2024-06-18T18:27:26,774 Created temporary directory: /tmp/pip-build-tracker-h_9q8t41 2024-06-18T18:27:26,775 Initialized build tracking at /tmp/pip-build-tracker-h_9q8t41 2024-06-18T18:27:26,776 Created build tracker: /tmp/pip-build-tracker-h_9q8t41 2024-06-18T18:27:26,776 Entered build tracker: /tmp/pip-build-tracker-h_9q8t41 2024-06-18T18:27:26,777 Created temporary directory: /tmp/pip-wheel-58l4znwo 2024-06-18T18:27:26,780 Created temporary directory: /tmp/pip-ephem-wheel-cache-74tgza7q 2024-06-18T18:27:26,802 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-06-18T18:27:26,806 2 location(s) to search for versions of streamd: 2024-06-18T18:27:26,806 * https://pypi.org/simple/streamd/ 2024-06-18T18:27:26,806 * https://www.piwheels.org/simple/streamd/ 2024-06-18T18:27:26,806 Fetching project page and analyzing links: https://pypi.org/simple/streamd/ 2024-06-18T18:27:26,807 Getting page https://pypi.org/simple/streamd/ 2024-06-18T18:27:26,809 Found index url https://pypi.org/simple/ 2024-06-18T18:27:27,020 Fetched page https://pypi.org/simple/streamd/ as application/vnd.pypi.simple.v1+json 2024-06-18T18:27:27,022 Found link https://files.pythonhosted.org/packages/8d/96/dd06d3cfc2b8f66a791d39120d88fc8a735168ebc8ff7e5638850a02bdb7/streamd-0.2.4.tar.gz (from https://pypi.org/simple/streamd/) (requires-python:>=3.6), version: 0.2.4 2024-06-18T18:27:27,023 Found link https://files.pythonhosted.org/packages/3c/33/e67ff9cffede4a4390020db9ba6f6823898845e3c8bba06b3b5ff85c9c70/streamd-0.2.5.tar.gz (from https://pypi.org/simple/streamd/) (requires-python:>=3.6), version: 0.2.5 2024-06-18T18:27:27,024 Fetching project page and analyzing links: https://www.piwheels.org/simple/streamd/ 2024-06-18T18:27:27,024 Getting page https://www.piwheels.org/simple/streamd/ 2024-06-18T18:27:27,026 Found index url https://www.piwheels.org/simple/ 2024-06-18T18:27:27,272 Fetched page https://www.piwheels.org/simple/streamd/ as text/html 2024-06-18T18:27:27,273 Skipping link: No binaries permitted for streamd: https://www.piwheels.org/simple/streamd/streamd-0.2.4-py3-none-any.whl#sha256=411cca8c59b01f0e7b8e18520e025a61e135cc2a6db0f374d2d5b80b171dbb2e (from https://www.piwheels.org/simple/streamd/) (requires-python:>=3.6) 2024-06-18T18:27:27,274 Skipping link: not a file: https://www.piwheels.org/simple/streamd/ 2024-06-18T18:27:27,274 Skipping link: not a file: https://pypi.org/simple/streamd/ 2024-06-18T18:27:27,292 Given no hashes to check 1 links for project 'streamd': discarding no candidates 2024-06-18T18:27:27,311 Collecting streamd==0.2.5 2024-06-18T18:27:27,313 Created temporary directory: /tmp/pip-unpack-4nttk8bi 2024-06-18T18:27:27,524 Downloading streamd-0.2.5.tar.gz (141 kB) 2024-06-18T18:27:27,713 Added streamd==0.2.5 from https://files.pythonhosted.org/packages/3c/33/e67ff9cffede4a4390020db9ba6f6823898845e3c8bba06b3b5ff85c9c70/streamd-0.2.5.tar.gz to build tracker '/tmp/pip-build-tracker-h_9q8t41' 2024-06-18T18:27:27,715 Running setup.py (path:/tmp/pip-wheel-58l4znwo/streamd_09359e9952fe420f93166d2f132566af/setup.py) egg_info for package streamd 2024-06-18T18:27:27,716 Created temporary directory: /tmp/pip-pip-egg-info-vt10hd_5 2024-06-18T18:27:27,717 Preparing metadata (setup.py): started 2024-06-18T18:27:27,718 Running command python setup.py egg_info 2024-06-18T18:27:28,875 running egg_info 2024-06-18T18:27:28,876 creating /tmp/pip-pip-egg-info-vt10hd_5/streamd.egg-info 2024-06-18T18:27:28,901 writing /tmp/pip-pip-egg-info-vt10hd_5/streamd.egg-info/PKG-INFO 2024-06-18T18:27:28,906 writing dependency_links to /tmp/pip-pip-egg-info-vt10hd_5/streamd.egg-info/dependency_links.txt 2024-06-18T18:27:28,908 writing entry points to /tmp/pip-pip-egg-info-vt10hd_5/streamd.egg-info/entry_points.txt 2024-06-18T18:27:28,910 writing requirements to /tmp/pip-pip-egg-info-vt10hd_5/streamd.egg-info/requires.txt 2024-06-18T18:27:28,911 writing top-level names to /tmp/pip-pip-egg-info-vt10hd_5/streamd.egg-info/top_level.txt 2024-06-18T18:27:28,912 writing manifest file '/tmp/pip-pip-egg-info-vt10hd_5/streamd.egg-info/SOURCES.txt' 2024-06-18T18:27:29,001 reading manifest file '/tmp/pip-pip-egg-info-vt10hd_5/streamd.egg-info/SOURCES.txt' 2024-06-18T18:27:29,003 reading manifest template 'MANIFEST.in' 2024-06-18T18:27:29,008 adding license file 'LICENSE.txt' 2024-06-18T18:27:29,011 writing manifest file '/tmp/pip-pip-egg-info-vt10hd_5/streamd.egg-info/SOURCES.txt' 2024-06-18T18:27:29,134 Preparing metadata (setup.py): finished with status 'done' 2024-06-18T18:27:29,138 Source in /tmp/pip-wheel-58l4znwo/streamd_09359e9952fe420f93166d2f132566af has version 0.2.5, which satisfies requirement streamd==0.2.5 from https://files.pythonhosted.org/packages/3c/33/e67ff9cffede4a4390020db9ba6f6823898845e3c8bba06b3b5ff85c9c70/streamd-0.2.5.tar.gz 