/decompose_tree.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2024-01-09T02:48:31,133 copying build/lib/witch_msa/gcmm/merger.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2024-01-09T02:48:31,135 copying build/lib/witch_msa/gcmm/aligner.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2024-01-09T02:48:31,137 copying build/lib/witch_msa/gcmm/task.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2024-01-09T02:48:31,139 copying build/lib/witch_msa/gcmm/tree.py -> build/bdist.linux-armv7l/wheel/witch_msa/gcmm 2024-01-09T02:48:31,142 copying build/lib/witch_msa/default.config -> build/bdist.linux-armv7l/wheel/witch_msa 2024-01-09T02:48:31,144 copying build/lib/witch_msa/__init__.py -> build/bdist.linux-armv7l/wheel/witch_msa 2024-01-09T02:48:31,147 copying build/lib/witch_msa/init_configs.py -> build/bdist.linux-armv7l/wheel/witch_msa 2024-01-09T02:48:31,149 running install_egg_info 2024-01-09T02:48:31,154 Copying witch_msa.egg-info to build/bdist.linux-armv7l/wheel/witch_msa-1.0.2-py3.11.egg-info 2024-01-09T02:48:31,168 running install_scripts 2024-01-09T02:48:31,169 creating build/bdist.linux-armv7l/wheel/witch_msa-1.0.2.data 2024-01-09T02:48:31,170 creating build/bdist.linux-armv7l/wheel/witch_msa-1.0.2.data/scripts 2024-01-09T02:48:31,172 copying build/scripts-3.11/witch.py -> build/bdist.linux-armv7l/wheel/witch_msa-1.0.2.data/scripts 2024-01-09T02:48:31,174 copying build/scripts-3.11/witch-msa -> build/bdist.linux-armv7l/wheel/witch_msa-1.0.2.data/scripts 2024-01-09T02:48:31,176 changing mode of build/bdist.linux-armv7l/wheel/witch_msa-1.0.2.data/scripts/witch.py to 755 2024-01-09T02:48:31,177 changing mode of build/bdist.linux-armv7l/wheel/witch_msa-1.0.2.data/scripts/witch-msa to 755 2024-01-09T02:48:31,204 creating build/bdist.linux-armv7l/wheel/witch_msa-1.0.2.dist-info/WHEEL 2024-01-09T02:48:31,207 creating '/tmp/pip-wheel-mt9b1vzu/.tmp-e6kprb_e/witch_msa-1.0.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-01-09T02:48:31,211 adding 'witch_msa/__init__.py' 2024-01-09T02:48:31,214 adding 'witch_msa/configs.py' 2024-01-09T02:48:31,216 adding 'witch_msa/default.config' 2024-01-09T02:48:31,218 adding 'witch_msa/init_configs.py' 2024-01-09T02:48:31,220 adding 'witch_msa/gcmm/__init__.py' 2024-01-09T02:48:31,224 adding 'witch_msa/gcmm/algorithm.py' 2024-01-09T02:48:31,228 adding 'witch_msa/gcmm/aligner.py' 2024-01-09T02:48:31,231 adding 'witch_msa/gcmm/backbone.py' 2024-01-09T02:48:31,233 adding 'witch_msa/gcmm/callback.py' 2024-01-09T02:48:31,235 adding 'witch_msa/gcmm/decompose_tree.py' 2024-01-09T02:48:31,237 adding 'witch_msa/gcmm/gcmm.py' 2024-01-09T02:48:31,240 adding 'witch_msa/gcmm/loader.py' 2024-01-09T02:48:31,242 adding 'witch_msa/gcmm/merger.py' 2024-01-09T02:48:31,244 adding 'witch_msa/gcmm/results_handler.py' 2024-01-09T02:48:31,245 adding 'witch_msa/gcmm/task.py' 2024-01-09T02:48:31,248 adding 'witch_msa/gcmm/tree.py' 2024-01-09T02:48:31,249 adding 'witch_msa/gcmm/weighting.py' 2024-01-09T02:48:31,251 adding 'witch_msa/helpers/__init__.py' 2024-01-09T02:48:31,257 adding 'witch_msa/helpers/alignment_tools.py' 2024-01-09T02:48:31,258 adding 'witch_msa/helpers/general_tools.py' 2024-01-09T02:48:31,260 adding 'witch_msa/helpers/math_utils.py' 2024-01-09T02:48:31,261 adding 'witch_msa/helpers/pyhmmer_tools.py' 2024-01-09T02:48:31,317 adding 'witch_msa/tools/macOS/FastTreeMP' 2024-01-09T02:48:31,464 adding 'witch_msa/tools/macOS/hmmalign' 