2026-07-25T15:32:16,617 Created temporary directory: /tmp/pip-ephem-wheel-cache-n_fv_lpt
2026-07-25T15:32:16,619 Created temporary directory: /tmp/pip-build-tracker-smkxz8p3
2026-07-25T15:32:16,619 Initialized build tracking at /tmp/pip-build-tracker-smkxz8p3
2026-07-25T15:32:16,620 Created build tracker: /tmp/pip-build-tracker-smkxz8p3
2026-07-25T15:32:16,620 Entered build tracker: /tmp/pip-build-tracker-smkxz8p3
2026-07-25T15:32:16,621 Created temporary directory: /tmp/pip-wheel-dj6qnve3
2026-07-25T15:32:16,624 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2026-07-25T15:32:16,626 Created temporary directory: /tmp/pip-ephem-wheel-cache-1mxtkihh
2026-07-25T15:32:16,650 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-07-25T15:32:16,653 2 location(s) to search for versions of shephard:
2026-07-25T15:32:16,653 * https://pypi.org/simple/shephard/
2026-07-25T15:32:16,653 * https://www.piwheels.org/simple/shephard/
2026-07-25T15:32:16,654 Fetching project page and analyzing links: https://pypi.org/simple/shephard/
2026-07-25T15:32:16,655 Getting page https://pypi.org/simple/shephard/
2026-07-25T15:32:16,656 Found index url https://pypi.org/simple
2026-07-25T15:32:16,900 Fetched page https://pypi.org/simple/shephard/ as application/vnd.pypi.simple.v1+json
2026-07-25T15:32:16,903   Found link https://files.pythonhosted.org/packages/a9/95/cbdbdeb72c0c4970872dc8b61c9df622274cc80602640b478e234c921234/shephard-0.1.5.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.5
2026-07-25T15:32:16,904   Found link https://files.pythonhosted.org/packages/e9/11/69a637d6d4e0cb3a2addc9c06587e781747dfee014076fdaab76d466c46f/shephard-0.1.7.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.7
2026-07-25T15:32:16,905   Found link https://files.pythonhosted.org/packages/b7/90/ea0b27088b3586d48ecaaae9743f8289d28c8e602c4aee5bb4e342b06fc5/shephard-0.1.8.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.8
2026-07-25T15:32:16,906   Found link https://files.pythonhosted.org/packages/2d/0b/2c408626a7f199cb04f61d0fffb3372420ad5564e6bffb942646d140232a/shephard-0.1.12.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.12
2026-07-25T15:32:16,906   Found link https://files.pythonhosted.org/packages/60/78/e58f5c608c7cc8363648b8466f262582a7de95a0331f7b3e87085cf31179/shephard-0.1.14.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.14
2026-07-25T15:32:16,907   Found link https://files.pythonhosted.org/packages/78/01/9fc9805f42e59bdf8a00197d349471405e1f27c254562ef81a79f0c67a18/shephard-0.1.15.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.15
2026-07-25T15:32:16,908   Found link https://files.pythonhosted.org/packages/c6/9c/5920ae7fe8ea8af0aa79d7d2554018f6408462d68ac30b501933c9870bc9/shephard-0.1.16.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.16
2026-07-25T15:32:16,909   Found link https://files.pythonhosted.org/packages/b9/7c/03b2d14b68bd74d6dbdef3acd2a59faa9eebb74bc9b5bd623488ae60bf0c/shephard-0.1.17.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.17
2026-07-25T15:32:16,910   Found link https://files.pythonhosted.org/packages/78/a1/eda32772db5f73f89f29c1827f159ee9715a2adb6c0cd7d4d8272fde7c0a/shephard-0.1.20.tar.gz (from https://pypi.org/simple/shephard/) (requires-python:>=3.7,<3.12.0), version: 0.1.20
2026-07-25T15:32:16,911   Found link https://files.pythonhosted.org/packages/1d/74/63cf0dc536cee0215cdee8ea059f7fa2207748646d24e93de829ac0f9b1f/shephard-0.1.21.tar.gz (from https://pypi.org/simple/shephard/) (requires-python:>=3.7,<3.12.0), version: 0.1.21
2026-07-25T15:32:16,912   Found link https://files.pythonhosted.org/packages/68/39/e27dc8f28f0b456c82c497b702bf945bc6596ccf72665cbfe873ecfbcc58/shephard-0.2.0.tar.gz (from https://pypi.org/simple/shephard/) (requires-python:>=3.7), version: 0.2.0
2026-07-25T15:32:16,913   Found link https://files.pythonhosted.org/packages/5f/73/f7cd4bfd9dda99aec6247051206598c1cf2684faca7b90a06660a540ab1f/shephard-0.2.1.tar.gz (from https://pypi.org/simple/shephard/) (requires-python:>=3.7), version: 0.2.1
2026-07-25T15:32:16,914   Found link https://files.pythonhosted.org/packages/f8/16/aa35d7ab6fa18f8b58edb4213a080f01f43ce1c3ec87ddb4ab533601cdaf/shephard-0.2.2.tar.gz (from https://pypi.org/simple/shephard/) (requires-python:>=3.7), version: 0.2.2
2026-07-25T15:32:16,915   Skipping link: No binaries permitted for shephard: https://files.pythonhosted.org/packages/d6/f5/a3e2a50fccff77e44759d1866b05d689ebb92ec62b5998a5cfe844196a04/shephard-0.2.3-py3-none-any.whl (from https://pypi.org/simple/shephard/) (requires-python:>=3.10)
2026-07-25T15:32:16,916   Found link https://files.pythonhosted.org/packages/08/b2/7df159885a6ad070ae8a733f96d4fb9a760ee784124ae03db919458e63bc/shephard-0.2.3.tar.gz (from https://pypi.org/simple/shephard/) (requires-python:>=3.10), version: 0.2.3
2026-07-25T15:32:16,916 Fetching project page and analyzing links: https://www.piwheels.org/simple/shephard/
2026-07-25T15:32:16,917 Getting page https://www.piwheels.org/simple/shephard/
2026-07-25T15:32:16,918 Found index url https://www.piwheels.org/simple
2026-07-25T15:32:17,120 Fetched page https://www.piwheels.org/simple/shephard/ as text/html
2026-07-25T15:32:17,125   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/SHEPHARD-0.2.2-py3-none-any.whl#sha256=439b7a735d0a7049a0e6221661fc776137c9e179ad5f2a320e5392bb8069f20b (from https://www.piwheels.org/simple/shephard/) (requires-python:>=3.7)
2026-07-25T15:32:17,125   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/SHEPHARD-0.2.1-py3-none-any.whl#sha256=c2938ecde6fe46680cbd7eaeaaac9786f78306fc45827bc64fc01bacedebf1aa (from https://www.piwheels.org/simple/shephard/) (requires-python:>=3.7)
2026-07-25T15:32:17,126   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/SHEPHARD-0.2.0-py3-none-any.whl#sha256=bf25de7957cfc8245aa838a5f45de3b9493736e1329249b856aca74b167a11d2 (from https://www.piwheels.org/simple/shephard/) (requires-python:>=3.7)
2026-07-25T15:32:17,126   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.21-py3-none-any.whl#sha256=a7b74868e7b3d7a863c6bcb667f0f6e90071dfcfc14fedffb0f42d538e6cb261 (from https://www.piwheels.org/simple/shephard/) (requires-python:>=3.7,<3.12.0)
