2024-06-12T12:36:41,026 Created temporary directory: /tmp/pip-build-tracker-i4mnh8v9 2024-06-12T12:36:41,027 Initialized build tracking at /tmp/pip-build-tracker-i4mnh8v9 2024-06-12T12:36:41,027 Created build tracker: /tmp/pip-build-tracker-i4mnh8v9 2024-06-12T12:36:41,028 Entered build tracker: /tmp/pip-build-tracker-i4mnh8v9 2024-06-12T12:36:41,029 Created temporary directory: /tmp/pip-wheel-sbv1co8k 2024-06-12T12:36:41,032 Created temporary directory: /tmp/pip-ephem-wheel-cache-7vjz0qyc 2024-06-12T12:36:41,054 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-06-12T12:36:41,057 2 location(s) to search for versions of streamd: 2024-06-12T12:36:41,057 * https://pypi.org/simple/streamd/ 2024-06-12T12:36:41,057 * https://www.piwheels.org/simple/streamd/ 2024-06-12T12:36:41,058 Fetching project page and analyzing links: https://pypi.org/simple/streamd/ 2024-06-12T12:36:41,059 Getting page https://pypi.org/simple/streamd/ 2024-06-12T12:36:41,060 Found index url https://pypi.org/simple/ 2024-06-12T12:36:41,266 Fetched page https://pypi.org/simple/streamd/ as application/vnd.pypi.simple.v1+json 2024-06-12T12:36:41,268 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 2024-06-12T12:36:41,269 Fetching project page and analyzing links: https://www.piwheels.org/simple/streamd/ 2024-06-12T12:36:41,270 Getting page https://www.piwheels.org/simple/streamd/ 2024-06-12T12:36:41,271 Found index url https://www.piwheels.org/simple/ 2024-06-12T12:36:41,448 Fetched page https://www.piwheels.org/simple/streamd/ as text/html 2024-06-12T12:36:41,450 Skipping link: not a file: https://www.piwheels.org/simple/streamd/ 2024-06-12T12:36:41,452 Skipping link: not a file: https://pypi.org/simple/streamd/ 2024-06-12T12:36:41,473 Given no hashes to check 1 links for project 'streamd': discarding no candidates 2024-06-12T12:36:41,492 Collecting streamd==0.2.4 2024-06-12T12:36:41,495 Created temporary directory: /tmp/pip-unpack-won0m9xb 2024-06-12T12:36:41,700 Downloading streamd-0.2.4.tar.gz (140 kB) 2024-06-12T12:36:41,911 Added streamd==0.2.4 from https://files.pythonhosted.org/packages/8d/96/dd06d3cfc2b8f66a791d39120d88fc8a735168ebc8ff7e5638850a02bdb7/streamd-0.2.4.tar.gz to build tracker '/tmp/pip-build-tracker-i4mnh8v9' 2024-06-12T12:36:41,913 Running setup.py (path:/tmp/pip-wheel-sbv1co8k/streamd_e705f87998f0456780b9b60fdbe722bc/setup.py) egg_info for package streamd 2024-06-12T12:36:41,914 Created temporary directory: /tmp/pip-pip-egg-info-n6a9uy66 2024-06-12T12:36:41,914 Preparing metadata (setup.py): started 2024-06-12T12:36:41,916 Running command python setup.py egg_info 2024-06-12T12:36:42,873 running egg_info 2024-06-12T12:36:42,874 creating /tmp/pip-pip-egg-info-n6a9uy66/streamd.egg-info 2024-06-12T12:36:42,901 writing /tmp/pip-pip-egg-info-n6a9uy66/streamd.egg-info/PKG-INFO 2024-06-12T12:36:42,906 writing dependency_links to /tmp/pip-pip-egg-info-n6a9uy66/streamd.egg-info/dependency_links.txt 2024-06-12T12:36:42,908 writing entry points to /tmp/pip-pip-egg-info-n6a9uy66/streamd.egg-info/entry_points.txt 2024-06-12T12:36:42,910 writing requirements to /tmp/pip-pip-egg-info-n6a9uy66/streamd.egg-info/requires.txt 2024-06-12T12:36:42,911 writing top-level names to /tmp/pip-pip-egg-info-n6a9uy66/streamd.egg-info/top_level.txt 2024-06-12T12:36:42,913 writing manifest file '/tmp/pip-pip-egg-info-n6a9uy66/streamd.egg-info/SOURCES.txt' 2024-06-12T12:36:43,004 reading manifest file '/tmp/pip-pip-egg-info-n6a9uy66/streamd.egg-info/SOURCES.txt' 2024-06-12T12:36:43,008 reading manifest template 'MANIFEST.in' 2024-06-12T12:36:43,016 adding license file 'LICENSE.txt' 2024-06-12T12:36:43,019 writing manifest file '/tmp/pip-pip-egg-info-n6a9uy66/streamd.egg-info/SOURCES.txt' 2024-06-12T12:36:43,127 Preparing metadata (setup.py): finished with status 'done' 2024-06-12T12:36:43,131 Source in /tmp/pip-wheel-sbv1co8k/streamd_e705f87998f0456780b9b60fdbe722bc has version 0.2.4, which satisfies requirement streamd==0.2.4 from https://files.pythonhosted.org/packages/8d/96/dd06d3cfc2b8f66a791d39120d88fc8a735168ebc8ff7e5638850a02bdb7/streamd-0.2.4.tar.gz 2024-06-12T12:36:43,132 Removed streamd==0.2.4 from https://files.pythonhosted.org/packages/8d/96/dd06d3cfc2b8f66a791d39120d88fc8a735168ebc8ff7e5638850a02bdb7/streamd-0.2.4.tar.gz from build tracker '/tmp/pip-build-tracker-i4mnh8v9' 2024-06-12T12:36:43,139 Created temporary directory: /tmp/pip-unpack-rlqhmrin 2024-06-12T12:36:43,140 Created temporary directory: /tmp/pip-unpack-8bck3n0v 2024-06-12T12:36:43,149 Building wheels for collected packages: streamd 2024-06-12T12:36:43,155 Created temporary directory: /tmp/pip-wheel-96ojefvk 2024-06-12T12:36:43,155 