2025-09-02T15:59:22,774 Created temporary directory: /tmp/pip-build-tracker-7by9rejx
2025-09-02T15:59:22,775 Initialized build tracking at /tmp/pip-build-tracker-7by9rejx
2025-09-02T15:59:22,775 Created build tracker: /tmp/pip-build-tracker-7by9rejx
2025-09-02T15:59:22,776 Entered build tracker: /tmp/pip-build-tracker-7by9rejx
2025-09-02T15:59:22,777 Created temporary directory: /tmp/pip-wheel-iw49cyar
2025-09-02T15:59:22,781 Created temporary directory: /tmp/pip-ephem-wheel-cache-77t8z2xn
2025-09-02T15:59:22,832 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-09-02T15:59:22,834 2 location(s) to search for versions of streamd:
2025-09-02T15:59:22,834 * https://pypi.org/simple/streamd/
2025-09-02T15:59:22,834 * https://www.piwheels.org/simple/streamd/
2025-09-02T15:59:22,835 Fetching project page and analyzing links: https://pypi.org/simple/streamd/
2025-09-02T15:59:22,836 Getting page https://pypi.org/simple/streamd/
2025-09-02T15:59:22,837 Found index url https://pypi.org/simple/
2025-09-02T15:59:23,066 Fetched page https://pypi.org/simple/streamd/ as application/vnd.pypi.simple.v1+json
2025-09-02T15:59:23,072   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
2025-09-02T15:59:23,074   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
2025-09-02T15:59:23,075   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)
2025-09-02T15:59:23,076   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
2025-09-02T15:59:23,077   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)
2025-09-02T15:59:23,078   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
2025-09-02T15:59:23,079   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)
2025-09-02T15:59:23,080   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
2025-09-02T15:59:23,082   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)
2025-09-02T15:59:23,083   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
2025-09-02T15:59:23,084   Skipping link: No binaries permitted for streamd: https://files.pythonhosted.org/packages/53/88/c0feb4fb4b51196ef79a72380bb22ec9b2e2f0674f034e2520aba9d563eb/streamd-0.3-py3-none-any.whl (from https://pypi.org/simple/streamd/) (requires-python:>=3.6)
2025-09-02T15:59:23,085   Found link https://files.pythonhosted.org/packages/bf/ba/70cf2cfbe64e43048424f29dd196db07250247d0aae797fb5a083054e3fe/streamd-0.3.tar.gz (from https://pypi.org/simple/streamd/) (requires-python:>=3.6), version: 0.3
2025-09-02T15:59:23,085   Skipping link: No binaries permitted for streamd: https://files.pythonhosted.org/packages/d9/8c/3204260f6b7c1a12eda43b914f90ea2a79e896c072dc6e9230ea1beae77a/streamd-0.4-py3-none-any.whl (from https://pypi.org/simple/streamd/) (requires-python:>=3.6)
2025-09-02T15:59:23,086   Found link https://files.pythonhosted.org/packages/bd/90/bae892ae6c75b409a16281d5d0c5f3cb6d68711e349160cf6a277e6ac164/streamd-0.4.tar.gz (from https://pypi.org/simple/streamd/) (requires-python:>=3.6), version: 0.4
2025-09-02T15:59:23,087 Fetching project page and analyzing links: https://www.piwheels.org/simple/streamd/
2025-09-02T15:59:23,088 Getting page https://www.piwheels.org/simple/streamd/
2025-09-02T15:59:23,089 Found index url https://www.piwheels.org/simple/
2025-09-02T15:59:23,270 Fetched page https://www.piwheels.org/simple/streamd/ as text/html
2025-09-02T15:59:23,273   Skipping link: No binaries permitted for streamd: https://archive1.piwheels.org/simple/streamd/streamd-0.3-py3-none-any.whl#sha256=2bf8c22e8b7ef687a394e66f26ce21ad2982fa8c67b633298d4e929f198753f2 (from https://www.piwheels.org/simple/streamd/) (requires-python:>=3.6)
2025-09-02T15:59:23,274   Skipping link: No binaries permitted for streamd: https://archive1.piwheels.org/simple/streamd/streamd-0.2.9-py3-none-any.whl#sha256=2f5cf07ac089ea46fefb860397b396a55254233e996ad7572c92226ed1d2dfc4 (from https://www.piwheels.org/simple/streamd/) (requires-python:>=3.6)
2025-09-02T15:59:23,274   Skipping link: No binaries permitted for streamd: https://archive1.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)
2025-09-02T15:59:23,275   Skipping link: No binaries permitted for streamd: https://archive1.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)
2025-09-02T15:59:23,275   Skipping link: No binaries permitted for streamd: https://archive1.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)
2025-09-02T15:59:23,276   Skipping link: No binaries permitted for streamd: https://archive1.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)
2025-09-02T15:59:23,277   Skipping link: No binaries permitted for streamd: https://archive1.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)
2025-09-02T15:59:23,277 Skipping link: not a file: https://www.piwheels.org/simple/streamd/
2025-09-02T15:59:23,278 Skipping link: not a file: https://pypi.org/simple/streamd/
2025-09-02T15:59:23,303 Given no hashes to check 1 links for project 'streamd': discarding no candidates
2025-09-02T15:59:23,306 Collecting streamd==0.4
2025-09-02T15:59:23,308   Created temporary directory: /tmp/pip-unpack-n8555miy
2025-09-02T15:59:23,532   Downloading streamd-0.4.tar.gz (201 kB)
2025-09-02T15:59:23,804   Added streamd==0.4 from https://files.pythonhosted.org/packages/bd/90/bae892ae6c75b409a16281d5d0c5f3cb6d68711e349160cf6a277e6ac164/streamd-0.4.tar.gz to build tracker '/tmp/pip-build-tracker-7by9rejx'
2025-09-02T15:59:23,806   Running setup.py (path:/tmp/pip-wheel-iw49cyar/streamd_3edb0fbbceaf43a1983fcb1073aa2581/setup.py) egg_info for package streamd
2025-09-02T15:59:23,807   Created temporary directory: /tmp/pip-pip-egg-info-hd2jjzyf
2025-09-02T15:59:23,808   Preparing metadata (setup.py): started
2025-09-02T15:59:23,810   Running command python setup.py egg_info
2025-09-02T15:59:24,934   running egg_info
2025-09-02T15:59:24,963   creating /tmp/pip-pip-egg-info-hd2jjzyf/streamd.egg-info
2025-09-02T15:59:24,964   writing /tmp/pip-pip-egg-info-hd2jjzyf/streamd.egg-info/PKG-INFO
2025-09-02T15:59:24,969   writing dependency_links to /tmp/pip-pip-egg-info-hd2jjzyf/streamd.egg-info/dependency_links.txt
2025-09-02T15:59:24,970   writing entry points to /tmp/pip-pip-egg-info-hd2jjzyf/streamd.egg-info/entry_points.txt
2025-09-02T15:59:24,972   writing requirements to /tmp/pip-pip-egg-info-hd2jjzyf/streamd.egg-info/requires.txt
2025-09-02T15:59:24,973   writing top-level names to /tmp/pip-pip-egg-info-hd2jjzyf/streamd.egg-info/top_level.txt
2025-09-02T15:59:24,975   writing manifest file '/tmp/pip-pip-egg-info-hd2jjzyf/streamd.egg-info/SOURCES.txt'
2025-09-02T15:59:25,075   reading manifest file '/tmp/pip-pip-egg-info-hd2jjzyf/streamd.egg-info/SOURCES.txt'
2025-09-02T15:59:25,077   reading manifest template 'MANIFEST.in'
2025-09-02T15:59:25,082   adding license file 'LICENSE.txt'
