Read the Docs build information Build id: 2079085 Project: institute-for-disease-modeling-emodpy-hiv Version: 199 Commit: 1d761ace739da60657255f96481ad79aa56914b2 Date: 2024-03-12T18:15:04.621306Z State: finished Success: True [rtd-command-info] start-time: 2024-03-12T18:15:05.723169Z, end-time: 2024-03-12T18:15:07.340464Z, duration: 1, exit-code: 0 git clone --depth 1 git@github.com:InstituteforDiseaseModeling/emodpy-hiv.git . Cloning into '.'... Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. [rtd-command-info] start-time: 2024-03-12T18:15:07.408042Z, end-time: 2024-03-12T18:15:11.085119Z, duration: 3, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/199/head:external-199 Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. From github.com:InstituteforDiseaseModeling/emodpy-hiv * [new ref] refs/pull/199/head -> external-199 Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. * [new tag] v1.0.2 -> v1.0.2 [rtd-command-info] start-time: 2024-03-12T18:15:11.215361Z, end-time: 2024-03-12T18:15:11.384287Z, duration: 0, exit-code: 0 git checkout --force 1d761ace739da60657255f96481ad79aa56914b2 Note: switching to '1d761ace739da60657255f96481ad79aa56914b2'. 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 1d761ac update and fix hiv.py and rename to coc.py [rtd-command-info] start-time: 2024-03-12T18:15:11.449010Z, end-time: 2024-03-12T18:15:11.510774Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2024-03-12T18:15:11.577639Z, end-time: 2024-03-12T18:15:11.637291Z, 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 # Set the version of Python and other tools you might need build: os: ubuntu-20.04 tools: python: "3.9" # 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 # Optionally set the version of Python and requirements required to build your docs python: install: - requirements: requirements.txt - requirements: docs/requirements.txt - method: setuptools path: . # Optionally rank topics in search results, between -10 (lower) and 10 (higher). # 0 is normal rank, not no rank # search: # ranking: [rtd-command-info] start-time: 2024-03-12T18:15:17.468005Z, end-time: 2024-03-12T18:15:17.546296Z, duration: 0, exit-code: 0 asdf global python 3.9.18 [rtd-command-info] start-time: 2024-03-12T18:15:17.969559Z, end-time: 2024-03-12T18:15:19.101694Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.18.final.0-64 in 834ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2024-03-12T18:15:19.169089Z, end-time: 2024-03-12T18:15:32.753450Z, duration: 13, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (23.1) Collecting pip Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/8a/6a/19e9fe04fca059ccf770861c7d5721ab4c2aebc539889e97c7977528a53b/pip-24.0-py3-none-any.whl (2.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 11.5 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (67.6.1) Collecting setuptools Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c0/7a/3da654f49c95d0cc6e9549a855b5818e66a917e852ec608e77550c8dc08b/setuptools-69.1.1-py3-none-any.whl (819 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 819.3/819.3 kB 15.8 MB/s eta 0:00:00 Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 67.6.1 Uninstalling setuptools-67.6.1: Successfully uninstalled setuptools-67.6.1 Attempting uninstall: pip Found existing installation: pip 23.1 Uninstalling pip-23.1: Successfully uninstalled pip-23.1 Successfully installed pip-24.0 setuptools-69.1.1 [rtd-command-info] start-time: 2024-03-12T18:15:32.837126Z, end-time: 2024-03-12T18:15:43.698185Z, duration: 10, exit-code: 0 python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Collecting sphinx Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/b2/b6/8ed35256aa530a9d3da15d20bdc0ba888d5364441bb50a5a83ee7827affe/sphinx-7.2.6-py3-none-any.whl (3.