Building wheel for streamd (setup.py): started 2024-06-12T12:36:43,157 Destination directory: /tmp/pip-wheel-96ojefvk 2024-06-12T12:36:43,157 Running command python setup.py bdist_wheel 2024-06-12T12:36:44,048 running bdist_wheel 2024-06-12T12:36:44,184 running build 2024-06-12T12:36:44,185 running build_py 2024-06-12T12:36:44,213 creating build 2024-06-12T12:36:44,214 creating build/lib 2024-06-12T12:36:44,214 creating build/lib/streamd 2024-06-12T12:36:44,215 copying streamd/run_md.py -> build/lib/streamd 2024-06-12T12:36:44,218 copying streamd/__init__.py -> build/lib/streamd 2024-06-12T12:36:44,220 copying streamd/md_analysis.py -> build/lib/streamd 2024-06-12T12:36:44,222 copying streamd/run_gbsa.py -> build/lib/streamd 2024-06-12T12:36:44,224 creating build/lib/streamd/utils 2024-06-12T12:36:44,225 copying streamd/utils/utils.py -> build/lib/streamd/utils 2024-06-12T12:36:44,227 copying streamd/utils/__init__.py -> build/lib/streamd/utils 2024-06-12T12:36:44,228 copying streamd/utils/dask_init.py -> build/lib/streamd/utils 2024-06-12T12:36:44,231 creating build/lib/streamd/scripts 2024-06-12T12:36:44,232 copying streamd/scripts/mol2_fix_coordsbonds.py -> build/lib/streamd/scripts 2024-06-12T12:36:44,234 copying streamd/scripts/getcharge.py -> build/lib/streamd/scripts 2024-06-12T12:36:44,236 copying streamd/scripts/__init__.py -> build/lib/streamd/scripts 2024-06-12T12:36:44,237 copying streamd/scripts/prepare_Gaussian_input.py -> build/lib/streamd/scripts 2024-06-12T12:36:44,239 copying streamd/scripts/pmed_amb2gmx.py -> build/lib/streamd/scripts 2024-06-12T12:36:44,240 copying streamd/scripts/pdb2mol.py -> build/lib/streamd/scripts 2024-06-12T12:36:44,242 copying streamd/scripts/xvg2png.py -> build/lib/streamd/scripts 2024-06-12T12:36:44,244 creating build/lib/streamd/preparation 2024-06-12T12:36:44,245 copying streamd/preparation/complex_preparation.py -> build/lib/streamd/preparation 2024-06-12T12:36:44,247 copying streamd/preparation/mcpbpy_preparation.py -> build/lib/streamd/preparation 2024-06-12T12:36:44,249 copying streamd/preparation/ligand_preparation.py -> build/lib/streamd/preparation 2024-06-12T12:36:44,252 copying streamd/preparation/md_files_preparation.py -> build/lib/streamd/preparation 2024-06-12T12:36:44,254 copying streamd/preparation/__init__.py -> build/lib/streamd/preparation 2024-06-12T12:36:44,256 creating build/lib/streamd/prolif 2024-06-12T12:36:44,257 copying streamd/prolif/prolif_frame_map.py -> build/lib/streamd/prolif 2024-06-12T12:36:44,259 copying streamd/prolif/__init__.py -> build/lib/streamd/prolif 2024-06-12T12:36:44,261 copying streamd/prolif/prolif2png.py -> build/lib/streamd/prolif 2024-06-12T12:36:44,263 copying streamd/prolif/run_prolif.py -> build/lib/streamd/prolif 2024-06-12T12:36:44,265 creating build/lib/streamd/mcpbpy_md 2024-06-12T12:36:44,266 copying streamd/mcpbpy_md/mcbpy_md.py -> build/lib/streamd/mcpbpy_md 2024-06-12T12:36:44,269 copying streamd/mcpbpy_md/__init__.py -> build/lib/streamd/mcpbpy_md 2024-06-12T12:36:44,270 running egg_info 2024-06-12T12:36:44,299 writing streamd.egg-info/PKG-INFO 2024-06-12T12:36:44,304 writing dependency_links to streamd.egg-info/dependency_links.txt 2024-06-12T12:36:44,305 writing entry points to streamd.egg-info/entry_points.txt 2024-06-12T12:36:44,307 writing requirements to streamd.egg-info/requires.txt 2024-06-12T12:36:44,309 writing top-level names to streamd.egg-info/top_level.txt 2024-06-12T12:36:44,340 reading manifest file 'streamd.egg-info/SOURCES.txt' 2024-06-12T12:36:44,343 reading manifest template 'MANIFEST.in' 2024-06-12T12:36:44,346 adding license file 'LICENSE.txt' 2024-06-12T12:36:44,350 writing manifest file 'streamd.egg-info/SOURCES.txt' 2024-06-12T12:36:44,352 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'streamd.example' is absent from the `packages` configuration. 2024-06-12T12:36:44,353 !! 2024-06-12T12:36:44,354 ******************************************************************************** 2024-06-12T12:36:44,354 ############################ 2024-06-12T12:36:44,355 # Package would be ignored # 2024-06-12T12:36:44,355 ############################ 2024-06-12T12:36:44,355 Python recognizes 'streamd.example' as an importable package[^1], 2024-06-12T12:36:44,356 but it is absent from setuptools' `packages` configuration. 2024-06-12T12:36:44,357 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-12T12:36:44,357 package, please make sure that 'streamd.example' is explicitly added 2024-06-12T12:36:44,358 to the `packages` configuration field. 2024-06-12T12:36:44,359 Alternatively, you can also rely on setuptools' discovery methods 2024-06-12T12:36:44,359 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-12T12:36:44,360 instead of `find_packages(...)