2025-09-02T15:59:25,086   writing manifest file '/tmp/pip-pip-egg-info-hd2jjzyf/streamd.egg-info/SOURCES.txt'
2025-09-02T15:59:25,190   Preparing metadata (setup.py): finished with status 'done'
2025-09-02T15:59:25,196   Source in /tmp/pip-wheel-iw49cyar/streamd_3edb0fbbceaf43a1983fcb1073aa2581 has version 0.4, which satisfies requirement streamd==0.4 from https://files.pythonhosted.org/packages/bd/90/bae892ae6c75b409a16281d5d0c5f3cb6d68711e349160cf6a277e6ac164/streamd-0.4.tar.gz
2025-09-02T15:59:25,197   Removed streamd==0.4 from https://files.pythonhosted.org/packages/bd/90/bae892ae6c75b409a16281d5d0c5f3cb6d68711e349160cf6a277e6ac164/streamd-0.4.tar.gz from build tracker '/tmp/pip-build-tracker-7by9rejx'
2025-09-02T15:59:25,207 Created temporary directory: /tmp/pip-unpack-dtoh6pru
2025-09-02T15:59:25,208 Created temporary directory: /tmp/pip-unpack-5ea5lfdk
2025-09-02T15:59:25,209 Building wheels for collected packages: streamd
2025-09-02T15:59:25,213   Created temporary directory: /tmp/pip-wheel-rtum93wu
2025-09-02T15:59:25,214   DEPRECATION: Building 'streamd' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'streamd'. Discussion can be found at https://github.com/pypa/pip/issues/6334
2025-09-02T15:59:25,216   Building wheel for streamd (setup.py): started
2025-09-02T15:59:25,217   Destination directory: /tmp/pip-wheel-rtum93wu
2025-09-02T15:59:25,218   Running command python setup.py bdist_wheel
2025-09-02T15:59:26,077   running bdist_wheel
2025-09-02T15:59:26,214   running build
2025-09-02T15:59:26,215   running build_py
2025-09-02T15:59:26,246   creating build/lib/streamd
2025-09-02T15:59:26,248   copying streamd/run_gbsa.py -> build/lib/streamd
2025-09-02T15:59:26,251   copying streamd/run_md.py -> build/lib/streamd
2025-09-02T15:59:26,256   copying streamd/__init__.py -> build/lib/streamd
2025-09-02T15:59:26,258   creating build/lib/streamd/analysis
2025-09-02T15:59:26,259   copying streamd/analysis/md_system_analysis.py -> build/lib/streamd/analysis
2025-09-02T15:59:26,261   copying streamd/analysis/plot_build.py -> build/lib/streamd/analysis
2025-09-02T15:59:26,264   copying streamd/analysis/run_analysis.py -> build/lib/streamd/analysis
2025-09-02T15:59:26,266   copying streamd/analysis/xvg2png.py -> build/lib/streamd/analysis
2025-09-02T15:59:26,269   copying streamd/analysis/__init__.py -> build/lib/streamd/analysis
2025-09-02T15:59:26,271   creating build/lib/streamd/tests
2025-09-02T15:59:26,272   copying streamd/tests/analysis_test.py -> build/lib/streamd/tests
2025-09-02T15:59:26,275   copying streamd/tests/conftest.py -> build/lib/streamd/tests
2025-09-02T15:59:26,278   copying streamd/tests/decomp_dat_parser_test.py -> build/lib/streamd/tests
2025-09-02T15:59:26,280   copying streamd/tests/system_name_test.py -> build/lib/streamd/tests
2025-09-02T15:59:26,282   copying streamd/tests/config_cli_test.py -> build/lib/streamd/tests
2025-09-02T15:59:26,285   copying streamd/tests/md_test.py -> build/lib/streamd/tests
2025-09-02T15:59:26,287   copying streamd/tests/plot_build_test.py -> build/lib/streamd/tests
2025-09-02T15:59:26,289   copying streamd/tests/import_test.py -> build/lib/streamd/tests
2025-09-02T15:59:26,291   copying streamd/tests/preparation_test.py -> build/lib/streamd/tests
2025-09-02T15:59:26,293   copying streamd/tests/__init__.py -> build/lib/streamd/tests
2025-09-02T15:59:26,295   copying streamd/tests/prolif_test.py -> build/lib/streamd/tests
2025-09-02T15:59:26,298   copying streamd/tests/gbsa_test.py -> build/lib/streamd/tests
2025-09-02T15:59:26,301   creating build/lib/streamd/preparation
2025-09-02T15:59:26,302   copying streamd/preparation/md_files_preparation.py -> build/lib/streamd/preparation
2025-09-02T15:59:26,305   copying streamd/preparation/complex_preparation.py -> build/lib/streamd/preparation
2025-09-02T15:59:26,307   copying streamd/preparation/mcpbpy_preparation.py -> build/lib/streamd/preparation
2025-09-02T15:59:26,310   copying streamd/preparation/__init__.py -> build/lib/streamd/preparation
2025-09-02T15:59:26,312   copying streamd/preparation/ligand_preparation.py -> build/lib/streamd/preparation
2025-09-02T15:59:26,315   copying streamd/preparation/nonstandard_solvent_preparation.py -> build/lib/streamd/preparation
2025-09-02T15:59:26,317   creating build/lib/streamd/mcpbpy_md
2025-09-02T15:59:26,318   copying streamd/mcpbpy_md/mcbpy_md.py -> build/lib/streamd/mcpbpy_md
2025-09-02T15:59:26,321   copying streamd/mcpbpy_md/__init__.py -> build/lib/streamd/mcpbpy_md
2025-09-02T15:59:26,324   creating build/lib/streamd/scripts
2025-09-02T15:59:26,325   copying streamd/scripts/pmed_amb2gmx.py -> build/lib/streamd/scripts
2025-09-02T15:59:26,328   copying streamd/scripts/mol2_fix_coordsbonds.py -> build/lib/streamd/scripts
2025-09-02T15:59:26,330   copying streamd/scripts/pdb2mol.py -> build/lib/streamd/scripts
2025-09-02T15:59:26,333   copying streamd/scripts/getcharge.py -> build/lib/streamd/scripts
2025-09-02T15:59:26,334   copying streamd/scripts/prepare_Gaussian_input.py -> build/lib/streamd/scripts
2025-09-02T15:59:26,337   copying streamd/scripts/__init__.py -> build/lib/streamd/scripts
2025-09-02T15:59:26,339   creating build/lib/streamd/utils
2025-09-02T15:59:26,340   copying streamd/utils/utils.py -> build/lib/streamd/utils
2025-09-02T15:59:26,343   copying streamd/utils/__init__.py -> build/lib/streamd/utils
2025-09-02T15:59:26,345   copying streamd/utils/dask_init.py -> build/lib/streamd/utils
2025-09-02T15:59:26,348   creating build/lib/streamd/prolif
2025-09-02T15:59:26,349   copying streamd/prolif/run_prolif.py -> build/lib/streamd/prolif
2025-09-02T15:59:26,352   copying streamd/prolif/prolif2png.py -> build/lib/streamd/prolif
2025-09-02T15:59:26,355   copying streamd/prolif/prolif_frame_map.py -> build/lib/streamd/prolif
2025-09-02T15:59:26,357   copying streamd/prolif/__init__.py -> build/lib/streamd/prolif
2025-09-02T15:59:26,359   running egg_info
2025-09-02T15:59:26,391   writing streamd.egg-info/PKG-INFO
2025-09-02T15:59:26,397   writing dependency_links to streamd.egg-info/dependency_links.txt
2025-09-02T15:59:26,399   writing entry points to streamd.egg-info/entry_points.txt
2025-09-02T15:59:26,401   writing requirements to streamd.egg-info/requires.txt
2025-09-02T15:59:26,402   writing top-level names to streamd.egg-info/top_level.txt
2025-09-02T15:59:26,442   reading manifest file 'streamd.egg-info/SOURCES.txt'
2025-09-02T15:59:26,449   reading manifest template 'MANIFEST.in'
2025-09-02T15:59:26,452   adding license file 'LICENSE.txt'
2025-09-02T15:59:26,458   writing manifest file 'streamd.egg-info/SOURCES.txt'
2025-09-02T15:59:26,460   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'streamd.example' is absent from the `packages` configuration.
2025-09-02T15:59:26,461   !!