2024-06-18T18:27:29,139 Removed streamd==0.2.5 from https://files.pythonhosted.org/packages/3c/33/e67ff9cffede4a4390020db9ba6f6823898845e3c8bba06b3b5ff85c9c70/streamd-0.2.5.tar.gz from build tracker '/tmp/pip-build-tracker-h_9q8t41' 2024-06-18T18:27:29,146 Created temporary directory: /tmp/pip-unpack-2g83ivyv 2024-06-18T18:27:29,147 Created temporary directory: /tmp/pip-unpack-juzm2l7y 2024-06-18T18:27:29,155 Building wheels for collected packages: streamd 2024-06-18T18:27:29,159 Created temporary directory: /tmp/pip-wheel-o5ijg3vo 2024-06-18T18:27:29,159 Building wheel for streamd (setup.py): started 2024-06-18T18:27:29,161 Destination directory: /tmp/pip-wheel-o5ijg3vo 2024-06-18T18:27:29,161 Running command python setup.py bdist_wheel 2024-06-18T18:27:30,236 running bdist_wheel 2024-06-18T18:27:30,338 running build 2024-06-18T18:27:30,339 running build_py 2024-06-18T18:27:30,367 creating build 2024-06-18T18:27:30,368 creating build/lib 2024-06-18T18:27:30,368 creating build/lib/streamd 2024-06-18T18:27:30,370 copying streamd/run_md.py -> build/lib/streamd 2024-06-18T18:27:30,373 copying streamd/__init__.py -> build/lib/streamd 2024-06-18T18:27:30,374 copying streamd/run_gbsa.py -> build/lib/streamd 2024-06-18T18:27:30,377 copying streamd/md_analysis.py -> build/lib/streamd 2024-06-18T18:27:30,379 creating build/lib/streamd/preparation 2024-06-18T18:27:30,380 copying streamd/preparation/ligand_preparation.py -> build/lib/streamd/preparation 2024-06-18T18:27:30,383 copying streamd/preparation/complex_preparation.py -> build/lib/streamd/preparation 2024-06-18T18:27:30,385 copying streamd/preparation/__init__.py -> build/lib/streamd/preparation 2024-06-18T18:27:30,386 copying streamd/preparation/md_files_preparation.py -> build/lib/streamd/preparation 2024-06-18T18:27:30,388 copying streamd/preparation/mcpbpy_preparation.py -> build/lib/streamd/preparation 2024-06-18T18:27:30,391 creating build/lib/streamd/scripts 2024-06-18T18:27:30,392 copying streamd/scripts/getcharge.py -> build/lib/streamd/scripts 2024-06-18T18:27:30,394 copying streamd/scripts/prepare_Gaussian_input.py -> build/lib/streamd/scripts 2024-06-18T18:27:30,396 copying streamd/scripts/__init__.py -> build/lib/streamd/scripts 2024-06-18T18:27:30,397 copying streamd/scripts/mol2_fix_coordsbonds.py -> build/lib/streamd/scripts 2024-06-18T18:27:30,400 copying streamd/scripts/pmed_amb2gmx.py -> build/lib/streamd/scripts 2024-06-18T18:27:30,402 copying streamd/scripts/xvg2png.py -> build/lib/streamd/scripts 2024-06-18T18:27:30,403 copying streamd/scripts/pdb2mol.py -> build/lib/streamd/scripts 2024-06-18T18:27:30,406 creating build/lib/streamd/prolif 2024-06-18T18:27:30,407 copying streamd/prolif/prolif2png.py -> build/lib/streamd/prolif 2024-06-18T18:27:30,409 copying streamd/prolif/run_prolif.py -> build/lib/streamd/prolif 2024-06-18T18:27:30,412 copying streamd/prolif/__init__.py -> build/lib/streamd/prolif 2024-06-18T18:27:30,413 copying streamd/prolif/prolif_frame_map.py -> build/lib/streamd/prolif 2024-06-18T18:27:30,416 creating build/lib/streamd/mcpbpy_md 2024-06-18T18:27:30,417 copying streamd/mcpbpy_md/__init__.py -> build/lib/streamd/mcpbpy_md 2024-06-18T18:27:30,419 copying streamd/mcpbpy_md/mcbpy_md.py -> build/lib/streamd/mcpbpy_md 2024-06-18T18:27:30,421 creating build/lib/streamd/utils 2024-06-18T18:27:30,423 copying streamd/utils/utils.py -> build/lib/streamd/utils 2024-06-18T18:27:30,424 copying streamd/utils/__init__.py -> build/lib/streamd/utils 2024-06-18T18:27:30,426 copying streamd/utils/dask_init.py -> build/lib/streamd/utils 2024-06-18T18:27:30,427 running egg_info 2024-06-18T18:27:30,487 writing streamd.egg-info/PKG-INFO 2024-06-18T18:27:30,491 writing dependency_links to streamd.egg-info/dependency_links.txt 2024-06-18T18:27:30,493 writing entry points to streamd.egg-info/entry_points.txt 2024-06-18T18:27:30,494 writing requirements to streamd.egg-info/requires.txt 2024-06-18T18:27:30,496 writing top-level names to streamd.egg-info/top_level.txt 2024-06-18T18:27:30,528 reading manifest file 'streamd.egg-info/SOURCES.txt' 2024-06-18T18:27:30,531 reading manifest template 'MANIFEST.in' 2024-06-18T18:27:30,535 adding license file 'LICENSE.txt' 2024-06-18T18:27:30,539 writing manifest file 'streamd.egg-info/SOURCES.txt' 2024-06-18T18:27:30,541 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'streamd.example' is absent from the `packages` configuration. 2024-06-18T18:27:30,541 !! 2024-06-18T18:27:30,542 ******************************************************************************** 2024-06-18T18:27:30,543 ############################ 2024-06-18T18:27:30,543 # Package would be ignored # 2024-06-18T18:27:30,544 ############################ 2024-06-18T18:27:30,544 Python recognizes 'streamd.example' as an importable package[^1], 2024-06-18T18:27:30,544 but it is absent from setuptools' `packages` configuration. 