2026-07-25T15:32:17,127   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.20-py3-none-any.whl#sha256=24e0e6400e28f09571d88701fe01ae333e945fde39dac06662db18acf07102f7 (from https://www.piwheels.org/simple/shephard/) (requires-python:>=3.7,<3.12.0)
2026-07-25T15:32:17,128   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.17-py3-none-any.whl#sha256=e58970e02d8a29858bffaa02f2b81a682a9ff647ab2d40add23077b69f3ac021 (from https://www.piwheels.org/simple/shephard/)
2026-07-25T15:32:17,129   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.16-py3-none-any.whl#sha256=f8e78c819d4b0150399cc6bb2176f78cba05e409f65559ce80fd765577c27f81 (from https://www.piwheels.org/simple/shephard/)
2026-07-25T15:32:17,129   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.15-py3-none-any.whl#sha256=79ddd35e1cf2c5fc12afbbb7ccd13a338a58db5b7af8b2777c70a6ec6c6a5e6f (from https://www.piwheels.org/simple/shephard/)
2026-07-25T15:32:17,130   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.14-py3-none-any.whl#sha256=475a3c0e8212f4d337f0f1dc4abe953595d119c3b46c8cc25fcc63502c39ac2d (from https://www.piwheels.org/simple/shephard/)
2026-07-25T15:32:17,130   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.12-py3-none-any.whl#sha256=11352de9001ada56ef480863bdad4b36727295a16dfd6bdbbb8b4c13523d07ba (from https://www.piwheels.org/simple/shephard/)
2026-07-25T15:32:17,131   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.8-py3-none-any.whl#sha256=affda4c08aba9e71908aa718a3fdb9851faff0a49135550c7741cbeb0d804582 (from https://www.piwheels.org/simple/shephard/)
2026-07-25T15:32:17,132   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.7-py3-none-any.whl#sha256=e515f924da74d106bd56b75ebb3d14350dfd59ecae19d4004c155b7894558ee9 (from https://www.piwheels.org/simple/shephard/)
2026-07-25T15:32:17,132   Skipping link: No binaries permitted for shephard: https://archive1.piwheels.org/simple/shephard/shephard-0.1.5-py3-none-any.whl#sha256=920236db73af811e8085b5527ca1713d3434695a2dc7a8a4da603b7034a40f67 (from https://www.piwheels.org/simple/shephard/)
2026-07-25T15:32:17,133 Skipping link: not a file: https://www.piwheels.org/simple/shephard/
2026-07-25T15:32:17,133 Skipping link: not a file: https://pypi.org/simple/shephard/
2026-07-25T15:32:17,153 Given no hashes to check 1 links for project 'shephard': discarding no candidates
2026-07-25T15:32:17,171 Collecting shephard==0.2.3
2026-07-25T15:32:17,173   Created temporary directory: /tmp/pip-unpack-j9__1etd
2026-07-25T15:32:17,339   Downloading shephard-0.2.3.tar.gz (224 kB)
2026-07-25T15:32:17,689   Added shephard==0.2.3 from https://files.pythonhosted.org/packages/08/b2/7df159885a6ad070ae8a733f96d4fb9a760ee784124ae03db919458e63bc/shephard-0.2.3.tar.gz to build tracker '/tmp/pip-build-tracker-smkxz8p3'
2026-07-25T15:32:17,696   Created temporary directory: /tmp/pip-build-env-uz0zk_d4
2026-07-25T15:32:17,700   Installing build dependencies: started
2026-07-25T15:32:17,701   Running command pip subprocess to install build dependencies
2026-07-25T15:32:18,840   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-07-25T15:32:19,299   DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2026-07-25T15:32:19,322   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-07-25T15:32:21,119   Collecting setuptools>=77
2026-07-25T15:32:21,121     Obtaining dependency information for setuptools>=77 from https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata
2026-07-25T15:32:21,136     Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata (6.6 kB)
2026-07-25T15:32:21,265   Collecting versioningit~=2.0
2026-07-25T15:32:21,267     Obtaining dependency information for versioningit~=2.0 from https://archive1.piwheels.org/simple/versioningit/versioningit-2.3.0-py3-none-any.whl.metadata
2026-07-25T15:32:21,560     Downloading https://archive1.piwheels.org/simple/versioningit/versioningit-2.3.0-py3-none-any.whl.metadata (9.4 kB)
2026-07-25T15:32:21,766   Collecting packaging>=17.1
2026-07-25T15:32:21,768     Obtaining dependency information for packaging>=17.1 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata
2026-07-25T15:32:21,781     Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
2026-07-25T15:32:21,988   Downloading https://archive1.piwheels.org/simple/versioningit/versioningit-2.3.0-py3-none-any.whl (35 kB)
2026-07-25T15:32:22,015   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-07-25T15:32:22,115   Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB)
2026-07-25T15:32:22,153   Using cached https://archive1.piwheels.org/simple/versioningit/versioningit-2.3.0-py3-none-any.whl (35 kB)
2026-07-25T15:32:22,179   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-07-25T15:32:22,285   Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB)
2026-07-25T15:32:25,025   Installing collected packages: setuptools, packaging, versioningit
2026-07-25T15:32:28,427     Creating /tmp/pip-build-env-uz0zk_d4/overlay/local/bin
2026-07-25T15:32:28,429     changing mode of /tmp/pip-build-env-uz0zk_d4/overlay/local/bin/versioningit to 755
2026-07-25T15:32:28,451   Successfully installed packaging-26.2 setuptools-83.0.0 versioningit-2.3.0
2026-07-25T15:32:28,735   Installing build dependencies: finished with status 'done'
2026-07-25T15:32:28,741   Getting requirements to build wheel: started
2026-07-25T15:32:28,742   Running command Getting requirements to build wheel
2026-07-25T15:32:29,479   running egg_info
2026-07-25T15:32:29,486   writing SHEPHARD.egg-info/PKG-INFO
2026-07-25T15:32:29,490   writing dependency_links to SHEPHARD.egg-info/dependency_links.txt
2026-07-25T15:32:29,492   writing requirements to SHEPHARD.egg-info/requires.txt
2026-07-25T15:32:29,493   writing top-level names to SHEPHARD.egg-info/top_level.txt
2026-07-25T15:32:29,528   reading manifest file 'SHEPHARD.egg-info/SOURCES.txt'
2026-07-25T15:32:29,535   reading manifest template 'MANIFEST.in'
2026-07-25T15:32:29,544   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2026-07-25T15:32:29,546   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2026-07-25T15:32:29,547   warning: no previously-included files matching '*.so' found anywhere in distribution
2026-07-25T15:32:29,548   adding license file 'LICENSE'
2026-07-25T15:32:29,555   writing manifest file 'SHEPHARD.egg-info/SOURCES.txt'