`/`find:`). 2024-06-12T12:36:44,361 You can read more about "package discovery" on setuptools documentation page: 2024-06-12T12:36:44,362 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-12T12:36:44,363 If you don't want 'streamd.example' to be distributed and are 2024-06-12T12:36:44,364 already explicitly excluding 'streamd.example' via 2024-06-12T12:36:44,364 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-12T12:36:44,365 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-12T12:36:44,365 combination with a more fine grained `package-data` configuration. 2024-06-12T12:36:44,366 You can read more about "package data files" on setuptools documentation page: 2024-06-12T12:36:44,367 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-12T12:36:44,370 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-12T12:36:44,373 even if it does not contain any `.py` files. 2024-06-12T12:36:44,374 On the other hand, currently there is no concept of package data 2024-06-12T12:36:44,375 directory, all directories are treated like packages. 2024-06-12T12:36:44,375 ******************************************************************************** 2024-06-12T12:36:44,376 !! 2024-06-12T12:36:44,377 check.warn(importable) 2024-06-12T12:36:44,377 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'streamd.scripts.com' is absent from the `packages` configuration. 2024-06-12T12:36:44,378 !! 2024-06-12T12:36:44,379 ******************************************************************************** 2024-06-12T12:36:44,380 ############################ 2024-06-12T12:36:44,380 # Package would be ignored # 2024-06-12T12:36:44,381 ############################ 2024-06-12T12:36:44,382 Python recognizes 'streamd.scripts.com' as an importable package[^1], 2024-06-12T12:36:44,382 but it is absent from setuptools' `packages` configuration. 2024-06-12T12:36:44,383 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-12T12:36:44,384 package, please make sure that 'streamd.scripts.com' is explicitly added 2024-06-12T12:36:44,385 to the `packages` configuration field. 2024-06-12T12:36:44,386 Alternatively, you can also rely on setuptools' discovery methods 2024-06-12T12:36:44,386 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-12T12:36:44,387 instead of `find_packages(...)`/`find:`). 2024-06-12T12:36:44,387 You can read more about "package discovery" on setuptools documentation page: 2024-06-12T12:36:44,389 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-12T12:36:44,390 If you don't want 'streamd.scripts.com' to be distributed and are 2024-06-12T12:36:44,390 already explicitly excluding 'streamd.scripts.com' via 2024-06-12T12:36:44,390 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-12T12:36:44,391 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-12T12:36:44,391 combination with a more fine grained `package-data` configuration. 2024-06-12T12:36:44,392 You can read more about "package data files" on setuptools documentation page: 2024-06-12T12:36:44,393 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-12T12:36:44,395 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-12T12:36:44,396 even if it does not contain any `.py` files. 2024-06-12T12:36:44,396 On the other hand, currently there is no concept of package data 2024-06-12T12:36:44,397 directory, all directories are treated like packages. 2024-06-12T12:36:44,398 ******************************************************************************** 2024-06-12T12:36:44,399 !! 2024-06-12T12:36:44,400 check.warn(importable) 2024-06-12T12:36:44,401 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'streamd.scripts.gbsa' is absent from the `packages` configuration. 2024-06-12T12:36:44,401 !! 2024-06-12T12:36:44,403 ******************************************************************************** 2024-06-12T12:36:44,403 ############################ 2024-06-12T12:36:44,404 # Package would be ignored # 2024-06-12T12:36:44,404 ############################ 2024-06-12T12:36:44,405 Python recognizes 'streamd.scripts.gbsa' as an importable package[^1], 2024-06-12T12:36:44,406 but it is absent from setuptools' `packages` configuration. 2024-06-12T12:36:44,407 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-12T12:36:44,408 package, please make sure that 'streamd.scripts.gbsa' is explicitly added 2024-06-12T12:36:44,409 to the `packages` configuration field. 2024-06-12T12:36:44,410 Alternatively, you can also rely on setuptools' discovery methods 2024-06-12T12:36:44,410 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-12T12:36:44,411 instead of `find_packages(...)