2024-06-18T18:27:30,546 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-18T18:27:30,546 package, please make sure that 'streamd.example' is explicitly added 2024-06-18T18:27:30,547 to the `packages` configuration field. 2024-06-18T18:27:30,548 Alternatively, you can also rely on setuptools' discovery methods 2024-06-18T18:27:30,548 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-18T18:27:30,549 instead of `find_packages(...)`/`find:`). 2024-06-18T18:27:30,550 You can read more about "package discovery" on setuptools documentation page: 2024-06-18T18:27:30,551 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-18T18:27:30,552 If you don't want 'streamd.example' to be distributed and are 2024-06-18T18:27:30,552 already explicitly excluding 'streamd.example' via 2024-06-18T18:27:30,553 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-18T18:27:30,553 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-18T18:27:30,554 combination with a more fine grained `package-data` configuration. 2024-06-18T18:27:30,555 You can read more about "package data files" on setuptools documentation page: 2024-06-18T18:27:30,556 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-18T18:27:30,558 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-18T18:27:30,558 even if it does not contain any `.py` files. 2024-06-18T18:27:30,559 On the other hand, currently there is no concept of package data 2024-06-18T18:27:30,560 directory, all directories are treated like packages. 2024-06-18T18:27:30,561 ******************************************************************************** 2024-06-18T18:27:30,562 !! 2024-06-18T18:27:30,563 check.warn(importable) 2024-06-18T18:27:30,564 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'streamd.scripts.com' is absent from the `packages` configuration. 2024-06-18T18:27:30,564 !! 2024-06-18T18:27:30,566 ******************************************************************************** 2024-06-18T18:27:30,567 ############################ 2024-06-18T18:27:30,568 # Package would be ignored # 2024-06-18T18:27:30,568 ############################ 2024-06-18T18:27:30,569 Python recognizes 'streamd.scripts.com' as an importable package[^1], 2024-06-18T18:27:30,569 but it is absent from setuptools' `packages` configuration. 2024-06-18T18:27:30,570 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-18T18:27:30,570 package, please make sure that 'streamd.scripts.com' is explicitly added 2024-06-18T18:27:30,571 to the `packages` configuration field. 2024-06-18T18:27:30,572 Alternatively, you can also rely on setuptools' discovery methods 2024-06-18T18:27:30,572 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-18T18:27:30,572 instead of `find_packages(...)`/`find:`). 2024-06-18T18:27:30,573 You can read more about "package discovery" on setuptools documentation page: 2024-06-18T18:27:30,574 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-18T18:27:30,575 If you don't want 'streamd.scripts.com' to be distributed and are 2024-06-18T18:27:30,575 already explicitly excluding 'streamd.scripts.com' via 2024-06-18T18:27:30,576 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-18T18:27:30,576 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-18T18:27:30,577 combination with a more fine grained `package-data` configuration. 2024-06-18T18:27:30,578 You can read more about "package data files" on setuptools documentation page: 2024-06-18T18:27:30,579 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-18T18:27:30,580 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-18T18:27:30,581 even if it does not contain any `.py` files. 2024-06-18T18:27:30,581 On the other hand, currently there is no concept of package data 2024-06-18T18:27:30,582 directory, all directories are treated like packages. 2024-06-18T18:27:30,582 ******************************************************************************** 2024-06-18T18:27:30,583 !! 2024-06-18T18:27:30,584 check.warn(importable) 2024-06-18T18:27:30,584 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'streamd.scripts.gbsa' is absent from the `packages` configuration. 2024-06-18T18:27:30,585 !! 2024-06-18T18:27:30,586 ******************************************************************************** 2024-06-18T18:27:30,586 ############################ 2024-06-18T18:27:30,587 # Package would be ignored # 2024-06-18T18:27:30,587 ############################ 2024-06-18T18:27:30,588 Python recognizes 'streamd.scripts.gbsa' as an importable package[^1], 2024-06-18T18:27:30,588 but it is absent from setuptools' `packages` configuration. 