2025-06-02T21:24:58,810 Created temporary directory: /tmp/pip-build-tracker-gkp4v1kd 2025-06-02T21:24:58,811 Initialized build tracking at /tmp/pip-build-tracker-gkp4v1kd 2025-06-02T21:24:58,812 Created build tracker: /tmp/pip-build-tracker-gkp4v1kd 2025-06-02T21:24:58,812 Entered build tracker: /tmp/pip-build-tracker-gkp4v1kd 2025-06-02T21:24:58,813 Created temporary directory: /tmp/pip-wheel-6zojxd8m 2025-06-02T21:24:58,818 Created temporary directory: /tmp/pip-ephem-wheel-cache-3x7o611m 2025-06-02T21:24:58,877 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-02T21:24:58,880 2 location(s) to search for versions of pichemist: 2025-06-02T21:24:58,880 * https://pypi.org/simple/pichemist/ 2025-06-02T21:24:58,880 * https://www.piwheels.org/simple/pichemist/ 2025-06-02T21:24:58,881 Fetching project page and analyzing links: https://pypi.org/simple/pichemist/ 2025-06-02T21:24:58,881 Getting page https://pypi.org/simple/pichemist/ 2025-06-02T21:24:58,883 Found index url https://pypi.org/simple/ 2025-06-02T21:24:59,108 Fetched page https://pypi.org/simple/pichemist/ as application/vnd.pypi.simple.v1+json 2025-06-02T21:24:59,111 Skipping link: No binaries permitted for pichemist: https://files.pythonhosted.org/packages/87/1a/bb171094da5c6a6829a2043fc67059297628311a144d79b7aa7dc156d8fd/pichemist-0.1.0-py3-none-any.whl (from https://pypi.org/simple/pichemist/) 2025-06-02T21:24:59,112 Found link https://files.pythonhosted.org/packages/0d/d8/1621751aa5081e2b1fa62f4cef7de3a2c38a3cad4e4a2b21fc35e08103b0/pichemist-0.1.0.tar.gz (from https://pypi.org/simple/pichemist/), version: 0.1.0 2025-06-02T21:24:59,113 Skipping link: No binaries permitted for pichemist: https://files.pythonhosted.org/packages/76/3d/a5bfd0d8d48f95fb95fa503e6a79651c547d9bd4802d8335db181b6434f3/pichemist-0.2.0-py3-none-any.whl (from https://pypi.org/simple/pichemist/) 2025-06-02T21:24:59,115 Found link https://files.pythonhosted.org/packages/4b/b4/28c15528b9742ec95abdec64b71e2bbf7fed2e0fcf8efdd1dfa817482f4d/pichemist-0.2.0.tar.gz (from https://pypi.org/simple/pichemist/), version: 0.2.0 2025-06-02T21:24:59,116 Fetching project page and analyzing links: https://www.piwheels.org/simple/pichemist/ 2025-06-02T21:24:59,117 Getting page https://www.piwheels.org/simple/pichemist/ 2025-06-02T21:24:59,119 Found index url https://www.piwheels.org/simple/ 2025-06-02T21:24:59,277 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/pichemist/ 2025-06-02T21:24:59,935 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/pichemist/ 2025-06-02T21:25:01,121 WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/pichemist/ 2025-06-02T21:25:03,294 WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/pichemist/ 2025-06-02T21:25:07,464 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/pichemist/ 2025-06-02T21:25:07,638 Could not fetch URL https://www.piwheels.org/simple/pichemist/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/pichemist/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping 2025-06-02T21:25:07,640 Skipping link: not a file: https://www.piwheels.org/simple/pichemist/ 2025-06-02T21:25:07,641 Skipping link: not a file: https://pypi.org/simple/pichemist/ 2025-06-02T21:25:07,660 Given no hashes to check 1 links for project 'pichemist': discarding no candidates 2025-06-02T21:25:07,662 Collecting pichemist==0.2.0 2025-06-02T21:25:07,664 Created temporary directory: /tmp/pip-unpack-mra4g9je 2025-06-02T21:25:07,887 Downloading pichemist-0.2.0.tar.gz (49 kB) 2025-06-02T21:25:08,117 Added pichemist==0.2.0 from https://files.pythonhosted.org/packages/4b/b4/28c15528b9742ec95abdec64b71e2bbf7fed2e0fcf8efdd1dfa817482f4d/pichemist-0.2.0.tar.gz to build tracker '/tmp/pip-build-tracker-gkp4v1kd' 2025-06-02T21:25:08,119 Running setup.py (path:/tmp/pip-wheel-6zojxd8m/pichemist_98e976b6c74d4637a6ed534384426097/setup.py) egg_info for package pichemist 2025-06-02T21:25:08,120 Created temporary directory: /tmp/pip-pip-egg-info-_3c45n78 2025-06-02T21:25:08,121 Preparing metadata (setup.py): started 2025-06-02T21:25:08,122 Running command python setup.py egg_info 2025-06-02T21:25:08,724 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-06-02T21:25:08,725 !! 2025-06-02T21:25:08,726 ******************************************************************************** 2025-06-02T21:25:08,726 Requirements should be satisfied by a PEP 517 installer. 2025-06-02T21:25:08,729 If you are using pip, you can try `pip install --use-pep517`. 2025-06-02T21:25:08,730 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-02T21:25:08,730 or your builds will no longer be supported. 2025-06-02T21:25:08,731 ******************************************************************************** 2025-06-02T21:25:08,732 !! 2025-06-02T21:25:08,733 dist.fetch_build_eggs(dist.setup_requires) 2025-06-02T21:25:14,226 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-06-02T21:25:14,227 warnings.warn(msg) 2025-06-02T21:25:14,227 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-06-02T21:25:14,228 warnings.warn(msg) 2025-06-02T21:25:14,325 running egg_info 2025-06-02T21:25:14,357 creating /tmp/pip-pip-egg-info-_3c45n78/pichemist.egg-info 2025-06-02T21:25:14,358 writing /tmp/pip-pip-egg-info-_3c45n78/pichemist.egg-info/PKG-INFO 2025-06-02T21:25:14,361 writing dependency_links to /tmp/pip-pip-egg-info-_3c45n78/pichemist.egg-info/dependency_links.txt 2025-06-02T21:25:14,363 writing entry points to /tmp/pip-pip-egg-info-_3c45n78/pichemist.egg-info/entry_points.txt 2025-06-02T21:25:14,364 writing requirements to /tmp/pip-pip-egg-info-_3c45n78/pichemist.egg-info/requires.txt 2025-06-02T21:25:14,365 writing top-level names to /tmp/pip-pip-egg-info-_3c45n78/pichemist.egg-info/top_level.txt 2025-06-02T21:25:14,367 writing manifest file '/tmp/pip-pip-egg-info-_3c45n78/pichemist.egg-info/SOURCES.txt' 2025-06-02T21:25:14,476 reading manifest file '/tmp/pip-pip-egg-info-_3c45n78/pichemist.egg-info/SOURCES.txt' 2025-06-02T21:25:14,478 reading manifest template 'MANIFEST.in' 2025-06-02T21:25:14,503 adding license file 'LICENSE' 2025-06-02T21:25:14,508 writing manifest file '/tmp/pip-pip-egg-info-_3c45n78/pichemist.egg-info/SOURCES.txt' 2025-06-02T21:25:14,618 Preparing metadata (setup.py): finished with status 'done' 2025-06-02T21:25:14,622 Source in /tmp/pip-wheel-6zojxd8m/pichemist_98e976b6c74d4637a6ed534384426097 has version 0.2.0, which satisfies requirement pichemist==0.2.0 from https://files.pythonhosted.org/packages/4b/b4/28c15528b9742ec95abdec64b71e2bbf7fed2e0fcf8efdd1dfa817482f4d/pichemist-0.2.0.tar.gz 2025-06-02T21:25:14,623 Removed pichemist==0.2.0 from https://files.pythonhosted.org/packages/4b/b4/28c15528b9742ec95abdec64b71e2bbf7fed2e0fcf8efdd1dfa817482f4d/pichemist-0.2.0.tar.gz from build tracker '/tmp/pip-build-tracker-gkp4v1kd' 2025-06-02T21:25:14,629 Created temporary directory: /tmp/pip-unpack-o26hsk8y 2025-06-02T21:25:14,630 Created temporary directory: /tmp/pip-unpack-31dlrg5a 2025-06-02T21:25:14,630 Building wheels for collected packages: pichemist 2025-06-02T21:25:14,635 Created temporary directory: /tmp/pip-wheel-8b8qbtmw 2025-06-02T21:25:14,635 DEPRECATION: Building 'pichemist' 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 'pichemist'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-06-02T21:25:14,637 Building wheel for pichemist (setup.py): started 2025-06-02T21:25:14,638 Destination directory: /tmp/pip-wheel-8b8qbtmw 2025-06-02T21:25:14,638 Running command python setup.py bdist_wheel 2025-06-02T21:25:15,180 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-06-02T21:25:15,180 !! 