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 15.1 MB/s eta 0:00:00 Collecting readthedocs-sphinx-ext Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/64/71/c89e7709a0d4f93af1848e9855112299a820b470d84f917b4dd5998bdd07/readthedocs_sphinx_ext-2.2.5-py2.py3-none-any.whl (11 kB) Collecting sphinxcontrib-applehelp (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/56/89/fea3fbf6785b388e6cb8a1beaf62f96e80b37311bdeed6e133388a732426/sphinxcontrib_applehelp-1.0.8-py3-none-any.whl (120 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 120.0/120.0 kB 214.1 MB/s eta 0:00:00 Collecting sphinxcontrib-devhelp (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a0/52/1049d918d1d1c72857d285c3f0c64c1cbe0be394ce1c93a3d2aa4f39fe3b/sphinxcontrib_devhelp-1.0.6-py3-none-any.whl (83 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 83.5/83.5 kB 199.8 MB/s eta 0:00:00 Collecting sphinxcontrib-jsmath (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c2/42/4c8646762ee83602e3fb3fbe774c2fac12f317deb0b5dbeeedd2d3ba4b77/sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting sphinxcontrib-htmlhelp>=2.0.0 (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c2/e9/74c4cda5b409af3222fda38f0774e616011bc935f639dbc0da5ca2d1be7d/sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl (99 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 99.2/99.2 kB 209.0 MB/s eta 0:00:00 Collecting sphinxcontrib-serializinghtml>=1.1.9 (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/38/24/228bb903ea87b9e08ab33470e6102402a644127108c7117ac9c00d849f82/sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl (92 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 92.7/92.7 kB 205.2 MB/s eta 0:00:00 Collecting sphinxcontrib-qthelp (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/80/b3/1beac14a88654d2e5120d0143b49be5ad450b86eb1963523d8dbdcc51eb2/sphinxcontrib_qthelp-1.0.7-py3-none-any.whl (89 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 89.4/89.4 kB 207.6 MB/s eta 0:00:00 Collecting Jinja2>=3.0 (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/30/6d/6de6be2d02603ab56e72997708809e8a5b0fbfee080735109b40a3564843/Jinja2-3.1.3-py3-none-any.whl (133 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.2/133.2 kB 18.1 MB/s eta 0:00:00 Collecting Pygments>=2.14 (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/97/9c/372fef8377a6e340b1704768d20daaded98bf13282b5327beb2e2fe2c7ef/pygments-2.17.2-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 15.6 MB/s eta 0:00:00 Collecting docutils<0.21,>=0.18.1 (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/26/87/f238c0670b94533ac0353a4e2a1a771a0cc73277b88bff23d3ae35a256c1/docutils-0.20.1-py3-none-any.whl (572 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 572.7/572.7 kB 16.3 MB/s eta 0:00:00 Collecting snowballstemmer>=2.0 (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ed/dc/c02e01294f7265e63a7315fe086dd1df7dacb9f840a804da846b96d01b96/snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 207.5 MB/s eta 0:00:00 Collecting babel>=2.9 (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/0d/35/4196b21041e29a42dc4f05866d0c94fa26c9da88ce12c38c2265e42c82fb/Babel-2.14.0-py3-none-any.whl (11.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.0/11.0 MB 15.2 MB/s eta 0:00:00 Collecting alabaster<0.8,>=0.7 (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/32/34/d4e1c02d3bee589efb5dfa17f88ea08bdb3e3eac12bc475462aec52ed223/alabaster-0.7.16-py3-none-any.whl (13 kB) Collecting imagesize>=1.3 (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ff/62/85c4c919272577931d407be5ba5d71c20f0b616d31a0befe0ae45bb79abd/imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Collecting requests>=2.25.0 (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/70/8e/0e2d847013cb52cd35b38c009bb167a1a26b2ce6cd6965bf26b47bc0bf44/requests-2.31.0-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.6/62.6 kB 185.7 MB/s eta 0:00:00 Collecting packaging>=21.0 (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/49/df/1fceb2f8900f8639e278b056416d49134fb8d84c5942ffaa01ad34782422/packaging-24.0-py3-none-any.whl (53 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.5/53.5 kB 145.0 MB/s eta 0:00:00 Collecting importlib-metadata>=4.8 (from sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/db/62/6879ab53ad4997b627fc67241a41eabf7163299c59580c6ca4aa5ae6b677/importlib_metadata-7.0.2-py3-none-any.whl (24 kB) Collecting zipp>=0.5 (from importlib-metadata>=4.8->sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d9/66/48866fc6b158c81cc2bfecc04c480f105c6040e8b077bc54c634b4a67926/zipp-3.17.0-py3-none-any.whl (7.4 kB) Collecting MarkupSafe>=2.0 (from Jinja2>=3.0->sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/5f/5a/360da85076688755ea0cceb92472923086993e86b5613bbae9fbc14136b0/MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Collecting charset-normalizer<4,>=2 (from requests>=2.25.0->sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/98/69/5d8751b4b670d623aa7a47bef061d69c279e9f922f6705147983aa76c3ce/charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 142.3/142.3 kB 19.4 MB/s eta 0:00:00 Collecting idna<4,>=2.5 (from requests>=2.25.0->sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c2/e7/a82b05cf63a603df6e68d59ae6a68bf5064484a0718ea5033660af4b54a9/idna-3.6-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.6/61.6 kB 181.8 MB/s eta 0:00:00 Collecting urllib3<3,>=1.21.1 (from requests>=2.25.0->sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a2/73/a68704750a7679d0b6d3ad7aa8d4da8e14e151ae82e6fee774e6e0d05ec8/urllib3-2.2.1-py3-none-any.whl (121 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.1/121.1 kB 219.6 MB/s eta 0:00:00 Collecting certifi>=2017.4.17 (from requests>=2.25.0->sphinx) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ba/06/a07f096c664aeb9f01624f858c3add0a4e913d6c96257acb4fce61e7de14/certifi-2024.2.2-py3-none-any.whl (163 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 163.8/163.8 kB 17.4 MB/s eta 0:00:00 Installing collected packages: snowballstemmer, zipp, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext Successfully installed Jinja2-3.1.3 MarkupSafe-2.1.5 Pygments-2.17.2 alabaster-0.7.16 babel-2.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.6 imagesize-1.4.1 importlib-metadata-7.0.2 packaging-24.0 readthedocs-sphinx-ext-2.2.5 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.8 sphinxcontrib-devhelp-1.0.6 sphinxcontrib-htmlhelp-2.0.5 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.7 sphinxcontrib-serializinghtml-1.1.10 urllib3-2.2.1 zipp-3.17.0 [rtd-command-info] start-time: 2024-03-12T18:15:43.783115Z, end-time: 2024-03-12T18:16:31.029748Z, duration: 47, 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 emodpy~=1.15 (from -r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/emodpy/1.22.0/emodpy-1.22.0-py3-none-any.whl (122 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 122.6/122.6 kB 5.9 MB/s eta 0:00:00 Collecting emod-hiv==1.0.1 (from -r requirements.txt (line 3)) Downloading https://packages.idmod.org/api/pypi/pypi-production/emod-hiv/1.0.1/emod_hiv-1.0.1-py3-none-any.whl (2.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.5/2.5 MB 12.6 MB/s eta 0:00:00 Collecting click~=7.1 (from emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d2/3d/fa76db83bf75c4f8d338c2fd15c8d33fdd7ad23a9b5e57eb6c5de26b430e/click-7.1.2-py2.py3-none-any.whl (82 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 82.8/82.8 kB 214.9 MB/s eta 0:00:00 Collecting idmtools~=1.7 (from emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools/1.7.9/idmtools-1.7.9-py3-none-any.whl (168 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 168.6/168.6 kB 18.6 MB/s eta 0:00:00 Collecting idmtools-platform-comps~=1.7 (from emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools-platform-comps/1.7.9/idmtools_platform_comps-1.7.9-py3-none-any.whl (188 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 188.5/188.5 kB 20.0 MB/s eta 0:00:00 Collecting idmtools-models~=1.7 (from emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/idmtools-models/1.7.9/idmtools_models-1.7.9.tar.gz (12 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting emod-api~=1.24 (from emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/emod-api/1.30.1/emod_api-1.30.1-py3-none-any.whl (166 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 166.6/166.6 kB 19.1 MB/s eta 0:00:00 Collecting matplotlib (from emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/35/82/ca05c3e3ec4a38eaf49a9bfa1a700658284ddaaa2e2523fa91fbb96d207a/matplotlib-3.8.