`/`find:`). 2024-06-12T12:36:44,413 You can read more about "package discovery" on setuptools documentation page: 2024-06-12T12:36:44,414 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-12T12:36:44,415 If you don't want 'streamd.scripts.gbsa' to be distributed and are 2024-06-12T12:36:44,416 already explicitly excluding 'streamd.scripts.gbsa' via 2024-06-12T12:36:44,416 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-12T12:36:44,417 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-12T12:36:44,418 combination with a more fine grained `package-data` configuration. 2024-06-12T12:36:44,419 You can read more about "package data files" on setuptools documentation page: 2024-06-12T12:36:44,420 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-12T12:36:44,422 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-12T12:36:44,423 even if it does not contain any `.py` files. 2024-06-12T12:36:44,423 On the other hand, currently there is no concept of package data 2024-06-12T12:36:44,424 directory, all directories are treated like packages. 2024-06-12T12:36:44,425 ******************************************************************************** 2024-06-12T12:36:44,426 !! 2024-06-12T12:36:44,426 check.warn(importable) 2024-06-12T12:36:44,427 /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. 2024-06-12T12:36:44,428 !! 2024-06-12T12:36:44,429 ******************************************************************************** 2024-06-12T12:36:44,429 ############################ 2024-06-12T12:36:44,430 # Package would be ignored # 2024-06-12T12:36:44,430 ############################ 2024-06-12T12:36:44,431 Python recognizes 'streamd.scripts.mcpbpy_scripts' as an importable package[^1], 2024-06-12T12:36:44,432 but it is absent from setuptools' `packages` configuration. 2024-06-12T12:36:44,433 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-12T12:36:44,434 package, please make sure that 'streamd.scripts.mcpbpy_scripts' is explicitly added 2024-06-12T12:36:44,434 to the `packages` configuration field. 2024-06-12T12:36:44,436 Alternatively, you can also rely on setuptools' discovery methods 2024-06-12T12:36:44,436 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-12T12:36:44,437 instead of `find_packages(...)`/`find:`). 2024-06-12T12:36:44,439 You can read more about "package discovery" on setuptools documentation page: 2024-06-12T12:36:44,440 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-12T12:36:44,442 If you don't want 'streamd.scripts.mcpbpy_scripts' to be distributed and are 2024-06-12T12:36:44,442 already explicitly excluding 'streamd.scripts.mcpbpy_scripts' via 2024-06-12T12:36:44,443 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-12T12:36:44,444 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-12T12:36:44,446 combination with a more fine grained `package-data` configuration. 2024-06-12T12:36:44,447 You can read more about "package data files" on setuptools documentation page: 2024-06-12T12:36:44,449 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-12T12:36:44,451 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-12T12:36:44,451 even if it does not contain any `.py` files. 2024-06-12T12:36:44,452 On the other hand, currently there is no concept of package data 2024-06-12T12:36:44,453 directory, all directories are treated like packages. 2024-06-12T12:36:44,453 ******************************************************************************** 2024-06-12T12:36:44,454 !! 2024-06-12T12:36:44,455 check.warn(importable) 2024-06-12T12:36:44,455 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'streamd.scripts.mdp' is absent from the `packages` configuration. 2024-06-12T12:36:44,456 !! 2024-06-12T12:36:44,457 ******************************************************************************** 2024-06-12T12:36:44,458 ############################ 2024-06-12T12:36:44,458 # Package would be ignored # 2024-06-12T12:36:44,459 ############################ 2024-06-12T12:36:44,460 Python recognizes 'streamd.scripts.mdp' as an importable package[^1], 2024-06-12T12:36:44,460 but it is absent from setuptools' `packages` configuration. 2024-06-12T12:36:44,461 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-12T12:36:44,461 package, please make sure that 'streamd.scripts.mdp' is explicitly added 2024-06-12T12:36:44,462 to the `packages` configuration field. 2024-06-12T12:36:44,463 Alternatively, you can also rely on setuptools' discovery methods 2024-06-12T12:36:44,463 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-12T12:36:44,464 instead of `find_packages(...)`/`find:`). 