2026-07-25T15:32:29,655   Getting requirements to build wheel: finished with status 'done'
2026-07-25T15:32:29,658   Created temporary directory: /tmp/pip-modern-metadata-cxu44ox1
2026-07-25T15:32:29,661   Preparing metadata (pyproject.toml): started
2026-07-25T15:32:29,662   Running command Preparing metadata (pyproject.toml)
2026-07-25T15:32:30,390   running dist_info
2026-07-25T15:32:30,402   creating /tmp/pip-modern-metadata-cxu44ox1/SHEPHARD.egg-info
2026-07-25T15:32:30,403   writing /tmp/pip-modern-metadata-cxu44ox1/SHEPHARD.egg-info/PKG-INFO
2026-07-25T15:32:30,408   writing dependency_links to /tmp/pip-modern-metadata-cxu44ox1/SHEPHARD.egg-info/dependency_links.txt
2026-07-25T15:32:30,411   writing requirements to /tmp/pip-modern-metadata-cxu44ox1/SHEPHARD.egg-info/requires.txt
2026-07-25T15:32:30,411   writing top-level names to /tmp/pip-modern-metadata-cxu44ox1/SHEPHARD.egg-info/top_level.txt
2026-07-25T15:32:30,413   writing manifest file '/tmp/pip-modern-metadata-cxu44ox1/SHEPHARD.egg-info/SOURCES.txt'
2026-07-25T15:32:30,444   reading manifest file '/tmp/pip-modern-metadata-cxu44ox1/SHEPHARD.egg-info/SOURCES.txt'
2026-07-25T15:32:30,446   reading manifest template 'MANIFEST.in'
2026-07-25T15:32:30,454   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2026-07-25T15:32:30,455   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2026-07-25T15:32:30,456   warning: no previously-included files matching '*.so' found anywhere in distribution
2026-07-25T15:32:30,457   adding license file 'LICENSE'
2026-07-25T15:32:30,463   writing manifest file '/tmp/pip-modern-metadata-cxu44ox1/SHEPHARD.egg-info/SOURCES.txt'
2026-07-25T15:32:30,465   creating '/tmp/pip-modern-metadata-cxu44ox1/shephard-0.2.3.dist-info'
2026-07-25T15:32:30,592   Preparing metadata (pyproject.toml): finished with status 'done'
2026-07-25T15:32:30,597   Source in /tmp/pip-wheel-dj6qnve3/shephard_14825fbda667481b8b9abd3859f5ee9d has version 0.2.3, which satisfies requirement shephard==0.2.3 from https://files.pythonhosted.org/packages/08/b2/7df159885a6ad070ae8a733f96d4fb9a760ee784124ae03db919458e63bc/shephard-0.2.3.tar.gz
2026-07-25T15:32:30,598   Removed shephard==0.2.3 from https://files.pythonhosted.org/packages/08/b2/7df159885a6ad070ae8a733f96d4fb9a760ee784124ae03db919458e63bc/shephard-0.2.3.tar.gz from build tracker '/tmp/pip-build-tracker-smkxz8p3'
2026-07-25T15:32:30,604 Created temporary directory: /tmp/pip-unpack-n0t53ind
2026-07-25T15:32:30,604 Building wheels for collected packages: shephard
2026-07-25T15:32:30,609   Created temporary directory: /tmp/pip-wheel-dvjscffi
2026-07-25T15:32:30,609   Destination directory: /tmp/pip-wheel-dvjscffi
2026-07-25T15:32:30,612   Building wheel for shephard (pyproject.toml): started
2026-07-25T15:32:30,613   Running command Building wheel for shephard (pyproject.toml)
2026-07-25T15:32:31,288   running bdist_wheel
2026-07-25T15:32:31,310   running build
2026-07-25T15:32:31,310   running build_py
2026-07-25T15:32:31,317   creating build/lib/shephard
2026-07-25T15:32:31,319   copying shephard/exceptions.py -> build/lib/shephard
2026-07-25T15:32:31,321   copying shephard/protein.py -> build/lib/shephard
2026-07-25T15:32:31,325   copying shephard/_version.py -> build/lib/shephard
2026-07-25T15:32:31,327   copying shephard/proteome.py -> build/lib/shephard
2026-07-25T15:32:31,330   copying shephard/site.py -> build/lib/shephard
2026-07-25T15:32:31,332   copying shephard/sequence_utilities.py -> build/lib/shephard
2026-07-25T15:32:31,334   copying shephard/track.py -> build/lib/shephard
2026-07-25T15:32:31,337   copying shephard/general_utilities.py -> build/lib/shephard
2026-07-25T15:32:31,339   copying shephard/domain.py -> build/lib/shephard
2026-07-25T15:32:31,341   copying shephard/__init__.py -> build/lib/shephard
2026-07-25T15:32:31,344   creating build/lib/shephard/tools
2026-07-25T15:32:31,345   copying shephard/tools/domain_tools.py -> build/lib/shephard/tools
2026-07-25T15:32:31,347   copying shephard/tools/site_tools.py -> build/lib/shephard/tools
2026-07-25T15:32:31,350   copying shephard/tools/experimental.py -> build/lib/shephard/tools
2026-07-25T15:32:31,352   copying shephard/tools/sequence_tools.py -> build/lib/shephard/tools
2026-07-25T15:32:31,354   copying shephard/tools/attribute_tools.py -> build/lib/shephard/tools
2026-07-25T15:32:31,356   copying shephard/tools/track_tools.py -> build/lib/shephard/tools
2026-07-25T15:32:31,358   copying shephard/tools/__init__.py -> build/lib/shephard/tools
2026-07-25T15:32:31,360   creating build/lib/shephard/apis
2026-07-25T15:32:31,361   copying shephard/apis/uniprot.py -> build/lib/shephard/apis
2026-07-25T15:32:31,364   copying shephard/apis/albatross_api.py -> build/lib/shephard/apis
2026-07-25T15:32:31,366   copying shephard/apis/metapredict_api.py -> build/lib/shephard/apis
2026-07-25T15:32:31,369   copying shephard/apis/fasta.py -> build/lib/shephard/apis
2026-07-25T15:32:31,371   copying shephard/apis/__init__.py -> build/lib/shephard/apis
2026-07-25T15:32:31,374   creating build/lib/shephard/interfaces
2026-07-25T15:32:31,375   copying shephard/interfaces/si_proteins.py -> build/lib/shephard/interfaces
2026-07-25T15:32:31,378   copying shephard/interfaces/interface_tools.py -> build/lib/shephard/interfaces
2026-07-25T15:32:31,380   copying shephard/interfaces/si_protein_attributes.py -> build/lib/shephard/interfaces
2026-07-25T15:32:31,383   copying shephard/interfaces/si_domains.py -> build/lib/shephard/interfaces
2026-07-25T15:32:31,386   copying shephard/interfaces/si_tracks.py -> build/lib/shephard/interfaces
2026-07-25T15:32:31,388   copying shephard/interfaces/si_sites.py -> build/lib/shephard/interfaces
2026-07-25T15:32:31,391   copying shephard/interfaces/__init__.py -> build/lib/shephard/interfaces
2026-07-25T15:32:31,394   creating build/lib/shephard/tests
2026-07-25T15:32:31,395   copying shephard/tests/test_comprehensive_track.py -> build/lib/shephard/tests
2026-07-25T15:32:31,398   copying shephard/tests/test_comprehensive_interfaces.py -> build/lib/shephard/tests
2026-07-25T15:32:31,400   copying shephard/tests/test_bugfix_regressions.py -> build/lib/shephard/tests
