2024-09-18T11:54:58,090 Created temporary directory: /tmp/pip-build-tracker-p3bmeljm 2024-09-18T11:54:58,091 Initialized build tracking at /tmp/pip-build-tracker-p3bmeljm 2024-09-18T11:54:58,092 Created build tracker: /tmp/pip-build-tracker-p3bmeljm 2024-09-18T11:54:58,092 Entered build tracker: /tmp/pip-build-tracker-p3bmeljm 2024-09-18T11:54:58,093 Created temporary directory: /tmp/pip-wheel-mi9w0_69 2024-09-18T11:54:58,097 Created temporary directory: /tmp/pip-ephem-wheel-cache-2mx3xexj 2024-09-18T11:54:58,140 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-09-18T11:54:58,143 2 location(s) to search for versions of streamd: 2024-09-18T11:54:58,143 * https://pypi.org/simple/streamd/ 2024-09-18T11:54:58,143 * https://www.piwheels.org/simple/streamd/ 2024-09-18T11:54:58,144 Fetching project page and analyzing links: https://pypi.org/simple/streamd/ 2024-09-18T11:54:58,145 Getting page https://pypi.org/simple/streamd/ 2024-09-18T11:54:58,146 Found index url https://pypi.org/simple/ 2024-09-18T11:54:58,359 Fetched page https://pypi.org/simple/streamd/ as application/vnd.pypi.simple.v1+json 2024-09-18T11:54:58,361 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 2024-09-18T11:54:58,362 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 2024-09-18T11:54:58,363 Skipping link: No binaries permitted for streamd: https://files.pythonhosted.org/packages/44/4e/ff6c13b62f53b4037ae42649009dce5a32b8ac0ad0eac5eec3df5cfbb557/streamd-0.2.6-py3-none-any.whl (from https://pypi.org/simple/streamd/) (requires-python:>=3.6) 2024-09-18T11:54:58,364 Found link https://files.pythonhosted.org/packages/72/53/dc71d524afdcfe34821f994e1affe793bbc44b984a73134cdea2ef641300/streamd-0.2.6.tar.gz (from https://pypi.org/simple/streamd/) (requires-python:>=3.6), version: 0.2.6 2024-09-18T11:54:58,365 Fetching project page and analyzing links: https://www.piwheels.org/simple/streamd/ 2024-09-18T11:54:58,366 Getting page https://www.piwheels.org/simple/streamd/ 2024-09-18T11:54:58,367 Found index url https://www.piwheels.org/simple/ 2024-09-18T11:54:58,525 Fetched page https://www.piwheels.org/simple/streamd/ as text/html 2024-09-18T11:54:58,527 Skipping link: No binaries permitted for streamd: https://www.piwheels.org/simple/streamd/streamd-0.2.5-py3-none-any.whl#sha256=23e92bac46dff5622fbf91e611c2277c5c87967d2a26965933d6f33e03b63818 (from https://www.piwheels.org/simple/streamd/) (requires-python:>=3.6) 2024-09-18T11:54:58,528 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) 2024-09-18T11:54:58,529 Skipping link: not a file: https://www.piwheels.org/simple/streamd/ 2024-09-18T11:54:58,529 Skipping link: not a file: https://pypi.org/simple/streamd/ 2024-09-18T11:54:58,549 Given no hashes to check 1 links for project 'streamd': discarding no candidates 2024-09-18T11:54:58,550 Collecting streamd==0.2.6 2024-09-18T11:54:58,553 Created temporary directory: /tmp/pip-unpack-fd0oju8a 2024-09-18T11:54:58,687 Downloading streamd-0.2.6.tar.gz (147 kB) 2024-09-18T11:54:58,886 Added streamd==0.2.6 from https://files.pythonhosted.org/packages/72/53/dc71d524afdcfe34821f994e1affe793bbc44b984a73134cdea2ef641300/streamd-0.2.6.tar.gz to build tracker '/tmp/pip-build-tracker-p3bmeljm' 2024-09-18T11:54:58,888 Running setup.py (path:/tmp/pip-wheel-mi9w0_69/streamd_1313e983237a4886bef727a1a39fda86/setup.py) egg_info for package streamd 2024-09-18T11:54:58,889 Created temporary directory: /tmp/pip-pip-egg-info-k0xibfzs 2024-09-18T11:54:58,890 Preparing metadata (setup.py): started 2024-09-18T11:54:58,891 Running command python setup.py egg_info 2024-09-18T11:55:00,022 running egg_info 2024-09-18T11:55:00,023 creating /tmp/pip-pip-egg-info-k0xibfzs/streamd.egg-info 2024-09-18T11:55:00,050 writing /tmp/pip-pip-egg-info-k0xibfzs/streamd.egg-info/PKG-INFO 2024-09-18T11:55:00,055 writing dependency_links to /tmp/pip-pip-egg-info-k0xibfzs/streamd.egg-info/dependency_links.txt 2024-09-18T11:55:00,056 writing entry points to /tmp/pip-pip-egg-info-k0xibfzs/streamd.egg-info/entry_points.txt 2024-09-18T11:55:00,058 writing requirements to /tmp/pip-pip-egg-info-k0xibfzs/streamd.egg-info/requires.txt 2024-09-18T11:55:00,059 writing top-level names to /tmp/pip-pip-egg-info-k0xibfzs/streamd.egg-info/top_level.txt 2024-09-18T11:55:00,060 writing manifest file '/tmp/pip-pip-egg-info-k0xibfzs/streamd.egg-info/SOURCES.txt' 2024-09-18T11:55:00,153 reading manifest file '/tmp/pip-pip-egg-info-k0xibfzs/streamd.egg-info/SOURCES.txt' 2024-09-18T11:55:00,155 reading manifest template 'MANIFEST.in' 2024-09-18T11:55:00,160 adding license file 'LICENSE.txt' 2024-09-18T11:55:00,163 writing manifest file '/tmp/pip-pip-egg-info-k0xibfzs/streamd.egg-info/SOURCES.txt' 2024-09-18T11:55:00,275 Preparing metadata (setup.py): finished with status 'done' 2024-09-18T11:55:00,279 Source in /tmp/pip-wheel-mi9w0_69/streamd_1313e983237a4886bef727a1a39fda86 