2024-06-18T18:27:30,589 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-18T18:27:30,590 package, please make sure that 'streamd.scripts.gbsa' is explicitly added 2024-06-18T18:27:30,590 to the `packages` configuration field. 2024-06-18T18:27:30,591 Alternatively, you can also rely on setuptools' discovery methods 2024-06-18T18:27:30,592 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-18T18:27:30,592 instead of `find_packages(...)`/`find:`). 2024-06-18T18:27:30,593 You can read more about "package discovery" on setuptools documentation page: 2024-06-18T18:27:30,594 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-18T18:27:30,596 If you don't want 'streamd.scripts.gbsa' to be distributed and are 2024-06-18T18:27:30,596 already explicitly excluding 'streamd.scripts.gbsa' via 2024-06-18T18:27:30,596 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-18T18:27:30,597 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-18T18:27:30,597 combination with a more fine grained `package-data` configuration. 2024-06-18T18:27:30,598 You can read more about "package data files" on setuptools documentation page: 2024-06-18T18:27:30,599 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-18T18:27:30,600 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-18T18:27:30,601 even if it does not contain any `.py` files. 2024-06-18T18:27:30,601 On the other hand, currently there is no concept of package data 2024-06-18T18:27:30,602 directory, all directories are treated like packages. 2024-06-18T18:27:30,602 ******************************************************************************** 2024-06-18T18:27:30,603 !! 2024-06-18T18:27:30,603 check.warn(importable) 2024-06-18T18:27:30,604 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'streamd.scripts.mcpbpy_scripts' is absent from the `packages` configuration. 2024-06-18T18:27:30,604 !! 2024-06-18T18:27:30,605 ******************************************************************************** 2024-06-18T18:27:30,606 ############################ 2024-06-18T18:27:30,606 # Package would be ignored # 2024-06-18T18:27:30,607 ############################ 2024-06-18T18:27:30,607 Python recognizes 'streamd.scripts.mcpbpy_scripts' as an importable package[^1], 2024-06-18T18:27:30,607 but it is absent from setuptools' `packages` configuration. 2024-06-18T18:27:30,608 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-18T18:27:30,609 package, please make sure that 'streamd.scripts.mcpbpy_scripts' is explicitly added 2024-06-18T18:27:30,609 to the `packages` configuration field. 2024-06-18T18:27:30,610 Alternatively, you can also rely on setuptools' discovery methods 2024-06-18T18:27:30,611 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-18T18:27:30,611 instead of `find_packages(...)`/`find:`). 2024-06-18T18:27:30,612 You can read more about "package discovery" on setuptools documentation page: 2024-06-18T18:27:30,613 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-18T18:27:30,614 If you don't want 'streamd.scripts.mcpbpy_scripts' to be distributed and are 2024-06-18T18:27:30,615 already explicitly excluding 'streamd.scripts.mcpbpy_scripts' via 2024-06-18T18:27:30,615 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-18T18:27:30,616 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-18T18:27:30,616 combination with a more fine grained `package-data` configuration. 2024-06-18T18:27:30,617 You can read more about "package data files" on setuptools documentation page: 2024-06-18T18:27:30,618 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-18T18:27:30,620 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-18T18:27:30,620 even if it does not contain any `.py` files. 2024-06-18T18:27:30,621 On the other hand, currently there is no concept of package data 2024-06-18T18:27:30,621 directory, all directories are treated like packages. 2024-06-18T18:27:30,622 ******************************************************************************** 2024-06-18T18:27:30,623 !! 2024-06-18T18:27:30,624 check.warn(importable) 2024-06-18T18:27:30,624 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'streamd.scripts.mdp' is absent from the `packages` configuration. 2024-06-18T18:27:30,624 !! 2024-06-18T18:27:30,625 ******************************************************************************** 2024-06-18T18:27:30,626 ############################ 2024-06-18T18:27:30,626 # Package would be ignored # 2024-06-18T18:27:30,626 ############################ 2024-06-18T18:27:30,627 Python recognizes 'streamd.scripts.mdp' as an importable package[^1], 2024-06-18T18:27:30,627 but it is absent from setuptools' `packages` configuration. 2024-06-18T18:27:30,628 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-18T18:27:30,629 package, please make sure that 'streamd.scripts.mdp' is explicitly added 2024-06-18T18:27:30,629 to the `packages` configuration field. 