2025-01-24T08:11:40,619 Created temporary directory: /tmp/pip-build-tracker-3hr39tc8 2025-01-24T08:11:40,621 Initialized build tracking at /tmp/pip-build-tracker-3hr39tc8 2025-01-24T08:11:40,621 Created build tracker: /tmp/pip-build-tracker-3hr39tc8 2025-01-24T08:11:40,622 Entered build tracker: /tmp/pip-build-tracker-3hr39tc8 2025-01-24T08:11:40,622 Created temporary directory: /tmp/pip-wheel-ppin0evb 2025-01-24T08:11:40,626 Created temporary directory: /tmp/pip-ephem-wheel-cache-4elrodtp 2025-01-24T08:11:40,670 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-01-24T08:11:40,673 2 location(s) to search for versions of streamd: 2025-01-24T08:11:40,673 * https://pypi.org/simple/streamd/ 2025-01-24T08:11:40,673 * https://www.piwheels.org/simple/streamd/ 2025-01-24T08:11:40,674 Fetching project page and analyzing links: https://pypi.org/simple/streamd/ 2025-01-24T08:11:40,674 Getting page https://pypi.org/simple/streamd/ 2025-01-24T08:11:40,676 Found index url https://pypi.org/simple/ 2025-01-24T08:11:40,896 Fetched page https://pypi.org/simple/streamd/ as application/vnd.pypi.simple.v1+json 2025-01-24T08:11:40,899 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 2025-01-24T08:11:40,901 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 2025-01-24T08:11:40,901 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) 2025-01-24T08:11:40,902 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 2025-01-24T08:11:40,903 Skipping link: No binaries permitted for streamd: https://files.pythonhosted.org/packages/4f/10/22028ea2fffc91921a979a6e5ac95b1f2b490e16abb5942b8ed978990ef7/streamd-0.2.7-py3-none-any.whl (from https://pypi.org/simple/streamd/) (requires-python:>=3.6) 2025-01-24T08:11:40,904 Found link https://files.pythonhosted.org/packages/0f/8e/371666f0b05ae834174fb94cf0f7bd3871c13f87754cb346c767547c4fd6/streamd-0.2.7.tar.gz (from https://pypi.org/simple/streamd/) (requires-python:>=3.6), version: 0.2.7 2025-01-24T08:11:40,904 Skipping link: No binaries permitted for streamd: https://files.pythonhosted.org/packages/c2/f5/430a5c7a0d58e87a183780df143edaea3c8926826fbe74855b67dc603ac8/streamd-0.2.8-py3-none-any.whl (from https://pypi.org/simple/streamd/) (requires-python:>=3.6) 2025-01-24T08:11:40,906 Found link https://files.pythonhosted.org/packages/19/63/5b4a036a2830d533730fefed020bcd0451328786b9d3de3e28b3b4f9ce5a/streamd-0.2.8.tar.gz (from https://pypi.org/simple/streamd/) (requires-python:>=3.6), version: 0.2.8 2025-01-24T08:11:40,906 Skipping link: No binaries permitted for streamd: https://files.pythonhosted.org/packages/0d/0e/56e8fb1a84d82e7f36c107fd07d780f29b3be32de62ab14af1cd1ebf030b/streamd-0.2.9-py3-none-any.whl (from https://pypi.org/simple/streamd/) (requires-python:>=3.6) 2025-01-24T08:11:40,907 Found link https://files.pythonhosted.org/packages/4b/a2/ba16665fe440ea86118621cdcd0510b4d700139c70b1b2597469cbc652c5/streamd-0.2.9.tar.gz (from https://pypi.org/simple/streamd/) (requires-python:>=3.6), version: 0.2.9 2025-01-24T08:11:40,908 Fetching project page and analyzing links: https://www.piwheels.org/simple/streamd/ 2025-01-24T08:11:40,909 Getting page https://www.piwheels.org/simple/streamd/ 2025-01-24T08:11:40,910 Found index url https://www.piwheels.org/simple/ 2025-01-24T08:11:41,071 Fetched page https://www.piwheels.org/simple/streamd/ as text/html 2025-01-24T08:11:41,073 Skipping link: No binaries permitted for streamd: https://www.piwheels.org/simple/streamd/streamd-0.2.8-py3-none-any.whl#sha256=a342054bdd211653becf34ee37509df59f9e3cc54a5ff152aff02627d172df19 (from https://www.piwheels.org/simple/streamd/) (requires-python:>=3.6) 2025-01-24T08:11:41,074 Skipping link: No binaries permitted for streamd: https://www.piwheels.org/simple/streamd/streamd-0.2.7-py3-none-any.whl#sha256=b7a066f4959ff075f96580ed0af8feed31c39d59ca32f5706f79c6503d02d3f7 (from https://www.piwheels.org/simple/streamd/) (requires-python:>=3.6) 2025-01-24T08:11:41,075 Skipping link: No binaries permitted for streamd: https://www.piwheels.org/simple/streamd/streamd-0.2.6-py3-none-any.whl#sha256=f7888c07d9836354ded91c5e344bbb7b1d4552d11e37e32321cde4b50262a040 (from https://www.piwheels.org/simple/streamd/) (requires-python:>=3.6) 2025-01-24T08:11:41,075 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) 2025-01-24T08:11:41,076 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) 2025-01-24T08:11:41,076 Skipping link: not a file: https://www.piwheels.org/simple/streamd/ 2025-01-24T08:11:41,077 Skipping link: not a file: https://pypi.org/simple/streamd/ 2025-01-24T08:11:41,096 Given no hashes to check 1 links for project 'streamd': discarding no candidates 2025-01-24T08:11:41,098 Collecting streamd==0.2.9 2025-01-24T08:11:41,100 Created temporary directory: /tmp/pip-unpack-anzb8pdf 2025-01-24T08:11:41,319 Downloading streamd-0.2.9.tar.gz (176 kB) 2025-01-24T08:11:41,534 Added streamd==0.2.9 from https://files.pythonhosted.org/packages/4b/a2/ba16665fe440ea86118621cdcd0510b4d700139c70b1b2597469cbc652c5/streamd-0.2.9.tar.gz to build tracker '/tmp/pip-build-tracker-3hr39tc8' 2025-01-24T08:11:41,535 Running setup.py (path:/tmp/pip-wheel-ppin0evb/streamd_621fd759c1084bd6882cd48f62926c9f/setup.py) egg_info for package streamd 2025-01-24T08:11:41,536 Created temporary directory: /tmp/pip-pip-egg-info-qtelk_vy 2025-01-24T08:11:41,537 Preparing metadata (setup.py): started 2025-01-24T08:11:41,538 Running command python setup.py egg_info 2025-01-24T08:11:42,584 running egg_info 2025-01-24T08:11:42,611 creating /tmp/pip-pip-egg-info-qtelk_vy/streamd.egg-info 