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 12.4 MB/s eta 0:00:00 Collecting astor (from emodpy~=1.15->-r requirements.txt (line 2)) 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->-r requirements.txt (line 2)) 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->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/51/bb/bf7aab772a159614954d84aa832c129624ba6c32faa559dfb200a534e50b/bs4-0.0.2-py2.py3-none-any.whl (1.2 kB) Collecting keyring (from emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/7c/23/d557507915181687e4a613e1c8a01583fd6d7cb7590e1f039e357fe3b304/keyring-24.3.1-py3-none-any.whl (38 kB) Collecting pyCOMPS~=2.6 (from emodpy~=1.15->-r requirements.txt (line 2)) 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 177.8 MB/s eta 0:00:00 Collecting requests==2.29.0 (from emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/cf/e1/2aa539876d9ed0ddc95882451deb57cfd7aa8dbf0b8dbce68e045549ba56/requests-2.29.0-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.5/62.5 kB 201.9 MB/s eta 0:00:00 Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from requests==2.29.0->emodpy~=1.15->-r requirements.txt (line 2)) (3.3.2) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from requests==2.29.0->emodpy~=1.15->-r requirements.txt (line 2)) (3.6) Collecting urllib3<1.27,>=1.21.1 (from requests==2.29.0->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/b0/53/aa91e163dcfd1e5b82d8a890ecf13314e3e149c05270cc644581f77f17fd/urllib3-1.26.18-py2.py3-none-any.whl (143 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 143.8/143.8 kB 16.3 MB/s eta 0:00:00 Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from requests==2.29.0->emodpy~=1.15->-r requirements.txt (line 2)) (2024.2.2) Collecting numpy!=1.19.4 (from emod-api~=1.24->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/54/30/c2a907b9443cf42b90c17ad10c1e8fa801975f01cb9764f3f8eb8aea638b/numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 18.2/18.2 MB 12.4 MB/s eta 0:00:00 Collecting pyyaml (from emod-api~=1.24->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/7d/39/472f2554a0f1e825bd7c5afc11c817cd7a2f3657460f7159f691fbb37c51/PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (738 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 738.9/738.9 kB 14.4 MB/s eta 0:00:00 Collecting pandas (from emod-api~=1.24->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1a/5e/71bb0eef0dc543f7516d9ddeca9ee8dc98207043784e3f7e6c08b4a6b3d9/pandas-2.2.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.0/13.0 MB 12.4 MB/s eta 0:00:00 Collecting scipy (from emod-api~=1.24->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a6/9d/f864266894b67cdb5731ab531afba68713da3d6d8252f698ccab775d3f68/scipy-1.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (38.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.5/38.5 MB 12.5 MB/s eta 0:00:00 Collecting shapely (from emod-api~=1.24->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a7/c6/ff0ac1df8d9e806e8c710b08600cd7764f2cf794e6cc5749992298a1c9f2/shapely-2.0.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.5/2.5 MB 12.9 MB/s eta 0:00:00 Collecting pyproj (from emod-api~=1.24->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/97/0a/b1525be9680369cc06dd288e12c59d24d5798b4afcdcf1b0915836e1caa6/pyproj-3.6.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.3/8.3 MB 12.5 MB/s eta 0:00:00 Collecting geographiclib (from emod-api~=1.24->emodpy~=1.15->-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 160.5 MB/s eta 0:00:00 Collecting scikit-learn (from emod-api~=1.24->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f0/e8/c95689d74c61f558e9e7d4ef21173811dc2ae303d1307090f85bf5a3b70b/scikit_learn-1.4.1.post1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.2/12.2 MB 12.4 MB/s eta 0:00:00 Collecting lz4 (from emod-api~=1.24->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/10/39/baa1138796c410449ec1d8942cd8105c1ed41745e2b16f64dbe02ff10ee3/lz4-4.3.