2025-06-02T21:25:15,181 ******************************************************************************** 2025-06-02T21:25:15,182 Requirements should be satisfied by a PEP 517 installer. 2025-06-02T21:25:15,182 If you are using pip, you can try `pip install --use-pep517`. 2025-06-02T21:25:15,183 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-02T21:25:15,184 or your builds will no longer be supported. 2025-06-02T21:25:15,184 ******************************************************************************** 2025-06-02T21:25:15,186 !! 2025-06-02T21:25:15,186 dist.fetch_build_eggs(dist.setup_requires) 2025-06-02T21:25:15,569 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-06-02T21:25:15,570 warnings.warn(msg) 2025-06-02T21:25:15,570 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-06-02T21:25:15,571 warnings.warn(msg) 2025-06-02T21:25:15,857 running bdist_wheel 2025-06-02T21:25:16,018 running build 2025-06-02T21:25:16,018 running build_py 2025-06-02T21:25:16,055 creating build/lib/pichemist 2025-06-02T21:25:16,057 copying pichemist/api.py -> build/lib/pichemist 2025-06-02T21:25:16,060 copying pichemist/isoelectric.py -> build/lib/pichemist 2025-06-02T21:25:16,062 copying pichemist/__init__.py -> build/lib/pichemist 2025-06-02T21:25:16,064 copying pichemist/charges.py -> build/lib/pichemist 2025-06-02T21:25:16,066 copying pichemist/cli.py -> build/lib/pichemist 2025-06-02T21:25:16,068 copying pichemist/config.py -> build/lib/pichemist 2025-06-02T21:25:16,070 copying pichemist/model.py -> build/lib/pichemist 2025-06-02T21:25:16,072 copying pichemist/plot.py -> build/lib/pichemist 2025-06-02T21:25:16,074 copying pichemist/core.py -> build/lib/pichemist 2025-06-02T21:25:16,076 copying pichemist/molecule.py -> build/lib/pichemist 2025-06-02T21:25:16,078 copying pichemist/utils.py -> build/lib/pichemist 2025-06-02T21:25:16,080 copying pichemist/stats.py -> build/lib/pichemist 2025-06-02T21:25:16,082 copying pichemist/io.py -> build/lib/pichemist 2025-06-02T21:25:16,085 creating build/lib/pichemist/fasta 2025-06-02T21:25:16,086 copying pichemist/fasta/__init__.py -> build/lib/pichemist/fasta 2025-06-02T21:25:16,088 copying pichemist/fasta/scrambler.py -> build/lib/pichemist/fasta 2025-06-02T21:25:16,090 copying pichemist/fasta/matcher.py -> build/lib/pichemist/fasta 2025-06-02T21:25:16,093 copying pichemist/fasta/helpers.py -> build/lib/pichemist/fasta 2025-06-02T21:25:16,095 copying pichemist/fasta/pka_sets.py -> build/lib/pichemist/fasta 2025-06-02T21:25:16,097 copying pichemist/fasta/smarts.py -> build/lib/pichemist/fasta 2025-06-02T21:25:16,099 creating build/lib/pichemist/pka 2025-06-02T21:25:16,100 copying pichemist/pka/acd.py -> build/lib/pichemist/pka 2025-06-02T21:25:16,102 copying pichemist/pka/__init__.py -> build/lib/pichemist/pka 2025-06-02T21:25:16,104 copying pichemist/pka/pkamatcher.py -> build/lib/pichemist/pka 2025-06-02T21:25:16,106 copying pichemist/pka/utils.py -> build/lib/pichemist/pka 2025-06-02T21:25:16,108 creating build/lib/pichemist/smarts 2025-06-02T21:25:16,109 copying pichemist/smarts/__init__.py -> build/lib/pichemist/smarts 2025-06-02T21:25:16,111 copying pichemist/smarts/pka_set.py -> build/lib/pichemist/smarts 2025-06-02T21:25:16,112 running egg_info 2025-06-02T21:25:16,146 writing pichemist.egg-info/PKG-INFO 2025-06-02T21:25:16,149 writing dependency_links to pichemist.egg-info/dependency_links.txt 2025-06-02T21:25:16,151 writing entry points to pichemist.egg-info/entry_points.txt 2025-06-02T21:25:16,152 writing requirements to pichemist.egg-info/requires.txt 2025-06-02T21:25:16,153 writing top-level names to pichemist.egg-info/top_level.txt 2025-06-02T21:25:16,192 reading manifest file 'pichemist.egg-info/SOURCES.txt' 2025-06-02T21:25:16,199 reading manifest template 'MANIFEST.in' 2025-06-02T21:25:16,219 adding license file 'LICENSE' 2025-06-02T21:25:16,226 writing manifest file 'pichemist.egg-info/SOURCES.txt' 2025-06-02T21:25:16,229 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.fasta' is absent from the `packages` configuration. 2025-06-02T21:25:16,230 !! 2025-06-02T21:25:16,231 ******************************************************************************** 2025-06-02T21:25:16,231 ############################ 2025-06-02T21:25:16,232 # Package would be ignored # 2025-06-02T21:25:16,232 ############################ 2025-06-02T21:25:16,233 Python recognizes 'pichemist.data.fasta' as an importable package[^1], 2025-06-02T21:25:16,234 but it is absent from setuptools' `packages` configuration. 2025-06-02T21:25:16,235 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-02T21:25:16,236 package, please make sure that 'pichemist.data.fasta' is explicitly added 2025-06-02T21:25:16,236 to the `packages` configuration field. 2025-06-02T21:25:16,238 Alternatively, you can also rely on setuptools' discovery methods 2025-06-02T21:25:16,238 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-02T21:25:16,239 instead of `find_packages(...)`/`find:`). 2025-06-02T21:25:16,240 You can read more about "package discovery" on setuptools documentation page: 2025-06-02T21:25:16,241 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-02T21:25:16,242 If you don't want 'pichemist.data.fasta' to be distributed and are 2025-06-02T21:25:16,243 already explicitly excluding 'pichemist.data.fasta' via 2025-06-02T21:25:16,244 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-02T21:25:16,244 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-02T21:25:16,245 combination with a more fine grained `package-data` configuration. 2025-06-02T21:25:16,246 You can read more about "package data files" on setuptools documentation page: 2025-06-02T21:25:16,247 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-02T21:25:16,249 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-02T21:25:16,249 even if it does not contain any `.py` files. 2025-06-02T21:25:16,250 On the other hand, currently there is no concept of package data 2025-06-02T21:25:16,250 directory, all directories are treated like packages. 2025-06-02T21:25:16,251 ******************************************************************************** 2025-06-02T21:25:16,252 !! 2025-06-02T21:25:16,252 check.warn(importable) 2025-06-02T21:25:16,253 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.fasta.legacy' is absent from the `packages` configuration. 2025-06-02T21:25:16,253 !! 2025-06-02T21:25:16,254 ******************************************************************************** 2025-06-02T21:25:16,255 ############################ 2025-06-02T21:25:16,255 # Package would be ignored # 2025-06-02T21:25:16,255 ############################ 2025-06-02T21:25:16,256 Python recognizes 'pichemist.data.fasta.legacy' as an importable package[^1], 2025-06-02T21:25:16,256 but it is absent from setuptools' `packages` configuration. 