2025-01-24T08:11:42,613 writing /tmp/pip-pip-egg-info-qtelk_vy/streamd.egg-info/PKG-INFO 2025-01-24T08:11:42,617 writing dependency_links to /tmp/pip-pip-egg-info-qtelk_vy/streamd.egg-info/dependency_links.txt 2025-01-24T08:11:42,619 writing entry points to /tmp/pip-pip-egg-info-qtelk_vy/streamd.egg-info/entry_points.txt 2025-01-24T08:11:42,621 writing requirements to /tmp/pip-pip-egg-info-qtelk_vy/streamd.egg-info/requires.txt 2025-01-24T08:11:42,622 writing top-level names to /tmp/pip-pip-egg-info-qtelk_vy/streamd.egg-info/top_level.txt 2025-01-24T08:11:42,623 writing manifest file '/tmp/pip-pip-egg-info-qtelk_vy/streamd.egg-info/SOURCES.txt' 2025-01-24T08:11:42,716 reading manifest file '/tmp/pip-pip-egg-info-qtelk_vy/streamd.egg-info/SOURCES.txt' 2025-01-24T08:11:42,718 reading manifest template 'MANIFEST.in' 2025-01-24T08:11:42,722 adding license file 'LICENSE.txt' 2025-01-24T08:11:42,726 writing manifest file '/tmp/pip-pip-egg-info-qtelk_vy/streamd.egg-info/SOURCES.txt' 2025-01-24T08:11:42,836 Preparing metadata (setup.py): finished with status 'done' 2025-01-24T08:11:42,841 Source in /tmp/pip-wheel-ppin0evb/streamd_621fd759c1084bd6882cd48f62926c9f has version 0.2.9, which satisfies requirement streamd==0.2.9 from https://files.pythonhosted.org/packages/4b/a2/ba16665fe440ea86118621cdcd0510b4d700139c70b1b2597469cbc652c5/streamd-0.2.9.tar.gz 2025-01-24T08:11:42,842 Removed streamd==0.2.9 from https://files.pythonhosted.org/packages/4b/a2/ba16665fe440ea86118621cdcd0510b4d700139c70b1b2597469cbc652c5/streamd-0.2.9.tar.gz from build tracker '/tmp/pip-build-tracker-3hr39tc8' 2025-01-24T08:11:42,851 Created temporary directory: /tmp/pip-unpack-73qp3bzg 2025-01-24T08:11:42,852 Created temporary directory: /tmp/pip-unpack-7ergst7q 2025-01-24T08:11:42,853 Building wheels for collected packages: streamd 2025-01-24T08:11:42,857 Created temporary directory: /tmp/pip-wheel-3h0n2hcy 2025-01-24T08:11:42,857 Building wheel for streamd (setup.py): started 2025-01-24T08:11:42,859 Destination directory: /tmp/pip-wheel-3h0n2hcy 2025-01-24T08:11:42,859 Running command python setup.py bdist_wheel 2025-01-24T08:11:43,896 running bdist_wheel 2025-01-24T08:11:44,027 running build 2025-01-24T08:11:44,028 running build_py 2025-01-24T08:11:44,057 creating build/lib/streamd 2025-01-24T08:11:44,059 copying streamd/__init__.py -> build/lib/streamd 2025-01-24T08:11:44,061 copying streamd/run_gbsa.py -> build/lib/streamd 2025-01-24T08:11:44,064 copying streamd/run_md.py -> build/lib/streamd 2025-01-24T08:11:44,068 creating build/lib/streamd/scripts 2025-01-24T08:11:44,069 copying streamd/scripts/prepare_Gaussian_input.py -> build/lib/streamd/scripts 2025-01-24T08:11:44,071 copying streamd/scripts/pdb2mol.py -> build/lib/streamd/scripts 2025-01-24T08:11:44,073 copying streamd/scripts/getcharge.py -> build/lib/streamd/scripts 2025-01-24T08:11:44,075 copying streamd/scripts/__init__.py -> build/lib/streamd/scripts 2025-01-24T08:11:44,076 copying streamd/scripts/pmed_amb2gmx.py -> build/lib/streamd/scripts 2025-01-24T08:11:44,078 copying streamd/scripts/mol2_fix_coordsbonds.py -> build/lib/streamd/scripts 2025-01-24T08:11:44,081 creating build/lib/streamd/utils 2025-01-24T08:11:44,082 copying streamd/utils/__init__.py -> build/lib/streamd/utils 2025-01-24T08:11:44,084 copying streamd/utils/dask_init.py -> build/lib/streamd/utils 2025-01-24T08:11:44,086 copying streamd/utils/utils.py -> build/lib/streamd/utils 2025-01-24T08:11:44,089 creating build/lib/streamd/analysis 2025-01-24T08:11:44,090 copying streamd/analysis/md_system_analysis.py -> build/lib/streamd/analysis 2025-01-24T08:11:44,092 copying streamd/analysis/__init__.py -> build/lib/streamd/analysis 2025-01-24T08:11:44,095 copying streamd/analysis/xvg2png.py -> build/lib/streamd/analysis 2025-01-24T08:11:44,097 copying streamd/analysis/run_analysis.py -> build/lib/streamd/analysis 2025-01-24T08:11:44,099 copying streamd/analysis/plot_build.py -> build/lib/streamd/analysis 2025-01-24T08:11:44,102 creating build/lib/streamd/preparation 2025-01-24T08:11:44,103 copying streamd/preparation/__init__.py -> build/lib/streamd/preparation 2025-01-24T08:11:44,105 copying streamd/preparation/md_files_preparation.py -> build/lib/streamd/preparation 2025-01-24T08:11:44,108 copying streamd/preparation/nonstandard_solvent_preparation.py -> build/lib/streamd/preparation 2025-01-24T08:11:44,110 copying streamd/preparation/complex_preparation.py -> build/lib/streamd/preparation 2025-01-24T08:11:44,113 copying streamd/preparation/mcpbpy_preparation.py -> build/lib/streamd/preparation 2025-01-24T08:11:44,115 copying streamd/preparation/ligand_preparation.py -> build/lib/streamd/preparation 2025-01-24T08:11:44,118 creating build/lib/streamd/mcpbpy_md 2025-01-24T08:11:44,120 copying streamd/mcpbpy_md/mcbpy_md.py -> build/lib/streamd/mcpbpy_md 2025-01-24T08:11:44,123 copying streamd/mcpbpy_md/__init__.py -> build/lib/streamd/mcpbpy_md 2025-01-24T08:11:44,125 creating build/lib/streamd/tests 2025-01-24T08:11:44,127 copying streamd/tests/conftest.py -> build/lib/streamd/tests 2025-01-24T08:11:44,129 copying streamd/tests/__init__.py -> build/lib/streamd/tests 2025-01-24T08:11:44,131 copying streamd/tests/analysis_test.py -> build/lib/streamd/tests 2025-01-24T08:11:44,134 copying streamd/tests/gbsa_test.py -> build/lib/streamd/tests 2025-01-24T08:11:44,136 copying streamd/tests/prolif_test.py -> build/lib/streamd/tests 2025-01-24T08:11:44,139 copying streamd/tests/preparation_test.py -> build/lib/streamd/tests 