has version 0.2.6, which satisfies requirement streamd==0.2.6 from https://files.pythonhosted.org/packages/72/53/dc71d524afdcfe34821f994e1affe793bbc44b984a73134cdea2ef641300/streamd-0.2.6.tar.gz 2024-09-18T11:55:00,280 Removed streamd==0.2.6 from https://files.pythonhosted.org/packages/72/53/dc71d524afdcfe34821f994e1affe793bbc44b984a73134cdea2ef641300/streamd-0.2.6.tar.gz from build tracker '/tmp/pip-build-tracker-p3bmeljm' 2024-09-18T11:55:00,288 Created temporary directory: /tmp/pip-unpack-jvy7zbbx 2024-09-18T11:55:00,289 Created temporary directory: /tmp/pip-unpack-wfqf86p_ 2024-09-18T11:55:00,290 Building wheels for collected packages: streamd 2024-09-18T11:55:00,294 Created temporary directory: /tmp/pip-wheel-ztd4_p9f 2024-09-18T11:55:00,294 Building wheel for streamd (setup.py): started 2024-09-18T11:55:00,296 Destination directory: /tmp/pip-wheel-ztd4_p9f 2024-09-18T11:55:00,296 Running command python setup.py bdist_wheel 2024-09-18T11:55:01,361 running bdist_wheel 2024-09-18T11:55:01,509 running build 2024-09-18T11:55:01,510 running build_py 2024-09-18T11:55:01,542 creating build 2024-09-18T11:55:01,543 creating build/lib 2024-09-18T11:55:01,544 creating build/lib/streamd 2024-09-18T11:55:01,546 copying streamd/run_gbsa.py -> build/lib/streamd 2024-09-18T11:55:01,549 copying streamd/run_md.py -> build/lib/streamd 2024-09-18T11:55:01,552 copying streamd/__init__.py -> build/lib/streamd 2024-09-18T11:55:01,553 copying streamd/md_analysis.py -> build/lib/streamd 2024-09-18T11:55:01,556 creating build/lib/streamd/utils 2024-09-18T11:55:01,557 copying streamd/utils/utils.py -> build/lib/streamd/utils 2024-09-18T11:55:01,559 copying streamd/utils/__init__.py -> build/lib/streamd/utils 2024-09-18T11:55:01,563 copying streamd/utils/dask_init.py -> build/lib/streamd/utils 2024-09-18T11:55:01,566 creating build/lib/streamd/mcpbpy_md 2024-09-18T11:55:01,567 copying streamd/mcpbpy_md/__init__.py -> build/lib/streamd/mcpbpy_md 2024-09-18T11:55:01,569 copying streamd/mcpbpy_md/mcbpy_md.py -> build/lib/streamd/mcpbpy_md 2024-09-18T11:55:01,572 creating build/lib/streamd/preparation 2024-09-18T11:55:01,573 copying streamd/preparation/ligand_preparation.py -> build/lib/streamd/preparation 2024-09-18T11:55:01,575 copying streamd/preparation/complex_preparation.py -> build/lib/streamd/preparation 2024-09-18T11:55:01,577 copying streamd/preparation/__init__.py -> build/lib/streamd/preparation 2024-09-18T11:55:01,579 copying streamd/preparation/mcpbpy_preparation.py -> build/lib/streamd/preparation 2024-09-18T11:55:01,582 copying streamd/preparation/md_files_preparation.py -> build/lib/streamd/preparation 2024-09-18T11:55:01,585 creating build/lib/streamd/scripts 2024-09-18T11:55:01,586 copying streamd/scripts/getcharge.py -> build/lib/streamd/scripts 2024-09-18T11:55:01,588 copying streamd/scripts/pdb2mol.py -> build/lib/streamd/scripts 2024-09-18T11:55:01,590 copying streamd/scripts/__init__.py -> build/lib/streamd/scripts 2024-09-18T11:55:01,592 copying streamd/scripts/mol2_fix_coordsbonds.py -> build/lib/streamd/scripts 2024-09-18T11:55:01,594 copying streamd/scripts/prepare_Gaussian_input.py -> build/lib/streamd/scripts 2024-09-18T11:55:01,596 copying streamd/scripts/xvg2png.py -> build/lib/streamd/scripts 2024-09-18T11:55:01,598 copying streamd/scripts/pmed_amb2gmx.py -> build/lib/streamd/scripts 2024-09-18T11:55:01,600 creating build/lib/streamd/prolif 2024-09-18T11:55:01,602 copying streamd/prolif/run_prolif.py -> build/lib/streamd/prolif 2024-09-18T11:55:01,604 copying streamd/prolif/__init__.py -> build/lib/streamd/prolif 2024-09-18T11:55:01,606 copying streamd/prolif/prolif2png.py -> build/lib/streamd/prolif 2024-09-18T11:55:01,608 copying streamd/prolif/prolif_frame_map.py -> build/lib/streamd/prolif 2024-09-18T11:55:01,611 running egg_info 2024-09-18T11:55:01,638 writing streamd.egg-info/PKG-INFO 2024-09-18T11:55:01,642 writing dependency_links to streamd.egg-info/dependency_links.txt 2024-09-18T11:55:01,644 writing entry points to streamd.egg-info/entry_points.txt 2024-09-18T11:55:01,646 writing requirements to streamd.egg-info/requires.txt 2024-09-18T11:55:01,647 writing top-level names to streamd.egg-info/top_level.txt 2024-09-18T11:55:01,682 reading manifest file 'streamd.egg-info/SOURCES.txt' 2024-09-18T11:55:01,687 reading manifest template 'MANIFEST.in' 2024-09-18T11:55:01,691 adding license file 'LICENSE.txt' 2024-09-18T11:55:01,695 writing manifest file 'streamd.egg-info/SOURCES.txt' 2024-09-18T11:55:01,697 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'streamd.example' is absent from the `packages` configuration. 2024-09-18T11:55:01,697 !! 