2024-06-12T12:36:44,464 You can read more about "package discovery" on setuptools documentation page: 2024-06-12T12:36:44,465 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-12T12:36:44,466 If you don't want 'streamd.scripts.mdp' to be distributed and are 2024-06-12T12:36:44,467 already explicitly excluding 'streamd.scripts.mdp' via 2024-06-12T12:36:44,467 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-12T12:36:44,468 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-12T12:36:44,468 combination with a more fine grained `package-data` configuration. 2024-06-12T12:36:44,469 You can read more about "package data files" on setuptools documentation page: 2024-06-12T12:36:44,471 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-12T12:36:44,472 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-12T12:36:44,473 even if it does not contain any `.py` files. 2024-06-12T12:36:44,473 On the other hand, currently there is no concept of package data 2024-06-12T12:36:44,474 directory, all directories are treated like packages. 2024-06-12T12:36:44,475 ******************************************************************************** 2024-06-12T12:36:44,476 !! 2024-06-12T12:36:44,477 check.warn(importable) 2024-06-12T12:36:44,477 /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. 2024-06-12T12:36:44,478 !! 2024-06-12T12:36:44,479 ******************************************************************************** 2024-06-12T12:36:44,480 ############################ 2024-06-12T12:36:44,480 # Package would be ignored # 2024-06-12T12:36:44,481 ############################ 2024-06-12T12:36:44,481 Python recognizes 'streamd.scripts.script_sh' as an importable package[^1], 2024-06-12T12:36:44,482 but it is absent from setuptools' `packages` configuration. 2024-06-12T12:36:44,483 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-12T12:36:44,484 package, please make sure that 'streamd.scripts.script_sh' is explicitly added 2024-06-12T12:36:44,484 to the `packages` configuration field. 2024-06-12T12:36:44,486 Alternatively, you can also rely on setuptools' discovery methods 2024-06-12T12:36:44,486 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-12T12:36:44,487 instead of `find_packages(...)`/`find:`). 2024-06-12T12:36:44,488 You can read more about "package discovery" on setuptools documentation page: 2024-06-12T12:36:44,489 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-12T12:36:44,490 If you don't want 'streamd.scripts.script_sh' to be distributed and are 2024-06-12T12:36:44,491 already explicitly excluding 'streamd.scripts.script_sh' via 2024-06-12T12:36:44,492 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-12T12:36:44,492 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-12T12:36:44,493 combination with a more fine grained `package-data` configuration. 2024-06-12T12:36:44,494 You can read more about "package data files" on setuptools documentation page: 2024-06-12T12:36:44,495 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-12T12:36:44,496 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-12T12:36:44,497 even if it does not contain any `.py` files. 2024-06-12T12:36:44,497 On the other hand, currently there is no concept of package data 2024-06-12T12:36:44,498 directory, all directories are treated like packages. 2024-06-12T12:36:44,498 ******************************************************************************** 2024-06-12T12:36:44,499 !! 2024-06-12T12:36:44,499 check.warn(importable) 2024-06-12T12:36:44,500 creating build/lib/streamd/example 2024-06-12T12:36:44,501 copying streamd/example/instructions.txt -> build/lib/streamd/example 2024-06-12T12:36:44,501 copying streamd/example/ligand.mol -> build/lib/streamd/example 2024-06-12T12:36:44,501 copying streamd/example/protein_HIS.pdb -> build/lib/streamd/example 2024-06-12T12:36:44,502 copying streamd/scripts/tleap.in -> build/lib/streamd/scripts 2024-06-12T12:36:44,502 creating build/lib/streamd/scripts/com 2024-06-12T12:36:44,503 copying streamd/scripts/com/1.com -> build/lib/streamd/scripts/com 2024-06-12T12:36:44,503 copying streamd/scripts/com/2.com -> build/lib/streamd/scripts/com 2024-06-12T12:36:44,504 copying streamd/scripts/com/3.com -> build/lib/streamd/scripts/com 2024-06-12T12:36:44,504 creating build/lib/streamd/scripts/gbsa 2024-06-12T12:36:44,505 copying streamd/scripts/gbsa/mmpbsa.in -> build/lib/streamd/scripts/gbsa 2024-06-12T12:36:44,505 creating build/lib/streamd/scripts/mcpbpy_scripts 2024-06-12T12:36:44,506 copying streamd/scripts/mcpbpy_scripts/protein.in -> build/lib/streamd/scripts/mcpbpy_scripts 2024-06-12T12:36:44,506 creating build/lib/streamd/scripts/mdp 2024-06-12T12:36:44,507 copying