Read the Docs build information Build id: 1635301 Project: institute-for-disease-modeling-hiv-workflow Version: latest Commit: 3bd471af18e6b04648aa550f323db0162e1ac162 Date: 2023-08-02T00:10:30.117996Z State: finished Success: False [rtd-command-info] start-time: 2023-08-02T00:27:51.542470Z, end-time: 2023-08-02T00:27:57.901985Z, duration: 6, exit-code: 0 git clone --depth 1 git@github.com:InstituteforDiseaseModeling/hiv_workflow.git . Cloning into '.'... Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. 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[rtd-command-info] start-time: 2023-08-02T00:27:58.302133Z, end-time: 2023-08-02T00:27:59.938530Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. [rtd-command-info] start-time: 2023-08-02T00:28:00.190010Z, end-time: 2023-08-02T00:28:02.121495Z, duration: 1, exit-code: 0 git checkout --force origin/main Note: switching to 'origin/main'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 3bd471a clarifying a variable name to make the code safer and more understandable [rtd-command-info] start-time: 2023-08-02T00:28:02.487366Z, end-time: 2023-08-02T00:28:02.599528Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-08-02T00:28:02.900167Z, end-time: 2023-08-02T00:28:02.985359Z, duration: 0, exit-code: 0 cat .readthedocs.yml # .readthedocs.yml # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details # Required version: 2 # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py fail_on_warning: true # Build documentation with MkDocs #mkdocs: # configuration: mkdocs.yml # Optionally build your docs in additional formats such as PDF formats: - htmlzip - pdf # Optionally set the version of Python and requirements required to build your docs python: version: 3.7 install: - requirements: requirements.txt - method: setuptools path: . - requirements: docs/requirements.txt system_packages: true # Optionally rank topics in search results, between -10 (lower) and 10 (higher). # 0 is normal rank, not no rank search: ranking: index.html: 3 modules.html: 2 [rtd-command-info] start-time: 2023-08-02T00:28:06.317696Z, end-time: 2023-08-02T00:28:17.684436Z, duration: 11, exit-code: 0 python3.7 -mvirtualenv --system-site-packages $READTHEDOCS_VIRTUALENV_PATH Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/bin/python Installing setuptools, pip, wheel... done. 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wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23771 sha256=c43a80abf3d768756539cc494728266e9e2c212790aa37d329d26f5c873dc5ff Stored in directory: /tmp/pip-ephem-wheel-cache-kdb7n3u_/wheels/39/db/d5/e22e622f3ac6beb40ab992464b2b5ae38526942ed4ffff7c05 Successfully built mock Installing collected packages: snowballstemmer, pytz, mock, commonmark, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, setuptools, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext, sphinxcontrib-jquery, recommonmark, sphinx-rtd-theme ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. matplotlib 3.5.3 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible. Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.3 Pygments-2.15.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.7.22 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.18.1 idna-3.4 imagesize-1.4.1 importlib-metadata-6.7.0 mock-1.0.1 packaging-23.1 pillow-5.4.1 pytz-2023.3 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 setuptools-58.2.0 snowballstemmer-2.2.0 sphinx-5.3.0 sphinx-rtd-theme-1.2.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jquery-4.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 typing-extensions-4.7.1 urllib3-2.0.4 zipp-3.15.0 [rtd-command-info] start-time: 2023-08-02T00:28:44.951306Z, end-time: 2023-08-02T00:29:31.221062Z, duration: 46, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Looking in indexes: https://packages.idmod.org/api/pypi/pypi-production/simple Collecting idmtools_calibra~=1.0.5 (from -r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools-calibra/1.0.10/idmtools_calibra-1.0.10-py3-none-any.whl (153 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 154.0/154.0 kB 4.6 MB/s eta 0:00:00 Collecting emodpy-hiv~=1.0.2 (from -r requirements.txt (line 3)) Downloading https://packages.idmod.org/api/pypi/pypi-production/emodpy-hiv/1.0.2/emodpy_hiv-1.0.2-py3-none-any.whl (46 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 46.3/46.3 kB 5.4 MB/s eta 0:00:00 Collecting openpyxl (from -r requirements.txt (line 4)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/6a/94/a59521de836ef0da54aaf50da6c4da8fb4072fb3053fa71f052fd9399e7a/openpyxl-3.1.2-py2.py3-none-any.whl (249 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 250.0/250.0 kB 5.0 MB/s eta 0:00:00 Collecting lz4 (from -r requirements.txt (line 5)) Downloading 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Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools/1.7.8/idmtools-1.7.8-py3-none-any.whl (168 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 