2024-09-18T11:55:01,699 ******************************************************************************** 2024-09-18T11:55:01,699 ############################ 2024-09-18T11:55:01,700 # Package would be ignored # 2024-09-18T11:55:01,701 ############################ 2024-09-18T11:55:01,701 Python recognizes 'streamd.example' as an importable package[^1], 2024-09-18T11:55:01,702 but it is absent from setuptools' `packages` configuration. 2024-09-18T11:55:01,703 This leads to an ambiguous overall configuration. If you want to distribute this 2024-09-18T11:55:01,704 package, please make sure that 'streamd.example' is explicitly added 2024-09-18T11:55:01,704 to the `packages` configuration field. 2024-09-18T11:55:01,705 Alternatively, you can also rely on setuptools' discovery methods 2024-09-18T11:55:01,706 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-09-18T11:55:01,706 instead of `find_packages(...)`/`find:`). 2024-09-18T11:55:01,707 You can read more about "package discovery" on setuptools documentation page: 2024-09-18T11:55:01,708 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-09-18T11:55:01,709 If you don't want 'streamd.example' to be distributed and are 2024-09-18T11:55:01,710 already explicitly excluding 'streamd.example' via 2024-09-18T11:55:01,710 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-09-18T11:55:01,711 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-09-18T11:55:01,711 combination with a more fine grained `package-data` configuration. 2024-09-18T11:55:01,712 You can read more about "package data files" on setuptools documentation page: 2024-09-18T11:55:01,713 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-09-18T11:55:01,717 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-09-18T11:55:01,719 even if it does not contain any `.py` files. 2024-09-18T11:55:01,719 On the other hand, currently there is no concept of package data 2024-09-18T11:55:01,720 directory, all directories are treated like packages. 2024-09-18T11:55:01,720 ******************************************************************************** 2024-09-18T11:55:01,721 !! 2024-09-18T11:55:01,721 check.warn(importable) 2024-09-18T11:55:01,722 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'streamd.scripts.com' is absent from the `packages` configuration. 2024-09-18T11:55:01,722 !! 2024-09-18T11:55:01,724 ******************************************************************************** 2024-09-18T11:55:01,724 ############################ 2024-09-18T11:55:01,725 # Package would be ignored # 2024-09-18T11:55:01,725 ############################ 2024-09-18T11:55:01,725 Python recognizes 'streamd.scripts.com' as an importable package[^1], 2024-09-18T11:55:01,726 but it is absent from setuptools' `packages` configuration. 2024-09-18T11:55:01,727 This leads to an ambiguous overall configuration. If you want to distribute this 2024-09-18T11:55:01,727 package, please make sure that 'streamd.scripts.com' is explicitly added 2024-09-18T11:55:01,728 to the `packages` configuration field. 2024-09-18T11:55:01,729 Alternatively, you can also rely on setuptools' discovery methods 2024-09-18T11:55:01,729 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-09-18T11:55:01,730 instead of `find_packages(...)`/`find:`). 2024-09-18T11:55:01,731 You can read more about "package discovery" on setuptools documentation page: 2024-09-18T11:55:01,732 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-09-18T11:55:01,733 If you don't want 'streamd.scripts.com' to be distributed and are 2024-09-18T11:55:01,733 already explicitly excluding 'streamd.scripts.com' via 2024-09-18T11:55:01,734 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-09-18T11:55:01,734 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-09-18T11:55:01,735 combination with a more fine grained `package-data` configuration. 2024-09-18T11:55:01,736 You can read more about "package data files" on setuptools documentation page: 2024-09-18T11:55:01,737 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-09-18T11:55:01,738 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-09-18T11:55:01,739 even if it does not contain any `.py` files. 2024-09-18T11:55:01,739 On the other hand, currently there is no concept of package data 2024-09-18T11:55:01,740 directory, all directories are treated like packages. 2024-09-18T11:55:01,740 ******************************************************************************** 2024-09-18T11:55:01,741 !! 2024-09-18T11:55:01,742 check.warn(importable) 2024-09-18T11:55:01,742 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'streamd.scripts.gbsa' is absent from the `packages` configuration. 2024-09-18T11:55:01,743 !! 2024-09-18T11:55:01,744 ******************************************************************************** 2024-09-18T11:55:01,744 ############################ 2024-09-18T11:55:01,745 # Package would be ignored # 2024-09-18T11:55:01,746 ############################ 2024-09-18T11:55:01,746 Python recognizes 'streamd.scripts.gbsa' as an importable package[^1], 2024-09-18T11:55:01,747 but it is absent from setuptools' `packages` configuration. 