2025-01-24T08:11:44,141 copying streamd/tests/import_test.py -> build/lib/streamd/tests 2025-01-24T08:11:44,143 copying streamd/tests/md_test.py -> build/lib/streamd/tests 2025-01-24T08:11:44,146 creating build/lib/streamd/prolif 2025-01-24T08:11:44,147 copying streamd/prolif/__init__.py -> build/lib/streamd/prolif 2025-01-24T08:11:44,149 copying streamd/prolif/prolif_frame_map.py -> build/lib/streamd/prolif 2025-01-24T08:11:44,151 copying streamd/prolif/prolif2png.py -> build/lib/streamd/prolif 2025-01-24T08:11:44,154 copying streamd/prolif/run_prolif.py -> build/lib/streamd/prolif 2025-01-24T08:11:44,156 running egg_info 2025-01-24T08:11:44,184 writing streamd.egg-info/PKG-INFO 2025-01-24T08:11:44,189 writing dependency_links to streamd.egg-info/dependency_links.txt 2025-01-24T08:11:44,191 writing entry points to streamd.egg-info/entry_points.txt 2025-01-24T08:11:44,193 writing requirements to streamd.egg-info/requires.txt 2025-01-24T08:11:44,194 writing top-level names to streamd.egg-info/top_level.txt 2025-01-24T08:11:44,233 reading manifest file 'streamd.egg-info/SOURCES.txt' 2025-01-24T08:11:44,238 reading manifest template 'MANIFEST.in' 2025-01-24T08:11:44,242 adding license file 'LICENSE.txt' 2025-01-24T08:11:44,247 writing manifest file 'streamd.egg-info/SOURCES.txt' 2025-01-24T08:11:44,250 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'streamd.example' is absent from the `packages` configuration. 2025-01-24T08:11:44,251 !! 2025-01-24T08:11:44,252 ******************************************************************************** 2025-01-24T08:11:44,252 ############################ 2025-01-24T08:11:44,253 # Package would be ignored # 2025-01-24T08:11:44,253 ############################ 2025-01-24T08:11:44,254 Python recognizes 'streamd.example' as an importable package[^1], 2025-01-24T08:11:44,255 but it is absent from setuptools' `packages` configuration. 2025-01-24T08:11:44,256 This leads to an ambiguous overall configuration. If you want to distribute this 2025-01-24T08:11:44,256 package, please make sure that 'streamd.example' is explicitly added 2025-01-24T08:11:44,257 to the `packages` configuration field. 2025-01-24T08:11:44,258 Alternatively, you can also rely on setuptools' discovery methods 2025-01-24T08:11:44,259 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-01-24T08:11:44,260 instead of `find_packages(...)`/`find:`). 2025-01-24T08:11:44,261 You can read more about "package discovery" on setuptools documentation page: 2025-01-24T08:11:44,262 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-01-24T08:11:44,263 If you don't want 'streamd.example' to be distributed and are 2025-01-24T08:11:44,264 already explicitly excluding 'streamd.example' via 2025-01-24T08:11:44,264 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-01-24T08:11:44,265 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-01-24T08:11:44,265 combination with a more fine grained `package-data` configuration. 2025-01-24T08:11:44,267 You can read more about "package data files" on setuptools documentation page: 2025-01-24T08:11:44,268 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-01-24T08:11:44,269 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-01-24T08:11:44,270 even if it does not contain any `.py` files. 2025-01-24T08:11:44,270 On the other hand, currently there is no concept of package data 2025-01-24T08:11:44,271 directory, all directories are treated like packages. 2025-01-24T08:11:44,272 ******************************************************************************** 2025-01-24T08:11:44,273 !! 2025-01-24T08:11:44,274 check.warn(importable) 2025-01-24T08:11:44,274 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'streamd.scripts.com' is absent from the `packages` configuration. 2025-01-24T08:11:44,274 !! 2025-01-24T08:11:44,275 ******************************************************************************** 2025-01-24T08:11:44,276 ############################ 2025-01-24T08:11:44,276 # Package would be ignored # 2025-01-24T08:11:44,276 ############################ 2025-01-24T08:11:44,277 Python recognizes 'streamd.scripts.com' as an importable package[^1], 2025-01-24T08:11:44,277 but it is absent from setuptools' `packages` configuration. 2025-01-24T08:11:44,278 This leads to an ambiguous overall configuration. If you want to distribute this 2025-01-24T08:11:44,278 package, please make sure that 'streamd.scripts.com' is explicitly added 2025-01-24T08:11:44,279 to the `packages` configuration field. 2025-01-24T08:11:44,280 Alternatively, you can also rely on setuptools' discovery methods 2025-01-24T08:11:44,280 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-01-24T08:11:44,281 instead of `find_packages(...)`/`find:`). 2025-01-24T08:11:44,281 You can read more about "package discovery" on setuptools documentation page: 2025-01-24T08:11:44,282 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-01-24T08:11:44,283 If you don't want 'streamd.scripts.com' to be distributed and are 2025-01-24T08:11:44,284 already explicitly excluding 'streamd.scripts.com' via 2025-01-24T08:11:44,284 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-01-24T08:11:44,285 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-01-24T08:11:44,285 combination with a more fine grained `package-data` configuration. 2025-01-24T08:11:44,286 You can read more about "package data files" on setuptools documentation page: 2025-01-24T08:11:44,287 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-01-24T08:11:44,290 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-01-24T08:11:44,291 even if it does not contain any `.py` files. 