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 12.9 MB/s eta 0:00:00 Collecting prodict (from emod-api~=1.24->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/5a/0b/594c85ac539dda877198e7d5541982127d0929e3b0e8e6018004cfbd9ac9/prodict-0.8.18.tar.gz (4.2 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting graphviz (from emod-api~=1.24->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/de/5e/fcbb22c68208d39edff467809d06c9d81d7d27426460ebc598e55130c1aa/graphviz-0.20.1-py3-none-any.whl (47 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.0/47.0 kB 143.9 MB/s eta 0:00:00 Collecting parse (from emod-api~=1.24->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ce/f0/30fe1494f1910ad3ea40639b13ac48cdb16a8600e8861cbfc2c560661ddf/parse-1.20.1-py2.py3-none-any.whl (20 kB) Collecting backoff<2.3,>=1.10.0 (from idmtools~=1.7->emodpy~=1.15->-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->emodpy~=1.15->-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 161.1 MB/s eta 0:00:00 Collecting diskcache~=5.4.0 (from idmtools~=1.7->emodpy~=1.15->-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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.0/45.0 kB 144.2 MB/s eta 0:00:00 Collecting filelock (from idmtools~=1.7->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/81/54/84d42a0bee35edba99dee7b59a8d4970eccdd44b99fe728ed912106fc781/filelock-3.13.1-py3-none-any.whl (11 kB) Collecting more-itertools~=9.1.0 (from idmtools~=1.7->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/85/01/e2678ee4e0d7eed4fd6be9e5b043fff9d22d245d06c8c91def8ced664189/more_itertools-9.1.0-py3-none-any.whl (54 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.2/54.2 kB 175.0 MB/s eta 0:00:00 Collecting pipreqs<0.5,>=0.4.10 (from idmtools~=1.7->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d9/ea/74c89d786cf3403bfbf8fb70142fdf501af9517d0bb8c1acce3ee5ab613e/pipreqs-0.4.13-py2.py3-none-any.whl (33 kB) Collecting pluggy~=1.2.0 (from idmtools~=1.7->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/51/32/4a79112b8b87b21450b066e102d6608907f4c885ed7b04c3fdb085d4d6ae/pluggy-1.2.0-py3-none-any.whl (17 kB) Collecting tabulate<0.10,>=0.8.9 (from idmtools~=1.7->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/40/44/4a5f08c96eb108af5cb50b41f76142f0afa346dfa99d5296fe7202a11854/tabulate-0.9.0-py3-none-any.whl (35 kB) Collecting tqdm<5,>=4.52.0 (from idmtools~=1.7->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2a/14/e75e52d521442e2fcc9f1df3c5e456aead034203d4797867980de558ab34/tqdm-4.66.2-py3-none-any.whl (78 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.3/78.3 kB 181.2 MB/s eta 0:00:00 Requirement already satisfied: jinja2~=3.1.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from idmtools~=1.7->emodpy~=1.15->-r requirements.txt (line 2)) (3.1.3) Collecting packaging<22.0,>=20.4 (from idmtools~=1.7->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/05/8e/8de486cbd03baba4deef4142bd643a3e7bbe954a784dc1bb17142572d127/packaging-21.3-py3-none-any.whl (40 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 161.8 MB/s eta 0:00:00 Collecting pygit2<=1.10.1,>=1.4.0 (from idmtools~=1.7->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1b/4a/06d4b23dfb374e5de0f5fc3ec1d469a68e13d942ced6b978fa6d5826f35e/pygit2-1.10.