2024-09-18T11:55:01,748 This leads to an ambiguous overall configuration. If you want to distribute this 2024-09-18T11:55:01,749 package, please make sure that 'streamd.scripts.gbsa' is explicitly added 2024-09-18T11:55:01,749 to the `packages` configuration field. 2024-09-18T11:55:01,750 Alternatively, you can also rely on setuptools' discovery methods 2024-09-18T11:55:01,750 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-09-18T11:55:01,751 instead of `find_packages(...)`/`find:`). 2024-09-18T11:55:01,751 You can read more about "package discovery" on setuptools documentation page: 2024-09-18T11:55:01,752 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-09-18T11:55:01,753 If you don't want 'streamd.scripts.gbsa' to be distributed and are 2024-09-18T11:55:01,753 already explicitly excluding 'streamd.scripts.gbsa' via 2024-09-18T11:55:01,754 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-09-18T11:55:01,754 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-09-18T11:55:01,755 combination with a more fine grained `package-data` configuration. 2024-09-18T11:55:01,756 You can read more about "package data files" on setuptools documentation page: 2024-09-18T11:55:01,757 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-09-18T11:55:01,758 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-09-18T11:55:01,758 even if it does not contain any `.py` files. 2024-09-18T11:55:01,759 On the other hand, currently there is no concept of package data 2024-09-18T11:55:01,759 directory, all directories are treated like packages. 2024-09-18T11:55:01,760 ******************************************************************************** 2024-09-18T11:55:01,761 !! 2024-09-18T11:55:01,761 check.warn(importable) 2024-09-18T11:55:01,761 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'streamd.scripts.mcpbpy_scripts' is absent from the `packages` configuration. 2024-09-18T11:55:01,762 !! 2024-09-18T11:55:01,763 ******************************************************************************** 2024-09-18T11:55:01,763 ############################ 2024-09-18T11:55:01,764 # Package would be ignored # 2024-09-18T11:55:01,764 ############################ 2024-09-18T11:55:01,765 Python recognizes 'streamd.scripts.mcpbpy_scripts' as an importable package[^1], 2024-09-18T11:55:01,765 but it is absent from setuptools' `packages` configuration. 2024-09-18T11:55:01,766 This leads to an ambiguous overall configuration. If you want to distribute this 2024-09-18T11:55:01,766 package, please make sure that 'streamd.scripts.mcpbpy_scripts' is explicitly added 2024-09-18T11:55:01,767 to the `packages` configuration field. 2024-09-18T11:55:01,768 Alternatively, you can also rely on setuptools' discovery methods 2024-09-18T11:55:01,769 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-09-18T11:55:01,769 instead of `find_packages(...)`/`find:`). 2024-09-18T11:55:01,770 You can read more about "package discovery" on setuptools documentation page: 2024-09-18T11:55:01,771 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-09-18T11:55:01,773 If you don't want 'streamd.scripts.mcpbpy_scripts' to be distributed and are 2024-09-18T11:55:01,773 already explicitly excluding 'streamd.scripts.mcpbpy_scripts' via 2024-09-18T11:55:01,774 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-09-18T11:55:01,774 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-09-18T11:55:01,775 combination with a more fine grained `package-data` configuration. 2024-09-18T11:55:01,776 You can read more about "package data files" on setuptools documentation page: 2024-09-18T11:55:01,777 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-09-18T11:55:01,778 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-09-18T11:55:01,779 even if it does not contain any `.py` files. 2024-09-18T11:55:01,779 On the other hand, currently there is no concept of package data 2024-09-18T11:55:01,780 directory, all directories are treated like packages. 2024-09-18T11:55:01,780 ******************************************************************************** 2024-09-18T11:55:01,781 !! 2024-09-18T11:55:01,781 check.warn(importable) 2024-09-18T11:55:01,782 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'streamd.scripts.mdp' is absent from the `packages` configuration. 2024-09-18T11:55:01,782 !! 2024-09-18T11:55:01,783 ******************************************************************************** 2024-09-18T11:55:01,784 ############################ 2024-09-18T11:55:01,784 # Package would be ignored # 2024-09-18T11:55:01,785 ############################ 2024-09-18T11:55:01,785 Python recognizes 'streamd.scripts.mdp' as an importable package[^1], 2024-09-18T11:55:01,786 but it is absent from setuptools' `packages` configuration. 