2025-01-24T08:11:44,292 On the other hand, currently there is no concept of package data 2025-01-24T08:11:44,292 directory, all directories are treated like packages. 2025-01-24T08:11:44,293 ******************************************************************************** 2025-01-24T08:11:44,294 !! 2025-01-24T08:11:44,295 check.warn(importable) 2025-01-24T08:11:44,295 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'streamd.scripts.gbsa' is absent from the `packages` configuration. 2025-01-24T08:11:44,296 !! 2025-01-24T08:11:44,297 ******************************************************************************** 2025-01-24T08:11:44,297 ############################ 2025-01-24T08:11:44,298 # Package would be ignored # 2025-01-24T08:11:44,299 ############################ 2025-01-24T08:11:44,299 Python recognizes 'streamd.scripts.gbsa' as an importable package[^1], 2025-01-24T08:11:44,300 but it is absent from setuptools' `packages` configuration. 2025-01-24T08:11:44,301 This leads to an ambiguous overall configuration. If you want to distribute this 2025-01-24T08:11:44,301 package, please make sure that 'streamd.scripts.gbsa' is explicitly added 2025-01-24T08:11:44,302 to the `packages` configuration field. 2025-01-24T08:11:44,303 Alternatively, you can also rely on setuptools' discovery methods 2025-01-24T08:11:44,303 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-01-24T08:11:44,304 instead of `find_packages(...)`/`find:`). 2025-01-24T08:11:44,304 You can read more about "package discovery" on setuptools documentation page: 2025-01-24T08:11:44,305 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-01-24T08:11:44,306 If you don't want 'streamd.scripts.gbsa' to be distributed and are 2025-01-24T08:11:44,307 already explicitly excluding 'streamd.scripts.gbsa' via 2025-01-24T08:11:44,307 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-01-24T08:11:44,307 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-01-24T08:11:44,308 combination with a more fine grained `package-data` configuration. 2025-01-24T08:11:44,309 You can read more about "package data files" on setuptools documentation page: 2025-01-24T08:11:44,309 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-01-24T08:11:44,311 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-01-24T08:11:44,311 even if it does not contain any `.py` files. 2025-01-24T08:11:44,311 On the other hand, currently there is no concept of package data 2025-01-24T08:11:44,312 directory, all directories are treated like packages. 2025-01-24T08:11:44,312 ******************************************************************************** 2025-01-24T08:11:44,313 !! 2025-01-24T08:11:44,314 check.warn(importable) 2025-01-24T08:11:44,314 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'streamd.scripts.mcpbpy_scripts' is absent from the `packages` configuration. 2025-01-24T08:11:44,315 !! 2025-01-24T08:11:44,316 ******************************************************************************** 2025-01-24T08:11:44,316 ############################ 2025-01-24T08:11:44,316 # Package would be ignored # 2025-01-24T08:11:44,317 ############################ 2025-01-24T08:11:44,318 Python recognizes 'streamd.scripts.mcpbpy_scripts' as an importable package[^1], 2025-01-24T08:11:44,318 but it is absent from setuptools' `packages` configuration. 2025-01-24T08:11:44,319 This leads to an ambiguous overall configuration. If you want to distribute this 2025-01-24T08:11:44,320 package, please make sure that 'streamd.scripts.mcpbpy_scripts' is explicitly added 2025-01-24T08:11:44,320 to the `packages` configuration field. 2025-01-24T08:11:44,321 Alternatively, you can also rely on setuptools' discovery methods 2025-01-24T08:11:44,322 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-01-24T08:11:44,322 instead of `find_packages(...)`/`find:`). 2025-01-24T08:11:44,323 You can read more about "package discovery" on setuptools documentation page: 2025-01-24T08:11:44,324 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-01-24T08:11:44,325 If you don't want 'streamd.scripts.mcpbpy_scripts' to be distributed and are 2025-01-24T08:11:44,326 already explicitly excluding 'streamd.scripts.mcpbpy_scripts' via 2025-01-24T08:11:44,326 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-01-24T08:11:44,327 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-01-24T08:11:44,327 combination with a more fine grained `package-data` configuration. 2025-01-24T08:11:44,329 You can read more about "package data files" on setuptools documentation page: 2025-01-24T08:11:44,330 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-01-24T08:11:44,331 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-01-24T08:11:44,332 even if it does not contain any `.py` files. 2025-01-24T08:11:44,332 On the other hand, currently there is no concept of package data 2025-01-24T08:11:44,332 directory, all directories are treated like packages. 2025-01-24T08:11:44,333 ******************************************************************************** 2025-01-24T08:11:44,334 !! 2025-01-24T08:11:44,334 check.warn(importable) 2025-01-24T08:11:44,334 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'streamd.scripts.mdp' is absent from the `packages` configuration. 2025-01-24T08:11:44,335 !! 