2026-07-25T15:32:31,403   copying shephard/tests/test_si_domains.py -> build/lib/shephard/tests
2026-07-25T15:32:31,405   copying shephard/tests/test_bugfix_regressions_0_2_3.py -> build/lib/shephard/tests
2026-07-25T15:32:31,408   copying shephard/tests/test_proteome.py -> build/lib/shephard/tests
2026-07-25T15:32:31,410   copying shephard/tests/test_domain_tools.py -> build/lib/shephard/tests
2026-07-25T15:32:31,412   copying shephard/tests/test_apis_fasta.py -> build/lib/shephard/tests
2026-07-25T15:32:31,414   copying shephard/tests/test_tracks.py -> build/lib/shephard/tests
2026-07-25T15:32:31,415   copying shephard/tests/test_comprehensive_site.py -> build/lib/shephard/tests
2026-07-25T15:32:31,417   copying shephard/tests/test_ProteinAttributesInterface.py -> build/lib/shephard/tests
2026-07-25T15:32:31,419   copying shephard/tests/test_si_tracks.py -> build/lib/shephard/tests
2026-07-25T15:32:31,422   copying shephard/tests/test_comprehensive_proteome.py -> build/lib/shephard/tests
2026-07-25T15:32:31,424   copying shephard/tests/test_attribute_tools.py -> build/lib/shephard/tests
2026-07-25T15:32:31,426   copying shephard/tests/test_comprehensive_protein.py -> build/lib/shephard/tests
2026-07-25T15:32:31,429   copying shephard/tests/test_si_sites.py -> build/lib/shephard/tests
2026-07-25T15:32:31,431   copying shephard/tests/test_sites.py -> build/lib/shephard/tests
2026-07-25T15:32:31,433   copying shephard/tests/test_ProteinInterface.py -> build/lib/shephard/tests
2026-07-25T15:32:31,435   copying shephard/tests/test_api_uniprot_live.py -> build/lib/shephard/tests
2026-07-25T15:32:31,437   copying shephard/tests/test_SiteInterface.py -> build/lib/shephard/tests
2026-07-25T15:32:31,439   copying shephard/tests/test_interfaces.py -> build/lib/shephard/tests
2026-07-25T15:32:31,440   copying shephard/tests/test_sequence_tools.py -> build/lib/shephard/tests
2026-07-25T15:32:31,442   copying shephard/tests/test_track_tools.py -> build/lib/shephard/tests
2026-07-25T15:32:31,444   copying shephard/tests/test_api_metapredict.py -> build/lib/shephard/tests
2026-07-25T15:32:31,447   copying shephard/tests/test_DomainInterface.py -> build/lib/shephard/tests
2026-07-25T15:32:31,448   copying shephard/tests/test_domains.py -> build/lib/shephard/tests
2026-07-25T15:32:31,451   copying shephard/tests/example_test_function.py -> build/lib/shephard/tests
2026-07-25T15:32:31,453   copying shephard/tests/conftest.py -> build/lib/shephard/tests
2026-07-25T15:32:31,455   copying shephard/tests/test_comprehensive_domain.py -> build/lib/shephard/tests
2026-07-25T15:32:31,457   copying shephard/tests/test_add_remove_annotations.py -> build/lib/shephard/tests
2026-07-25T15:32:31,459   copying shephard/tests/test_protein_site_functions.py -> build/lib/shephard/tests
2026-07-25T15:32:31,461   copying shephard/tests/test_TrackInterface.py -> build/lib/shephard/tests
2026-07-25T15:32:31,463   copying shephard/tests/test_shephard.py -> build/lib/shephard/tests
2026-07-25T15:32:31,465   copying shephard/tests/test_protein.py -> build/lib/shephard/tests
2026-07-25T15:32:31,467   copying shephard/tests/test_api_albatross.py -> build/lib/shephard/tests
2026-07-25T15:32:31,469   copying shephard/tests/test_comprehensive_apis.py -> build/lib/shephard/tests
2026-07-25T15:32:31,472   copying shephard/tests/__init__.py -> build/lib/shephard/tests
2026-07-25T15:32:31,473   copying shephard/tests/test_api_uniprot_annotation.py -> build/lib/shephard/tests
2026-07-25T15:32:31,477   copying shephard/tests/test_comprehensive_tools.py -> build/lib/shephard/tests
2026-07-25T15:32:31,480   running egg_info
2026-07-25T15:32:31,492   writing SHEPHARD.egg-info/PKG-INFO
2026-07-25T15:32:31,496   writing dependency_links to SHEPHARD.egg-info/dependency_links.txt
2026-07-25T15:32:31,497   writing requirements to SHEPHARD.egg-info/requires.txt
2026-07-25T15:32:31,498   writing top-level names to SHEPHARD.egg-info/top_level.txt
2026-07-25T15:32:31,519   reading manifest file 'SHEPHARD.egg-info/SOURCES.txt'
2026-07-25T15:32:31,527   reading manifest template 'MANIFEST.in'
2026-07-25T15:32:31,535   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2026-07-25T15:32:31,536   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2026-07-25T15:32:31,538   warning: no previously-included files matching '*.so' found anywhere in distribution
2026-07-25T15:32:31,538   adding license file 'LICENSE'
2026-07-25T15:32:31,546   writing manifest file 'SHEPHARD.egg-info/SOURCES.txt'
2026-07-25T15:32:31,557   copying shephard/.DS_Store -> build/lib/shephard
2026-07-25T15:32:31,559   copying shephard/py.typed -> build/lib/shephard
2026-07-25T15:32:31,561   creating build/lib/shephard/data
2026-07-25T15:32:31,562   copying shephard/data/README.md -> build/lib/shephard/data
2026-07-25T15:32:31,564   copying shephard/data/look_and_say.dat -> build/lib/shephard/data
2026-07-25T15:32:31,566   creating build/lib/shephard/data/test_data
2026-07-25T15:32:31,567   copying shephard/data/test_data/ts1_bonus_sites_bad.tsv -> build/lib/shephard/data/test_data
2026-07-25T15:32:31,569   copying shephard/data/test_data/TS1_protein_attributes.tsv -> build/lib/shephard/data/test_data
2026-07-25T15:32:31,571   copying shephard/data/test_data/TS1_domains_pscore.tsv -> build/lib/shephard/data/test_data
2026-07-25T15:32:31,574   copying shephard/data/test_data/ts1_bonus_sites_bad2.tsv -> build/lib/shephard/data/test_data
2026-07-25T15:32:31,576   copying shephard/data/test_data/TS1_domains_idr_and_others.tsv -> build/lib/shephard/data/test_data
2026-07-25T15:32:31,578   copying shephard/data/test_data/TS1_tracks_pscore.tsv -> build/lib/shephard/data/test_data
2026-07-25T15:32:31,581   copying shephard/data/test_data/names.txt -> build/lib/shephard/data/test_data
2026-07-25T15:32:31,583   copying shephard/data/test_data/TS1_protein_attributes_several.tsv -> build/lib/shephard/data/test_data
2026-07-25T15:32:31,585   copying shephard/data/test_data/TS1_domains_idr.tsv -> build/lib/shephard/data/test_data
2026-07-25T15:32:31,587   copying shephard/data/test_data/testset_1.fasta -> build/lib/shephard/data/test_data
2026-07-25T15:32:31,590   copying shephard/data/test_data/seqs.fasta -> build/lib/shephard/data/test_data