2024-01-09T02:48:31,633 adding 'witch_msa/tools/macOS/hmmbuild' 2024-01-09T02:48:31,811 adding 'witch_msa/tools/macOS/hmmsearch' 2024-01-09T02:48:31,827 adding 'witch_msa/tools/macOS/mafft' 2024-01-09T02:48:31,896 adding 'witch_msa/tools/macOS/mcl' 2024-01-09T02:48:31,901 adding 'witch_msa/tools/magus/README.md' 2024-01-09T02:48:31,902 adding 'witch_msa/tools/magus/configuration.py' 2024-01-09T02:48:31,904 adding 'witch_msa/tools/magus/magus.py' 2024-01-09T02:48:31,906 adding 'witch_msa/tools/magus/align/__init__.py' 2024-01-09T02:48:31,907 adding 'witch_msa/tools/magus/align/aligner.py' 2024-01-09T02:48:31,909 adding 'witch_msa/tools/magus/align/alignment_context.py' 2024-01-09T02:48:31,910 adding 'witch_msa/tools/magus/align/decompose/__init__.py' 2024-01-09T02:48:31,912 adding 'witch_msa/tools/magus/align/decompose/decomposer.py' 2024-01-09T02:48:31,913 adding 'witch_msa/tools/magus/align/decompose/initial_tree.py' 2024-01-09T02:48:31,915 adding 'witch_msa/tools/magus/align/decompose/kmh.py' 2024-01-09T02:48:31,916 adding 'witch_msa/tools/magus/align/merge/__init__.py' 2024-01-09T02:48:31,918 adding 'witch_msa/tools/magus/align/merge/alignment_graph.py' 2024-01-09T02:48:31,920 adding 'witch_msa/tools/magus/align/merge/alignment_writer.py' 2024-01-09T02:48:31,921 adding 'witch_msa/tools/magus/align/merge/merger.py' 2024-01-09T02:48:31,924 adding 'witch_msa/tools/magus/align/merge/optimizer.py' 2024-01-09T02:48:31,926 adding 'witch_msa/tools/magus/align/merge/graph_build/__init__.py' 2024-01-09T02:48:31,927 adding 'witch_msa/tools/magus/align/merge/graph_build/graph_builder.py' 2024-01-09T02:48:31,929 adding 'witch_msa/tools/magus/align/merge/graph_cluster/__init__.py' 2024-01-09T02:48:31,930 adding 'witch_msa/tools/magus/align/merge/graph_cluster/clean_clusters.py' 2024-01-09T02:48:31,932 adding 'witch_msa/tools/magus/align/merge/graph_cluster/clusterer.py' 2024-01-09T02:48:31,933 adding 'witch_msa/tools/magus/align/merge/graph_cluster/mcl.py' 2024-01-09T02:48:31,934 adding 'witch_msa/tools/magus/align/merge/graph_cluster/mlr_mcl.py' 2024-01-09T02:48:31,935 adding 'witch_msa/tools/magus/align/merge/graph_cluster/rg.py' 2024-01-09T02:48:31,937 adding 'witch_msa/tools/magus/align/merge/graph_trace/__init__.py' 2024-01-09T02:48:31,939 adding 'witch_msa/tools/magus/align/merge/graph_trace/fm.py' 2024-01-09T02:48:31,941 adding 'witch_msa/tools/magus/align/merge/graph_trace/min_clusters.py' 2024-01-09T02:48:31,943 adding 'witch_msa/tools/magus/align/merge/graph_trace/mwt_search.py' 2024-01-09T02:48:31,945 adding 'witch_msa/tools/magus/align/merge/graph_trace/naive.py' 2024-01-09T02:48:31,946 adding 'witch_msa/tools/magus/align/merge/graph_trace/rg_fast_search.py' 2024-01-09T02:48:31,948 adding 'witch_msa/tools/magus/align/merge/graph_trace/rg_search.py' 2024-01-09T02:48:31,949 adding 'witch_msa/tools/magus/align/merge/graph_trace/tracer.py' 2024-01-09T02:48:31,951 adding 'witch_msa/tools/magus/helpers/__init__.py' 2024-01-09T02:48:31,952 adding 'witch_msa/tools/magus/helpers/hmmutils.py' 2024-01-09T02:48:31,954 adding 'witch_msa/tools/magus/helpers/sequenceutils.py' 2024-01-09T02:48:31,955 adding 'witch_msa/tools/magus/helpers/treeutils.py' 2024-01-09T02:48:31,957 adding 'witch_msa/tools/magus/tasks/__init__.py' 2024-01-09T02:48:31,958 adding 'witch_msa/tools/magus/tasks/controller.py' 2024-01-09T02:48:31,959 adding 'witch_msa/tools/magus/tasks/files.py' 2024-01-09T02:48:31,961 adding 