2025-06-02T21:25:16,257 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-02T21:25:16,258 package, please make sure that 'pichemist.data.fasta.legacy' is explicitly added 2025-06-02T21:25:16,258 to the `packages` configuration field. 2025-06-02T21:25:16,259 Alternatively, you can also rely on setuptools' discovery methods 2025-06-02T21:25:16,259 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-02T21:25:16,260 instead of `find_packages(...)`/`find:`). 2025-06-02T21:25:16,261 You can read more about "package discovery" on setuptools documentation page: 2025-06-02T21:25:16,262 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-02T21:25:16,263 If you don't want 'pichemist.data.fasta.legacy' to be distributed and are 2025-06-02T21:25:16,264 already explicitly excluding 'pichemist.data.fasta.legacy' via 2025-06-02T21:25:16,264 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-02T21:25:16,264 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-02T21:25:16,265 combination with a more fine grained `package-data` configuration. 2025-06-02T21:25:16,266 You can read more about "package data files" on setuptools documentation page: 2025-06-02T21:25:16,267 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-02T21:25:16,269 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-02T21:25:16,269 even if it does not contain any `.py` files. 2025-06-02T21:25:16,270 On the other hand, currently there is no concept of package data 2025-06-02T21:25:16,270 directory, all directories are treated like packages. 2025-06-02T21:25:16,271 ******************************************************************************** 2025-06-02T21:25:16,272 !! 2025-06-02T21:25:16,272 check.warn(importable) 2025-06-02T21:25:16,273 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.fasta.original_enriched' is absent from the `packages` configuration. 2025-06-02T21:25:16,273 !! 2025-06-02T21:25:16,275 ******************************************************************************** 2025-06-02T21:25:16,275 ############################ 2025-06-02T21:25:16,276 # Package would be ignored # 2025-06-02T21:25:16,276 ############################ 2025-06-02T21:25:16,277 Python recognizes 'pichemist.data.fasta.original_enriched' as an importable package[^1], 2025-06-02T21:25:16,277 but it is absent from setuptools' `packages` configuration. 2025-06-02T21:25:16,279 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-02T21:25:16,279 package, please make sure that 'pichemist.data.fasta.original_enriched' is explicitly added 2025-06-02T21:25:16,280 to the `packages` configuration field. 2025-06-02T21:25:16,281 Alternatively, you can also rely on setuptools' discovery methods 2025-06-02T21:25:16,282 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-02T21:25:16,282 instead of `find_packages(...)`/`find:`). 2025-06-02T21:25:16,283 You can read more about "package discovery" on setuptools documentation page: 2025-06-02T21:25:16,284 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-02T21:25:16,285 If you don't want 'pichemist.data.fasta.original_enriched' to be distributed and are 2025-06-02T21:25:16,286 already explicitly excluding 'pichemist.data.fasta.original_enriched' via 2025-06-02T21:25:16,286 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-02T21:25:16,287 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-02T21:25:16,287 combination with a more fine grained `package-data` configuration. 2025-06-02T21:25:16,288 You can read more about "package data files" on setuptools documentation page: 2025-06-02T21:25:16,289 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-02T21:25:16,291 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-02T21:25:16,291 even if it does not contain any `.py` files. 2025-06-02T21:25:16,292 On the other hand, currently there is no concept of package data 2025-06-02T21:25:16,292 directory, all directories are treated like packages. 2025-06-02T21:25:16,293 ******************************************************************************** 2025-06-02T21:25:16,294 !! 2025-06-02T21:25:16,294 check.warn(importable) 2025-06-02T21:25:16,295 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.fasta.original_short' is absent from the `packages` configuration. 2025-06-02T21:25:16,295 !! 2025-06-02T21:25:16,296 ******************************************************************************** 2025-06-02T21:25:16,297 ############################ 2025-06-02T21:25:16,297 # Package would be ignored # 2025-06-02T21:25:16,298 ############################ 2025-06-02T21:25:16,299 Python recognizes 'pichemist.data.fasta.original_short' as an importable package[^1], 2025-06-02T21:25:16,299 but it is absent from setuptools' `packages` configuration. 2025-06-02T21:25:16,300 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-02T21:25:16,301 package, please make sure that 'pichemist.data.fasta.original_short' is explicitly added 2025-06-02T21:25:16,301 to the `packages` configuration field. 2025-06-02T21:25:16,302 Alternatively, you can also rely on setuptools' discovery methods 2025-06-02T21:25:16,303 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-02T21:25:16,304 instead of `find_packages(...)`/`find:`). 2025-06-02T21:25:16,305 You can read more about "package discovery" on setuptools documentation page: 2025-06-02T21:25:16,306 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-02T21:25:16,307 If you don't want 'pichemist.data.fasta.original_short' to be distributed and are 2025-06-02T21:25:16,308 already explicitly excluding 'pichemist.data.fasta.original_short' via 2025-06-02T21:25:16,308 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-02T21:25:16,309 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-02T21:25:16,310 combination with a more fine grained `package-data` configuration. 2025-06-02T21:25:16,311 You can read more about "package data files" on setuptools documentation page: 2025-06-02T21:25:16,312 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-02T21:25:16,313 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-02T21:25:16,314 even if it does not contain any `.py` files. 2025-06-02T21:25:16,314 On the other hand, currently there is no concept of package data 2025-06-02T21:25:16,315 directory, all directories are treated like packages. 2025-06-02T21:25:16,315 ******************************************************************************** 2025-06-02T21:25:16,316 !! 2025-06-02T21:25:16,317 check.warn(importable) 2025-06-02T21:25:16,317 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.fasta.standardised' is absent from the `packages` configuration. 2025-06-02T21:25:16,318 !! 2025-06-02T21:25:16,319 ******************************************************************************** 2025-06-02T21:25:16,319 ############################ 2025-06-02T21:25:16,320 # Package would be ignored # 2025-06-02T21:25:16,320 ############################ 2025-06-02T21:25:16,321 Python recognizes 'pichemist.data.fasta.standardised' as an importable package[^1], 2025-06-02T21:25:16,321 but it is absent from setuptools' `packages` configuration. 