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 12.6 MB/s eta 0:00:00 Collecting natsort~=8.4.0 (from idmtools-platform-comps~=1.7->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ef/82/7a9d0550484a62c6da82858ee9419f3dd1ccc9aa1c26a1e43da3ecd20b0d/natsort-8.4.0-py3-none-any.whl (38 kB) Collecting pytz>=2016.3 (from pyCOMPS~=2.6->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9c/3d/a121f284241f08268b21359bd425f7d4825cffc5ac5cd0e1b3d82ffd2b10/pytz-2024.1-py2.py3-none-any.whl (505 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 505.5/505.5 kB 15.1 MB/s eta 0:00:00 Collecting future>=0.16.0 (from pyCOMPS~=2.6->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/da/71/ae30dadffc90b9006d77af76b393cb9dfbfc9629f339fc1574a1c52e6806/future-1.0.0-py3-none-any.whl (491 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 491.3/491.3 kB 14.9 MB/s eta 0:00:00 Collecting xdg>=4.0.1 (from pyCOMPS~=2.6->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/dd/54/3516c1cf349060fc3578686d271eba242f10ec00b4530c2985af9faac49b/xdg-6.0.0-py3-none-any.whl (3.9 kB) Requirement already satisfied: wheel<1.0,>=0.23.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from astunparse->emodpy~=1.15->-r requirements.txt (line 2)) (0.40.0) Collecting six<2.0,>=1.6.1 (from astunparse->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d9/5a/e7c31adbe875f2abbb91bd84cf2dc52d792b5a01506781dbcf25c91daf11/six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting beautifulsoup4 (from bs4->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/b1/fe/e8c672695b37eecc5cbf43e1d0638d88d66ba3a44c4d321c796f4e59167f/beautifulsoup4-4.12.3-py3-none-any.whl (147 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 147.9/147.9 kB 12.9 MB/s eta 0:00:00 Collecting jaraco.classes (from keyring->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/eb/57/d3590a153d7c1970f466f69fa2570e1a93a34d8f88f23c11411df73729bf/jaraco.classes-3.3.1-py3-none-any.whl (6.8 kB) Requirement already satisfied: importlib-metadata>=4.11.4 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from keyring->emodpy~=1.15->-r requirements.txt (line 2)) (7.0.2) Collecting SecretStorage>=3.2 (from keyring->emodpy~=1.15->-r requirements.txt (line 2)) 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->-r requirements.txt (line 2)) 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 160.7 MB/s eta 0:00:00 Collecting contourpy>=1.0.1 (from matplotlib->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a9/ba/d8fd1380876f1e9114157606302e3644c85f6d116aeba354c212ee13edc7/contourpy-1.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (310 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 311.0/311.0 kB 14.1 MB/s eta 0:00:00 Collecting cycler>=0.10 (from matplotlib->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e7/05/c19819d5e3d95294a6f5947fb9b9629efb316b96de511b418c53d245aae6/cycler-0.12.1-py3-none-any.whl (8.3 kB) Collecting fonttools>=4.22.0 (from matplotlib->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d8/d7/0f4563ea45c14c84fde44aca3cb0896e49d1d960ba1298e789b75b1d2625/fonttools-4.49.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 12.5 MB/s eta 0:00:00 Collecting kiwisolver>=1.3.1 (from matplotlib->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c0/a8/841594f11d0b88d8aeb26991bc4dac38baa909dc58d0c4262a4f7893bcbf/kiwisolver-1.4.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 13.4 MB/s eta 0:00:00 Collecting pillow>=8 (from matplotlib->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/87/0d/8f5136a5481731c342a901ff155c587ce7804114db069345e1894ab4978a/pillow-10.2.0-cp39-cp39-manylinux_2_28_x86_64.whl (4.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 13.4 MB/s eta 0:00:00 Collecting pyparsing>=2.3.1 (from matplotlib->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9d/ea/6d76df31432a0e6fdf81681a895f009a4bb47b3c39036db3e1b528191d52/pyparsing-3.1.2-py3-none-any.whl (103 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.2/103.2 kB 208.6 MB/s eta 0:00:00 Collecting python-dateutil>=2.7 (from matplotlib->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ec/57/56b9bcc3c9c6a792fcbaf139543cee77261f3651ca9da0c93f5c1221264b/python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 229.9/229.9 kB 20.8 MB/s eta 0:00:00 Collecting importlib-resources>=3.2.0 (from matplotlib->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f3/3e/a01c6de9853a7d73672926e01966f979723386f0ba83d62e5db3cdf4c097/importlib_resources-6.1.3-py3-none-any.whl (34 kB) Collecting humanfriendly>=9.1 (from