2025-01-24T08:11:44,336 ******************************************************************************** 2025-01-24T08:11:44,336 ############################ 2025-01-24T08:11:44,336 # Package would be ignored # 2025-01-24T08:11:44,337 ############################ 2025-01-24T08:11:44,337 Python recognizes 'streamd.scripts.mdp' as an importable package[^1], 2025-01-24T08:11:44,338 but it is absent from setuptools' `packages` configuration. 2025-01-24T08:11:44,339 This leads to an ambiguous overall configuration. If you want to distribute this 2025-01-24T08:11:44,339 package, please make sure that 'streamd.scripts.mdp' is explicitly added 2025-01-24T08:11:44,339 to the `packages` configuration field. 2025-01-24T08:11:44,340 Alternatively, you can also rely on setuptools' discovery methods 2025-01-24T08:11:44,341 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-01-24T08:11:44,341 instead of `find_packages(...)`/`find:`). 2025-01-24T08:11:44,342 You can read more about "package discovery" on setuptools documentation page: 2025-01-24T08:11:44,343 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-01-24T08:11:44,344 If you don't want 'streamd.scripts.mdp' to be distributed and are 2025-01-24T08:11:44,345 already explicitly excluding 'streamd.scripts.mdp' via 2025-01-24T08:11:44,345 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-01-24T08:11:44,345 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-01-24T08:11:44,346 combination with a more fine grained `package-data` configuration. 2025-01-24T08:11:44,347 You can read more about "package data files" on setuptools documentation page: 2025-01-24T08:11:44,348 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-01-24T08:11:44,349 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-01-24T08:11:44,350 even if it does not contain any `.py` files. 2025-01-24T08:11:44,350 On the other hand, currently there is no concept of package data 2025-01-24T08:11:44,351 directory, all directories are treated like packages. 2025-01-24T08:11:44,351 ******************************************************************************** 2025-01-24T08:11:44,352 !! 2025-01-24T08:11:44,353 check.warn(importable) 2025-01-24T08:11:44,353 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'streamd.scripts.script_sh' is absent from the `packages` configuration. 2025-01-24T08:11:44,354 !! 2025-01-24T08:11:44,355 ******************************************************************************** 2025-01-24T08:11:44,355 ############################ 2025-01-24T08:11:44,356 # Package would be ignored # 2025-01-24T08:11:44,356 ############################ 2025-01-24T08:11:44,357 Python recognizes 'streamd.scripts.script_sh' as an importable package[^1], 2025-01-24T08:11:44,357 but it is absent from setuptools' `packages` configuration. 2025-01-24T08:11:44,358 This leads to an ambiguous overall configuration. If you want to distribute this 2025-01-24T08:11:44,359 package, please make sure that 'streamd.scripts.script_sh' is explicitly added 2025-01-24T08:11:44,360 to the `packages` configuration field. 2025-01-24T08:11:44,360 Alternatively, you can also rely on setuptools' discovery methods 2025-01-24T08:11:44,361 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-01-24T08:11:44,361 instead of `find_packages(...)`/`find:`). 2025-01-24T08:11:44,362 You can read more about "package discovery" on setuptools documentation page: 2025-01-24T08:11:44,363 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-01-24T08:11:44,364 If you don't want 'streamd.scripts.script_sh' to be distributed and are 2025-01-24T08:11:44,364 already explicitly excluding 'streamd.scripts.script_sh' via 2025-01-24T08:11:44,365 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-01-24T08:11:44,365 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-01-24T08:11:44,366 combination with a more fine grained `package-data` configuration. 2025-01-24T08:11:44,366 You can read more about "package data files" on setuptools documentation page: 2025-01-24T08:11:44,367 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-01-24T08:11:44,369 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-01-24T08:11:44,369 even if it does not contain any `.py` files. 2025-01-24T08:11:44,370 On the other hand, currently there is no concept of package data 2025-01-24T08:11:44,370 directory, all directories are treated like packages. 2025-01-24T08:11:44,371 ******************************************************************************** 2025-01-24T08:11:44,372 !! 2025-01-24T08:11:44,373 check.warn(importable) 2025-01-24T08:11:44,373 creating build/lib/streamd/example 2025-01-24T08:11:44,374 copying streamd/example/instructions.txt -> build/lib/streamd/example 2025-01-24T08:11:44,375 copying streamd/example/ligand.mol -> build/lib/streamd/example 2025-01-24T08:11:44,375 copying streamd/example/protein_HIS.pdb -> build/lib/streamd/example 2025-01-24T08:11:44,376 copying streamd/scripts/tleap.in -> build/lib/streamd/scripts 2025-01-24T08:11:44,376 creating build/lib/streamd/scripts/com 2025-01-24T08:11:44,377 copying streamd/scripts/com/1.com -> build/lib/streamd/scripts/com 2025-01-24T08:11:44,378 copying streamd/scripts/com/2.com -> build/lib/streamd/scripts/com 2025-01-24T08:11:44,378 copying streamd/scripts/com/3.com -> build/lib/streamd/scripts/com 2025-01-24T08:11:44,379 creating build/lib/streamd/scripts/gbsa 2025-01-24T08:11:44,379 copying streamd/scripts/gbsa/mmpbsa.in -> build/lib/streamd/scripts/gbsa 2025-01-24T08:11:44,380 creating build/lib/streamd/scripts/mcpbpy_scripts 2025-01-24T08:11:44,381 copying streamd/scripts/mcpbpy_scripts/protein.in -> build/lib/streamd/scripts/mcpbpy_scripts 