2026-07-25T15:32:31,592   copying shephard/data/test_data/TS1_small_proteins.tsv -> build/lib/shephard/data/test_data
2026-07-25T15:32:31,595   copying shephard/data/test_data/ts1_bonus_sites.tsv -> build/lib/shephard/data/test_data
2026-07-25T15:32:31,597   copying shephard/data/test_data/testset_1.fasta.fai -> build/lib/shephard/data/test_data
2026-07-25T15:32:31,599   copying shephard/data/test_data/TS1_sites.tsv -> build/lib/shephard/data/test_data
2026-07-25T15:32:31,601   copying shephard/data/test_data/testset_1_ptms.tsv -> build/lib/shephard/data/test_data
2026-07-25T15:32:31,604   copying shephard/tools/attribute_tools.py~ -> build/lib/shephard/tools
2026-07-25T15:32:31,607   copying shephard/tests/test_scratchpad.ipynb -> build/lib/shephard/tests
2026-07-25T15:32:31,609   creating build/lib/shephard/tests/.ipynb_checkpoints
2026-07-25T15:32:31,610   copying shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb -> build/lib/shephard/tests/.ipynb_checkpoints
2026-07-25T15:32:31,619   creating build/lib/shephard/tests/output_test
2026-07-25T15:32:31,620   copying shephard/tests/output_test/all_symbols_test.tsv -> build/lib/shephard/tests/output_test
2026-07-25T15:32:31,622   copying shephard/tests/output_test/all_values_test.tsv -> build/lib/shephard/tests/output_test
2026-07-25T15:32:31,625   copying shephard/tests/output_test/all_values_test_from_list.tsv -> build/lib/shephard/tests/output_test
2026-07-25T15:32:31,628   copying shephard/tests/output_test/out_tracks.tsv -> build/lib/shephard/tests/output_test
2026-07-25T15:32:31,631   copying shephard/tests/output_test/readme.md -> build/lib/shephard/tests/output_test
2026-07-25T15:32:31,634   copying shephard/tests/output_test/shephard_track_phosres.tsv -> build/lib/shephard/tests/output_test
2026-07-25T15:32:31,636   copying shephard/tests/output_test/shephard_track_pscore.tsv -> build/lib/shephard/tests/output_test
2026-07-25T15:32:31,639   copying shephard/tests/output_test/test_domains.tsv -> build/lib/shephard/tests/output_test
2026-07-25T15:32:31,641   copying shephard/tests/output_test/test_domains_types.tsv -> build/lib/shephard/tests/output_test
2026-07-25T15:32:31,643   copying shephard/tests/output_test/test_sites.tsv -> build/lib/shephard/tests/output_test
2026-07-25T15:32:31,647   copying shephard/tests/output_test/track_phospho_track.tsv -> build/lib/shephard/tests/output_test
2026-07-25T15:32:31,649   copying shephard/tests/output_test/track_random_vals.tsv -> build/lib/shephard/tests/output_test
2026-07-25T15:32:31,667   installing to build/bdist.linux-armv7l/wheel
2026-07-25T15:32:31,667   running install
2026-07-25T15:32:31,690   running install_lib
2026-07-25T15:32:31,697   creating build/bdist.linux-armv7l/wheel
2026-07-25T15:32:31,699   creating build/bdist.linux-armv7l/wheel/shephard
2026-07-25T15:32:31,701   copying build/lib/shephard/.DS_Store -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-25T15:32:31,703   creating build/bdist.linux-armv7l/wheel/shephard/tools
2026-07-25T15:32:31,704   copying build/lib/shephard/tools/domain_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tools
2026-07-25T15:32:31,707   copying build/lib/shephard/tools/site_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tools
2026-07-25T15:32:31,709   copying build/lib/shephard/tools/experimental.py -> build/bdist.linux-armv7l/wheel/./shephard/tools
2026-07-25T15:32:31,711   copying build/lib/shephard/tools/sequence_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tools
2026-07-25T15:32:31,713   copying build/lib/shephard/tools/attribute_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tools
2026-07-25T15:32:31,715   copying build/lib/shephard/tools/track_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tools
2026-07-25T15:32:31,717   copying build/lib/shephard/tools/attribute_tools.py~ -> build/bdist.linux-armv7l/wheel/./shephard/tools
2026-07-25T15:32:31,719   copying build/lib/shephard/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./shephard/tools
2026-07-25T15:32:31,721   creating build/bdist.linux-armv7l/wheel/shephard/apis
2026-07-25T15:32:31,722   copying build/lib/shephard/apis/uniprot.py -> build/bdist.linux-armv7l/wheel/./shephard/apis
2026-07-25T15:32:31,726   copying build/lib/shephard/apis/albatross_api.py -> build/bdist.linux-armv7l/wheel/./shephard/apis
2026-07-25T15:32:31,728   copying build/lib/shephard/apis/metapredict_api.py -> build/bdist.linux-armv7l/wheel/./shephard/apis
2026-07-25T15:32:31,730   copying build/lib/shephard/apis/fasta.py -> build/bdist.linux-armv7l/wheel/./shephard/apis
2026-07-25T15:32:31,733   copying build/lib/shephard/apis/__init__.py -> build/bdist.linux-armv7l/wheel/./shephard/apis
2026-07-25T15:32:31,735   creating build/bdist.linux-armv7l/wheel/shephard/data
2026-07-25T15:32:31,736   copying build/lib/shephard/data/README.md -> build/bdist.linux-armv7l/wheel/./shephard/data
2026-07-25T15:32:31,739   creating build/bdist.linux-armv7l/wheel/shephard/data/test_data
2026-07-25T15:32:31,740   copying build/lib/shephard/data/test_data/ts1_bonus_sites_bad.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-25T15:32:31,742   copying build/lib/shephard/data/test_data/TS1_protein_attributes.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-25T15:32:31,744   copying build/lib/shephard/data/test_data/TS1_domains_pscore.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-25T15:32:31,746   copying build/lib/shephard/data/test_data/ts1_bonus_sites_bad2.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-25T15:32:31,748   copying build/lib/shephard/data/test_data/TS1_domains_idr_and_others.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-25T15:32:31,750   copying build/lib/shephard/data/test_data/TS1_tracks_pscore.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-25T15:32:31,752   copying build/lib/shephard/data/test_data/names.txt -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-25T15:32:31,754   copying build/lib/shephard/data/test_data/TS1_protein_attributes_several.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-25T15:32:31,756   copying build/lib/shephard/data/test_data/TS1_domains_idr.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-25T15:32:31,758   copying build/lib/shephard/data/test_data/testset_1.fasta -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-25T15:32:31,760   copying build/lib/shephard/data/test_data/seqs.fasta -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-25T15:32:31,762   copying build/lib/shephard/data/test_data/TS1_small_proteins.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-25T15:32:31,764   copying build/lib/shephard/data/test_data/ts1_bonus_sites.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-25T15:32:31,766   copying build/lib/shephard/data/test_data/testset_1.fasta.fai -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-25T15:32:31,767   copying build/lib/shephard/data/test_data/TS1_sites.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-25T15:32:31,769   copying build/lib/shephard/data/test_data/testset_1_ptms.tsv -> build/bdist.linux-armv7l/wheel/./shephard/data/test_data