coloredlogs~=15.0->idmtools~=1.7->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f0/0f/310fb31e39e2d734ccaa2c0fb981ee41f7bd5056ce9bc29b2248bd569169/humanfriendly-10.0-py2.py3-none-any.whl (86 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.8/86.8 kB 195.3 MB/s eta 0:00:00 Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from importlib-metadata>=4.11.4->keyring->emodpy~=1.15->-r requirements.txt (line 2)) (3.17.0) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from jinja2~=3.1.2->idmtools~=1.7->emodpy~=1.15->-r requirements.txt (line 2)) (2.1.5) Collecting tzdata>=2022.7 (from pandas->emod-api~=1.24->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/65/58/f9c9e6be752e9fcb8b6a0ee9fb87e6e7a1f6bcab2cdc73f02bb7ba91ada0/tzdata-2024.1-py2.py3-none-any.whl (345 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 345.4/345.4 kB 16.4 MB/s eta 0:00:00 Collecting docopt (from pipreqs<0.5,>=0.4.10->idmtools~=1.7->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a2/55/8f8cab2afd404cf578136ef2cc5dfb50baa1761b68c9da1fb1e4eed343c9/docopt-0.6.2.tar.gz (25 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting yarg (from pipreqs<0.5,>=0.4.10->idmtools~=1.7->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/8b/90/89a2ff242ccab6a24fbab18dbbabc67c51a6f0ed01f9a0f41689dc177419/yarg-0.1.9-py2.py3-none-any.whl (19 kB) Collecting cffi>=1.9.1 (from pygit2<=1.10.1,>=1.4.0->idmtools~=1.7->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ea/ac/e9e77bc385729035143e54cc8c4785bd480eaca9df17565963556b0b7a93/cffi-1.16.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (443 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 443.4/443.4 kB 14.5 MB/s eta 0:00:00 Collecting cryptography>=2.0 (from SecretStorage>=3.2->keyring->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/48/c8/c0962598c43d3cff2c9d6ac66d0c612bdfb1975be8d87b8889960cf8c81d/cryptography-42.0.5-cp39-abi3-manylinux_2_28_x86_64.whl (4.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 13.4 MB/s eta 0:00:00 Collecting soupsieve>1.2 (from beautifulsoup4->bs4->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/4c/f3/038b302fdfbe3be7da016777069f26ceefe11a681055ea1f7817546508e3/soupsieve-2.5-py3-none-any.whl (36 kB) Collecting joblib>=1.2.0 (from scikit-learn->emod-api~=1.24->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/10/40/d551139c85db202f1f384ba8bcf96aca2f329440a844f924c8a0040b6d02/joblib-1.3.2-py3-none-any.whl (302 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 302.2/302.2 kB 14.7 MB/s eta 0:00:00 Collecting threadpoolctl>=2.0.0 (from scikit-learn->emod-api~=1.24->emodpy~=1.15->-r requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/b1/2c/f504e55d98418f2fcf756a56877e6d9a45dd5ed28b3d7c267b300e85ad5b/threadpoolctl-3.3.0-py3-none-any.whl (17 kB) Collecting pycparser (from cffi>=1.9.1->pygit2<=1.10.1,>=1.4.0->idmtools~=1.7->emodpy~=1.15->-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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 118.7/118.7 kB 218.5 MB/s eta 0:00:00 Building wheels for collected packages: idmtools-models, prodict, docopt Building wheel for idmtools-models (setup.py): started Building wheel for idmtools-models (setup.py): finished with status 'done' Created wheel for idmtools-models: filename=idmtools_models-1.7.9-py3-none-any.whl size=18203 sha256=f73da4bd25dfc6b84d2fe51001765529a6294deb412d5ad1bbf4fabc49ebbab0 Stored in directory: /tmp/pip-ephem-wheel-cache-phgqs91n/wheels/45/89/0f/d22c2ae7e95145614a035133233281200ff8036033c3e183a7 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=4203 sha256=5095a458e3b3903b54f0f618aef0c3952ed520989683b6ae69b48e81e3b2dc7e Stored in directory: /tmp/pip-ephem-wheel-cache-phgqs91n/wheels/b0/9c/b9/694dc9fa35b338adf315c91781d2150a3bccd224174d897720 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=13707 sha256=6e5ac1ba9be063d5416836555b0128a9d276afd3e0c9269056ae0674af13bca5 Stored in directory: /tmp/pip-ephem-wheel-cache-phgqs91n/wheels/8d/59/3a/894ec22b85063f7b617ea5956e702fa119c6b14d7e6208a419 