'witch_msa/tools/magus/tasks/manager.py' 2024-01-09T02:48:31,962 adding 'witch_msa/tools/magus/tasks/task.py' 2024-01-09T02:48:31,964 adding 'witch_msa/tools/magus/tools/__init__.py' 2024-01-09T02:48:31,965 adding 'witch_msa/tools/magus/tools/external_tools.py' 2024-01-09T02:48:32,786 adding 'witch_msa/tools/magus/tools/clustal/clustalo' 2024-01-09T02:48:32,884 adding 'witch_msa/tools/magus/tools/fasttree/FastTree' 2024-01-09T02:48:32,956 adding 'witch_msa/tools/magus/tools/fasttree/FastTreeMP' 2024-01-09T02:48:33,166 adding 'witch_msa/tools/magus/tools/hmmer/hmmalign' 2024-01-09T02:48:33,392 adding 'witch_msa/tools/magus/tools/hmmer/hmmbuild' 2024-01-09T02:48:33,638 adding 'witch_msa/tools/magus/tools/hmmer/hmmsearch' 2024-01-09T02:48:33,649 adding 'witch_msa/tools/magus/tools/mafft/mafft' 2024-01-09T02:48:33,660 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/bin/mafft' 2024-01-09T02:48:33,915 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/addsingle' 2024-01-09T02:48:34,095 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/contrafoldwrap' 2024-01-09T02:48:34,221 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/countlen' 2024-01-09T02:48:35,045 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dash_client' 2024-01-09T02:48:35,328 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/disttbfast' 2024-01-09T02:48:35,511 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndblast' 2024-01-09T02:48:35,692 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndfast7' 2024-01-09T02:48:35,871 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dndpre' 2024-01-09T02:48:36,124 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/dvtditr' 2024-01-09T02:48:36,265 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/f2cl' 2024-01-09T02:48:36,502 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/getlag' 2024-01-09T02:48:36,612 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/hex2maffttext' 2024-01-09T02:48:36,791 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-distance' 2024-01-09T02:48:36,798 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-homologs.1' 2024-01-09T02:48:37,031 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft-profile' 2024-01-09T02:48:37,041 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafft.1' 2024-01-09T02:48:37,043 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mafftash_premafft.pl' 2024-01-09T02:48:37,148 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/maffttext2hex' 2024-01-09T02:48:37,388 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/makedirectionlist' 2024-01-09T02:48:37,568 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/mccaskillwrap' 2024-01-09T02:48:37,759 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/multi2hat3s' 2024-01-09T02:48:38,009 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/nodepair' 2024-01-09T02:48:38,252 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairash' 2024-01-09T02:48:38,498 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/pairlocalalign' 2024-01-09T02:48:38,669 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/regtable2seq' 2024-01-09T02:48:38,837 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/replaceu' 2024-01-09T02:48:39,007 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/restoreu' 2024-01-09T02:48:39,184 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/score' 2024-01-09T02:48:39,192 