2024-06-18T18:27:30,630 Alternatively, you can also rely on setuptools' discovery methods 2024-06-18T18:27:30,631 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-18T18:27:30,631 instead of `find_packages(...)`/`find:`). 2024-06-18T18:27:30,632 You can read more about "package discovery" on setuptools documentation page: 2024-06-18T18:27:30,633 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-18T18:27:30,635 If you don't want 'streamd.scripts.mdp' to be distributed and are 2024-06-18T18:27:30,635 already explicitly excluding 'streamd.scripts.mdp' via 2024-06-18T18:27:30,636 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-18T18:27:30,636 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-18T18:27:30,637 combination with a more fine grained `package-data` configuration. 2024-06-18T18:27:30,639 You can read more about "package data files" on setuptools documentation page: 2024-06-18T18:27:30,640 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-18T18:27:30,641 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-18T18:27:30,642 even if it does not contain any `.py` files. 2024-06-18T18:27:30,643 On the other hand, currently there is no concept of package data 2024-06-18T18:27:30,643 directory, all directories are treated like packages. 2024-06-18T18:27:30,644 ******************************************************************************** 2024-06-18T18:27:30,645 !! 2024-06-18T18:27:30,646 check.warn(importable) 2024-06-18T18:27:30,646 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'streamd.scripts.script_sh' is absent from the `packages` configuration. 2024-06-18T18:27:30,647 !! 2024-06-18T18:27:30,648 ******************************************************************************** 2024-06-18T18:27:30,648 ############################ 2024-06-18T18:27:30,649 # Package would be ignored # 2024-06-18T18:27:30,650 ############################ 2024-06-18T18:27:30,650 Python recognizes 'streamd.scripts.script_sh' as an importable package[^1], 2024-06-18T18:27:30,651 but it is absent from setuptools' `packages` configuration. 2024-06-18T18:27:30,652 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-18T18:27:30,653 package, please make sure that 'streamd.scripts.script_sh' is explicitly added 2024-06-18T18:27:30,653 to the `packages` configuration field. 2024-06-18T18:27:30,654 Alternatively, you can also rely on setuptools' discovery methods 2024-06-18T18:27:30,655 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-18T18:27:30,656 instead of `find_packages(...)`/`find:`). 2024-06-18T18:27:30,657 You can read more about "package discovery" on setuptools documentation page: 2024-06-18T18:27:30,658 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-18T18:27:30,658 If you don't want 'streamd.scripts.script_sh' to be distributed and are 2024-06-18T18:27:30,659 already explicitly excluding 'streamd.scripts.script_sh' via 2024-06-18T18:27:30,659 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-18T18:27:30,660 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-18T18:27:30,660 combination with a more fine grained `package-data` configuration. 2024-06-18T18:27:30,661 You can read more about "package data files" on setuptools documentation page: 2024-06-18T18:27:30,662 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-18T18:27:30,663 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-18T18:27:30,664 even if it does not contain any `.py` files. 2024-06-18T18:27:30,664 On the other hand, currently there is no concept of package data 2024-06-18T18:27:30,664 directory, all directories are treated like packages. 2024-06-18T18:27:30,665 ******************************************************************************** 2024-06-18T18:27:30,666 !! 2024-06-18T18:27:30,667 check.warn(importable) 2024-06-18T18:27:30,667 creating build/lib/streamd/example 2024-06-18T18:27:30,668 copying streamd/example/instructions.txt -> build/lib/streamd/example 2024-06-18T18:27:30,668 copying streamd/example/ligand.mol -> build/lib/streamd/example 2024-06-18T18:27:30,669 copying streamd/example/protein_HIS.pdb -> build/lib/streamd/example 2024-06-18T18:27:30,670 copying streamd/scripts/tleap.in -> build/lib/streamd/scripts 2024-06-18T18:27:30,670 creating build/lib/streamd/scripts/com 2024-06-18T18:27:30,671 copying streamd/scripts/com/1.com -> build/lib/streamd/scripts/com 2024-06-18T18:27:30,671 copying streamd/scripts/com/2.com -> build/lib/streamd/scripts/com 2024-06-18T18:27:30,672 copying streamd/scripts/com/3.com -> build/lib/streamd/scripts/com 2024-06-18T18:27:30,672 creating build/lib/streamd/scripts/gbsa 2024-06-18T18:27:30,673 copying streamd/scripts/gbsa/mmpbsa.in -> build/lib/streamd/scripts/gbsa 2024-06-18T18:27:30,674 creating build/lib/streamd/scripts/mcpbpy_scripts 2024-06-18T18:27:30,674 copying streamd/scripts/mcpbpy_scripts/protein.in -> build/lib/streamd/scripts/mcpbpy_scripts 2024-06-18T18:27:30,675 creating build/lib/streamd/scripts/mdp 2024-06-18T18:27:30,676 copying streamd/scripts/mdp/ions.mdp -> build/lib/streamd/scripts/mdp 2024-06-18T18:27:30,676 copying streamd/scripts/mdp/md.mdp -> build/lib/streamd/scripts/mdp 2024-06-18T18:27:30,677 copying streamd/scripts/mdp/minim.mdp -> build/lib/streamd/scripts/mdp 2024-06-18T18:27:30,677 copying streamd/scripts/mdp/npt.mdp -> build/lib/streamd/scripts/mdp 2024-06-18T18:27:30,678 copying streamd/scripts/mdp/nvt.mdp -> build/lib/streamd/scripts/mdp 2024-06-18T18:27:30,678 creating build/lib/streamd/scripts/script_sh 2024-06-18T18:27:30,679 copying streamd/scripts/script_sh/continue_md.sh -> build/lib/streamd/scripts/script_sh 2024-06-18T18:27:30,679 copying streamd/scripts/script_sh/equlibration.sh -> build/lib/streamd/scripts/script_sh 2024-06-18T18:27:30,680 copying streamd/scripts/script_sh/ligand_mol2prep.sh -> build/lib/streamd/scripts/script_sh 2024-06-18T18:27:30,681 copying streamd/scripts/script_sh/ligand_mol2prep_by_gaussian.sh -> build/lib/streamd/scripts/script_sh 2024-06-18T18:27:30,681 copying streamd/scripts/script_sh/ligand_prep.sh -> build/lib/streamd/scripts/script_sh 2024-06-18T18:27:30,682 copying streamd/scripts/script_sh/md.sh -> build/lib/streamd/scripts/script_sh 2024-06-18T18:27:30,683 copying streamd/scripts/script_sh/md_analysis.sh -> build/lib/streamd/scripts/script_sh 2024-06-18T18:27:30,683 copying streamd/scripts/script_sh/md_ligand_analysis.sh -> build/lib/streamd/scripts/script_sh 2024-06-18T18:27:30,684 copying streamd/scripts/script_sh/solv_ions.sh -> build/lib/streamd/scripts/script_sh 2024-06-18T18:27:30,684 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-06-18T18:27:30,685 !! 2024-06-18T18:27:30,686 ******************************************************************************** 2024-06-18T18:27:30,686 Please avoid running ``setup.py`` directly. 2024-06-18T18:27:30,687 Instead, use pypa/build, pypa/installer or other 2024-06-18T18:27:30,687 standards-based tools. 2024-06-18T18:27:30,688 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-06-18T18:27:30,688 ******************************************************************************** 2024-06-18T18:27:30,689 !! 2024-06-18T18:27:30,690 self.initialize_options() 2024-06-18T18:27:30,710 installing to build/bdist.linux-armv7l/wheel 2024-06-18T18:27:30,711 running install 2024-06-18T18:27:30,735 running install_lib 2024-06-18T18:27:30,761 creating build/bdist.linux-armv7l 2024-06-18T18:27:30,761 creating build/bdist.linux-armv7l/wheel 2024-06-18T18:27:30,763 creating build/bdist.linux-armv7l/wheel/streamd 2024-06-18T18:27:30,764 copying build/lib/streamd/run_md.py -> build/bdist.linux-armv7l/wheel/streamd 2024-06-18T18:27:30,768 creating build/bdist.linux-armv7l/wheel/streamd/preparation 2024-06-18T18:27:30,769 copying build/lib/streamd/preparation/ligand_preparation.py -> build/bdist.linux-armv7l/wheel/streamd/preparation 2024-06-18T18:27:30,772 copying build/lib/streamd/preparation/complex_preparation.py -> build/bdist.linux-armv7l/wheel/streamd/preparation 2024-06-18T18:27:30,774 copying build/lib/streamd/preparation/__init__.py -> build/bdist.linux-armv7l/wheel/streamd/preparation 2024-06-18T18:27:30,776 copying build/lib/streamd/preparation/md_files_preparation.py -> build/bdist.linux-armv7l/wheel/streamd/preparation 2024-06-18T18:27:30,778 copying build/lib/streamd/preparation/mcpbpy_preparation.py -> build/bdist.linux-armv7l/wheel/streamd/preparation 2024-06-18T18:27:30,781 creating build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-18T18:27:30,782 copying build/lib/streamd/scripts/getcharge.py -> build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-18T18:27:30,784 copying build/lib/streamd/scripts/prepare_Gaussian_input.py -> build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-18T18:27:30,787 creating build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-18T18:27:30,788 copying build/lib/streamd/scripts/script_sh/md.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-18T18:27:30,790 copying build/lib/streamd/scripts/script_sh/ligand_mol2prep_by_gaussian.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-18T18:27:30,792 copying build/lib/streamd/scripts/script_sh/ligand_prep.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-18T18:27:30,794 copying build/lib/streamd/scripts/script_sh/continue_md.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-18T18:27:30,796 copying build/lib/streamd/scripts/script_sh/equlibration.