2025-09-02T15:59:26,462           ********************************************************************************
2025-09-02T15:59:26,462           ############################
2025-09-02T15:59:26,463           # Package would be ignored #
2025-09-02T15:59:26,463           ############################
2025-09-02T15:59:26,464           Python recognizes 'streamd.example' as an importable package[^1],
2025-09-02T15:59:26,464           but it is absent from setuptools' `packages` configuration.

2025-09-02T15:59:26,465           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-02T15:59:26,465           package, please make sure that 'streamd.example' is explicitly added
2025-09-02T15:59:26,466           to the `packages` configuration field.

2025-09-02T15:59:26,467           Alternatively, you can also rely on setuptools' discovery methods
2025-09-02T15:59:26,467           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-02T15:59:26,468           instead of `find_packages(...)`/`find:`).

2025-09-02T15:59:26,469           You can read more about "package discovery" on setuptools documentation page:

2025-09-02T15:59:26,470           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-02T15:59:26,471           If you don't want 'streamd.example' to be distributed and are
2025-09-02T15:59:26,471           already explicitly excluding 'streamd.example' via
2025-09-02T15:59:26,472           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-02T15:59:26,472           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-02T15:59:26,473           combination with a more fine grained `package-data` configuration.

2025-09-02T15:59:26,473           You can read more about "package data files" on setuptools documentation page:

2025-09-02T15:59:26,474           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-02T15:59:26,476           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-02T15:59:26,476                 even if it does not contain any `.py` files.
2025-09-02T15:59:26,477                 On the other hand, currently there is no concept of package data
2025-09-02T15:59:26,477                 directory, all directories are treated like packages.
2025-09-02T15:59:26,478           ********************************************************************************

2025-09-02T15:59:26,479   !!
2025-09-02T15:59:26,480     check.warn(importable)
2025-09-02T15:59:26,483   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'streamd.scripts.com' is absent from the `packages` configuration.
2025-09-02T15:59:26,484   !!

2025-09-02T15:59:26,485           ********************************************************************************
2025-09-02T15:59:26,486           ############################
2025-09-02T15:59:26,486           # Package would be ignored #
2025-09-02T15:59:26,487           ############################
2025-09-02T15:59:26,487           Python recognizes 'streamd.scripts.com' as an importable package[^1],
2025-09-02T15:59:26,488           but it is absent from setuptools' `packages` configuration.

2025-09-02T15:59:26,489           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-02T15:59:26,489           package, please make sure that 'streamd.scripts.com' is explicitly added
2025-09-02T15:59:26,490           to the `packages` configuration field.

2025-09-02T15:59:26,491           Alternatively, you can also rely on setuptools' discovery methods
2025-09-02T15:59:26,492           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-02T15:59:26,492           instead of `find_packages(...)`/`find:`).

2025-09-02T15:59:26,493           You can read more about "package discovery" on setuptools documentation page:

2025-09-02T15:59:26,494           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-02T15:59:26,496           If you don't want 'streamd.scripts.com' to be distributed and are
2025-09-02T15:59:26,496           already explicitly excluding 'streamd.scripts.com' via
2025-09-02T15:59:26,496           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-02T15:59:26,497           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-02T15:59:26,497           combination with a more fine grained `package-data` configuration.