2026-07-25T15:32:31,771   copying build/lib/shephard/data/look_and_say.dat -> build/bdist.linux-armv7l/wheel/./shephard/data
2026-07-25T15:32:31,773   copying build/lib/shephard/exceptions.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-25T15:32:31,775   copying build/lib/shephard/protein.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-25T15:32:31,779   creating build/bdist.linux-armv7l/wheel/shephard/interfaces
2026-07-25T15:32:31,780   copying build/lib/shephard/interfaces/si_proteins.py -> build/bdist.linux-armv7l/wheel/./shephard/interfaces
2026-07-25T15:32:31,782   copying build/lib/shephard/interfaces/interface_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/interfaces
2026-07-25T15:32:31,784   copying build/lib/shephard/interfaces/si_protein_attributes.py -> build/bdist.linux-armv7l/wheel/./shephard/interfaces
2026-07-25T15:32:31,787   copying build/lib/shephard/interfaces/si_domains.py -> build/bdist.linux-armv7l/wheel/./shephard/interfaces
2026-07-25T15:32:31,789   copying build/lib/shephard/interfaces/si_tracks.py -> build/bdist.linux-armv7l/wheel/./shephard/interfaces
2026-07-25T15:32:31,792   copying build/lib/shephard/interfaces/si_sites.py -> build/bdist.linux-armv7l/wheel/./shephard/interfaces
2026-07-25T15:32:31,795   copying build/lib/shephard/interfaces/__init__.py -> build/bdist.linux-armv7l/wheel/./shephard/interfaces
2026-07-25T15:32:31,797   creating build/bdist.linux-armv7l/wheel/shephard/tests
2026-07-25T15:32:31,798   copying build/lib/shephard/tests/test_comprehensive_track.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,801   copying build/lib/shephard/tests/test_comprehensive_interfaces.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,803   copying build/lib/shephard/tests/test_bugfix_regressions.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,805   copying build/lib/shephard/tests/test_si_domains.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,808   copying build/lib/shephard/tests/test_bugfix_regressions_0_2_3.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,810   copying build/lib/shephard/tests/test_proteome.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,812   copying build/lib/shephard/tests/test_domain_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,815   copying build/lib/shephard/tests/test_apis_fasta.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,817   copying build/lib/shephard/tests/test_tracks.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,818   copying build/lib/shephard/tests/test_comprehensive_site.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,821   copying build/lib/shephard/tests/test_ProteinAttributesInterface.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,822   copying build/lib/shephard/tests/test_si_tracks.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,825   copying build/lib/shephard/tests/test_comprehensive_proteome.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,827   copying build/lib/shephard/tests/test_attribute_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,829   copying build/lib/shephard/tests/test_comprehensive_protein.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,831   copying build/lib/shephard/tests/test_si_sites.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,834   creating build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2026-07-25T15:32:31,835   copying build/lib/shephard/tests/output_test/out_tracks.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-25T15:32:31,838   copying build/lib/shephard/tests/output_test/track_random_vals.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-25T15:32:31,840   copying build/lib/shephard/tests/output_test/test_domains.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-25T15:32:31,841   copying build/lib/shephard/tests/output_test/readme.md -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-25T15:32:31,843   copying build/lib/shephard/tests/output_test/test_sites.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-25T15:32:31,847   copying build/lib/shephard/tests/output_test/all_symbols_test.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-25T15:32:31,849   copying build/lib/shephard/tests/output_test/all_values_test_from_list.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-25T15:32:31,852   copying build/lib/shephard/tests/output_test/shephard_track_pscore.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-25T15:32:31,855   copying build/lib/shephard/tests/output_test/all_values_test.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-25T15:32:31,857   copying build/lib/shephard/tests/output_test/shephard_track_phosres.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-25T15:32:31,859   copying build/lib/shephard/tests/output_test/test_domains_types.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-25T15:32:31,861   copying build/lib/shephard/tests/output_test/track_phospho_track.tsv -> build/bdist.linux-armv7l/wheel/./shephard/tests/output_test