2024-09-18T11:55:01,786 This leads to an ambiguous overall configuration. If you want to distribute this 2024-09-18T11:55:01,787 package, please make sure that 'streamd.scripts.mdp' is explicitly added 2024-09-18T11:55:01,787 to the `packages` configuration field. 2024-09-18T11:55:01,789 Alternatively, you can also rely on setuptools' discovery methods 2024-09-18T11:55:01,789 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-09-18T11:55:01,790 instead of `find_packages(...)`/`find:`). 2024-09-18T11:55:01,791 You can read more about "package discovery" on setuptools documentation page: 2024-09-18T11:55:01,792 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-09-18T11:55:01,793 If you don't want 'streamd.scripts.mdp' to be distributed and are 2024-09-18T11:55:01,794 already explicitly excluding 'streamd.scripts.mdp' via 2024-09-18T11:55:01,794 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-09-18T11:55:01,795 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-09-18T11:55:01,795 combination with a more fine grained `package-data` configuration. 2024-09-18T11:55:01,797 You can read more about "package data files" on setuptools documentation page: 2024-09-18T11:55:01,798 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-09-18T11:55:01,799 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-09-18T11:55:01,800 even if it does not contain any `.py` files. 2024-09-18T11:55:01,801 On the other hand, currently there is no concept of package data 2024-09-18T11:55:01,801 directory, all directories are treated like packages. 2024-09-18T11:55:01,802 ******************************************************************************** 2024-09-18T11:55:01,803 !! 2024-09-18T11:55:01,803 check.warn(importable) 2024-09-18T11:55:01,804 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'streamd.scripts.script_sh' is absent from the `packages` configuration. 2024-09-18T11:55:01,805 !! 2024-09-18T11:55:01,806 ******************************************************************************** 2024-09-18T11:55:01,807 ############################ 2024-09-18T11:55:01,807 # Package would be ignored # 2024-09-18T11:55:01,808 ############################ 2024-09-18T11:55:01,808 Python recognizes 'streamd.scripts.script_sh' as an importable package[^1], 2024-09-18T11:55:01,809 but it is absent from setuptools' `packages` configuration. 2024-09-18T11:55:01,810 This leads to an ambiguous overall configuration. If you want to distribute this 2024-09-18T11:55:01,810 package, please make sure that 'streamd.scripts.script_sh' is explicitly added 2024-09-18T11:55:01,811 to the `packages` configuration field. 2024-09-18T11:55:01,811 Alternatively, you can also rely on setuptools' discovery methods 2024-09-18T11:55:01,812 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-09-18T11:55:01,813 instead of `find_packages(...)`/`find:`). 2024-09-18T11:55:01,813 You can read more about "package discovery" on setuptools documentation page: 2024-09-18T11:55:01,814 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-09-18T11:55:01,815 If you don't want 'streamd.scripts.script_sh' to be distributed and are 2024-09-18T11:55:01,816 already explicitly excluding 'streamd.scripts.script_sh' via 2024-09-18T11:55:01,816 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-09-18T11:55:01,817 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-09-18T11:55:01,817 combination with a more fine grained `package-data` configuration. 2024-09-18T11:55:01,818 You can read more about "package data files" on setuptools documentation page: 2024-09-18T11:55:01,819 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-09-18T11:55:01,821 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-09-18T11:55:01,821 even if it does not contain any `.py` files. 2024-09-18T11:55:01,822 On the other hand, currently there is no concept of package data 2024-09-18T11:55:01,822 directory, all directories are treated like packages. 2024-09-18T11:55:01,823 ******************************************************************************** 2024-09-18T11:55:01,824 !! 2024-09-18T11:55:01,825 check.warn(importable) 2024-09-18T11:55:01,825 creating build/lib/streamd/example 2024-09-18T11:55:01,826 copying streamd/example/instructions.txt -> build/lib/streamd/example 2024-09-18T11:55:01,826 copying streamd/example/ligand.mol -> build/lib/streamd/example 2024-09-18T11:55:01,827 copying streamd/example/protein_HIS.pdb -> build/lib/streamd/example 2024-09-18T11:55:01,827 copying streamd/scripts/tleap.in -> build/lib/streamd/scripts 2024-09-18T11:55:01,828 creating build/lib/streamd/scripts/com 2024-09-18T11:55:01,828 copying streamd/scripts/com/1.com -> build/lib/streamd/scripts/com 2024-09-18T11:55:01,829 copying streamd/scripts/com/2.com -> build/lib/streamd/scripts/com 2024-09-18T11:55:01,829 copying streamd/scripts/com/3.com -> build/lib/streamd/scripts/com 