168.4/168.4 kB 7.1 MB/s eta 0:00:00 Requirement already satisfied: scipy~=1.5 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from idmtools_calibra~=1.0.5->-r requirements.txt (line 2)) (1.7.3) Collecting seaborn~=0.11 (from idmtools_calibra~=1.0.5->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/8f/2e/17bbb83fbf102687bb2aa3d808add39da820a7698159302a1a69bb82e01c/seaborn-0.12.2-py3-none-any.whl (293 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 293.3/293.3 kB 10.4 MB/s eta 0:00:00 Collecting scikit-learn (from idmtools_calibra~=1.0.5->-r requirements.txt (line 2)) Downloading 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https://packages.idmod.org/api/pypi/pypi-production/emodpy/1.21.1/emodpy-1.21.1-py3-none-any.whl (121 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.7/121.7 kB 104.5 MB/s eta 0:00:00 Collecting emod-hiv==0.0.4 (from emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) Downloading https://packages.idmod.org/api/pypi/pypi-production/emod-hiv/0.0.4/emod_hiv-0.0.4-py3-none-any.whl (44.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 44.0/44.0 MB 14.8 MB/s eta 0:00:00 Collecting et-xmlfile (from openpyxl->-r requirements.txt (line 4)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/96/c2/3dd434b0108730014f1b96fd286040dc3bcb70066346f7e01ec2ac95865f/et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB) Collecting click~=7.1 (from emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d2/3d/fa76db83bf75c4f8d338c2fd15c8d33fdd7ad23a9b5e57eb6c5de26b430e/click-7.1.2-py2.py3-none-any.whl (82 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/home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) (3.5.3) Collecting astor (from emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c3/88/97eef84f48fa04fbd6750e62dcceafba6c63c81b7ac1420856c8dcc0a3f9/astor-0.8.1-py2.py3-none-any.whl (27 kB) Collecting astunparse (from emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2b/03/13dde6512ad7b4557eb792fbcf0c653af6076b81e5941d36ec61f7ce6028/astunparse-1.6.3-py2.py3-none-any.whl (12 kB) Collecting bs4 (from emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/10/ed/7e8b97591f6f456174139ec089c769f89a94a1a4025fe967691de971f314/bs4-0.0.1.tar.gz (1.1 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting keyring (from emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c5/9e/9517ad9978abfd2c579c0f7bd6ff3c549b5e0ea8a0e7ad345879c83a5b87/keyring-24.1.1-py3-none-any.whl (37 kB) Collecting pyCOMPS~=2.6 (from emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) Downloading https://packages.idmod.org/api/pypi/pypi-production/pyCOMPS/2.10.0/pyCOMPS-2.10.0-py2.py3-none-any.whl (74 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 74.5/74.5 kB 85.5 MB/s eta 0:00:00 Collecting geographiclib<3,>=1.52 (from geopy~=2.0->idmtools_calibra~=1.0.5->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9f/5a/a26132406f1f40cf51ea349a5f11b0a46cec02a2031ff82e391c2537247a/geographiclib-2.0-py3-none-any.whl (40 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.3/40.3 kB 83.2 MB/s eta 0:00:00 Collecting backoff<2.3,>=1.10.0 (from idmtools~=1.7->idmtools_calibra~=1.0.5->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/df/73/b6e24bd22e6720ca8ee9a85a0c4a2971af8497d8f3193fa05390cbd46e09/backoff-2.2.1-py3-none-any.whl (15 kB) Collecting coloredlogs~=15.0 (from idmtools~=1.7->idmtools_calibra~=1.0.5->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a7/06/3d6badcf13db419e25b07041d9c7b4a2c331d3f4e7134445ec5df57714cd/coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 46.0/46.0 kB 76.6 MB/s eta 0:00:00 Collecting diskcache~=5.4.0 (from idmtools~=1.7->idmtools_calibra~=1.0.5->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a1/c4/80d38cf6852ba87f8b506a91f18b3a485c668f452700689add960d7e2ecc/diskcache-5.4.0-py3-none-any.whl (44 kB) 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Collecting SecretStorage>=3.2 (from keyring->emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/54/24/b4293291fa1dd830f353d2cb163295742fa87f179fcc8a20a306a81978b7/SecretStorage-3.3.3-py3-none-any.whl (15 kB) Collecting jeepney>=0.4.2 (from keyring->emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ae/72/2a1e2290f1ab1e06f71f3d0f1646c9e4634e70e1d37491535e19266e8dc9/jeepney-0.8.0-py3-none-any.whl (48 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.4/48.4 kB 82.7 MB/s eta 0:00:00 Collecting pycparser (from cffi>=1.9.1->pygit2<=1.10.1,>=1.4.0->idmtools~=1.7->idmtools_calibra~=1.0.5->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/62/d5/5f610ebe421e85889f2e55e33b7f9a6795bd982198517d912eb1c76e1a53/pycparser-2.21-py2.py3-none-any.whl (118 kB) 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Collecting soupsieve>1.2 (from beautifulsoup4->bs4->emodpy~=1.15->emodpy-hiv~=1.0.2->-r requirements.txt (line 3)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/49/37/673d6490efc51ec46d198c75903d99de59baffdd47aea3d071b80a9e4e89/soupsieve-2.4.1-py3-none-any.whl (36 kB) Building wheels for collected packages: bs4, future, docopt, prodict Building wheel for bs4 (setup.py): started Building wheel for bs4 (setup.py): finished with status 'done' Created wheel for bs4: filename=bs4-0.0.1-py3-none-any.whl size=1271 sha256=823e32e361c1846c02300fb06c58094c8f9f250f5ad29aaeae6a288a8f7ba6d3 Stored in directory: /tmp/pip-ephem-wheel-cache-_kykf971/wheels/f1/23/17/3fcd260137068c2aa94da5806487146928f092eae4c2405b28 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492036 sha256=564fce876f9ba36906ab8c34c08fb44b9fcbfa21e18bfec7890b340ca7b1533d Stored in directory: /tmp/pip-ephem-wheel-cache-_kykf971/wheels/c4/f7/54/ce38ea620e2cd4e42cac68b1ca4904d1989313cd96c0b06673 Building wheel for docopt (setup.py): started Building wheel for docopt (setup.py): finished with status 'done' Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13723 sha256=c63b59144097bf60cc41d30c669ca8fe7bfab9e8bfabf6841031f7b2d305b077 Stored in directory: /tmp/pip-ephem-wheel-cache-_kykf971/wheels/d8/15/92/75bdb77cd20ddf510bfcf61379c480591df059bcd22a084f6c Building wheel for prodict (setup.py): started Building wheel for prodict (setup.py): finished with status 'done' Created wheel for prodict: filename=prodict-0.8.18-py3-none-any.whl size=4222 sha256=51ba7a90ba9c8bd4030834551078ddc2d23957bc491ca129e71f3a6cf51dbe37 Stored in directory: /tmp/pip-ephem-wheel-cache-_kykf971/wheels/a1/47/0e/cbfbed83f6077c4d538850a09e49b8d78284632fc1d48bf122 Successfully built bs4 future docopt prodict Installing collected packages: prodict, parse, emod-hiv, docopt, cached-property, xdg, tqdm, threadpoolctl, tabulate, soupsieve, shapely, PyYaml, pyproj, pycparser, pillow, patsy, packaging, natsort, more-itertools, lz4, joblib, jeepney, importlib-resources, humanfriendly, graphviz, geographiclib, future, filelock, fasteners, et-xmlfile, diskcache, click, backoff, astunparse, astor, yarg, scikit-learn, pyCOMPS, pluggy, openpyxl, jaraco.classes, geopy, coloredlogs, cffi, beautifulsoup4, statsmodels, seaborn, pygit2, pipreqs, emod-api, cryptography, bs4, SecretStorage, idmtools, keyring, idmtools-platform-comps, idmtools-models, idmtools_calibra, emodpy, emodpy-hiv Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Attempting uninstall: packaging Found existing installation: packaging 23.1 Uninstalling packaging-23.1: Successfully uninstalled packaging-23.1 Successfully installed PyYaml-6.0.1 SecretStorage-3.3.3 astor-0.8.1 astunparse-1.6.3 backoff-2.2.1 beautifulsoup4-4.12.2 bs4-0.0.1 cached-property-1.5.2 cffi-1.15.1 click-7.1.2 coloredlogs-15.0.1 cryptography-41.0.3 diskcache-5.4.0 docopt-0.6.2 emod-api-1.29.7 emod-hiv-0.0.4 emodpy-1.21.1 emodpy-hiv-1.0.2 et-xmlfile-1.1.0 fasteners-0.18 filelock-3.12.2 future-0.18.3 geographiclib-2.0 geopy-2.3.0 graphviz-0.20.1 humanfriendly-10.0 idmtools-1.7.8 idmtools-models-1.7.8 idmtools-platform-comps-1.7.8 idmtools_calibra-1.0.10 importlib-resources-5.12.0 jaraco.classes-3.2.3 jeepney-0.8.0 joblib-1.3.1 keyring-24.1.1 lz4-4.3.2 more-itertools-9.0.0 natsort-8.2.0 openpyxl-3.1.2 packaging-21.3 parse-1.19.1 patsy-0.5.3 pillow-9.5.0 pipreqs-0.4.13 pluggy-1.0.0 prodict-0.8.18 pyCOMPS-2.10.0 pycparser-2.21 pygit2-1.10.1 pyproj-3.2.1 scikit-learn-1.0.2 seaborn-0.12.2 shapely-2.0.1 soupsieve-2.4.1 statsmodels-0.13.5 tabulate-0.9.0 threadpoolctl-3.1.0 tqdm-4.65.0 xdg-6.0.0 yarg-0.1.9 [rtd-command-info] start-time: 2023-08-02T00:29:31.466511Z, end-time: 2023-08-02T00:29:32.992282Z, duration: 1, exit-code: 1 python ./setup.py install --force running install running bdist_egg running egg_info creating hiv_workflow.egg-info writing hiv_workflow.egg-info/PKG-INFO writing dependency_links to hiv_workflow.egg-info/dependency_links.txt writing requirements to hiv_workflow.egg-info/requires.txt writing top-level names to hiv_workflow.egg-info/top_level.txt writing manifest file 'hiv_workflow.egg-info/SOURCES.txt' reading manifest file 'hiv_workflow.egg-info/SOURCES.txt' writing manifest file 'hiv_workflow.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib creating build/lib/hiv_workflow copying hiv_workflow/__init__.py -> build/lib/hiv_workflow creating build/lib/hiv_workflow/scripts copying hiv_workflow/scripts/calibrate.py -> build/lib/hiv_workflow/scripts copying hiv_workflow/scripts/resample.py -> build/lib/hiv_workflow/scripts copying hiv_workflow/scripts/run.py -> build/lib/hiv_workflow/scripts copying hiv_workflow/scripts/__init__.py -> build/lib/hiv_workflow/scripts copying hiv_workflow/scripts/available_parameters.py -> build/lib/hiv_workflow/scripts copying hiv_workflow/scripts/dtk_post_process.py -> build/lib/hiv_workflow/scripts copying hiv_workflow/scripts/download.py -> build/lib/hiv_workflow/scripts creating build/lib/hiv_workflow/lib copying hiv_workflow/lib/__init__.py -> build/lib/hiv_workflow/lib creating build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/download_analyzer_by_experiment.