2025-09-02T15:59:26,498           You can read more about "package data files" on setuptools documentation page:

2025-09-02T15:59:26,499           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-02T15:59:26,500           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-02T15:59:26,501                 even if it does not contain any `.py` files.
2025-09-02T15:59:26,501                 On the other hand, currently there is no concept of package data
2025-09-02T15:59:26,502                 directory, all directories are treated like packages.
2025-09-02T15:59:26,502           ********************************************************************************

2025-09-02T15:59:26,503   !!
2025-09-02T15:59:26,503     check.warn(importable)
2025-09-02T15:59:26,504   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'streamd.scripts.gbsa' is absent from the `packages` configuration.
2025-09-02T15:59:26,504   !!

2025-09-02T15:59:26,505           ********************************************************************************
2025-09-02T15:59:26,506           ############################
2025-09-02T15:59:26,506           # Package would be ignored #
2025-09-02T15:59:26,507           ############################
2025-09-02T15:59:26,507           Python recognizes 'streamd.scripts.gbsa' as an importable package[^1],
2025-09-02T15:59:26,508           but it is absent from setuptools' `packages` configuration.

2025-09-02T15:59:26,509           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-02T15:59:26,509           package, please make sure that 'streamd.scripts.gbsa' is explicitly added
2025-09-02T15:59:26,510           to the `packages` configuration field.

2025-09-02T15:59:26,511           Alternatively, you can also rely on setuptools' discovery methods
2025-09-02T15:59:26,511           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-02T15:59:26,512           instead of `find_packages(...)`/`find:`).

2025-09-02T15:59:26,513           You can read more about "package discovery" on setuptools documentation page:

2025-09-02T15:59:26,514           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-02T15:59:26,515           If you don't want 'streamd.scripts.gbsa' to be distributed and are
2025-09-02T15:59:26,516           already explicitly excluding 'streamd.scripts.gbsa' via
2025-09-02T15:59:26,516           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-02T15:59:26,517           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-02T15:59:26,517           combination with a more fine grained `package-data` configuration.

2025-09-02T15:59:26,518           You can read more about "package data files" on setuptools documentation page:

2025-09-02T15:59:26,519           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-02T15:59:26,521           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-02T15:59:26,521                 even if it does not contain any `.py` files.
2025-09-02T15:59:26,522                 On the other hand, currently there is no concept of package data
2025-09-02T15:59:26,522                 directory, all directories are treated like packages.
2025-09-02T15:59:26,523           ********************************************************************************

2025-09-02T15:59:26,524   !!
2025-09-02T15:59:26,525     check.warn(importable)
2025-09-02T15:59:26,525   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'streamd.scripts.mcpbpy_scripts' is absent from the `packages` configuration.
2025-09-02T15:59:26,526   !!

2025-09-02T15:59:26,526           ********************************************************************************
2025-09-02T15:59:26,527           ############################
2025-09-02T15:59:26,527           # Package would be ignored #
2025-09-02T15:59:26,528           ############################
2025-09-02T15:59:26,528           Python recognizes 'streamd.scripts.mcpbpy_scripts' as an importable package[^1],
2025-09-02T15:59:26,529           but it is absent from setuptools' `packages` configuration.

2025-09-02T15:59:26,529           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-02T15:59:26,530           package, please make sure that 'streamd.scripts.mcpbpy_scripts' is explicitly added
2025-09-02T15:59:26,530           to the `packages` configuration field.

2025-09-02T15:59:26,531           Alternatively, you can also rely on setuptools' discovery methods
2025-09-02T15:59:26,532           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-02T15:59:26,532           instead of `find_packages(...)`/`find:`).

2025-09-02T15:59:26,533           You can read more about "package discovery" on setuptools documentation page:

2025-09-02T15:59:26,534           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-02T15:59:26,535           If you don't want 'streamd.scripts.mcpbpy_scripts' to be distributed and are
2025-09-02T15:59:26,536           already explicitly excluding 'streamd.scripts.mcpbpy_scripts' via
2025-09-02T15:59:26,536           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-02T15:59:26,537           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-02T15:59:26,537           combination with a more fine grained `package-data` configuration.

2025-09-02T15:59:26,538           You can read more about "package data files" on setuptools documentation page:

2025-09-02T15:59:26,539           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-02T15:59:26,541           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-02T15:59:26,541                 even if it does not contain any `.py` files.
2025-09-02T15:59:26,542                 On the other hand, currently there is no concept of package data
2025-09-02T15:59:26,542                 directory, all directories are treated like packages.
2025-09-02T15:59:26,543           ********************************************************************************

2025-09-02T15:59:26,544   !!
2025-09-02T15:59:26,544     check.warn(importable)
2025-09-02T15:59:26,545   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'streamd.scripts.mdp' is absent from the `packages` configuration.
2025-09-02T15:59:26,545   !!

2025-09-02T15:59:26,546           ********************************************************************************
2025-09-02T15:59:26,547           ############################
2025-09-02T15:59:26,547           # Package would be ignored #
2025-09-02T15:59:26,548           ############################
2025-09-02T15:59:26,548           Python recognizes 'streamd.scripts.mdp' as an importable package[^1],
2025-09-02T15:59:26,549           but it is absent from setuptools' `packages` configuration.

2025-09-02T15:59:26,550           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-02T15:59:26,550           package, please make sure that 'streamd.scripts.mdp' is explicitly added
2025-09-02T15:59:26,551           to the `packages` configuration field.

2025-09-02T15:59:26,552           Alternatively, you can also rely on setuptools' discovery methods
2025-09-02T15:59:26,553           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-02T15:59:26,554           instead of `find_packages(...)`/`find:`).

2025-09-02T15:59:26,555           You can read more about "package discovery" on setuptools documentation page:

2025-09-02T15:59:26,556           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-02T15:59:26,556           If you don't want 'streamd.scripts.mdp' to be distributed and are
2025-09-02T15:59:26,557           already explicitly excluding 'streamd.scripts.mdp' via
2025-09-02T15:59:26,557           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-02T15:59:26,558           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-02T15:59:26,558           combination with a more fine grained `package-data` configuration.