2024-09-18T11:55:01,830 creating build/lib/streamd/scripts/gbsa 2024-09-18T11:55:01,830 copying streamd/scripts/gbsa/mmpbsa.in -> build/lib/streamd/scripts/gbsa 2024-09-18T11:55:01,831 creating build/lib/streamd/scripts/mcpbpy_scripts 2024-09-18T11:55:01,831 copying streamd/scripts/mcpbpy_scripts/protein.in -> build/lib/streamd/scripts/mcpbpy_scripts 2024-09-18T11:55:01,832 creating build/lib/streamd/scripts/mdp 2024-09-18T11:55:01,833 copying streamd/scripts/mdp/ions.mdp -> build/lib/streamd/scripts/mdp 2024-09-18T11:55:01,833 copying streamd/scripts/mdp/md.mdp -> build/lib/streamd/scripts/mdp 2024-09-18T11:55:01,834 copying streamd/scripts/mdp/minim.mdp -> build/lib/streamd/scripts/mdp 2024-09-18T11:55:01,834 copying streamd/scripts/mdp/npt.mdp -> build/lib/streamd/scripts/mdp 2024-09-18T11:55:01,835 copying streamd/scripts/mdp/nvt.mdp -> build/lib/streamd/scripts/mdp 2024-09-18T11:55:01,836 creating build/lib/streamd/scripts/script_sh 2024-09-18T11:55:01,836 copying streamd/scripts/script_sh/continue_md.sh -> build/lib/streamd/scripts/script_sh 2024-09-18T11:55:01,837 copying streamd/scripts/script_sh/equlibration.sh -> build/lib/streamd/scripts/script_sh 2024-09-18T11:55:01,837 copying streamd/scripts/script_sh/ligand_mol2prep.sh -> build/lib/streamd/scripts/script_sh 2024-09-18T11:55:01,838 copying streamd/scripts/script_sh/ligand_mol2prep_by_gaussian.sh -> build/lib/streamd/scripts/script_sh 2024-09-18T11:55:01,838 copying streamd/scripts/script_sh/ligand_prep.sh -> build/lib/streamd/scripts/script_sh 2024-09-18T11:55:01,838 copying streamd/scripts/script_sh/md.sh -> build/lib/streamd/scripts/script_sh 2024-09-18T11:55:01,839 copying streamd/scripts/script_sh/md_analysis.sh -> build/lib/streamd/scripts/script_sh 2024-09-18T11:55:01,839 copying streamd/scripts/script_sh/md_ligand_analysis.sh -> build/lib/streamd/scripts/script_sh 2024-09-18T11:55:01,840 copying streamd/scripts/script_sh/solv_ions.sh -> build/lib/streamd/scripts/script_sh 2024-09-18T11:55:01,840 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-09-18T11:55:01,841 !! 2024-09-18T11:55:01,842 ******************************************************************************** 2024-09-18T11:55:01,842 Please avoid running ``setup.py`` directly. 2024-09-18T11:55:01,843 Instead, use pypa/build, pypa/installer or other 2024-09-18T11:55:01,843 standards-based tools. 2024-09-18T11:55:01,844 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-09-18T11:55:01,845 ******************************************************************************** 2024-09-18T11:55:01,845 !! 2024-09-18T11:55:01,846 self.initialize_options() 2024-09-18T11:55:01,846 installing to build/bdist.linux-armv7l/wheel 2024-09-18T11:55:01,847 running install 2024-09-18T11:55:01,869 running install_lib 2024-09-18T11:55:01,897 creating build/bdist.linux-armv7l 2024-09-18T11:55:01,897 creating build/bdist.linux-armv7l/wheel 2024-09-18T11:55:01,899 creating build/bdist.linux-armv7l/wheel/streamd 2024-09-18T11:55:01,900 copying build/lib/streamd/run_gbsa.py -> build/bdist.linux-armv7l/wheel/./streamd 2024-09-18T11:55:01,905 creating build/bdist.linux-armv7l/wheel/streamd/utils 2024-09-18T11:55:01,906 copying build/lib/streamd/utils/utils.py -> build/bdist.linux-armv7l/wheel/./streamd/utils 2024-09-18T11:55:01,908 copying build/lib/streamd/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/utils 2024-09-18T11:55:01,910 copying build/lib/streamd/utils/dask_init.py -> build/bdist.linux-armv7l/wheel/./streamd/utils 2024-09-18T11:55:01,912 copying build/lib/streamd/run_md.py -> build/bdist.linux-armv7l/wheel/./streamd 2024-09-18T11:55:01,915 creating build/bdist.linux-armv7l/wheel/streamd/mcpbpy_md 2024-09-18T11:55:01,916 copying build/lib/streamd/mcpbpy_md/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/mcpbpy_md 2024-09-18T11:55:01,918 copying build/lib/streamd/mcpbpy_md/mcbpy_md.py -> build/bdist.linux-armv7l/wheel/./streamd/mcpbpy_md 2024-09-18T11:55:01,921 creating build/bdist.linux-armv7l/wheel/streamd/preparation 2024-09-18T11:55:01,922 copying build/lib/streamd/preparation/ligand_preparation.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation 2024-09-18T11:55:01,924 copying build/lib/streamd/preparation/complex_preparation.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation 2024-09-18T11:55:01,926 copying build/lib/streamd/preparation/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation 2024-09-18T11:55:01,928 copying build/lib/streamd/preparation/mcpbpy_preparation.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation 2024-09-18T11:55:01,930 copying build/lib/streamd/preparation/md_files_preparation.