2026-07-25T15:32:31,863   copying build/lib/shephard/tests/test_sites.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,865   copying build/lib/shephard/tests/test_ProteinInterface.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,866   copying build/lib/shephard/tests/test_api_uniprot_live.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,869   copying build/lib/shephard/tests/test_SiteInterface.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,870   copying build/lib/shephard/tests/test_interfaces.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,872   copying build/lib/shephard/tests/test_sequence_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,874   copying build/lib/shephard/tests/test_track_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,876   copying build/lib/shephard/tests/test_api_metapredict.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,879   copying build/lib/shephard/tests/test_DomainInterface.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,881   creating build/bdist.linux-armv7l/wheel/shephard/tests/.ipynb_checkpoints
2026-07-25T15:32:31,882   copying build/lib/shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb -> build/bdist.linux-armv7l/wheel/./shephard/tests/.ipynb_checkpoints
2026-07-25T15:32:31,884   copying build/lib/shephard/tests/test_domains.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,886   copying build/lib/shephard/tests/example_test_function.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,888   copying build/lib/shephard/tests/conftest.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,890   copying build/lib/shephard/tests/test_comprehensive_domain.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,892   copying build/lib/shephard/tests/test_add_remove_annotations.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,894   copying build/lib/shephard/tests/test_protein_site_functions.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,896   copying build/lib/shephard/tests/test_TrackInterface.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,898   copying build/lib/shephard/tests/test_shephard.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,900   copying build/lib/shephard/tests/test_protein.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,902   copying build/lib/shephard/tests/test_api_albatross.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,904   copying build/lib/shephard/tests/test_comprehensive_apis.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,906   copying build/lib/shephard/tests/test_scratchpad.ipynb -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,909   copying build/lib/shephard/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,910   copying build/lib/shephard/tests/test_api_uniprot_annotation.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,914   copying build/lib/shephard/tests/test_comprehensive_tools.py -> build/bdist.linux-armv7l/wheel/./shephard/tests
2026-07-25T15:32:31,916   copying build/lib/shephard/_version.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-25T15:32:31,918   copying build/lib/shephard/proteome.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-25T15:32:31,921   copying build/lib/shephard/site.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-25T15:32:31,924   copying build/lib/shephard/sequence_utilities.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-25T15:32:31,925   copying build/lib/shephard/track.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-25T15:32:31,928   copying build/lib/shephard/general_utilities.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-25T15:32:31,930   copying build/lib/shephard/py.typed -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-25T15:32:31,931   copying build/lib/shephard/domain.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-25T15:32:31,934   copying build/lib/shephard/__init__.py -> build/bdist.linux-armv7l/wheel/./shephard
2026-07-25T15:32:31,936   running install_egg_info
2026-07-25T15:32:31,942   Copying SHEPHARD.egg-info to build/bdist.linux-armv7l/wheel/./SHEPHARD-0.2.3-py3.11.egg-info
2026-07-25T15:32:31,953   running install_scripts
2026-07-25T15:32:31,963   creating build/bdist.linux-armv7l/wheel/shephard-0.2.3.dist-info/WHEEL
2026-07-25T15:32:31,966   creating '/tmp/pip-wheel-dvjscffi/.tmp-af6i0g20/shephard-0.2.3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-07-25T15:32:31,968   adding 'shephard/.DS_Store'
2026-07-25T15:32:31,970   adding 'shephard/__init__.py'
2026-07-25T15:32:31,971   adding 'shephard/_version.py'
2026-07-25T15:32:31,974   adding 'shephard/domain.py'
2026-07-25T15:32:31,975   adding 'shephard/exceptions.py'
2026-07-25T15:32:31,977   adding 'shephard/general_utilities.py'
2026-07-25T15:32:31,986   adding 'shephard/protein.py'
2026-07-25T15:32:31,992   adding 'shephard/proteome.py'
2026-07-25T15:32:31,994   adding 'shephard/py.typed'
2026-07-25T15:32:31,995   adding 'shephard/sequence_utilities.py'
2026-07-25T15:32:31,997   adding 'shephard/site.py'
2026-07-25T15:32:31,999   adding 'shephard/track.py'
2026-07-25T15:32:32,001   adding 'shephard/apis/__init__.py'
2026-07-25T15:32:32,002   adding 'shephard/apis/albatross_api.py'
2026-07-25T15:32:32,005   adding 'shephard/apis/fasta.py'
2026-07-25T15:32:32,007   adding 'shephard/apis/metapredict_api.py'
2026-07-25T15:32:32,014   adding 'shephard/apis/uniprot.py'
2026-07-25T15:32:32,016   adding 'shephard/data/README.md'
2026-07-25T15:32:32,017   adding 'shephard/data/look_and_say.dat'
2026-07-25T15:32:32,019   adding 'shephard/data/test_data/TS1_domains_idr.tsv'
2026-07-25T15:32:32,020   adding 'shephard/data/test_data/TS1_domains_idr_and_others.tsv'
2026-07-25T15:32:32,021   adding 'shephard/data/test_data/TS1_domains_pscore.tsv'
2026-07-25T15:32:32,023   adding 'shephard/data/test_data/TS1_protein_attributes.tsv'
2026-07-25T15:32:32,024   adding 'shephard/data/test_data/TS1_protein_attributes_several.tsv'
2026-07-25T15:32:32,025   adding 'shephard/data/test_data/TS1_sites.tsv'
2026-07-25T15:32:32,026   adding 'shephard/data/test_data/TS1_small_proteins.tsv'
2026-07-25T15:32:32,035   adding 'shephard/data/test_data/TS1_tracks_pscore.tsv'
2026-07-25T15:32:32,036   adding 'shephard/data/test_data/names.txt'
2026-07-25T15:32:32,038   adding 'shephard/data/test_data/seqs.fasta'
2026-07-25T15:32:32,039   adding 'shephard/data/test_data/testset_1.fasta'
2026-07-25T15:32:32,041   adding 'shephard/data/test_data/testset_1.fasta.fai'
2026-07-25T15:32:32,042   adding 'shephard/data/test_data/testset_1_ptms.tsv'