2025-09-02T15:59:26,559           You can read more about "package data files" on setuptools documentation page:

2025-09-02T15:59:26,560           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-02T15:59:26,562           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-02T15:59:26,562                 even if it does not contain any `.py` files.
2025-09-02T15:59:26,563                 On the other hand, currently there is no concept of package data
2025-09-02T15:59:26,563                 directory, all directories are treated like packages.
2025-09-02T15:59:26,564           ********************************************************************************

2025-09-02T15:59:26,565   !!
2025-09-02T15:59:26,565     check.warn(importable)
2025-09-02T15:59:26,566   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'streamd.scripts.script_sh' is absent from the `packages` configuration.
2025-09-02T15:59:26,567   !!

2025-09-02T15:59:26,568           ********************************************************************************
2025-09-02T15:59:26,568           ############################
2025-09-02T15:59:26,569           # Package would be ignored #
2025-09-02T15:59:26,569           ############################
2025-09-02T15:59:26,570           Python recognizes 'streamd.scripts.script_sh' as an importable package[^1],
2025-09-02T15:59:26,570           but it is absent from setuptools' `packages` configuration.

2025-09-02T15:59:26,571           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-02T15:59:26,572           package, please make sure that 'streamd.scripts.script_sh' is explicitly added
2025-09-02T15:59:26,572           to the `packages` configuration field.

2025-09-02T15:59:26,574           Alternatively, you can also rely on setuptools' discovery methods
2025-09-02T15:59:26,574           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-02T15:59:26,575           instead of `find_packages(...)`/`find:`).

2025-09-02T15:59:26,576           You can read more about "package discovery" on setuptools documentation page:

2025-09-02T15:59:26,577           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-02T15:59:26,578           If you don't want 'streamd.scripts.script_sh' to be distributed and are
2025-09-02T15:59:26,579           already explicitly excluding 'streamd.scripts.script_sh' via
2025-09-02T15:59:26,579           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-02T15:59:26,580           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-02T15:59:26,581           combination with a more fine grained `package-data` configuration.

2025-09-02T15:59:26,582           You can read more about "package data files" on setuptools documentation page:

2025-09-02T15:59:26,583           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-02T15:59:26,585           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-02T15:59:26,586                 even if it does not contain any `.py` files.
2025-09-02T15:59:26,586                 On the other hand, currently there is no concept of package data
2025-09-02T15:59:26,587                 directory, all directories are treated like packages.
2025-09-02T15:59:26,588           ********************************************************************************

2025-09-02T15:59:26,589   !!
2025-09-02T15:59:26,590     check.warn(importable)
2025-09-02T15:59:26,591   creating build/lib/streamd/example
2025-09-02T15:59:26,591   copying streamd/example/instructions.txt -> build/lib/streamd/example
2025-09-02T15:59:26,592   copying streamd/example/ligand.mol -> build/lib/streamd/example
2025-09-02T15:59:26,592   copying streamd/example/protein_HIS.pdb -> build/lib/streamd/example
2025-09-02T15:59:26,593   copying streamd/scripts/tleap.in -> build/lib/streamd/scripts
2025-09-02T15:59:26,593   creating build/lib/streamd/scripts/com
2025-09-02T15:59:26,594   copying streamd/scripts/com/1.com -> build/lib/streamd/scripts/com
2025-09-02T15:59:26,594   copying streamd/scripts/com/2.com -> build/lib/streamd/scripts/com
2025-09-02T15:59:26,594   copying streamd/scripts/com/3.com -> build/lib/streamd/scripts/com
2025-09-02T15:59:26,595   creating build/lib/streamd/scripts/gbsa
2025-09-02T15:59:26,595   copying streamd/scripts/gbsa/mmpbsa.in -> build/lib/streamd/scripts/gbsa
2025-09-02T15:59:26,596   creating build/lib/streamd/scripts/mcpbpy_scripts
2025-09-02T15:59:26,597   copying streamd/scripts/mcpbpy_scripts/protein.in -> build/lib/streamd/scripts/mcpbpy_scripts
2025-09-02T15:59:26,597   creating build/lib/streamd/scripts/mdp
2025-09-02T15:59:26,598   copying streamd/scripts/mdp/ions.mdp -> build/lib/streamd/scripts/mdp
2025-09-02T15:59:26,598   copying streamd/scripts/mdp/md.mdp -> build/lib/streamd/scripts/mdp
2025-09-02T15:59:26,599   copying streamd/scripts/mdp/minim.mdp -> build/lib/streamd/scripts/mdp
2025-09-02T15:59:26,599   copying streamd/scripts/mdp/npt.mdp -> build/lib/streamd/scripts/mdp
2025-09-02T15:59:26,600   copying streamd/scripts/mdp/nvt.mdp -> build/lib/streamd/scripts/mdp
2025-09-02T15:59:26,601   creating build/lib/streamd/scripts/script_sh
2025-09-02T15:59:26,601   copying streamd/scripts/script_sh/continue_md.sh -> build/lib/streamd/scripts/script_sh
2025-09-02T15:59:26,602   copying streamd/scripts/script_sh/equlibration.sh -> build/lib/streamd/scripts/script_sh
2025-09-02T15:59:26,603   copying streamd/scripts/script_sh/ligand_mol2prep.sh -> build/lib/streamd/scripts/script_sh
2025-09-02T15:59:26,603   copying streamd/scripts/script_sh/ligand_mol2prep_by_gaussian.sh -> build/lib/streamd/scripts/script_sh
2025-09-02T15:59:26,604   copying streamd/scripts/script_sh/ligand_prep.sh -> build/lib/streamd/scripts/script_sh
2025-09-02T15:59:26,605   copying streamd/scripts/script_sh/md.sh -> build/lib/streamd/scripts/script_sh
2025-09-02T15:59:26,605   copying streamd/scripts/script_sh/md_analysis.sh -> build/lib/streamd/scripts/script_sh
2025-09-02T15:59:26,606   copying streamd/scripts/script_sh/md_ligand_analysis.sh -> build/lib/streamd/scripts/script_sh
2025-09-02T15:59:26,607   copying streamd/scripts/script_sh/solv_ions.sh -> build/lib/streamd/scripts/script_sh
2025-09-02T15:59:26,607   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-09-02T15:59:26,608   !!