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seekquencer_premafft.pl' 2024-01-09T02:48:39,313 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/seq2regtable' 2024-01-09T02:48:39,549 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setcore' 2024-01-09T02:48:39,721 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/setdirection' 2024-01-09T02:48:39,901 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/sextet5' 2024-01-09T02:48:40,145 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/splittbfast' 2024-01-09T02:48:40,406 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/tbfast' 2024-01-09T02:48:40,521 adding 'witch_msa/tools/magus/tools/mafft/mafftdir/libexec/version' 2024-01-09T02:48:40,784 adding 'witch_msa/tools/magus/tools/mcl/bin/clm' 2024-01-09T02:48:41,017 adding 'witch_msa/tools/magus/tools/mcl/bin/clmformat' 2024-01-09T02:48:41,027 adding 'witch_msa/tools/magus/tools/mcl/bin/clxdo' 2024-01-09T02:48:41,234 adding 'witch_msa/tools/magus/tools/mcl/bin/mcl' 2024-01-09T02:48:41,242 adding 'witch_msa/tools/magus/tools/mcl/bin/mclblastline' 2024-01-09T02:48:41,458 adding 'witch_msa/tools/magus/tools/mcl/bin/mclcm' 2024-01-09T02:48:41,469 adding 'witch_msa/tools/magus/tools/mcl/bin/mclpipeline' 2024-01-09T02:48:41,728 adding 'witch_msa/tools/magus/tools/mcl/bin/mcx' 2024-01-09T02:48:41,957 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxarray' 2024-01-09T02:48:42,173 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxassemble' 2024-01-09T02:48:42,182 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxdeblast' 2024-01-09T02:48:42,392 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxdump' 2024-01-09T02:48:42,629 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxi' 2024-01-09T02:48:42,847 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxload' 2024-01-09T02:48:42,979 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxmap' 2024-01-09T02:48:43,110 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxrand' 2024-01-09T02:48:43,340 adding 'witch_msa/tools/magus/tools/mcl/bin/mcxsubs' 2024-01-09T02:48:43,350 adding 'witch_msa/tools/magus/tools/mlrmcl/README' 2024-01-09T02:48:43,371 adding 'witch_msa/tools/magus/tools/mlrmcl/mlrmcl' 2024-01-09T02:48:43,391 adding 'witch_msa/tools/magus/tools/mlrmcl/ncut' 2024-01-09T02:48:44,599 adding 'witch_msa/tools/magus/tools/raxmlng/raxml-ng' 2024-01-09T02:48:44,643 adding 'witch_msa-1.0.2.data/scripts/witch-msa' 2024-01-09T02:48:44,644 adding 'witch_msa-1.0.2.data/scripts/witch.py' 2024-01-09T02:48:44,651 adding 'witch_msa-1.0.2.dist-info/LICENSE' 2024-01-09T02:48:44,659 adding 'witch_msa-1.0.2.dist-info/METADATA' 2024-01-09T02:48:44,660 adding 'witch_msa-1.0.2.dist-info/WHEEL' 2024-01-09T02:48:44,661 adding 'witch_msa-1.0.2.dist-info/top_level.txt' 2024-01-09T02:48:44,664 adding 'witch_msa-1.0.2.dist-info/RECORD' 2024-01-09T02:48:44,962 removing build/bdist.linux-armv7l/wheel 2024-01-09T02:48:45,150 Building wheel for witch-msa (pyproject.toml): finished with status 'done' 2024-01-09T02:48:45,724 Created wheel for witch-msa: filename=witch_msa-1.0.2-py3-none-any.whl size=29117314 sha256=6c112c92ccb048e378cb6201a41fe7025037418782b80ea7b41046fac80fb81c 2024-01-09T02:48:45,726 Stored in directory: /tmp/pip-ephem-wheel-cache-xomq2ypa/wheels/2a/51/09/929b226d558df9ad15d0ad5842b3014b990901b4c027d9f695 2024-01-09T02:48:45,772 Successfully built witch-msa 2024-01-09T02:48:46,471 Removed build tracker: '/tmp/pip-build-tracker-87yb8sky'