streamd/scripts/mdp/ions.mdp -> build/lib/streamd/scripts/mdp 2024-06-12T12:36:44,508 copying streamd/scripts/mdp/md.mdp -> build/lib/streamd/scripts/mdp 2024-06-12T12:36:44,508 copying streamd/scripts/mdp/minim.mdp -> build/lib/streamd/scripts/mdp 2024-06-12T12:36:44,509 copying streamd/scripts/mdp/npt.mdp -> build/lib/streamd/scripts/mdp 2024-06-12T12:36:44,509 copying streamd/scripts/mdp/nvt.mdp -> build/lib/streamd/scripts/mdp 2024-06-12T12:36:44,510 creating build/lib/streamd/scripts/script_sh 2024-06-12T12:36:44,511 copying streamd/scripts/script_sh/continue_md.sh -> build/lib/streamd/scripts/script_sh 2024-06-12T12:36:44,511 copying streamd/scripts/script_sh/equlibration.sh -> build/lib/streamd/scripts/script_sh 2024-06-12T12:36:44,512 copying streamd/scripts/script_sh/ligand_mol2prep.sh -> build/lib/streamd/scripts/script_sh 2024-06-12T12:36:44,512 copying streamd/scripts/script_sh/ligand_mol2prep_by_gaussian.sh -> build/lib/streamd/scripts/script_sh 2024-06-12T12:36:44,513 copying streamd/scripts/script_sh/ligand_prep.sh -> build/lib/streamd/scripts/script_sh 2024-06-12T12:36:44,513 copying streamd/scripts/script_sh/md.sh -> build/lib/streamd/scripts/script_sh 2024-06-12T12:36:44,514 copying streamd/scripts/script_sh/md_analysis.sh -> build/lib/streamd/scripts/script_sh 2024-06-12T12:36:44,515 copying streamd/scripts/script_sh/md_ligand_analysis.sh -> build/lib/streamd/scripts/script_sh 2024-06-12T12:36:44,515 copying streamd/scripts/script_sh/solv_ions.sh -> build/lib/streamd/scripts/script_sh 2024-06-12T12:36:44,516 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-06-12T12:36:44,516 !! 2024-06-12T12:36:44,518 ******************************************************************************** 2024-06-12T12:36:44,518 Please avoid running ``setup.py`` directly. 2024-06-12T12:36:44,518 Instead, use pypa/build, pypa/installer or other 2024-06-12T12:36:44,519 standards-based tools. 2024-06-12T12:36:44,520 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-06-12T12:36:44,520 ******************************************************************************** 2024-06-12T12:36:44,521 !! 2024-06-12T12:36:44,521 self.initialize_options() 2024-06-12T12:36:44,522 installing to build/bdist.linux-armv7l/wheel 2024-06-12T12:36:44,522 running install 2024-06-12T12:36:44,532 running install_lib 2024-06-12T12:36:44,558 creating build/bdist.linux-armv7l 2024-06-12T12:36:44,559 creating build/bdist.linux-armv7l/wheel 2024-06-12T12:36:44,560 creating build/bdist.linux-armv7l/wheel/streamd 2024-06-12T12:36:44,561 creating build/bdist.linux-armv7l/wheel/streamd/utils 2024-06-12T12:36:44,562 copying build/lib/streamd/utils/utils.py -> build/bdist.linux-armv7l/wheel/streamd/utils 2024-06-12T12:36:44,564 copying build/lib/streamd/utils/__init__.py -> build/bdist.linux-armv7l/wheel/streamd/utils 2024-06-12T12:36:44,566 copying build/lib/streamd/utils/dask_init.py -> build/bdist.linux-armv7l/wheel/streamd/utils 2024-06-12T12:36:44,568 creating build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-12T12:36:44,569 creating build/bdist.linux-armv7l/wheel/streamd/scripts/mdp 2024-06-12T12:36:44,570 copying build/lib/streamd/scripts/mdp/minim.mdp -> build/bdist.linux-armv7l/wheel/streamd/scripts/mdp 2024-06-12T12:36:44,572 copying build/lib/streamd/scripts/mdp/nvt.mdp -> build/bdist.linux-armv7l/wheel/streamd/scripts/mdp 2024-06-12T12:36:44,574 copying build/lib/streamd/scripts/mdp/npt.mdp -> build/bdist.linux-armv7l/wheel/streamd/scripts/mdp 2024-06-12T12:36:44,576 copying build/lib/streamd/scripts/mdp/md.mdp -> build/bdist.linux-armv7l/wheel/streamd/scripts/mdp 2024-06-12T12:36:44,578 copying build/lib/streamd/scripts/mdp/ions.mdp -> build/bdist.linux-armv7l/wheel/streamd/scripts/mdp 2024-06-12T12:36:44,580 creating build/bdist.linux-armv7l/wheel/streamd/scripts/gbsa 2024-06-12T12:36:44,581 copying build/lib/streamd/scripts/gbsa/mmpbsa.in -> build/bdist.linux-armv7l/wheel/streamd/scripts/gbsa 2024-06-12T12:36:44,583 creating build/bdist.linux-armv7l/wheel/streamd/scripts/com 2024-06-12T12:36:44,584 copying build/lib/streamd/scripts/com/3.com -> build/bdist.linux-armv7l/wheel/streamd/scripts/com 2024-06-12T12:36:44,586 copying build/lib/streamd/scripts/com/1.com -> build/bdist.linux-armv7l/wheel/streamd/scripts/com 2024-06-12T12:36:44,588 copying build/lib/streamd/scripts/com/2.com -> build/bdist.linux-armv7l/wheel/streamd/scripts/com 2024-06-12T12:36:44,590 copying build/lib/streamd/scripts/mol2_fix_coordsbonds.py -> build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-12T12:36:44,592 creating build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-12T12:36:44,593 copying build/lib/streamd/scripts/script_sh/md_ligand_analysis.