2025-09-02T15:59:26,609           ********************************************************************************
2025-09-02T15:59:26,610           Please avoid running ``setup.py`` directly.
2025-09-02T15:59:26,611           Instead, use pypa/build, pypa/installer or other
2025-09-02T15:59:26,611           standards-based tools.

2025-09-02T15:59:26,613           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-09-02T15:59:26,613           or your builds will no longer be supported.

2025-09-02T15:59:26,615           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-09-02T15:59:26,616           ********************************************************************************

2025-09-02T15:59:26,617   !!
2025-09-02T15:59:26,618     self.initialize_options()
2025-09-02T15:59:26,632   installing to build/bdist.linux-armv7l/wheel
2025-09-02T15:59:26,632   running install
2025-09-02T15:59:26,659   running install_lib
2025-09-02T15:59:26,686   creating build/bdist.linux-armv7l/wheel
2025-09-02T15:59:26,689   creating build/bdist.linux-armv7l/wheel/streamd
2025-09-02T15:59:26,690   creating build/bdist.linux-armv7l/wheel/streamd/analysis
2025-09-02T15:59:26,692   copying build/lib/streamd/analysis/md_system_analysis.py -> build/bdist.linux-armv7l/wheel/./streamd/analysis
2025-09-02T15:59:26,694   copying build/lib/streamd/analysis/plot_build.py -> build/bdist.linux-armv7l/wheel/./streamd/analysis
2025-09-02T15:59:26,697   copying build/lib/streamd/analysis/run_analysis.py -> build/bdist.linux-armv7l/wheel/./streamd/analysis
2025-09-02T15:59:26,699   copying build/lib/streamd/analysis/xvg2png.py -> build/bdist.linux-armv7l/wheel/./streamd/analysis
2025-09-02T15:59:26,702   copying build/lib/streamd/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/analysis
2025-09-02T15:59:26,705   creating build/bdist.linux-armv7l/wheel/streamd/tests
2025-09-02T15:59:26,706   copying build/lib/streamd/tests/analysis_test.py -> build/bdist.linux-armv7l/wheel/./streamd/tests
2025-09-02T15:59:26,708   copying build/lib/streamd/tests/conftest.py -> build/bdist.linux-armv7l/wheel/./streamd/tests
2025-09-02T15:59:26,711   copying build/lib/streamd/tests/decomp_dat_parser_test.py -> build/bdist.linux-armv7l/wheel/./streamd/tests
2025-09-02T15:59:26,714   copying build/lib/streamd/tests/system_name_test.py -> build/bdist.linux-armv7l/wheel/./streamd/tests
2025-09-02T15:59:26,716   copying build/lib/streamd/tests/config_cli_test.py -> build/bdist.linux-armv7l/wheel/./streamd/tests
2025-09-02T15:59:26,718   copying build/lib/streamd/tests/md_test.py -> build/bdist.linux-armv7l/wheel/./streamd/tests
2025-09-02T15:59:26,721   copying build/lib/streamd/tests/plot_build_test.py -> build/bdist.linux-armv7l/wheel/./streamd/tests
2025-09-02T15:59:26,723   copying build/lib/streamd/tests/import_test.py -> build/bdist.linux-armv7l/wheel/./streamd/tests
2025-09-02T15:59:26,726   copying build/lib/streamd/tests/preparation_test.py -> build/bdist.linux-armv7l/wheel/./streamd/tests
2025-09-02T15:59:26,728   copying build/lib/streamd/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/tests
2025-09-02T15:59:26,730   copying build/lib/streamd/tests/prolif_test.py -> build/bdist.linux-armv7l/wheel/./streamd/tests
2025-09-02T15:59:26,733   copying build/lib/streamd/tests/gbsa_test.py -> build/bdist.linux-armv7l/wheel/./streamd/tests
2025-09-02T15:59:26,779   creating build/bdist.linux-armv7l/wheel/streamd/preparation
2025-09-02T15:59:26,781   copying build/lib/streamd/preparation/md_files_preparation.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation
2025-09-02T15:59:26,785   copying build/lib/streamd/preparation/complex_preparation.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation
2025-09-02T15:59:26,788   copying build/lib/streamd/preparation/mcpbpy_preparation.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation
2025-09-02T15:59:26,791   copying build/lib/streamd/preparation/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation
2025-09-02T15:59:26,794   copying build/lib/streamd/preparation/ligand_preparation.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation
2025-09-02T15:59:26,797   copying build/lib/streamd/preparation/nonstandard_solvent_preparation.py -> build/bdist.linux-armv7l/wheel/./streamd/preparation
2025-09-02T15:59:26,800   creating build/bdist.linux-armv7l/wheel/streamd/mcpbpy_md
2025-09-02T15:59:26,801   copying build/lib/streamd/mcpbpy_md/mcbpy_md.py -> build/bdist.linux-armv7l/wheel/./streamd/mcpbpy_md
2025-09-02T15:59:26,805   copying build/lib/streamd/mcpbpy_md/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/mcpbpy_md
2025-09-02T15:59:26,808   creating build/bdist.linux-armv7l/wheel/streamd/scripts
2025-09-02T15:59:26,809   copying build/lib/streamd/scripts/pmed_amb2gmx.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts
2025-09-02T15:59:26,811   copying build/lib/streamd/scripts/tleap.in -> build/bdist.linux-armv7l/wheel/./streamd/scripts
2025-09-02T15:59:26,813   copying build/lib/streamd/scripts/mol2_fix_coordsbonds.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts
2025-09-02T15:59:26,816   creating build/bdist.linux-armv7l/wheel/streamd/scripts/mcpbpy_scripts
2025-09-02T15:59:26,817   copying build/lib/streamd/scripts/mcpbpy_scripts/protein.in -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mcpbpy_scripts
2025-09-02T15:59:26,820   creating build/bdist.linux-armv7l/wheel/streamd/scripts/script_sh