2025-06-02T21:25:16,322 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-02T21:25:16,323 package, please make sure that 'pichemist.data.fasta.standardised' is explicitly added 2025-06-02T21:25:16,324 to the `packages` configuration field. 2025-06-02T21:25:16,325 Alternatively, you can also rely on setuptools' discovery methods 2025-06-02T21:25:16,326 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-02T21:25:16,326 instead of `find_packages(...)`/`find:`). 2025-06-02T21:25:16,327 You can read more about "package discovery" on setuptools documentation page: 2025-06-02T21:25:16,328 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-02T21:25:16,330 If you don't want 'pichemist.data.fasta.standardised' to be distributed and are 2025-06-02T21:25:16,330 already explicitly excluding 'pichemist.data.fasta.standardised' via 2025-06-02T21:25:16,331 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-02T21:25:16,332 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-02T21:25:16,332 combination with a more fine grained `package-data` configuration. 2025-06-02T21:25:16,333 You can read more about "package data files" on setuptools documentation page: 2025-06-02T21:25:16,334 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-02T21:25:16,336 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-02T21:25:16,337 even if it does not contain any `.py` files. 2025-06-02T21:25:16,337 On the other hand, currently there is no concept of package data 2025-06-02T21:25:16,338 directory, all directories are treated like packages. 2025-06-02T21:25:16,338 ******************************************************************************** 2025-06-02T21:25:16,339 !! 2025-06-02T21:25:16,340 check.warn(importable) 2025-06-02T21:25:16,340 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.smarts' is absent from the `packages` configuration. 2025-06-02T21:25:16,341 !! 2025-06-02T21:25:16,342 ******************************************************************************** 2025-06-02T21:25:16,343 ############################ 2025-06-02T21:25:16,343 # Package would be ignored # 2025-06-02T21:25:16,343 ############################ 2025-06-02T21:25:16,344 Python recognizes 'pichemist.data.smarts' as an importable package[^1], 2025-06-02T21:25:16,344 but it is absent from setuptools' `packages` configuration. 2025-06-02T21:25:16,345 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-02T21:25:16,346 package, please make sure that 'pichemist.data.smarts' is explicitly added 2025-06-02T21:25:16,346 to the `packages` configuration field. 2025-06-02T21:25:16,347 Alternatively, you can also rely on setuptools' discovery methods 2025-06-02T21:25:16,348 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-02T21:25:16,348 instead of `find_packages(...)`/`find:`). 2025-06-02T21:25:16,349 You can read more about "package discovery" on setuptools documentation page: 2025-06-02T21:25:16,350 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-02T21:25:16,352 If you don't want 'pichemist.data.smarts' to be distributed and are 2025-06-02T21:25:16,352 already explicitly excluding 'pichemist.data.smarts' via 2025-06-02T21:25:16,353 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-02T21:25:16,353 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-02T21:25:16,354 combination with a more fine grained `package-data` configuration. 2025-06-02T21:25:16,355 You can read more about "package data files" on setuptools documentation page: 2025-06-02T21:25:16,356 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-02T21:25:16,358 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-02T21:25:16,358 even if it does not contain any `.py` files. 2025-06-02T21:25:16,359 On the other hand, currently there is no concept of package data 2025-06-02T21:25:16,359 directory, all directories are treated like packages. 2025-06-02T21:25:16,360 ******************************************************************************** 2025-06-02T21:25:16,361 !! 2025-06-02T21:25:16,362 check.warn(importable) 2025-06-02T21:25:16,362 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.smarts.legacy' is absent from the `packages` configuration. 2025-06-02T21:25:16,363 !! 2025-06-02T21:25:16,364 ******************************************************************************** 2025-06-02T21:25:16,364 ############################ 2025-06-02T21:25:16,365 # Package would be ignored # 2025-06-02T21:25:16,366 ############################ 2025-06-02T21:25:16,366 Python recognizes 'pichemist.data.smarts.legacy' as an importable package[^1], 2025-06-02T21:25:16,367 but it is absent from setuptools' `packages` configuration. 2025-06-02T21:25:16,368 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-02T21:25:16,368 package, please make sure that 'pichemist.data.smarts.legacy' is explicitly added 2025-06-02T21:25:16,369 to the `packages` configuration field. 2025-06-02T21:25:16,370 Alternatively, you can also rely on setuptools' discovery methods 2025-06-02T21:25:16,371 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-02T21:25:16,371 instead of `find_packages(...)`/`find:`). 2025-06-02T21:25:16,372 You can read more about "package discovery" on setuptools documentation page: 2025-06-02T21:25:16,374 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-02T21:25:16,375 If you don't want 'pichemist.data.smarts.legacy' to be distributed and are 2025-06-02T21:25:16,376 already explicitly excluding 'pichemist.data.smarts.legacy' via 2025-06-02T21:25:16,376 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-02T21:25:16,377 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-02T21:25:16,377 combination with a more fine grained `package-data` configuration. 2025-06-02T21:25:16,378 You can read more about "package data files" on setuptools documentation page: 2025-06-02T21:25:16,379 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-02T21:25:16,380 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-02T21:25:16,381 even if it does not contain any `.py` files. 2025-06-02T21:25:16,381 On the other hand, currently there is no concept of package data 2025-06-02T21:25:16,382 directory, all directories are treated like packages. 2025-06-02T21:25:16,383 ******************************************************************************** 2025-06-02T21:25:16,384 !! 2025-06-02T21:25:16,384 check.warn(importable) 2025-06-02T21:25:16,385 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.smarts.standardised' is absent from the `packages` configuration. 2025-06-02T21:25:16,386 !! 2025-06-02T21:25:16,387 ******************************************************************************** 2025-06-02T21:25:16,387 ############################ 2025-06-02T21:25:16,388 # Package would be ignored # 2025-06-02T21:25:16,389 ############################ 2025-06-02T21:25:16,389 Python recognizes 'pichemist.data.smarts.standardised' as an importable package[^1], 2025-06-02T21:25:16,390 but it is absent from setuptools' `packages` configuration. 2025-06-02T21:25:16,391 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-02T21:25:16,391 package, please make sure that 'pichemist.data.smarts.standardised' is explicitly added 2025-06-02T21:25:16,392 to the `packages` configuration field. 