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-12T12:36:44,595 copying build/lib/streamd/scripts/script_sh/ligand_prep.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-12T12:36:44,597 copying build/lib/streamd/scripts/script_sh/equlibration.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-12T12:36:44,599 copying build/lib/streamd/scripts/script_sh/md.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-12T12:36:44,601 copying build/lib/streamd/scripts/script_sh/solv_ions.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-12T12:36:44,603 copying build/lib/streamd/scripts/script_sh/ligand_mol2prep.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-12T12:36:44,605 copying build/lib/streamd/scripts/script_sh/continue_md.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-12T12:36:44,606 copying build/lib/streamd/scripts/script_sh/ligand_mol2prep_by_gaussian.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-12T12:36:44,609 copying build/lib/streamd/scripts/script_sh/md_analysis.sh -> build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh 2024-06-12T12:36:44,610 copying build/lib/streamd/scripts/getcharge.py -> build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-12T12:36:44,612 copying build/lib/streamd/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-12T12:36:44,614 copying build/lib/streamd/scripts/prepare_Gaussian_input.py -> build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-12T12:36:44,616 creating build/bdist.linux-armv7l/wheel/streamd/scripts/mcpbpy_scripts 2024-06-12T12:36:44,617 copying build/lib/streamd/scripts/mcpbpy_scripts/protein.in -> build/bdist.linux-armv7l/wheel/streamd/scripts/mcpbpy_scripts 2024-06-12T12:36:44,618 copying build/lib/streamd/scripts/pmed_amb2gmx.py -> build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-12T12:36:44,620 copying build/lib/streamd/scripts/pdb2mol.py -> build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-12T12:36:44,622 copying build/lib/streamd/scripts/tleap.in -> build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-12T12:36:44,624 copying build/lib/streamd/scripts/xvg2png.py -> build/bdist.linux-armv7l/wheel/streamd/scripts 2024-06-12T12:36:44,626 creating build/bdist.linux-armv7l/wheel/streamd/example 2024-06-12T12:36:44,627 copying build/lib/streamd/example/instructions.txt -> build/bdist.linux-armv7l/wheel/streamd/example 2024-06-12T12:36:44,628 copying build/lib/streamd/example/ligand.mol -> build/bdist.linux-armv7l/wheel/streamd/example 2024-06-12T12:36:44,630 copying build/lib/streamd/example/protein_HIS.pdb -> build/bdist.linux-armv7l/wheel/streamd/example 2024-06-12T12:36:44,638 copying build/lib/streamd/run_md.py -> build/bdist.linux-armv7l/wheel/streamd 2024-06-12T12:36:44,641 creating build/bdist.linux-armv7l/wheel/streamd/preparation 2024-06-12T12:36:44,642 copying build/lib/streamd/preparation/complex_preparation.py -> build/bdist.linux-armv7l/wheel/streamd/preparation 2024-06-12T12:36:44,644 copying build/lib/streamd/preparation/mcpbpy_preparation.py -> build/bdist.linux-armv7l/wheel/streamd/preparation 2024-06-12T12:36:44,646 copying build/lib/streamd/preparation/ligand_preparation.py -> build/bdist.linux-armv7l/wheel/streamd/preparation 2024-06-12T12:36:44,649 copying build/lib/streamd/preparation/md_files_preparation.py -> build/bdist.linux-armv7l/wheel/streamd/preparation 2024-06-12T12:36:44,651 copying build/lib/streamd/preparation/__init__.py -> build/bdist.linux-armv7l/wheel/streamd/preparation 2024-06-12T12:36:44,653 creating build/bdist.linux-armv7l/wheel/streamd/prolif 2024-06-12T12:36:44,654 copying build/lib/streamd/prolif/prolif_frame_map.py -> build/bdist.linux-armv7l/wheel/streamd/prolif 2024-06-12T12:36:44,656 copying build/lib/streamd/prolif/__init__.py -> build/bdist.linux-armv7l/wheel/streamd/prolif 2024-06-12T12:36:44,658 copying build/lib/streamd/prolif/prolif2png.py -> build/bdist.linux-armv7l/wheel/streamd/prolif 2024-06-12T12:36:44,660 copying build/lib/streamd/prolif/run_prolif.py -> build/bdist.linux-armv7l/wheel/streamd/prolif 2024-06-12T12:36:44,662 copying build/lib/streamd/__init__.py -> build/bdist.linux-armv7l/wheel/streamd 2024-06-12T12:36:44,665 creating build/bdist.linux-armv7l/wheel/streamd/mcpbpy_md 2024-06-12T12:36:44,666 copying build/lib/streamd/mcpbpy_md/mcbpy_md.py -> build/bdist.linux-armv7l/wheel/streamd/mcpbpy_md 2024-06-12T12:36:44,668 copying build/lib/streamd/mcpbpy_md/__init__.py -> build/bdist.linux-armv7l/wheel/streamd/mcpbpy_md 2024-06-12T12:36:44,670 copying build/lib/streamd/md_analysis.py -> build/bdist.linux-armv7l/wheel/streamd 2024-06-12T12:36:44,672 copying build/lib/streamd/run_gbsa.py -> build/bdist.linux-armv7l/wheel/streamd 2024-06-12T12:36:44,674 running install_egg_info 2024-06-12T12:36:44,709 Copying streamd.egg-info to build/bdist.linux-armv7l/wheel/streamd-0.2.4-py3.11.egg-info 2024-06-12T12:36:44,721 running install_scripts 2024-06-12T12:36:44,738 creating build/bdist.linux-armv7l/wheel/streamd-0.2.4.dist-info/WHEEL 2024-06-12T12:36:44,740 creating '/tmp/pip-wheel-96ojefvk/streamd-0.2.