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/hiv_analyzer.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/age_bin.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/base_distribution.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/population_obs.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/data_frame_wrapper.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/__init__.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/gaussian_distribution.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/beta_distribution.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/channel.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/download_analyzer_by_experiment_receipt.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/condition.py -> build/lib/hiv_workflow/lib/analysis copying hiv_workflow/lib/analysis/hiv_calib_site.py -> build/lib/hiv_workflow/lib/analysis creating build/lib/hiv_workflow/lib/utils copying hiv_workflow/lib/utils/runtime.py -> build/lib/hiv_workflow/lib/utils copying hiv_workflow/lib/utils/wrappers.py -> build/lib/hiv_workflow/lib/utils copying hiv_workflow/lib/utils/__init__.py -> build/lib/hiv_workflow/lib/utils copying hiv_workflow/lib/utils/project_data.py -> build/lib/hiv_workflow/lib/utils copying hiv_workflow/lib/utils/analysis.py -> build/lib/hiv_workflow/lib/utils creating build/lib/hiv_workflow/lib/calibration copying hiv_workflow/lib/calibration/__init__.py -> build/lib/hiv_workflow/lib/calibration creating build/lib/hiv_workflow/lib/utils/io copying hiv_workflow/lib/utils/io/__init__.py -> build/lib/hiv_workflow/lib/utils/io copying hiv_workflow/lib/utils/io/excel.py -> build/lib/hiv_workflow/lib/utils/io creating build/lib/hiv_workflow/lib/utils/builders copying hiv_workflow/lib/utils/builders/demographics.py -> build/lib/hiv_workflow/lib/utils/builders copying hiv_workflow/lib/utils/builders/__init__.py -> build/lib/hiv_workflow/lib/utils/builders copying hiv_workflow/lib/utils/builders/general.py -> build/lib/hiv_workflow/lib/utils/builders creating build/lib/hiv_workflow/lib/calibration/algorithms copying hiv_workflow/lib/calibration/algorithms/__init__.py -> build/lib/hiv_workflow/lib/calibration/algorithms copying hiv_workflow/lib/calibration/algorithms/optim_tool.py -> build/lib/hiv_workflow/lib/calibration/algorithms creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/hiv_workflow copying build/lib/hiv_workflow/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow creating build/bdist.linux-x86_64/egg/hiv_workflow/scripts copying build/lib/hiv_workflow/scripts/calibrate.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts copying build/lib/hiv_workflow/scripts/resample.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts copying build/lib/hiv_workflow/scripts/run.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts copying build/lib/hiv_workflow/scripts/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts copying build/lib/hiv_workflow/scripts/available_parameters.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts copying build/lib/hiv_workflow/scripts/dtk_post_process.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts copying build/lib/hiv_workflow/scripts/download.py -> build/bdist.linux-x86_64/egg/hiv_workflow/scripts creating build/bdist.linux-x86_64/egg/hiv_workflow/lib creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/download_analyzer_by_experiment.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/hiv_analyzer.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/age_bin.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/base_distribution.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/population_obs.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/data_frame_wrapper.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/gaussian_distribution.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/beta_distribution.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/channel.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/download_analyzer_by_experiment_receipt.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/condition.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/analysis/hiv_calib_site.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis copying build/lib/hiv_workflow/lib/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils copying build/lib/hiv_workflow/lib/utils/runtime.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/io copying build/lib/hiv_workflow/lib/utils/io/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/io copying build/lib/hiv_workflow/lib/utils/io/excel.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/io copying build/lib/hiv_workflow/lib/utils/wrappers.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils copying build/lib/hiv_workflow/lib/utils/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders copying build/lib/hiv_workflow/lib/utils/builders/demographics.