2025-06-02T21:25:16,393 Alternatively, you can also rely on setuptools' discovery methods 2025-06-02T21:25:16,394 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-02T21:25:16,395 instead of `find_packages(...)`/`find:`). 2025-06-02T21:25:16,396 You can read more about "package discovery" on setuptools documentation page: 2025-06-02T21:25:16,397 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-02T21:25:16,399 If you don't want 'pichemist.data.smarts.standardised' to be distributed and are 2025-06-02T21:25:16,399 already explicitly excluding 'pichemist.data.smarts.standardised' via 2025-06-02T21:25:16,400 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-02T21:25:16,401 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-02T21:25:16,401 combination with a more fine grained `package-data` configuration. 2025-06-02T21:25:16,402 You can read more about "package data files" on setuptools documentation page: 2025-06-02T21:25:16,403 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-02T21:25:16,405 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-02T21:25:16,406 even if it does not contain any `.py` files. 2025-06-02T21:25:16,407 On the other hand, currently there is no concept of package data 2025-06-02T21:25:16,407 directory, all directories are treated like packages. 2025-06-02T21:25:16,408 ******************************************************************************** 2025-06-02T21:25:16,409 !! 2025-06-02T21:25:16,409 check.warn(importable) 2025-06-02T21:25:16,410 creating build/lib/pichemist/data/fasta 2025-06-02T21:25:16,410 copying pichemist/data/fasta/convert_legacy_gauci_to_original_and_standardised.py -> build/lib/pichemist/data/fasta 2025-06-02T21:25:16,411 copying pichemist/data/fasta/convert_legacy_promost_into_standardised.py -> build/lib/pichemist/data/fasta 2025-06-02T21:25:16,411 copying pichemist/data/fasta/convert_legacy_short_set_to_original.py -> build/lib/pichemist/data/fasta 2025-06-02T21:25:16,412 copying pichemist/data/fasta/convert_original_short_set_to_standardised.py -> build/lib/pichemist/data/fasta 2025-06-02T21:25:16,412 copying pichemist/data/fasta/legacy_conversion.py -> build/lib/pichemist/data/fasta 2025-06-02T21:25:16,413 creating build/lib/pichemist/data/fasta/legacy 2025-06-02T21:25:16,413 copying pichemist/data/fasta/legacy/aa_legend.tsv -> build/lib/pichemist/data/fasta/legacy 2025-06-02T21:25:16,414 copying pichemist/data/fasta/legacy/gauci.py -> build/lib/pichemist/data/fasta/legacy 2025-06-02T21:25:16,415 copying pichemist/data/fasta/legacy/promost.py -> build/lib/pichemist/data/fasta/legacy 2025-06-02T21:25:16,415 copying pichemist/data/fasta/legacy/short_pka_sets.py -> build/lib/pichemist/data/fasta/legacy 2025-06-02T21:25:16,416 creating build/lib/pichemist/data/fasta/original_enriched 2025-06-02T21:25:16,416 copying pichemist/data/fasta/original_enriched/pka_set_gauci_original.json -> build/lib/pichemist/data/fasta/original_enriched 2025-06-02T21:25:16,417 creating build/lib/pichemist/data/fasta/original_short 2025-06-02T21:25:16,417 copying pichemist/data/fasta/original_short/pka_set_bjellqvist_original.json -> build/lib/pichemist/data/fasta/original_short 2025-06-02T21:25:16,418 copying pichemist/data/fasta/original_short/pka_set_dawson_original.json -> build/lib/pichemist/data/fasta/original_short 2025-06-02T21:25:16,418 copying pichemist/data/fasta/original_short/pka_set_dtaselect_original.json -> build/lib/pichemist/data/fasta/original_short 2025-06-02T21:25:16,419 copying pichemist/data/fasta/original_short/pka_set_emboss_original.json -> build/lib/pichemist/data/fasta/original_short 2025-06-02T21:25:16,420 copying pichemist/data/fasta/original_short/pka_set_grimsley_original.json -> build/lib/pichemist/data/fasta/original_short 2025-06-02T21:25:16,420 copying pichemist/data/fasta/original_short/pka_set_ipc2_peptide_original.json -> build/lib/pichemist/data/fasta/original_short 2025-06-02T21:25:16,421 copying pichemist/data/fasta/original_short/pka_set_ipc_peptide_original.json -> build/lib/pichemist/data/fasta/original_short 2025-06-02T21:25:16,421 copying pichemist/data/fasta/original_short/pka_set_lehninger_original.json -> build/lib/pichemist/data/fasta/original_short 2025-06-02T21:25:16,422 copying pichemist/data/fasta/original_short/pka_set_nozaki_original.json -> build/lib/pichemist/data/fasta/original_short 2025-06-02T21:25:16,423 copying pichemist/data/fasta/original_short/pka_set_rodwell_original.json -> build/lib/pichemist/data/fasta/original_short 2025-06-02T21:25:16,423 copying pichemist/data/fasta/original_short/pka_set_sillero_original.json -> build/lib/pichemist/data/fasta/original_short 2025-06-02T21:25:16,424 copying pichemist/data/fasta/original_short/pka_set_solomon_original.json -> build/lib/pichemist/data/fasta/original_short 2025-06-02T21:25:16,424 copying pichemist/data/fasta/original_short/pka_set_thurlkill_original.json -> build/lib/pichemist/data/fasta/original_short 2025-06-02T21:25:16,425 copying pichemist/data/fasta/original_short/pka_set_toseland_original.json -> build/lib/pichemist/data/fasta/original_short 2025-06-02T21:25:16,426 creating build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,426 copying pichemist/data/fasta/standardised/pka_set_bjellqvist_standardised.json -> build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,427 copying pichemist/data/fasta/standardised/pka_set_dawson_standardised.json -> build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,428 copying pichemist/data/fasta/standardised/pka_set_dtaselect_standardised.json -> build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,428 copying pichemist/data/fasta/standardised/pka_set_emboss_standardised.json -> build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,429 copying pichemist/data/fasta/standardised/pka_set_gauci_standardised.json -> build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,429 copying pichemist/data/fasta/standardised/pka_set_grimsley_standardised.json -> build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,430 copying pichemist/data/fasta/standardised/pka_set_ipc2_peptide_standardised.json -> build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,430 copying pichemist/data/fasta/standardised/pka_set_ipc_peptide_standardised.json -> build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,431 copying pichemist/data/fasta/standardised/pka_set_lehninger_standardised.json -> build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,431 copying pichemist/data/fasta/standardised/pka_set_nozaki_standardised.json -> build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,432 copying pichemist/data/fasta/standardised/pka_set_promost_standardised.json -> build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,433 copying pichemist/data/fasta/standardised/pka_set_rodwell_standardised.json -> build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,433 copying pichemist/data/fasta/standardised/pka_set_sillero_standardised.json -> build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,434 copying