2025-09-02T15:59:26,821   copying build/lib/streamd/scripts/script_sh/ligand_mol2prep_by_gaussian.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh
2025-09-02T15:59:26,823   copying build/lib/streamd/scripts/script_sh/md.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh
2025-09-02T15:59:26,824   copying build/lib/streamd/scripts/script_sh/equlibration.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh
2025-09-02T15:59:26,827   copying build/lib/streamd/scripts/script_sh/ligand_prep.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh
2025-09-02T15:59:26,829   copying build/lib/streamd/scripts/script_sh/solv_ions.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh
2025-09-02T15:59:26,830   copying build/lib/streamd/scripts/script_sh/md_ligand_analysis.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh
2025-09-02T15:59:26,833   copying build/lib/streamd/scripts/script_sh/ligand_mol2prep.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh
2025-09-02T15:59:26,835   copying build/lib/streamd/scripts/script_sh/md_analysis.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh
2025-09-02T15:59:26,837   copying build/lib/streamd/scripts/script_sh/continue_md.sh -> build/bdist.linux-armv7l/wheel/./streamd/scripts/script_sh
2025-09-02T15:59:26,839   copying build/lib/streamd/scripts/pdb2mol.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts
2025-09-02T15:59:26,841   copying build/lib/streamd/scripts/getcharge.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts
2025-09-02T15:59:26,843   copying build/lib/streamd/scripts/prepare_Gaussian_input.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts
2025-09-02T15:59:26,846   creating build/bdist.linux-armv7l/wheel/streamd/scripts/mdp
2025-09-02T15:59:26,847   copying build/lib/streamd/scripts/mdp/md.mdp -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mdp
2025-09-02T15:59:26,849   copying build/lib/streamd/scripts/mdp/ions.mdp -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mdp
2025-09-02T15:59:26,851   copying build/lib/streamd/scripts/mdp/minim.mdp -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mdp
2025-09-02T15:59:26,853   copying build/lib/streamd/scripts/mdp/nvt.mdp -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mdp
2025-09-02T15:59:26,856   copying build/lib/streamd/scripts/mdp/npt.mdp -> build/bdist.linux-armv7l/wheel/./streamd/scripts/mdp
2025-09-02T15:59:26,859   creating build/bdist.linux-armv7l/wheel/streamd/scripts/com
2025-09-02T15:59:26,860   copying build/lib/streamd/scripts/com/1.com -> build/bdist.linux-armv7l/wheel/./streamd/scripts/com
2025-09-02T15:59:26,862   copying build/lib/streamd/scripts/com/2.com -> build/bdist.linux-armv7l/wheel/./streamd/scripts/com
2025-09-02T15:59:26,864   copying build/lib/streamd/scripts/com/3.com -> build/bdist.linux-armv7l/wheel/./streamd/scripts/com
2025-09-02T15:59:26,866   copying build/lib/streamd/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/scripts
2025-09-02T15:59:26,869   creating build/bdist.linux-armv7l/wheel/streamd/scripts/gbsa
2025-09-02T15:59:26,870   copying build/lib/streamd/scripts/gbsa/mmpbsa.in -> build/bdist.linux-armv7l/wheel/./streamd/scripts/gbsa
2025-09-02T15:59:26,872   copying build/lib/streamd/run_gbsa.py -> build/bdist.linux-armv7l/wheel/./streamd
2025-09-02T15:59:26,876   creating build/bdist.linux-armv7l/wheel/streamd/example
2025-09-02T15:59:26,877   copying build/lib/streamd/example/ligand.mol -> build/bdist.linux-armv7l/wheel/./streamd/example
2025-09-02T15:59:26,879   copying build/lib/streamd/example/instructions.txt -> build/bdist.linux-armv7l/wheel/./streamd/example
2025-09-02T15:59:26,881   copying build/lib/streamd/example/protein_HIS.pdb -> build/bdist.linux-armv7l/wheel/./streamd/example
2025-09-02T15:59:26,891   creating build/bdist.linux-armv7l/wheel/streamd/utils
2025-09-02T15:59:26,892   copying build/lib/streamd/utils/utils.py -> build/bdist.linux-armv7l/wheel/./streamd/utils
2025-09-02T15:59:26,895   copying build/lib/streamd/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/utils
2025-09-02T15:59:26,897   copying build/lib/streamd/utils/dask_init.py -> build/bdist.linux-armv7l/wheel/./streamd/utils
2025-09-02T15:59:26,899   copying build/lib/streamd/run_md.py -> build/bdist.linux-armv7l/wheel/./streamd
2025-09-02T15:59:26,903   creating build/bdist.linux-armv7l/wheel/streamd/prolif
2025-09-02T15:59:26,905   copying build/lib/streamd/prolif/run_prolif.py -> build/bdist.linux-armv7l/wheel/./streamd/prolif
2025-09-02T15:59:26,907   copying build/lib/streamd/prolif/prolif2png.py -> build/bdist.linux-armv7l/wheel/./streamd/prolif
2025-09-02T15:59:26,910   copying build/lib/streamd/prolif/prolif_frame_map.py -> build/bdist.linux-armv7l/wheel/./streamd/prolif
2025-09-02T15:59:26,912   copying build/lib/streamd/prolif/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd/prolif
2025-09-02T15:59:26,914   copying build/lib/streamd/__init__.py -> build/bdist.linux-armv7l/wheel/./streamd
2025-09-02T15:59:26,916   running install_egg_info
2025-09-02T15:59:26,955   Copying streamd.egg-info to build/bdist.linux-armv7l/wheel/./streamd-0.4-py3.11.egg-info
2025-09-02T15:59:26,967   running install_scripts
2025-09-02T15:59:26,983   creating build/bdist.linux-armv7l/wheel/streamd-0.4.dist-info/WHEEL