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation 2024-09-18T11:55:01,933 creating build/bdist.linux-armv7l/wheel/streamd/example 2024-09-18T11:55:01,934 copying build/lib/streamd/example/instructions.txt -> build/bdist.linux-armv7l/wheel/./streamd/example 2024-09-18T11:55:01,936 copying build/lib/streamd/example/ligand.mol -> build/bdist.linux-armv7l/wheel/./streamd/example 2024-09-18T11:55:01,938 copying build/lib/streamd/example/protein_HIS.pdb -> build/bdist.linux-armv7l/wheel/./streamd/example 2024-09-18T11:55:01,946 copying build/lib/streamd/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd 2024-09-18T11:55:01,948 creating build/bdist.linux-armv7l/wheel/streamd/scripts 2024-09-18T11:55:01,949 creating build/bdist.linux-armv7l/wheel/streamd/scripts/com 2024-09-18T11:55:01,950 copying build/lib/streamd/scripts/com/3.com -> build/bdist.linux-armv7l/wheel/./streamd/scripts/com 2024-09-18T11:55:01,952 copying build/lib/streamd/scripts/com/2.com -> build/bdist.linux-armv7l/wheel/./streamd/scripts/com 2024-09-18T11:55:01,954 copying build/lib/streamd/scripts/com/1.com -> build/bdist.linux-armv7l/wheel/./streamd/scripts/com 2024-09-18T11:55:01,955 copying build/lib/streamd/scripts/getcharge.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts 2024-09-18T11:55:01,957 copying build/lib/streamd/scripts/pdb2mol.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts 2024-09-18T11:55:01,960 creating build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-09-18T11:55:01,961 copying build/lib/streamd/scripts/script_sh/md_analysis.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2024-09-18T11:55:01,963 copying build/lib/streamd/scripts/script_sh/ligand_prep.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2024-09-18T11:55:01,965 copying build/lib/streamd/scripts/script_sh/equlibration.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2024-09-18T11:55:01,967 copying build/lib/streamd/scripts/script_sh/md_ligand_analysis.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2024-09-18T11:55:01,969 copying build/lib/streamd/scripts/script_sh/md.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2024-09-18T11:55:01,971 copying build/lib/streamd/scripts/script_sh/ligand_mol2prep_by_gaussian.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2024-09-18T11:55:01,973 copying build/lib/streamd/scripts/script_sh/continue_md.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2024-09-18T11:55:01,975 copying build/lib/streamd/scripts/script_sh/ligand_mol2prep.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2024-09-18T11:55:01,977 copying build/lib/streamd/scripts/script_sh/solv_ions.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2024-09-18T11:55:01,979 creating build/bdist.linux-armv7l/wheel/streamd/scripts/gbsa 2024-09-18T11:55:01,980 copying build/lib/streamd/scripts/gbsa/mmpbsa.in -> build/bdist.linux-armv7l/wheel/./streamd/scripts/gbsa 2024-09-18T11:55:01,983 creating build/bdist.linux-armv7l/wheel/streamd/scripts/mcpbpy_scripts 2024-09-18T11:55:01,984 copying build/lib/streamd/scripts/mcpbpy_scripts/protein.in -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mcpbpy_scripts 2024-09-18T11:55:01,986 copying build/lib/streamd/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts 2024-09-18T11:55:01,987 copying build/lib/streamd/scripts/mol2_fix_coordsbonds.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts 2024-09-18T11:55:01,989 copying build/lib/streamd/scripts/prepare_Gaussian_input.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts 2024-09-18T11:55:01,991 copying build/lib/streamd/scripts/xvg2png.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts 2024-09-18T11:55:01,994 copying build/lib/streamd/scripts/pmed_amb2gmx.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts 2024-09-18T11:55:01,995 copying build/lib/streamd/scripts/tleap.in -> build/bdist.linux-armv7l/wheel/./streamd/scripts 2024-09-18T11:55:01,998 creating build/bdist.linux-armv7l/wheel/streamd/scripts/mdp 2024-09-18T11:55:01,999 copying build/lib/streamd/scripts/mdp/nvt.mdp -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mdp 2024-09-18T11:55:02,001 copying build/lib/streamd/scripts/mdp/npt.mdp -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mdp 2024-09-18T11:55:02,003 copying build/lib/streamd/scripts/mdp/md.mdp -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mdp 2024-09-18T11:55:02,004 copying build/lib/streamd/scripts/mdp/minim.mdp -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mdp 2024-09-18T11:55:02,006 copying build/lib/streamd/scripts/mdp/ions.mdp -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mdp 2024-09-18T11:55:02,008 copying build/lib/streamd/md_analysis.py -> build/bdist.linux-armv7l/wheel/./streamd 2024-09-18T11:55:02,011 creating build/bdist.linux-armv7l/wheel/streamd/prolif 2024-09-18T11:55:02,011 copying build/lib/streamd/prolif/run_prolif.py -> build/bdist.linux-armv7l/wheel/./streamd/prolif 2024-09-18T11:55:02,014 copying build/lib/streamd/prolif/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/prolif 