pichemist/data/fasta/standardised/pka_set_solomon_standardised.json -> build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,435 copying pichemist/data/fasta/standardised/pka_set_thurlkill_standardised.json -> build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,435 copying pichemist/data/fasta/standardised/pka_set_toseland_standardised.json -> build/lib/pichemist/data/fasta/standardised 2025-06-02T21:25:16,436 creating build/lib/pichemist/data/smarts 2025-06-02T21:25:16,437 copying pichemist/data/smarts/convert_legacy_aa_smarts_to_standardised.py -> build/lib/pichemist/data/smarts 2025-06-02T21:25:16,437 copying pichemist/data/smarts/convert_legacy_ss_smarts_to_standardised.py -> build/lib/pichemist/data/smarts 2025-06-02T21:25:16,438 creating build/lib/pichemist/data/smarts/legacy 2025-06-02T21:25:16,439 copying pichemist/data/smarts/legacy/smarts_naturalAAs.py -> build/lib/pichemist/data/smarts/legacy 2025-06-02T21:25:16,439 copying pichemist/data/smarts/legacy/smarts_notes.py -> build/lib/pichemist/data/smarts/legacy 2025-06-02T21:25:16,440 copying pichemist/data/smarts/legacy/smarts_pKaMatcher.dat -> build/lib/pichemist/data/smarts/legacy 2025-06-02T21:25:16,441 copying pichemist/data/smarts/legacy/smarts_pKaMatcher.py -> build/lib/pichemist/data/smarts/legacy 2025-06-02T21:25:16,441 creating build/lib/pichemist/data/smarts/standardised 2025-06-02T21:25:16,442 copying pichemist/data/smarts/standardised/aa_smarts_set_standardised.json -> build/lib/pichemist/data/smarts/standardised 2025-06-02T21:25:16,442 copying pichemist/data/smarts/standardised/ss_smarts_set_standardised.json -> build/lib/pichemist/data/smarts/standardised 2025-06-02T21:25:16,458 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-02T21:25:16,459 !! 2025-06-02T21:25:16,460 ******************************************************************************** 2025-06-02T21:25:16,461 Please avoid running ``setup.py`` directly. 2025-06-02T21:25:16,461 Instead, use pypa/build, pypa/installer or other 2025-06-02T21:25:16,462 standards-based tools. 2025-06-02T21:25:16,464 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-02T21:25:16,465 or your builds will no longer be supported. 2025-06-02T21:25:16,466 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-02T21:25:16,467 ******************************************************************************** 2025-06-02T21:25:16,468 !! 2025-06-02T21:25:16,468 self.initialize_options() 2025-06-02T21:25:16,493 installing to build/bdist.linux-armv7l/wheel 2025-06-02T21:25:16,493 running install 2025-06-02T21:25:16,518 running install_lib 2025-06-02T21:25:16,548 creating build/bdist.linux-armv7l/wheel 2025-06-02T21:25:16,550 creating build/bdist.linux-armv7l/wheel/pichemist 2025-06-02T21:25:16,551 copying build/lib/pichemist/api.py -> build/bdist.linux-armv7l/wheel/./pichemist 2025-06-02T21:25:16,554 copying build/lib/pichemist/isoelectric.py -> build/bdist.linux-armv7l/wheel/./pichemist 2025-06-02T21:25:16,556 copying build/lib/pichemist/__init__.py -> build/bdist.linux-armv7l/wheel/./pichemist 2025-06-02T21:25:16,557 copying build/lib/pichemist/charges.py -> build/bdist.linux-armv7l/wheel/./pichemist 2025-06-02T21:25:16,559 copying build/lib/pichemist/cli.py -> build/bdist.linux-armv7l/wheel/./pichemist 2025-06-02T21:25:16,561 copying build/lib/pichemist/config.py -> build/bdist.linux-armv7l/wheel/./pichemist 2025-06-02T21:25:16,564 creating build/bdist.linux-armv7l/wheel/pichemist/fasta 2025-06-02T21:25:16,565 copying build/lib/pichemist/fasta/__init__.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta 2025-06-02T21:25:16,566 copying build/lib/pichemist/fasta/scrambler.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta 2025-06-02T21:25:16,568 copying build/lib/pichemist/fasta/matcher.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta 2025-06-02T21:25:16,571 copying build/lib/pichemist/fasta/helpers.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta 2025-06-02T21:25:16,573 copying build/lib/pichemist/fasta/pka_sets.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta 2025-06-02T21:25:16,575 copying build/lib/pichemist/fasta/smarts.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta 2025-06-02T21:25:16,577 copying build/lib/pichemist/model.py -> build/bdist.linux-armv7l/wheel/./pichemist 2025-06-02T21:25:16,579 copying build/lib/pichemist/plot.py -> build/bdist.linux-armv7l/wheel/./pichemist 2025-06-02T21:25:16,582 creating build/bdist.linux-armv7l/wheel/pichemist/data 2025-06-02T21:25:16,583 creating build/bdist.linux-armv7l/wheel/pichemist/data/fasta 2025-06-02T21:25:16,585 creating build/bdist.linux-armv7l/wheel/pichemist/data/fasta/original_enriched 2025-06-02T21:25:16,587 copying build/lib/pichemist/data/fasta/original_enriched/pka_set_gauci_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_enriched 2025-06-02T21:25:16,590 creating build/bdist.linux-armv7l/wheel/pichemist/data/fasta/legacy 2025-06-02T21:25:16,591 copying build/lib/pichemist/data/fasta/legacy/short_pka_sets.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/legacy 2025-06-02T21:25:16,593 copying build/lib/pichemist/data/fasta/legacy/aa_legend.tsv -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/legacy 2025-06-02T21:25:16,595 copying build/lib/pichemist/data/fasta/legacy/promost.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/legacy 2025-06-02T21:25:16,597 copying build/lib/pichemist/data/fasta/legacy/gauci.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/legacy 2025-06-02T21:25:16,599 copying build/lib/pichemist/data/fasta/legacy_conversion.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta 2025-06-02T21:25:16,601 copying build/lib/pichemist/data/fasta/convert_original_short_set_to_standardised.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta 2025-06-02T21:25:16,604 creating build/bdist.linux-armv7l/wheel/pichemist/data/fasta/standardised 2025-06-02T21:25:16,605 copying build/lib/pichemist/data/fasta/standardised/pka_set_nozaki_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised 2025-06-02T21:25:16,608 copying build/lib/pichemist/data/fasta/standardised/pka_set_sillero_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised 2025-06-02T21:25:16,610 copying build/lib/pichemist/data/fasta/standardised/pka_set_dtaselect_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised 2025-06-02T21:25:16,613 copying build/lib/pichemist/data/fasta/standardised/pka_set_promost_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised 2025-06-02T21:25:16,615 copying build/lib/pichemist/data/fasta/standardised/pka_set_bjellqvist_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised 2025-06-02T21:25:16,617 copying build/lib/pichemist/data/fasta/standardised/pka_set_ipc_peptide_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised 2025-06-02T21:25:16,620 copying build/lib/pichemist/data/fasta/standardised/pka_set_solomon_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised 2025-06-02T21:25:16,622 copying build/lib/pichemist/data/fasta/standardised/pka_set_dawson_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised 2025-06-02T21:25:16,624 copying