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders copying build/lib/hiv_workflow/lib/utils/builders/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders copying build/lib/hiv_workflow/lib/utils/builders/general.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders copying build/lib/hiv_workflow/lib/utils/project_data.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils copying build/lib/hiv_workflow/lib/utils/analysis.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration creating build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/algorithms copying build/lib/hiv_workflow/lib/calibration/algorithms/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/algorithms copying build/lib/hiv_workflow/lib/calibration/algorithms/optim_tool.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/algorithms copying build/lib/hiv_workflow/lib/calibration/__init__.py -> build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/calibrate.py to calibrate.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/resample.py to resample.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/run.py to run.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/available_parameters.py to available_parameters.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/dtk_post_process.py to dtk_post_process.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/scripts/download.py to download.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/download_analyzer_by_experiment.py to download_analyzer_by_experiment.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/hiv_analyzer.py to hiv_analyzer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/age_bin.py to age_bin.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/base_distribution.py to base_distribution.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/population_obs.py to population_obs.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/data_frame_wrapper.py to data_frame_wrapper.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/gaussian_distribution.py to gaussian_distribution.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/beta_distribution.py to beta_distribution.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/channel.py to channel.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/download_analyzer_by_experiment_receipt.py to download_analyzer_by_experiment_receipt.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/condition.py to condition.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/analysis/hiv_calib_site.py to hiv_calib_site.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/runtime.py to runtime.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/io/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/io/excel.py to excel.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/wrappers.py to wrappers.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders/demographics.py to demographics.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/builders/general.py to general.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/project_data.py to project_data.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/utils/analysis.py to analysis.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/algorithms/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/algorithms/optim_tool.py to optim_tool.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/hiv_workflow/lib/calibration/__init__.py to __init__.cpython-37.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying hiv_workflow.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying hiv_workflow.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying hiv_workflow.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying hiv_workflow.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying hiv_workflow.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... hiv_workflow.lib.analysis.__pycache__.base_distribution.cpython-37: module references __file__ hiv_workflow.lib.calibration.algorithms.__pycache__.optim_tool.cpython-37: module references __file__ hiv_workflow.lib.utils.__pycache__.runtime.cpython-37: module references __path__ hiv_workflow.scripts.__pycache__.available_parameters.cpython-37: module references __file__ hiv_workflow.scripts.__pycache__.calibrate.cpython-37: module references __file__ hiv_workflow.scripts.__pycache__.run.cpython-37: module references __file__ creating dist creating 'dist/hiv_workflow-1.0.0-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing hiv_workflow-1.0.0-py3.7.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages/hiv_workflow-1.0.0-py3.7.egg Extracting hiv_workflow-1.0.0-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages Adding hiv-workflow 1.0.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-hiv-workflow/envs/latest/lib/python3.7/site-packages/hiv_workflow-1.0.0-py3.7.egg Processing dependencies for hiv-workflow==1.0.0 error: packaging 23.1 is installed but packaging<22.0,>=20.4 is required by {'idmtools'}