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-18T18:27:30,798 copying build/lib/streamd/scripts/script_sh/solv_ions.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-18T18:27:30,800 copying build/lib/streamd/scripts/script_sh/ligand_mol2prep.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-18T18:27:30,802 copying build/lib/streamd/scripts/script_sh/md_analysis.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-18T18:27:30,804 copying build/lib/streamd/scripts/script_sh/md_ligand_analysis.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-18T18:27:30,806 creating build/bdist.linux-armv7l/wheel/streamd/scripts/com 2024-06-18T18:27:30,807 copying build/lib/streamd/scripts/com/2.com -> build/bdist.linux-armv7l/wheel/streamd/scripts/com 2024-06-18T18:27:30,810 copying build/lib/streamd/scripts/com/3.com -> build/bdist.linux-armv7l/wheel/streamd/scripts/com 2024-06-18T18:27:30,811 copying build/lib/streamd/scripts/com/1.com -> build/bdist.linux-armv7l/wheel/streamd/scripts/com 2024-06-18T18:27:30,813 copying build/lib/streamd/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-18T18:27:30,815 copying build/lib/streamd/scripts/mol2_fix_coordsbonds.py -> build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-18T18:27:30,818 copying build/lib/streamd/scripts/tleap.in -> build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-18T18:27:30,821 creating build/bdist.linux-armv7l/wheel/streamd/scripts/gbsa 2024-06-18T18:27:30,822 copying build/lib/streamd/scripts/gbsa/mmpbsa.in -> build/bdist.linux-armv7l/wheel/streamd/scripts/gbsa 2024-06-18T18:27:30,825 copying build/lib/streamd/scripts/pmed_amb2gmx.py -> build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-18T18:27:30,827 creating build/bdist.linux-armv7l/wheel/streamd/scripts/mdp 2024-06-18T18:27:30,828 copying build/lib/streamd/scripts/mdp/ions.mdp -> build/bdist.linux-armv7l/wheel/streamd/scripts/mdp 2024-06-18T18:27:30,830 copying build/lib/streamd/scripts/mdp/nvt.mdp -> build/bdist.linux-armv7l/wheel/streamd/scripts/mdp 2024-06-18T18:27:30,832 copying build/lib/streamd/scripts/mdp/npt.mdp -> build/bdist.linux-armv7l/wheel/streamd/scripts/mdp 2024-06-18T18:27:30,834 copying build/lib/streamd/scripts/mdp/minim.mdp -> build/bdist.linux-armv7l/wheel/streamd/scripts/mdp 2024-06-18T18:27:30,836 copying build/lib/streamd/scripts/mdp/md.mdp -> build/bdist.linux-armv7l/wheel/streamd/scripts/mdp 2024-06-18T18:27:30,838 copying build/lib/streamd/scripts/xvg2png.py -> build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-18T18:27:30,840 creating build/bdist.linux-armv7l/wheel/streamd/scripts/mcpbpy_scripts 2024-06-18T18:27:30,841 copying build/lib/streamd/scripts/mcpbpy_scripts/protein.in -> build/bdist.linux-armv7l/wheel/streamd/scripts/mcpbpy_scripts 2024-06-18T18:27:30,843 copying build/lib/streamd/scripts/pdb2mol.py -> build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-18T18:27:30,846 creating build/bdist.linux-armv7l/wheel/streamd/prolif 2024-06-18T18:27:30,846 copying build/lib/streamd/prolif/prolif2png.py -> build/bdist.linux-armv7l/wheel/streamd/prolif 2024-06-18T18:27:30,849 copying build/lib/streamd/prolif/run_prolif.py -> build/bdist.linux-armv7l/wheel/streamd/prolif 2024-06-18T18:27:30,851 copying build/lib/streamd/prolif/__init__.py -> build/bdist.linux-armv7l/wheel/streamd/prolif 2024-06-18T18:27:30,853 copying build/lib/streamd/prolif/prolif_frame_map.py -> build/bdist.linux-armv7l/wheel/streamd/prolif 2024-06-18T18:27:30,855 copying build/lib/streamd/__init__.py -> build/bdist.linux-armv7l/wheel/streamd 2024-06-18T18:27:30,857 creating build/bdist.linux-armv7l/wheel/streamd/mcpbpy_md 2024-06-18T18:27:30,858 copying build/lib/streamd/mcpbpy_md/__init__.py -> build/bdist.linux-armv7l/wheel/streamd/mcpbpy_md 2024-06-18T18:27:30,860 copying build/lib/streamd/mcpbpy_md/mcbpy_md.py -> build/bdist.linux-armv7l/wheel/streamd/mcpbpy_md 2024-06-18T18:27:30,862 creating build/bdist.linux-armv7l/wheel/streamd/utils 2024-06-18T18:27:30,863 copying build/lib/streamd/utils/utils.py -> build/bdist.linux-armv7l/wheel/streamd/utils 2024-06-18T18:27:30,866 copying build/lib/streamd/utils/__init__.py -> build/bdist.linux-armv7l/wheel/streamd/utils 2024-06-18T18:27:30,867 copying build/lib/streamd/utils/dask_init.py -> build/bdist.linux-armv7l/wheel/streamd/utils 2024-06-18T18:27:30,869 creating build/bdist.linux-armv7l/wheel/streamd/example 2024-06-18T18:27:30,870 copying build/lib/streamd/example/instructions.txt -> build/bdist.linux-armv7l/wheel/streamd/example 2024-06-18T18:27:30,872 copying build/lib/streamd/example/ligand.mol -> build/bdist.linux-armv7l/wheel/streamd/example 2024-06-18T18:27:30,874 copying build/lib/streamd/example/protein_HIS.pdb -> build/bdist.linux-armv7l/wheel/streamd/example 2024-06-18T18:27:30,883 copying