build/lib/pichemist/data/fasta/standardised/pka_set_rodwell_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised 2025-06-02T21:25:16,626 copying build/lib/pichemist/data/fasta/standardised/pka_set_ipc2_peptide_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised 2025-06-02T21:25:16,629 copying build/lib/pichemist/data/fasta/standardised/pka_set_grimsley_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised 2025-06-02T21:25:16,631 copying build/lib/pichemist/data/fasta/standardised/pka_set_toseland_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised 2025-06-02T21:25:16,634 copying build/lib/pichemist/data/fasta/standardised/pka_set_gauci_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised 2025-06-02T21:25:16,636 copying build/lib/pichemist/data/fasta/standardised/pka_set_thurlkill_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised 2025-06-02T21:25:16,638 copying build/lib/pichemist/data/fasta/standardised/pka_set_lehninger_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised 2025-06-02T21:25:16,641 copying build/lib/pichemist/data/fasta/standardised/pka_set_emboss_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised 2025-06-02T21:25:16,643 copying build/lib/pichemist/data/fasta/convert_legacy_short_set_to_original.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta 2025-06-02T21:25:16,645 copying build/lib/pichemist/data/fasta/convert_legacy_promost_into_standardised.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta 2025-06-02T21:25:16,648 creating build/bdist.linux-armv7l/wheel/pichemist/data/fasta/original_short 2025-06-02T21:25:16,649 copying build/lib/pichemist/data/fasta/original_short/pka_set_ipc_peptide_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short 2025-06-02T21:25:16,651 copying build/lib/pichemist/data/fasta/original_short/pka_set_thurlkill_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short 2025-06-02T21:25:16,653 copying build/lib/pichemist/data/fasta/original_short/pka_set_solomon_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short 2025-06-02T21:25:16,655 copying build/lib/pichemist/data/fasta/original_short/pka_set_toseland_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short 2025-06-02T21:25:16,657 copying build/lib/pichemist/data/fasta/original_short/pka_set_ipc2_peptide_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short 2025-06-02T21:25:16,659 copying build/lib/pichemist/data/fasta/original_short/pka_set_dtaselect_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short 2025-06-02T21:25:16,661 copying build/lib/pichemist/data/fasta/original_short/pka_set_emboss_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short 2025-06-02T21:25:16,663 copying build/lib/pichemist/data/fasta/original_short/pka_set_rodwell_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short 2025-06-02T21:25:16,665 copying build/lib/pichemist/data/fasta/original_short/pka_set_grimsley_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short 2025-06-02T21:25:16,667 copying build/lib/pichemist/data/fasta/original_short/pka_set_nozaki_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short 2025-06-02T21:25:16,669 copying build/lib/pichemist/data/fasta/original_short/pka_set_sillero_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short 2025-06-02T21:25:16,670 copying build/lib/pichemist/data/fasta/original_short/pka_set_bjellqvist_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short 2025-06-02T21:25:16,672 copying build/lib/pichemist/data/fasta/original_short/pka_set_lehninger_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short 2025-06-02T21:25:16,674 copying build/lib/pichemist/data/fasta/original_short/pka_set_dawson_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short 2025-06-02T21:25:16,676 copying build/lib/pichemist/data/fasta/convert_legacy_gauci_to_original_and_standardised.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta 2025-06-02T21:25:16,679 creating build/bdist.linux-armv7l/wheel/pichemist/data/smarts 2025-06-02T21:25:16,680 copying build/lib/pichemist/data/smarts/convert_legacy_ss_smarts_to_standardised.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts 2025-06-02T21:25:16,682 creating build/bdist.linux-armv7l/wheel/pichemist/data/smarts/legacy 2025-06-02T21:25:16,684 copying build/lib/pichemist/data/smarts/legacy/smarts_naturalAAs.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/legacy 2025-06-02T21:25:16,687 copying build/lib/pichemist/data/smarts/legacy/smarts_pKaMatcher.dat -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/legacy 2025-06-02T21:25:16,689 copying build/lib/pichemist/data/smarts/legacy/smarts_notes.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/legacy 2025-06-02T21:25:16,691 copying build/lib/pichemist/data/smarts/legacy/smarts_pKaMatcher.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/legacy 2025-06-02T21:25:16,694 copying build/lib/pichemist/data/smarts/convert_legacy_aa_smarts_to_standardised.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts 2025-06-02T21:25:16,696 creating build/bdist.linux-armv7l/wheel/pichemist/data/smarts/standardised 2025-06-02T21:25:16,698 copying build/lib/pichemist/data/smarts/standardised/ss_smarts_set_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/standardised 2025-06-02T21:25:16,701 copying build/lib/pichemist/data/smarts/standardised/aa_smarts_set_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/standardised 2025-06-02T21:25:16,706 creating build/bdist.linux-armv7l/wheel/pichemist/pka 2025-06-02T21:25:16,707 copying build/lib/pichemist/pka/acd.py -> build/bdist.linux-armv7l/wheel/./pichemist/pka 2025-06-02T21:25:16,710 copying build/lib/pichemist/pka/__init__.py -> build/bdist.linux-armv7l/wheel/./pichemist/pka 2025-06-02T21:25:16,712 copying build/lib/pichemist/pka/pkamatcher.py -> build/bdist.linux-armv7l/wheel/./pichemist/pka 2025-06-02T21:25:16,715 copying build/lib/pichemist/pka/utils.py -> build/bdist.linux-armv7l/wheel/./pichemist/pka 2025-06-02T21:25:16,718 copying build/lib/pichemist/core.py -> build/bdist.linux-armv7l/wheel/./pichemist 2025-06-02T21:25:16,721 creating build/bdist.linux-armv7l/wheel/pichemist/smarts 2025-06-02T21:25:16,722 copying build/lib/pichemist/smarts/__init__.py -> build/bdist.linux-armv7l/wheel/./pichemist/smarts 2025-06-02T21:25:16,724 copying build/lib/pichemist/smarts/pka_set.py -> build/bdist.linux-armv7l/wheel/./pichemist/smarts 2025-06-02T21:25:16,727 copying build/lib/pichemist/molecule.py -> build/bdist.linux-armv7l/wheel/./pichemist 2025-06-02T21:25:16,729 copying build/lib/pichemist/utils.py -> build/bdist.linux-armv7l/wheel/./pichemist 2025-06-02T21:25:16,731 copying build/lib/pichemist/stats.py -> build/bdist.linux-armv7l/wheel/./pichemist 2025-06-02T21:25:16,734 copying build/lib/pichemist/io.py -> build/bdist.linux-armv7l/wheel/./pichemist 2025-06-02T21:25:16,736 running install_egg_info 2025-06-02T21:25:16,776 Copying pichemist.egg-info to build/bdist.linux-armv7l/wheel/./pichemist-0.2.0-py3.11.egg-info 2025-06-02T21:25:16,788 running install_scripts 2025-06-02T21:25:16,801 creating build/bdist.linux-armv7l/wheel/pichemist-0.2.0.dist-info/WHEEL 2025-06-02T21:25:16,804 creating '/tmp/pip-wheel-8b8qbtmw/pichemist-0.2.