2025-01-24T08:11:44,381 creating build/lib/streamd/scripts/mdp 2025-01-24T08:11:44,382 copying streamd/scripts/mdp/ions.mdp -> build/lib/streamd/scripts/mdp 2025-01-24T08:11:44,382 copying streamd/scripts/mdp/md.mdp -> build/lib/streamd/scripts/mdp 2025-01-24T08:11:44,383 copying streamd/scripts/mdp/minim.mdp -> build/lib/streamd/scripts/mdp 2025-01-24T08:11:44,383 copying streamd/scripts/mdp/npt.mdp -> build/lib/streamd/scripts/mdp 2025-01-24T08:11:44,384 copying streamd/scripts/mdp/nvt.mdp -> build/lib/streamd/scripts/mdp 2025-01-24T08:11:44,385 creating build/lib/streamd/scripts/script_sh 2025-01-24T08:11:44,385 copying streamd/scripts/script_sh/continue_md.sh -> build/lib/streamd/scripts/script_sh 2025-01-24T08:11:44,386 copying streamd/scripts/script_sh/equlibration.sh -> build/lib/streamd/scripts/script_sh 2025-01-24T08:11:44,386 copying streamd/scripts/script_sh/ligand_mol2prep.sh -> build/lib/streamd/scripts/script_sh 2025-01-24T08:11:44,387 copying streamd/scripts/script_sh/ligand_mol2prep_by_gaussian.sh -> build/lib/streamd/scripts/script_sh 2025-01-24T08:11:44,388 copying streamd/scripts/script_sh/ligand_prep.sh -> build/lib/streamd/scripts/script_sh 2025-01-24T08:11:44,388 copying streamd/scripts/script_sh/md.sh -> build/lib/streamd/scripts/script_sh 2025-01-24T08:11:44,389 copying streamd/scripts/script_sh/md_analysis.sh -> build/lib/streamd/scripts/script_sh 2025-01-24T08:11:44,389 copying streamd/scripts/script_sh/md_ligand_analysis.sh -> build/lib/streamd/scripts/script_sh 2025-01-24T08:11:44,390 copying streamd/scripts/script_sh/solv_ions.sh -> build/lib/streamd/scripts/script_sh 2025-01-24T08:11:44,401 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-01-24T08:11:44,402 !! 2025-01-24T08:11:44,403 ******************************************************************************** 2025-01-24T08:11:44,403 Please avoid running ``setup.py`` directly. 2025-01-24T08:11:44,404 Instead, use pypa/build, pypa/installer or other 2025-01-24T08:11:44,404 standards-based tools. 2025-01-24T08:11:44,405 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-01-24T08:11:44,406 ******************************************************************************** 2025-01-24T08:11:44,407 !! 2025-01-24T08:11:44,407 self.initialize_options() 2025-01-24T08:11:44,430 installing to build/bdist.linux-armv7l/wheel 2025-01-24T08:11:44,431 running install 2025-01-24T08:11:44,456 running install_lib 2025-01-24T08:11:44,483 creating build/bdist.linux-armv7l/wheel 2025-01-24T08:11:44,486 creating build/bdist.linux-armv7l/wheel/streamd 2025-01-24T08:11:44,487 copying build/lib/streamd/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd 2025-01-24T08:11:44,489 copying build/lib/streamd/run_gbsa.py -> build/bdist.linux-armv7l/wheel/./streamd 2025-01-24T08:11:44,492 creating build/bdist.linux-armv7l/wheel/streamd/scripts 2025-01-24T08:11:44,494 creating build/bdist.linux-armv7l/wheel/streamd/scripts/gbsa 2025-01-24T08:11:44,495 copying build/lib/streamd/scripts/gbsa/mmpbsa.in -> build/bdist.linux-armv7l/wheel/./streamd/scripts/gbsa 2025-01-24T08:11:44,498 creating build/bdist.linux-armv7l/wheel/streamd/scripts/mcpbpy_scripts 2025-01-24T08:11:44,499 copying build/lib/streamd/scripts/mcpbpy_scripts/protein.in -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mcpbpy_scripts 2025-01-24T08:11:44,501 copying build/lib/streamd/scripts/prepare_Gaussian_input.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts 2025-01-24T08:11:44,502 copying build/lib/streamd/scripts/pdb2mol.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts 2025-01-24T08:11:44,504 copying build/lib/streamd/scripts/getcharge.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts 2025-01-24T08:11:44,506 copying build/lib/streamd/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts 2025-01-24T08:11:44,508 copying build/lib/streamd/scripts/tleap.in -> build/bdist.linux-armv7l/wheel/./streamd/scripts 2025-01-24T08:11:44,509 copying build/lib/streamd/scripts/pmed_amb2gmx.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts 2025-01-24T08:11:44,512 creating build/bdist.linux-armv7l/wheel/streamd/scripts/mdp 2025-01-24T08:11:44,513 copying build/lib/streamd/scripts/mdp/minim.mdp -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mdp 2025-01-24T08:11:44,515 copying build/lib/streamd/scripts/mdp/md.mdp -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mdp 2025-01-24T08:11:44,517 copying build/lib/streamd/scripts/mdp/npt.mdp -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mdp 2025-01-24T08:11:44,519 copying build/lib/streamd/scripts/mdp/ions.mdp -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mdp 2025-01-24T08:11:44,520 copying build/lib/streamd/scripts/mdp/nvt.mdp -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mdp 2025-01-24T08:11:44,522 copying build/lib/streamd/scripts/mol2_fix_coordsbonds.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts 2025-01-24T08:11:44,525 creating build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2025-01-24T08:11:44,526 copying build/lib/streamd/scripts/script_sh/ligand_mol2prep_by_gaussian.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2025-01-24T08:11:44,528 copying build/lib/streamd/scripts/script_sh/ligand_mol2prep.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2025-01-24T08:11:44,530 copying build/lib/streamd/scripts/script_sh/ligand_prep.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2025-01-24T08:11:44,532 copying build/lib/streamd/scripts/script_sh/continue_md.