2026-07-25T15:32:32,043   adding 'shephard/data/test_data/ts1_bonus_sites.tsv'
2026-07-25T15:32:32,044   adding 'shephard/data/test_data/ts1_bonus_sites_bad.tsv'
2026-07-25T15:32:32,045   adding 'shephard/data/test_data/ts1_bonus_sites_bad2.tsv'
2026-07-25T15:32:32,047   adding 'shephard/interfaces/__init__.py'
2026-07-25T15:32:32,049   adding 'shephard/interfaces/interface_tools.py'
2026-07-25T15:32:32,052   adding 'shephard/interfaces/si_domains.py'
2026-07-25T15:32:32,055   adding 'shephard/interfaces/si_protein_attributes.py'
2026-07-25T15:32:32,057   adding 'shephard/interfaces/si_proteins.py'
2026-07-25T15:32:32,060   adding 'shephard/interfaces/si_sites.py'
2026-07-25T15:32:32,064   adding 'shephard/interfaces/si_tracks.py'
2026-07-25T15:32:32,066   adding 'shephard/tests/__init__.py'
2026-07-25T15:32:32,068   adding 'shephard/tests/conftest.py'
2026-07-25T15:32:32,069   adding 'shephard/tests/example_test_function.py'
2026-07-25T15:32:32,070   adding 'shephard/tests/test_DomainInterface.py'
2026-07-25T15:32:32,071   adding 'shephard/tests/test_ProteinAttributesInterface.py'
2026-07-25T15:32:32,073   adding 'shephard/tests/test_ProteinInterface.py'
2026-07-25T15:32:32,074   adding 'shephard/tests/test_SiteInterface.py'
2026-07-25T15:32:32,075   adding 'shephard/tests/test_TrackInterface.py'
2026-07-25T15:32:32,077   adding 'shephard/tests/test_add_remove_annotations.py'
2026-07-25T15:32:32,078   adding 'shephard/tests/test_api_albatross.py'
2026-07-25T15:32:32,080   adding 'shephard/tests/test_api_metapredict.py'
2026-07-25T15:32:32,084   adding 'shephard/tests/test_api_uniprot_annotation.py'
2026-07-25T15:32:32,085   adding 'shephard/tests/test_api_uniprot_live.py'
2026-07-25T15:32:32,087   adding 'shephard/tests/test_apis_fasta.py'
2026-07-25T15:32:32,088   adding 'shephard/tests/test_attribute_tools.py'
2026-07-25T15:32:32,090   adding 'shephard/tests/test_bugfix_regressions.py'
2026-07-25T15:32:32,092   adding 'shephard/tests/test_bugfix_regressions_0_2_3.py'
2026-07-25T15:32:32,094   adding 'shephard/tests/test_comprehensive_apis.py'
2026-07-25T15:32:32,096   adding 'shephard/tests/test_comprehensive_domain.py'
2026-07-25T15:32:32,098   adding 'shephard/tests/test_comprehensive_interfaces.py'
2026-07-25T15:32:32,100   adding 'shephard/tests/test_comprehensive_protein.py'
2026-07-25T15:32:32,102   adding 'shephard/tests/test_comprehensive_proteome.py'
2026-07-25T15:32:32,104   adding 'shephard/tests/test_comprehensive_site.py'
2026-07-25T15:32:32,105   adding 'shephard/tests/test_comprehensive_tools.py'
2026-07-25T15:32:32,107   adding 'shephard/tests/test_comprehensive_track.py'
2026-07-25T15:32:32,108   adding 'shephard/tests/test_domain_tools.py'
2026-07-25T15:32:32,110   adding 'shephard/tests/test_domains.py'
2026-07-25T15:32:32,111   adding 'shephard/tests/test_interfaces.py'
2026-07-25T15:32:32,113   adding 'shephard/tests/test_protein.py'
2026-07-25T15:32:32,114   adding 'shephard/tests/test_protein_site_functions.py'
2026-07-25T15:32:32,116   adding 'shephard/tests/test_proteome.py'
2026-07-25T15:32:32,118   adding 'shephard/tests/test_scratchpad.ipynb'
2026-07-25T15:32:32,120   adding 'shephard/tests/test_sequence_tools.py'
2026-07-25T15:32:32,121   adding 'shephard/tests/test_shephard.py'
2026-07-25T15:32:32,122   adding 'shephard/tests/test_si_domains.py'
2026-07-25T15:32:32,124   adding 'shephard/tests/test_si_sites.py'
2026-07-25T15:32:32,126   adding 'shephard/tests/test_si_tracks.py'
2026-07-25T15:32:32,127   adding 'shephard/tests/test_sites.py'
2026-07-25T15:32:32,128   adding 'shephard/tests/test_track_tools.py'
2026-07-25T15:32:32,129   adding 'shephard/tests/test_tracks.py'
2026-07-25T15:32:32,131   adding 'shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb'
2026-07-25T15:32:32,133   adding 'shephard/tests/output_test/all_symbols_test.tsv'
2026-07-25T15:32:32,135   adding 'shephard/tests/output_test/all_values_test.tsv'
2026-07-25T15:32:32,138   adding 'shephard/tests/output_test/all_values_test_from_list.tsv'
2026-07-25T15:32:32,147   adding 'shephard/tests/output_test/out_tracks.tsv'
2026-07-25T15:32:32,148   adding 'shephard/tests/output_test/readme.md'
2026-07-25T15:32:32,149   adding 'shephard/tests/output_test/shephard_track_phosres.tsv'
2026-07-25T15:32:32,158   adding 'shephard/tests/output_test/shephard_track_pscore.tsv'
2026-07-25T15:32:32,159   adding 'shephard/tests/output_test/test_domains.tsv'
2026-07-25T15:32:32,160   adding 'shephard/tests/output_test/test_domains_types.tsv'
2026-07-25T15:32:32,164   adding 'shephard/tests/output_test/test_sites.tsv'
2026-07-25T15:32:32,165   adding 'shephard/tests/output_test/track_phospho_track.tsv'
2026-07-25T15:32:32,167   adding 'shephard/tests/output_test/track_random_vals.tsv'
2026-07-25T15:32:32,169   adding 'shephard/tools/__init__.py'
2026-07-25T15:32:32,170   adding 'shephard/tools/attribute_tools.py'
2026-07-25T15:32:32,171   adding 'shephard/tools/attribute_tools.py~'
2026-07-25T15:32:32,174   adding 'shephard/tools/domain_tools.py'
2026-07-25T15:32:32,176   adding 'shephard/tools/experimental.py'
2026-07-25T15:32:32,178   adding 'shephard/tools/sequence_tools.py'
2026-07-25T15:32:32,179   adding 'shephard/tools/site_tools.py'
2026-07-25T15:32:32,181   adding 'shephard/tools/track_tools.py'
2026-07-25T15:32:32,184   adding 'shephard-0.2.3.dist-info/licenses/LICENSE'
2026-07-25T15:32:32,185   adding 'shephard-0.2.3.dist-info/METADATA'
2026-07-25T15:32:32,186   adding 'shephard-0.2.3.dist-info/WHEEL'
2026-07-25T15:32:32,187   adding 'shephard-0.2.3.dist-info/top_level.txt'
2026-07-25T15:32:32,189   adding 'shephard-0.2.3.dist-info/RECORD'
2026-07-25T15:32:32,195   removing build/bdist.linux-armv7l/wheel
2026-07-25T15:32:32,319   Building wheel for shephard (pyproject.toml): finished with status 'done'
2026-07-25T15:32:32,328   Created wheel for shephard: filename=shephard-0.2.3-py3-none-any.whl size=258431 sha256=5fc4d758d03e293d2abeca08ccf2b5d9d36ecdd842c63c24b5920ac46342b2de
2026-07-25T15:32:32,329   Stored in directory: /tmp/pip-ephem-wheel-cache-1mxtkihh/wheels/ef/67/1e/837c151801097a9c72e59cfaffefba1ef1bb0c68b4831a2e35
2026-07-25T15:32:32,343 Successfully built shephard
2026-07-25T15:32:32,352 Removed build tracker: '/tmp/pip-build-tracker-smkxz8p3'