2024-09-18T11:55:02,016 copying build/lib/streamd/prolif/prolif2png.py -> build/bdist.linux-armv7l/wheel/./streamd/prolif 2024-09-18T11:55:02,019 copying build/lib/streamd/prolif/prolif_frame_map.py -> build/bdist.linux-armv7l/wheel/./streamd/prolif 2024-09-18T11:55:02,021 running install_egg_info 2024-09-18T11:55:02,055 Copying streamd.egg-info to build/bdist.linux-armv7l/wheel/./streamd-0.2.6-py3.11.egg-info 2024-09-18T11:55:02,068 running install_scripts 2024-09-18T11:55:02,087 creating build/bdist.linux-armv7l/wheel/streamd-0.2.6.dist-info/WHEEL 2024-09-18T11:55:02,089 creating '/tmp/pip-wheel-ztd4_p9f/streamd-0.2.6-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-09-18T11:55:02,091 adding 'streamd/__init__.py' 2024-09-18T11:55:02,093 adding 'streamd/md_analysis.py' 2024-09-18T11:55:02,096 adding 'streamd/run_gbsa.py' 2024-09-18T11:55:02,100 adding 'streamd/run_md.py' 2024-09-18T11:55:02,102 adding 'streamd/example/instructions.txt' 2024-09-18T11:55:02,104 adding 'streamd/example/ligand.mol' 2024-09-18T11:55:02,165 adding 'streamd/example/protein_HIS.pdb' 2024-09-18T11:55:02,169 adding 'streamd/mcpbpy_md/__init__.py' 2024-09-18T11:55:02,171 adding 'streamd/mcpbpy_md/mcbpy_md.py' 2024-09-18T11:55:02,172 adding 'streamd/preparation/__init__.py' 2024-09-18T11:55:02,174 adding 'streamd/preparation/complex_preparation.py' 2024-09-18T11:55:02,176 adding 'streamd/preparation/ligand_preparation.py' 2024-09-18T11:55:02,178 adding 'streamd/preparation/mcpbpy_preparation.py' 2024-09-18T11:55:02,180 adding 'streamd/preparation/md_files_preparation.py' 2024-09-18T11:55:02,181 adding 'streamd/prolif/__init__.py' 2024-09-18T11:55:02,183 adding 'streamd/prolif/prolif2png.py' 2024-09-18T11:55:02,184 adding 'streamd/prolif/prolif_frame_map.py' 2024-09-18T11:55:02,186 adding 'streamd/prolif/run_prolif.py' 2024-09-18T11:55:02,188 adding 'streamd/scripts/__init__.py' 2024-09-18T11:55:02,189 adding 'streamd/scripts/getcharge.py' 2024-09-18T11:55:02,191 adding 'streamd/scripts/mol2_fix_coordsbonds.py' 2024-09-18T11:55:02,192 adding 'streamd/scripts/pdb2mol.py' 2024-09-18T11:55:02,194 adding 'streamd/scripts/pmed_amb2gmx.py' 2024-09-18T11:55:02,195 adding 'streamd/scripts/prepare_Gaussian_input.py' 2024-09-18T11:55:02,196 adding 'streamd/scripts/tleap.in' 2024-09-18T11:55:02,197 adding 'streamd/scripts/xvg2png.py' 2024-09-18T11:55:02,199 adding 'streamd/scripts/com/1.com' 2024-09-18T11:55:02,200 adding 'streamd/scripts/com/2.com' 2024-09-18T11:55:02,201 adding 'streamd/scripts/com/3.com' 2024-09-18T11:55:02,203 adding 'streamd/scripts/gbsa/mmpbsa.in' 2024-09-18T11:55:02,205 adding 'streamd/scripts/mcpbpy_scripts/protein.in' 2024-09-18T11:55:02,207 adding 'streamd/scripts/mdp/ions.mdp' 2024-09-18T11:55:02,208 adding 'streamd/scripts/mdp/md.mdp' 2024-09-18T11:55:02,210 adding 'streamd/scripts/mdp/minim.mdp' 2024-09-18T11:55:02,211 adding 'streamd/scripts/mdp/npt.mdp' 2024-09-18T11:55:02,212 adding 'streamd/scripts/mdp/nvt.mdp' 2024-09-18T11:55:02,214 adding 'streamd/scripts/script_sh/continue_md.sh' 2024-09-18T11:55:02,215 adding 'streamd/scripts/script_sh/equlibration.sh' 2024-09-18T11:55:02,216 adding 'streamd/scripts/script_sh/ligand_mol2prep.sh' 2024-09-18T11:55:02,218 adding 'streamd/scripts/script_sh/ligand_mol2prep_by_gaussian.sh' 2024-09-18T11:55:02,219 adding 'streamd/scripts/script_sh/ligand_prep.sh' 2024-09-18T11:55:02,220 adding 'streamd/scripts/script_sh/md.sh' 2024-09-18T11:55:02,221 adding 'streamd/scripts/script_sh/md_analysis.sh' 2024-09-18T11:55:02,222 adding 'streamd/scripts/script_sh/md_ligand_analysis.sh' 2024-09-18T11:55:02,224 adding 'streamd/scripts/script_sh/solv_ions.sh' 2024-09-18T11:55:02,225 adding 'streamd/utils/__init__.py' 2024-09-18T11:55:02,226 adding 'streamd/utils/dask_init.py' 2024-09-18T11:55:02,228 adding 'streamd/utils/utils.py' 2024-09-18T11:55:02,230 adding 'streamd-0.2.6.dist-info/LICENSE.txt' 2024-09-18T11:55:02,233 adding 'streamd-0.2.6.dist-info/METADATA' 2024-09-18T11:55:02,234 adding 'streamd-0.2.6.dist-info/WHEEL' 2024-09-18T11:55:02,235 adding 'streamd-0.2.6.dist-info/entry_points.txt' 2024-09-18T11:55:02,236 adding 'streamd-0.2.6.dist-info/top_level.txt' 2024-09-18T11:55:02,237 adding 'streamd-0.2.6.dist-info/RECORD' 2024-09-18T11:55:02,240 removing build/bdist.linux-armv7l/wheel 2024-09-18T11:55:02,371 Building wheel for streamd (setup.py): finished with status 'done' 2024-09-18T11:55:02,375 Created wheel for streamd: filename=streamd-0.2.6-py3-none-any.whl size=156174 sha256=f7888c07d9836354ded91c5e344bbb7b1d4552d11e37e32321cde4b50262a040 2024-09-18T11:55:02,377 Stored in directory: /tmp/pip-ephem-wheel-cache-2mx3xexj/wheels/27/0c/6a/a3c30fa96f30198b9480592d2f5ef27b6e2ddb3df8610e52a3 2024-09-18T11:55:02,392 Successfully built streamd 2024-09-18T11:55:02,399 Removed build tracker: '/tmp/pip-build-tracker-p3bmeljm'