build/lib/streamd/run_gbsa.py -> build/bdist.linux-armv7l/wheel/streamd 2024-06-18T18:27:30,885 copying build/lib/streamd/md_analysis.py -> build/bdist.linux-armv7l/wheel/streamd 2024-06-18T18:27:30,887 running install_egg_info 2024-06-18T18:27:30,918 Copying streamd.egg-info to build/bdist.linux-armv7l/wheel/streamd-0.2.5-py3.11.egg-info 2024-06-18T18:27:30,932 running install_scripts 2024-06-18T18:27:30,949 creating build/bdist.linux-armv7l/wheel/streamd-0.2.5.dist-info/WHEEL 2024-06-18T18:27:30,951 creating '/tmp/pip-wheel-o5ijg3vo/streamd-0.2.5-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-06-18T18:27:30,953 adding 'streamd/__init__.py' 2024-06-18T18:27:30,954 adding 'streamd/md_analysis.py' 2024-06-18T18:27:30,957 adding 'streamd/run_gbsa.py' 2024-06-18T18:27:30,961 adding 'streamd/run_md.py' 2024-06-18T18:27:30,963 adding 'streamd/example/instructions.txt' 2024-06-18T18:27:30,964 adding 'streamd/example/ligand.mol' 2024-06-18T18:27:31,026 adding 'streamd/example/protein_HIS.pdb' 2024-06-18T18:27:31,030 adding 'streamd/mcpbpy_md/__init__.py' 2024-06-18T18:27:31,031 adding 'streamd/mcpbpy_md/mcbpy_md.py' 2024-06-18T18:27:31,033 adding 'streamd/preparation/__init__.py' 2024-06-18T18:27:31,034 adding 'streamd/preparation/complex_preparation.py' 2024-06-18T18:27:31,036 adding 'streamd/preparation/ligand_preparation.py' 2024-06-18T18:27:31,038 adding 'streamd/preparation/mcpbpy_preparation.py' 2024-06-18T18:27:31,040 adding 'streamd/preparation/md_files_preparation.py' 2024-06-18T18:27:31,042 adding 'streamd/prolif/__init__.py' 2024-06-18T18:27:31,043 adding 'streamd/prolif/prolif2png.py' 2024-06-18T18:27:31,045 adding 'streamd/prolif/prolif_frame_map.py' 2024-06-18T18:27:31,047 adding 'streamd/prolif/run_prolif.py' 2024-06-18T18:27:31,048 adding 'streamd/scripts/__init__.py' 2024-06-18T18:27:31,050 adding 'streamd/scripts/getcharge.py' 2024-06-18T18:27:31,051 adding 'streamd/scripts/mol2_fix_coordsbonds.py' 2024-06-18T18:27:31,052 adding 'streamd/scripts/pdb2mol.py' 2024-06-18T18:27:31,054 adding 'streamd/scripts/pmed_amb2gmx.py' 2024-06-18T18:27:31,055 adding 'streamd/scripts/prepare_Gaussian_input.py' 2024-06-18T18:27:31,056 adding 'streamd/scripts/tleap.in' 2024-06-18T18:27:31,058 adding 'streamd/scripts/xvg2png.py' 2024-06-18T18:27:31,059 adding 'streamd/scripts/com/1.com' 2024-06-18T18:27:31,060 adding 'streamd/scripts/com/2.com' 2024-06-18T18:27:31,062 adding 'streamd/scripts/com/3.com' 2024-06-18T18:27:31,063 adding 'streamd/scripts/gbsa/mmpbsa.in' 2024-06-18T18:27:31,065 adding 'streamd/scripts/mcpbpy_scripts/protein.in' 2024-06-18T18:27:31,067 adding 'streamd/scripts/mdp/ions.mdp' 2024-06-18T18:27:31,068 adding 'streamd/scripts/mdp/md.mdp' 2024-06-18T18:27:31,070 adding 'streamd/scripts/mdp/minim.mdp' 2024-06-18T18:27:31,071 adding 'streamd/scripts/mdp/npt.mdp' 2024-06-18T18:27:31,073 adding 'streamd/scripts/mdp/nvt.mdp' 2024-06-18T18:27:31,075 adding 'streamd/scripts/script_sh/continue_md.sh' 2024-06-18T18:27:31,076 adding 'streamd/scripts/script_sh/equlibration.sh' 2024-06-18T18:27:31,077 adding 'streamd/scripts/script_sh/ligand_mol2prep.sh' 2024-06-18T18:27:31,079 adding 'streamd/scripts/script_sh/ligand_mol2prep_by_gaussian.sh' 2024-06-18T18:27:31,080 adding 'streamd/scripts/script_sh/ligand_prep.sh' 2024-06-18T18:27:31,082 adding 'streamd/scripts/script_sh/md.sh' 2024-06-18T18:27:31,083 adding 'streamd/scripts/script_sh/md_analysis.sh' 2024-06-18T18:27:31,084 adding 'streamd/scripts/script_sh/md_ligand_analysis.sh' 2024-06-18T18:27:31,086 adding 'streamd/scripts/script_sh/solv_ions.sh' 2024-06-18T18:27:31,088 adding 'streamd/utils/__init__.py' 2024-06-18T18:27:31,089 adding 'streamd/utils/dask_init.py' 2024-06-18T18:27:31,090 adding 'streamd/utils/utils.py' 2024-06-18T18:27:31,092 adding 'streamd-0.2.5.dist-info/LICENSE.txt' 2024-06-18T18:27:31,095 adding 'streamd-0.2.5.dist-info/METADATA' 2024-06-18T18:27:31,096 adding 'streamd-0.2.5.dist-info/WHEEL' 2024-06-18T18:27:31,097 adding 'streamd-0.2.5.dist-info/entry_points.txt' 2024-06-18T18:27:31,098 adding 'streamd-0.2.5.dist-info/top_level.txt' 2024-06-18T18:27:31,099 adding 'streamd-0.2.5.dist-info/RECORD' 2024-06-18T18:27:31,103 removing build/bdist.linux-armv7l/wheel 2024-06-18T18:27:31,241 Building wheel for streamd (setup.py): finished with status 'done' 2024-06-18T18:27:31,245 Created wheel for streamd: filename=streamd-0.2.5-py3-none-any.whl size=152587 sha256=23e92bac46dff5622fbf91e611c2277c5c87967d2a26965933d6f33e03b63818 2024-06-18T18:27:31,247 Stored in directory: /tmp/pip-ephem-wheel-cache-74tgza7q/wheels/c3/0d/5c/d4b8f03dfea6200cdce94ae52eecde8fbae2e4e7789ffb17c7 2024-06-18T18:27:31,261 Successfully built streamd 2024-06-18T18:27:31,268 Removed build tracker: '/tmp/pip-build-tracker-h_9q8t41'