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2025-01-24T08:11:44,533 copying build/lib/streamd/scripts/script_sh/md_analysis.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2025-01-24T08:11:44,535 copying build/lib/streamd/scripts/script_sh/md_ligand_analysis.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2025-01-24T08:11:44,537 copying build/lib/streamd/scripts/script_sh/equlibration.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2025-01-24T08:11:44,539 copying build/lib/streamd/scripts/script_sh/solv_ions.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2025-01-24T08:11:44,540 copying build/lib/streamd/scripts/script_sh/md.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh 2025-01-24T08:11:44,543 creating build/bdist.linux-armv7l/wheel/streamd/scripts/com 2025-01-24T08:11:44,544 copying build/lib/streamd/scripts/com/3.com -> build/bdist.linux-armv7l/wheel/./streamd/scripts/com 2025-01-24T08:11:44,546 copying build/lib/streamd/scripts/com/2.com -> build/bdist.linux-armv7l/wheel/./streamd/scripts/com 2025-01-24T08:11:44,548 copying build/lib/streamd/scripts/com/1.com -> build/bdist.linux-armv7l/wheel/./streamd/scripts/com 2025-01-24T08:11:44,550 creating build/bdist.linux-armv7l/wheel/streamd/utils 2025-01-24T08:11:44,551 copying build/lib/streamd/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/utils 2025-01-24T08:11:44,553 copying build/lib/streamd/utils/dask_init.py -> build/bdist.linux-armv7l/wheel/./streamd/utils 2025-01-24T08:11:44,555 copying build/lib/streamd/utils/utils.py -> build/bdist.linux-armv7l/wheel/./streamd/utils 2025-01-24T08:11:44,558 creating build/bdist.linux-armv7l/wheel/streamd/analysis 2025-01-24T08:11:44,559 copying build/lib/streamd/analysis/md_system_analysis.py -> build/bdist.linux-armv7l/wheel/./streamd/analysis 2025-01-24T08:11:44,561 copying build/lib/streamd/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/analysis 2025-01-24T08:11:44,563 copying build/lib/streamd/analysis/xvg2png.py -> build/bdist.linux-armv7l/wheel/./streamd/analysis 2025-01-24T08:11:44,565 copying build/lib/streamd/analysis/run_analysis.py -> build/bdist.linux-armv7l/wheel/./streamd/analysis 2025-01-24T08:11:44,567 copying build/lib/streamd/analysis/plot_build.py -> build/bdist.linux-armv7l/wheel/./streamd/analysis 2025-01-24T08:11:44,569 creating build/bdist.linux-armv7l/wheel/streamd/preparation 2025-01-24T08:11:44,570 copying build/lib/streamd/preparation/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation 2025-01-24T08:11:44,572 copying build/lib/streamd/preparation/md_files_preparation.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation 2025-01-24T08:11:44,574 copying build/lib/streamd/preparation/nonstandard_solvent_preparation.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation 2025-01-24T08:11:44,575 copying build/lib/streamd/preparation/complex_preparation.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation 2025-01-24T08:11:44,578 copying build/lib/streamd/preparation/mcpbpy_preparation.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation 2025-01-24T08:11:44,580 copying build/lib/streamd/preparation/ligand_preparation.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation 2025-01-24T08:11:44,583 copying build/lib/streamd/run_md.py -> build/bdist.linux-armv7l/wheel/./streamd 2025-01-24T08:11:44,587 creating build/bdist.linux-armv7l/wheel/streamd/mcpbpy_md 2025-01-24T08:11:44,588 copying build/lib/streamd/mcpbpy_md/mcbpy_md.py -> build/bdist.linux-armv7l/wheel/./streamd/mcpbpy_md 2025-01-24T08:11:44,590 copying build/lib/streamd/mcpbpy_md/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/mcpbpy_md 2025-01-24T08:11:44,592 creating build/bdist.linux-armv7l/wheel/streamd/example 2025-01-24T08:11:44,593 copying build/lib/streamd/example/protein_HIS.pdb -> build/bdist.linux-armv7l/wheel/./streamd/example 2025-01-24T08:11:44,601 copying build/lib/streamd/example/ligand.mol -> build/bdist.linux-armv7l/wheel/./streamd/example 2025-01-24T08:11:44,603 copying build/lib/streamd/example/instructions.txt -> build/bdist.linux-armv7l/wheel/./streamd/example 2025-01-24T08:11:44,605 creating build/bdist.linux-armv7l/wheel/streamd/tests 2025-01-24T08:11:44,606 copying build/lib/streamd/tests/conftest.py -> build/bdist.linux-armv7l/wheel/./streamd/tests 2025-01-24T08:11:44,609 copying build/lib/streamd/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/tests 2025-01-24T08:11:44,610 copying build/lib/streamd/tests/analysis_test.py -> build/bdist.linux-armv7l/wheel/./streamd/tests 2025-01-24T08:11:44,612 copying build/lib/streamd/tests/gbsa_test.py -> build/bdist.linux-armv7l/wheel/./streamd/tests 2025-01-24T08:11:44,615 copying build/lib/streamd/tests/prolif_test.py -> build/bdist.linux-armv7l/wheel/./streamd/tests 2025-01-24T08:11:44,617 copying build/lib/streamd/tests/preparation_test.py -> build/bdist.linux-armv7l/wheel/./streamd/tests 2025-01-24T08:11:44,619 copying build/lib/streamd/tests/import_test.py -> build/bdist.linux-armv7l/wheel/./streamd/tests 2025-01-24T08:11:44,620 copying build/lib/streamd/tests/md_test.py -> build/bdist.linux-armv7l/wheel/./streamd/tests 2025-01-24T08:11:44,623 creating build/bdist.linux-armv7l/wheel/streamd/prolif 2025-01-24T08:11:44,624 copying build/lib/streamd/prolif/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/prolif 2025-01-24T08:11:44,626 copying build/lib/streamd/prolif/prolif_frame_map.py -> build/bdist.linux-armv7l/wheel/./streamd/prolif 2025-01-24T08:11:44,628 copying build/lib/streamd/prolif/prolif2png.py -> build/bdist.linux-armv7l/wheel/./streamd/prolif 2025-01-24T08:11:44,630 copying build/lib/streamd/prolif/run_prolif.py -> build/bdist.linux-armv7l/wheel/./streamd/prolif 2025-01-24T08:11:44,633 running install_egg_info 2025-01-24T08:11:44,666 Copying streamd.egg-info to build/bdist.linux-armv7l/wheel/./streamd-0.2.9-py3.11.egg-info 2025-01-24T08:11:44,677 running install_scripts 2025-01-24T08:11:44,697 creating build/bdist.linux-armv7l/wheel/streamd-0.2.9.dist-info/WHEEL 2025-01-24T08:11:44,699 creating '/tmp/pip-wheel-3h0n2hcy/streamd-0.2.9-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-01-24T08:11:44,701 adding 'streamd/__init__.py' 2025-01-24T08:11:44,704 adding 'streamd/run_gbsa.py' 2025-01-24T08:11:44,709 adding 'streamd/run_md.py' 2025-01-24T08:11:44,711 adding 'streamd/analysis/__init__.py' 2025-01-24T08:11:44,713 adding 'streamd/analysis/md_system_analysis.py' 2025-01-24T08:11:44,714 adding 'streamd/analysis/plot_build.py' 2025-01-24T08:11:44,716 adding 'streamd/analysis/run_analysis.py' 2025-01-24T08:11:44,718 adding 'streamd/analysis/xvg2png.py' 2025-01-24T08:11:44,720 adding 'streamd/example/instructions.txt' 2025-01-24T08:11:44,721 adding 'streamd/example/ligand.mol' 2025-01-24T08:11:44,782 adding 'streamd/example/protein_HIS.pdb' 2025-01-24T08:11:44,786 adding 'streamd/mcpbpy_md/__init__.py' 2025-01-24T08:11:44,788 adding 'streamd/mcpbpy_md/mcbpy_md.py' 2025-01-24T08:11:44,790 adding 'streamd/preparation/__init__.py' 2025-01-24T08:11:44,791 adding 'streamd/preparation/complex_preparation.py' 2025-01-24T08:11:44,793 adding 'streamd/preparation/ligand_preparation.py' 2025-01-24T08:11:44,795 adding 'streamd/preparation/mcpbpy_preparation.py' 2025-01-24T08:11:44,797 adding 'streamd/preparation/md_files_preparation.py' 2025-01-24T08:11:44,798 adding 'streamd/preparation/nonstandard_solvent_preparation.py' 2025-01-24T08:11:44,800 adding 'streamd/prolif/__init__.py' 2025-01-24T08:11:44,802 adding 'streamd/prolif/prolif2png.py' 2025-01-24T08:11:44,803 adding 'streamd/prolif/prolif_frame_map.py' 2025-01-24T08:11:44,805 adding 'streamd/prolif/run_prolif.py' 2025-01-24T08:11:44,807 adding 'streamd/scripts/__init__.py' 2025-01-24T08:11:44,808 adding 'streamd/scripts/getcharge.py' 2025-01-24T08:11:44,810 adding 'streamd/scripts/mol2_fix_coordsbonds.py' 2025-01-24T08:11:44,811 adding 'streamd/scripts/pdb2mol.py' 2025-01-24T08:11:44,812 adding 'streamd/scripts/pmed_amb2gmx.py' 2025-01-24T08:11:44,814 adding 'streamd/scripts/prepare_Gaussian_input.py' 2025-01-24T08:11:44,815 adding 'streamd/scripts/tleap.in' 2025-01-24T08:11:44,816 adding 'streamd/scripts/com/1.com' 2025-01-24T08:11:44,818 adding 'streamd/scripts/com/2.com' 2025-01-24T08:11:44,819 adding 'streamd/scripts/com/3.com' 2025-01-24T08:11:44,820 adding 'streamd/scripts/gbsa/mmpbsa.in' 2025-01-24T08:11:44,822 adding 'streamd/scripts/mcpbpy_scripts/protein.in' 2025-01-24T08:11:44,824 adding 'streamd/scripts/mdp/ions.mdp' 2025-01-24T08:11:44,825 adding 'streamd/scripts/mdp/md.mdp' 2025-01-24T08:11:44,826 adding 'streamd/scripts/mdp/minim.mdp' 2025-01-24T08:11:44,827 adding 'streamd/scripts/mdp/npt.mdp' 2025-01-24T08:11:44,829 adding 'streamd/scripts/mdp/nvt.mdp' 2025-01-24T08:11:44,831 adding 'streamd/scripts/script_sh/continue_md.sh' 2025-01-24T08:11:44,832 adding 'streamd/scripts/script_sh/equlibration.sh' 2025-01-24T08:11:44,833 adding 'streamd/scripts/script_sh/ligand_mol2prep.sh' 2025-01-24T08:11:44,835 adding 'streamd/scripts/script_sh/ligand_mol2prep_by_gaussian.sh' 2025-01-24T08:11:44,836 adding 'streamd/scripts/script_sh/ligand_prep.sh' 2025-01-24T08:11:44,837 adding 'streamd/scripts/script_sh/md.sh' 2025-01-24T08:11:44,838 adding 'streamd/scripts/script_sh/md_analysis.sh' 2025-01-24T08:11:44,839 adding 'streamd/scripts/script_sh/md_ligand_analysis.sh' 2025-01-24T08:11:44,841 adding 'streamd/scripts/script_sh/solv_ions.sh' 2025-01-24T08:11:44,842 adding 'streamd/tests/__init__.py' 2025-01-24T08:11:44,844 adding 'streamd/tests/analysis_test.py' 2025-01-24T08:11:44,845 adding 'streamd/tests/conftest.py' 2025-01-24T08:11:44,847 adding 'streamd/tests/gbsa_test.py' 2025-01-24T08:11:44,848 adding 'streamd/tests/import_test.py' 2025-01-24T08:11:44,849 adding 'streamd/tests/md_test.py' 2025-01-24T08:11:44,850 adding 'streamd/tests/preparation_test.py' 2025-01-24T08:11:44,852 adding 'streamd/tests/prolif_test.py' 2025-01-24T08:11:44,853 adding 'streamd/utils/__init__.py' 2025-01-24T08:11:44,855 adding 'streamd/utils/dask_init.py' 2025-01-24T08:11:44,856 adding 'streamd/utils/utils.py' 2025-01-24T08:11:44,858 adding 'streamd-0.2.9.dist-info/LICENSE.txt' 2025-01-24T08:11:44,863 adding 'streamd-0.2.9.dist-info/METADATA' 2025-01-24T08:11:44,865 adding 'streamd-0.2.9.dist-info/WHEEL' 2025-01-24T08:11:44,866 adding 'streamd-0.2.9.dist-info/entry_points.txt' 2025-01-24T08:11:44,866 adding 'streamd-0.2.9.dist-info/top_level.txt' 2025-01-24T08:11:44,868 adding 'streamd-0.2.9.dist-info/RECORD' 2025-01-24T08:11:44,872 removing build/bdist.linux-armv7l/wheel 2025-01-24T08:11:45,001 Building wheel for streamd (setup.py): finished with status 'done' 2025-01-24T08:11:45,005 Created wheel for streamd: filename=streamd-0.2.9-py3-none-any.whl size=176930 sha256=2f5cf07ac089ea46fefb860397b396a55254233e996ad7572c92226ed1d2dfc4 2025-01-24T08:11:45,007 Stored in directory: /tmp/pip-ephem-wheel-cache-4elrodtp/wheels/f7/38/ae/cc52fa7da44d98de49e9bfff883da1f0334a9ed0ce2a9c55bb 2025-01-24T08:11:45,024 Successfully built streamd 2025-01-24T08:11:45,034 Removed build tracker: '/tmp/pip-build-tracker-3hr39tc8'