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-02T21:25:16,806 adding 'pichemist/__init__.py' 2025-06-02T21:25:16,808 adding 'pichemist/api.py' 2025-06-02T21:25:16,810 adding 'pichemist/charges.py' 2025-06-02T21:25:16,812 adding 'pichemist/cli.py' 2025-06-02T21:25:16,814 adding 'pichemist/config.py' 2025-06-02T21:25:16,816 adding 'pichemist/core.py' 2025-06-02T21:25:16,818 adding 'pichemist/io.py' 2025-06-02T21:25:16,820 adding 'pichemist/isoelectric.py' 2025-06-02T21:25:16,822 adding 'pichemist/model.py' 2025-06-02T21:25:16,823 adding 'pichemist/molecule.py' 2025-06-02T21:25:16,825 adding 'pichemist/plot.py' 2025-06-02T21:25:16,826 adding 'pichemist/stats.py' 2025-06-02T21:25:16,827 adding 'pichemist/utils.py' 2025-06-02T21:25:16,830 adding 'pichemist/data/fasta/convert_legacy_gauci_to_original_and_standardised.py' 2025-06-02T21:25:16,831 adding 'pichemist/data/fasta/convert_legacy_promost_into_standardised.py' 2025-06-02T21:25:16,832 adding 'pichemist/data/fasta/convert_legacy_short_set_to_original.py' 2025-06-02T21:25:16,834 adding 'pichemist/data/fasta/convert_original_short_set_to_standardised.py' 2025-06-02T21:25:16,835 adding 'pichemist/data/fasta/legacy_conversion.py' 2025-06-02T21:25:16,837 adding 'pichemist/data/fasta/legacy/aa_legend.tsv' 2025-06-02T21:25:16,838 adding 'pichemist/data/fasta/legacy/gauci.py' 2025-06-02T21:25:16,839 adding 'pichemist/data/fasta/legacy/promost.py' 2025-06-02T21:25:16,841 adding 'pichemist/data/fasta/legacy/short_pka_sets.py' 2025-06-02T21:25:16,843 adding 'pichemist/data/fasta/original_enriched/pka_set_gauci_original.json' 2025-06-02T21:25:16,845 adding 'pichemist/data/fasta/original_short/pka_set_bjellqvist_original.json' 2025-06-02T21:25:16,846 adding 'pichemist/data/fasta/original_short/pka_set_dawson_original.json' 2025-06-02T21:25:16,847 adding 'pichemist/data/fasta/original_short/pka_set_dtaselect_original.json' 2025-06-02T21:25:16,849 adding 'pichemist/data/fasta/original_short/pka_set_emboss_original.json' 2025-06-02T21:25:16,850 adding 'pichemist/data/fasta/original_short/pka_set_grimsley_original.json' 2025-06-02T21:25:16,851 adding 'pichemist/data/fasta/original_short/pka_set_ipc2_peptide_original.json' 2025-06-02T21:25:16,852 adding 'pichemist/data/fasta/original_short/pka_set_ipc_peptide_original.json' 2025-06-02T21:25:16,853 adding 'pichemist/data/fasta/original_short/pka_set_lehninger_original.json' 2025-06-02T21:25:16,855 adding 'pichemist/data/fasta/original_short/pka_set_nozaki_original.json' 2025-06-02T21:25:16,856 adding 'pichemist/data/fasta/original_short/pka_set_rodwell_original.json' 2025-06-02T21:25:16,857 adding 'pichemist/data/fasta/original_short/pka_set_sillero_original.json' 2025-06-02T21:25:16,858 adding 'pichemist/data/fasta/original_short/pka_set_solomon_original.json' 2025-06-02T21:25:16,859 adding 'pichemist/data/fasta/original_short/pka_set_thurlkill_original.json' 2025-06-02T21:25:16,861 adding 'pichemist/data/fasta/original_short/pka_set_toseland_original.json' 2025-06-02T21:25:16,863 adding 'pichemist/data/fasta/standardised/pka_set_bjellqvist_standardised.json' 2025-06-02T21:25:16,864 adding 'pichemist/data/fasta/standardised/pka_set_dawson_standardised.json' 2025-06-02T21:25:16,865 adding 'pichemist/data/fasta/standardised/pka_set_dtaselect_standardised.json' 2025-06-02T21:25:16,867 adding 'pichemist/data/fasta/standardised/pka_set_emboss_standardised.json' 2025-06-02T21:25:16,868 adding 'pichemist/data/fasta/standardised/pka_set_gauci_standardised.json' 2025-06-02T21:25:16,870 adding 'pichemist/data/fasta/standardised/pka_set_grimsley_standardised.json' 2025-06-02T21:25:16,871 adding 'pichemist/data/fasta/standardised/pka_set_ipc2_peptide_standardised.json' 2025-06-02T21:25:16,872 adding 'pichemist/data/fasta/standardised/pka_set_ipc_peptide_standardised.json' 2025-06-02T21:25:16,874 adding 'pichemist/data/fasta/standardised/pka_set_lehninger_standardised.json' 2025-06-02T21:25:16,875 adding 'pichemist/data/fasta/standardised/pka_set_nozaki_standardised.json' 2025-06-02T21:25:16,877 adding 'pichemist/data/fasta/standardised/pka_set_promost_standardised.json' 2025-06-02T21:25:16,878 adding 'pichemist/data/fasta/standardised/pka_set_rodwell_standardised.json' 2025-06-02T21:25:16,880 adding 'pichemist/data/fasta/standardised/pka_set_sillero_standardised.json' 2025-06-02T21:25:16,881 adding 'pichemist/data/fasta/standardised/pka_set_solomon_standardised.json' 2025-06-02T21:25:16,883 adding 'pichemist/data/fasta/standardised/pka_set_thurlkill_standardised.json' 2025-06-02T21:25:16,884 adding 'pichemist/data/fasta/standardised/pka_set_toseland_standardised.json' 2025-06-02T21:25:16,886 adding 'pichemist/data/smarts/convert_legacy_aa_smarts_to_standardised.py' 2025-06-02T21:25:16,887 adding 'pichemist/data/smarts/convert_legacy_ss_smarts_to_standardised.py' 2025-06-02T21:25:16,890 adding 'pichemist/data/smarts/legacy/smarts_naturalAAs.py' 2025-06-02T21:25:16,891 adding 'pichemist/data/smarts/legacy/smarts_notes.py' 2025-06-02T21:25:16,893 adding 'pichemist/data/smarts/legacy/smarts_pKaMatcher.dat' 2025-06-02T21:25:16,895 adding 'pichemist/data/smarts/legacy/smarts_pKaMatcher.py' 2025-06-02T21:25:16,898 adding 'pichemist/data/smarts/standardised/aa_smarts_set_standardised.json' 2025-06-02T21:25:16,901 adding 'pichemist/data/smarts/standardised/ss_smarts_set_standardised.json' 2025-06-02T21:25:16,903 adding 'pichemist/fasta/__init__.py' 2025-06-02T21:25:16,904 adding 'pichemist/fasta/helpers.py' 2025-06-02T21:25:16,906 adding 'pichemist/fasta/matcher.py' 2025-06-02T21:25:16,908 adding 'pichemist/fasta/pka_sets.py' 2025-06-02T21:25:16,909 adding 'pichemist/fasta/scrambler.py' 2025-06-02T21:25:16,911 adding 'pichemist/fasta/smarts.py' 2025-06-02T21:25:16,914 adding 'pichemist/pka/__init__.py' 2025-06-02T21:25:16,916 adding 'pichemist/pka/acd.py' 2025-06-02T21:25:16,918 adding 'pichemist/pka/pkamatcher.py' 2025-06-02T21:25:16,920 adding 'pichemist/pka/utils.py' 2025-06-02T21:25:16,922 adding 'pichemist/smarts/__init__.py' 2025-06-02T21:25:16,924 adding 'pichemist/smarts/pka_set.py' 2025-06-02T21:25:16,927 adding 'pichemist-0.2.0.dist-info/licenses/LICENSE' 2025-06-02T21:25:16,929 adding 'pichemist-0.2.0.dist-info/METADATA' 2025-06-02T21:25:16,930 adding 'pichemist-0.2.0.dist-info/WHEEL' 2025-06-02T21:25:16,931 adding 'pichemist-0.2.0.dist-info/entry_points.txt' 2025-06-02T21:25:16,932 adding 'pichemist-0.2.0.dist-info/top_level.txt' 2025-06-02T21:25:16,934 adding 'pichemist-0.2.0.dist-info/RECORD' 2025-06-02T21:25:16,938 removing build/bdist.linux-armv7l/wheel 2025-06-02T21:25:17,070 Building wheel for pichemist (setup.py): finished with status 'done' 2025-06-02T21:25:17,073 Created wheel for pichemist: filename=pichemist-0.2.0-py3-none-any.whl size=65588 sha256=3a9cc2439aeb60a99d3c9024d55885469d6ad761041e96c9c149b9ae25be981b 2025-06-02T21:25:17,074 Stored in directory: /tmp/pip-ephem-wheel-cache-3x7o611m/wheels/8a/e3/58/1d28426327f1b80c8227a757f2e9ad2cb28fbd3d7094af73f3 2025-06-02T21:25:17,091 Successfully built pichemist 2025-06-02T21:25:17,096 Removed build tracker: '/tmp/pip-build-tracker-gkp4v1kd'