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-06-12T12:36:44,742 adding 'streamd/__init__.py' 2024-06-12T12:36:44,744 adding 'streamd/md_analysis.py' 2024-06-12T12:36:44,746 adding 'streamd/run_gbsa.py' 2024-06-12T12:36:44,750 adding 'streamd/run_md.py' 2024-06-12T12:36:44,752 adding 'streamd/example/instructions.txt' 2024-06-12T12:36:44,753 adding 'streamd/example/ligand.mol' 2024-06-12T12:36:44,815 adding 'streamd/example/protein_HIS.pdb' 2024-06-12T12:36:44,819 adding 'streamd/mcpbpy_md/__init__.py' 2024-06-12T12:36:44,821 adding 'streamd/mcpbpy_md/mcbpy_md.py' 2024-06-12T12:36:44,822 adding 'streamd/preparation/__init__.py' 2024-06-12T12:36:44,824 adding 'streamd/preparation/complex_preparation.py' 2024-06-12T12:36:44,826 adding 'streamd/preparation/ligand_preparation.py' 2024-06-12T12:36:44,828 adding 'streamd/preparation/mcpbpy_preparation.py' 2024-06-12T12:36:44,830 adding 'streamd/preparation/md_files_preparation.py' 2024-06-12T12:36:44,831 adding 'streamd/prolif/__init__.py' 2024-06-12T12:36:44,833 adding 'streamd/prolif/prolif2png.py' 2024-06-12T12:36:44,834 adding 'streamd/prolif/prolif_frame_map.py' 2024-06-12T12:36:44,836 adding 'streamd/prolif/run_prolif.py' 2024-06-12T12:36:44,838 adding 'streamd/scripts/__init__.py' 2024-06-12T12:36:44,839 adding 'streamd/scripts/getcharge.py' 2024-06-12T12:36:44,841 adding 'streamd/scripts/mol2_fix_coordsbonds.py' 2024-06-12T12:36:44,842 adding 'streamd/scripts/pdb2mol.py' 2024-06-12T12:36:44,843 adding 'streamd/scripts/pmed_amb2gmx.py' 2024-06-12T12:36:44,845 adding 'streamd/scripts/prepare_Gaussian_input.py' 2024-06-12T12:36:44,846 adding 'streamd/scripts/tleap.in' 2024-06-12T12:36:44,847 adding 'streamd/scripts/xvg2png.py' 2024-06-12T12:36:44,849 adding 'streamd/scripts/com/1.com' 2024-06-12T12:36:44,850 adding 'streamd/scripts/com/2.com' 2024-06-12T12:36:44,851 adding 'streamd/scripts/com/3.com' 2024-06-12T12:36:44,853 adding 'streamd/scripts/gbsa/mmpbsa.in' 2024-06-12T12:36:44,854 adding 'streamd/scripts/mcpbpy_scripts/protein.in' 2024-06-12T12:36:44,856 adding 'streamd/scripts/mdp/ions.mdp' 2024-06-12T12:36:44,857 adding 'streamd/scripts/mdp/md.mdp' 2024-06-12T12:36:44,859 adding 'streamd/scripts/mdp/minim.mdp' 2024-06-12T12:36:44,860 adding 'streamd/scripts/mdp/npt.mdp' 2024-06-12T12:36:44,861 adding 'streamd/scripts/mdp/nvt.mdp' 2024-06-12T12:36:44,863 adding 'streamd/scripts/script_sh/continue_md.sh' 2024-06-12T12:36:44,864 adding 'streamd/scripts/script_sh/equlibration.sh' 2024-06-12T12:36:44,865 adding 'streamd/scripts/script_sh/ligand_mol2prep.sh' 2024-06-12T12:36:44,867 adding 'streamd/scripts/script_sh/ligand_mol2prep_by_gaussian.sh' 2024-06-12T12:36:44,868 adding 'streamd/scripts/script_sh/ligand_prep.sh' 2024-06-12T12:36:44,869 adding 'streamd/scripts/script_sh/md.sh' 2024-06-12T12:36:44,870 adding 'streamd/scripts/script_sh/md_analysis.sh' 2024-06-12T12:36:44,872 adding 'streamd/scripts/script_sh/md_ligand_analysis.sh' 2024-06-12T12:36:44,873 adding 'streamd/scripts/script_sh/solv_ions.sh' 2024-06-12T12:36:44,875 adding 'streamd/utils/__init__.py' 2024-06-12T12:36:44,876 adding 'streamd/utils/dask_init.py' 2024-06-12T12:36:44,877 adding 'streamd/utils/utils.py' 2024-06-12T12:36:44,879 adding 'streamd-0.2.4.dist-info/LICENSE.txt' 2024-06-12T12:36:44,882 adding 'streamd-0.2.4.dist-info/METADATA' 2024-06-12T12:36:44,883 adding 'streamd-0.2.4.dist-info/WHEEL' 2024-06-12T12:36:44,884 adding 'streamd-0.2.4.dist-info/entry_points.txt' 2024-06-12T12:36:44,885 adding 'streamd-0.2.4.dist-info/top_level.txt' 2024-06-12T12:36:44,886 adding 'streamd-0.2.4.dist-info/RECORD' 2024-06-12T12:36:44,891 removing build/bdist.linux-armv7l/wheel 2024-06-12T12:36:45,016 Building wheel for streamd (setup.py): finished with status 'done' 2024-06-12T12:36:45,020 Created wheel for streamd: filename=streamd-0.2.4-py3-none-any.whl size=151757 sha256=411cca8c59b01f0e7b8e18520e025a61e135cc2a6db0f374d2d5b80b171dbb2e 2024-06-12T12:36:45,021 Stored in directory: /tmp/pip-ephem-wheel-cache-7vjz0qyc/wheels/67/0d/72/744eef3d5d295b49bcfef8f29270c35015005cf4e0bf5510b4 2024-06-12T12:36:45,035 Successfully built streamd 2024-06-12T12:36:45,044 Removed build tracker: '/tmp/pip-build-tracker-i4mnh8v9'