2025-09-02T15:59:26,986   creating '/tmp/pip-wheel-rtum93wu/streamd-0.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-09-02T15:59:26,989   adding 'streamd/__init__.py'
2025-09-02T15:59:26,994   adding 'streamd/run_gbsa.py'
2025-09-02T15:59:27,002   adding 'streamd/run_md.py'
2025-09-02T15:59:27,004   adding 'streamd/analysis/__init__.py'
2025-09-02T15:59:27,006   adding 'streamd/analysis/md_system_analysis.py'
2025-09-02T15:59:27,008   adding 'streamd/analysis/plot_build.py'
2025-09-02T15:59:27,011   adding 'streamd/analysis/run_analysis.py'
2025-09-02T15:59:27,012   adding 'streamd/analysis/xvg2png.py'
2025-09-02T15:59:27,014   adding 'streamd/example/instructions.txt'
2025-09-02T15:59:27,016   adding 'streamd/example/ligand.mol'
2025-09-02T15:59:27,082   adding 'streamd/example/protein_HIS.pdb'
2025-09-02T15:59:27,086   adding 'streamd/mcpbpy_md/__init__.py'
2025-09-02T15:59:27,087   adding 'streamd/mcpbpy_md/mcbpy_md.py'
2025-09-02T15:59:27,089   adding 'streamd/preparation/__init__.py'
2025-09-02T15:59:27,091   adding 'streamd/preparation/complex_preparation.py'
2025-09-02T15:59:27,093   adding 'streamd/preparation/ligand_preparation.py'
2025-09-02T15:59:27,095   adding 'streamd/preparation/mcpbpy_preparation.py'
2025-09-02T15:59:27,097   adding 'streamd/preparation/md_files_preparation.py'
2025-09-02T15:59:27,098   adding 'streamd/preparation/nonstandard_solvent_preparation.py'
2025-09-02T15:59:27,100   adding 'streamd/prolif/__init__.py'
2025-09-02T15:59:27,102   adding 'streamd/prolif/prolif2png.py'
2025-09-02T15:59:27,104   adding 'streamd/prolif/prolif_frame_map.py'
2025-09-02T15:59:27,106   adding 'streamd/prolif/run_prolif.py'
2025-09-02T15:59:27,109   adding 'streamd/scripts/__init__.py'
2025-09-02T15:59:27,110   adding 'streamd/scripts/getcharge.py'
2025-09-02T15:59:27,112   adding 'streamd/scripts/mol2_fix_coordsbonds.py'
2025-09-02T15:59:27,114   adding 'streamd/scripts/pdb2mol.py'
2025-09-02T15:59:27,115   adding 'streamd/scripts/pmed_amb2gmx.py'
2025-09-02T15:59:27,116   adding 'streamd/scripts/prepare_Gaussian_input.py'
2025-09-02T15:59:27,118   adding 'streamd/scripts/tleap.in'
2025-09-02T15:59:27,119   adding 'streamd/scripts/com/1.com'
2025-09-02T15:59:27,120   adding 'streamd/scripts/com/2.com'
2025-09-02T15:59:27,121   adding 'streamd/scripts/com/3.com'
2025-09-02T15:59:27,123   adding 'streamd/scripts/gbsa/mmpbsa.in'
2025-09-02T15:59:27,125   adding 'streamd/scripts/mcpbpy_scripts/protein.in'
2025-09-02T15:59:27,126   adding 'streamd/scripts/mdp/ions.mdp'
2025-09-02T15:59:27,128   adding 'streamd/scripts/mdp/md.mdp'
2025-09-02T15:59:27,129   adding 'streamd/scripts/mdp/minim.mdp'
2025-09-02T15:59:27,131   adding 'streamd/scripts/mdp/npt.mdp'
2025-09-02T15:59:27,132   adding 'streamd/scripts/mdp/nvt.mdp'
2025-09-02T15:59:27,134   adding 'streamd/scripts/script_sh/continue_md.sh'
2025-09-02T15:59:27,135   adding 'streamd/scripts/script_sh/equlibration.sh'
2025-09-02T15:59:27,136   adding 'streamd/scripts/script_sh/ligand_mol2prep.sh'
2025-09-02T15:59:27,138   adding 'streamd/scripts/script_sh/ligand_mol2prep_by_gaussian.sh'
2025-09-02T15:59:27,139   adding 'streamd/scripts/script_sh/ligand_prep.sh'
2025-09-02T15:59:27,140   adding 'streamd/scripts/script_sh/md.sh'
2025-09-02T15:59:27,142   adding 'streamd/scripts/script_sh/md_analysis.sh'
2025-09-02T15:59:27,143   adding 'streamd/scripts/script_sh/md_ligand_analysis.sh'
2025-09-02T15:59:27,145   adding 'streamd/scripts/script_sh/solv_ions.sh'
2025-09-02T15:59:27,147   adding 'streamd/tests/__init__.py'
2025-09-02T15:59:27,148   adding 'streamd/tests/analysis_test.py'
2025-09-02T15:59:27,150   adding 'streamd/tests/config_cli_test.py'
2025-09-02T15:59:27,152   adding 'streamd/tests/conftest.py'
2025-09-02T15:59:27,153   adding 'streamd/tests/decomp_dat_parser_test.py'
2025-09-02T15:59:27,155   adding 'streamd/tests/gbsa_test.py'
2025-09-02T15:59:27,156   adding 'streamd/tests/import_test.py'
2025-09-02T15:59:27,158   adding 'streamd/tests/md_test.py'
2025-09-02T15:59:27,160   adding 'streamd/tests/plot_build_test.py'
2025-09-02T15:59:27,161   adding 'streamd/tests/preparation_test.py'
2025-09-02T15:59:27,162   adding 'streamd/tests/prolif_test.py'
2025-09-02T15:59:27,164   adding 'streamd/tests/system_name_test.py'
2025-09-02T15:59:27,165   adding 'streamd/utils/__init__.py'
2025-09-02T15:59:27,167   adding 'streamd/utils/dask_init.py'
2025-09-02T15:59:27,169   adding 'streamd/utils/utils.py'
2025-09-02T15:59:27,172   adding 'streamd-0.4.dist-info/licenses/LICENSE.txt'
2025-09-02T15:59:27,177   adding 'streamd-0.4.dist-info/METADATA'
2025-09-02T15:59:27,179   adding 'streamd-0.4.dist-info/WHEEL'
2025-09-02T15:59:27,180   adding 'streamd-0.4.dist-info/entry_points.txt'
2025-09-02T15:59:27,181   adding 'streamd-0.4.dist-info/top_level.txt'
2025-09-02T15:59:27,182   adding 'streamd-0.4.dist-info/RECORD'
2025-09-02T15:59:27,187   removing build/bdist.linux-armv7l/wheel
2025-09-02T15:59:27,317   Building wheel for streamd (setup.py): finished with status 'done'
2025-09-02T15:59:27,321   Created wheel for streamd: filename=streamd-0.4-py3-none-any.whl size=200088 sha256=afe1d3fb1d27b1f0bd3458d12ac85ed21d9eea86ae3f2a022a0a77607c5e5bb9
2025-09-02T15:59:27,322   Stored in directory: /tmp/pip-ephem-wheel-cache-77t8z2xn/wheels/9a/ce/bd/6fef1f51182cb01aec263cf66904930965487dd8a6c8d95f5d
2025-09-02T15:59:27,342 Successfully built streamd
2025-09-02T15:59:27,354 Removed build tracker: '/tmp/pip-build-tracker-7by9rejx'