Successfully built idmtools-models prodict docopt Installing collected packages: pytz, prodict, parse, emod-hiv, docopt, xdg, urllib3, tzdata, tqdm, threadpoolctl, tabulate, soupsieve, six, pyyaml, pyproj, pyparsing, pycparser, pluggy, pillow, numpy, natsort, more-itertools, lz4, kiwisolver, joblib, jeepney, importlib-resources, humanfriendly, graphviz, geographiclib, future, fonttools, filelock, diskcache, cycler, click, backoff, astor, shapely, scipy, requests, python-dateutil, packaging, jaraco.classes, contourpy, coloredlogs, cffi, beautifulsoup4, astunparse, yarg, scikit-learn, pygit2, pyCOMPS, pandas, matplotlib, cryptography, bs4, SecretStorage, pipreqs, emod-api, keyring, idmtools, idmtools-platform-comps, idmtools-models, emodpy Attempting uninstall: urllib3 Found existing installation: urllib3 2.2.1 Uninstalling urllib3-2.2.1: Successfully uninstalled urllib3-2.2.1 Attempting uninstall: requests Found existing installation: requests 2.31.0 Uninstalling requests-2.31.0: Successfully uninstalled requests-2.31.0 Attempting uninstall: packaging Found existing installation: packaging 24.0 Uninstalling packaging-24.0: Successfully uninstalled packaging-24.0 Successfully installed SecretStorage-3.3.3 astor-0.8.1 astunparse-1.6.3 backoff-2.2.1 beautifulsoup4-4.12.3 bs4-0.0.2 cffi-1.16.0 click-7.1.2 coloredlogs-15.0.1 contourpy-1.2.0 cryptography-42.0.5 cycler-0.12.1 diskcache-5.4.0 docopt-0.6.2 emod-api-1.30.1 emod-hiv-1.0.1 emodpy-1.22.0 filelock-3.13.1 fonttools-4.49.0 future-1.0.0 geographiclib-2.0 graphviz-0.20.1 humanfriendly-10.0 idmtools-1.7.9 idmtools-models-1.7.9 idmtools-platform-comps-1.7.9 importlib-resources-6.1.3 jaraco.classes-3.3.1 jeepney-0.8.0 joblib-1.3.2 keyring-24.3.1 kiwisolver-1.4.5 lz4-4.3.3 matplotlib-3.8.3 more-itertools-9.1.0 natsort-8.4.0 numpy-1.26.4 packaging-21.3 pandas-2.2.1 parse-1.20.1 pillow-10.2.0 pipreqs-0.4.13 pluggy-1.2.0 prodict-0.8.18 pyCOMPS-2.10.0 pycparser-2.21 pygit2-1.10.1 pyparsing-3.1.2 pyproj-3.6.1 python-dateutil-2.9.0.post0 pytz-2024.1 pyyaml-6.0.1 requests-2.29.0 scikit-learn-1.4.1.post1 scipy-1.12.0 shapely-2.0.3 six-1.16.0 soupsieve-2.5 tabulate-0.9.0 threadpoolctl-3.3.0 tqdm-4.66.2 tzdata-2024.1 urllib3-1.26.18 xdg-6.0.0 yarg-0.1.9 [rtd-command-info] start-time: 2024-03-12T18:16:31.128920Z, end-time: 2024-03-12T18:17:03.995676Z, duration: 32, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Collecting sphinxext.remoteliteralinclude~=0.4.0 (from -r docs/requirements.txt (line 1)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/13/0d/7e5009f48c33d5fd533dda80b42c4a79fce8dfdd1b617d0a9df9a9836145/sphinxext_remoteliteralinclude-0.4.0-py3-none-any.whl (6.4 kB) Collecting sphinx~=6.2.1 (from -r docs/requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/5f/d8/45ba6097c39ba44d9f0e1462fb232e13ca4ddb5aea93a385dcfa964687da/sphinx-6.2.1-py3-none-any.whl (3.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.0/3.0 MB 12.5 MB/s eta 0:00:00 Collecting sphinx-rtd-theme~=1.2.2 (from -r docs/requirements.txt (line 3)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/85/32/9ccebf3a82c085e8fc12b67cc3dbf840789fb6c7835ed0d61686d6509aa9/sphinx_rtd_theme-1.2.2-py2.py3-none-any.whl (2.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 12.7 MB/s eta 0:00:00 Collecting sphinxcontrib-napoleon~=0.7 (from -r docs/requirements.txt (line 4)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/75/f2/6b7627dfe7b4e418e295e254bb15c3a6455f11f8c0ad0d43113f678049c3/sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Collecting plantweb~=1.2.1 (from -r docs/requirements.txt (line 5)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d6/6f/9ab1a1c3e33aaa0c0931983578c09336b092c75dce777ea666d3032f756e/plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting sphinxcontrib-programoutput~=0.17 (from -r docs/requirements.txt (line 6)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/30/ee/b7be4b3f45f4e36bfa6c444cd234098e0d09880379c67a43e6bb9ab99a86/sphinxcontrib_programoutput-0.17-py2.py3-none-any.whl (22 kB) Collecting nbsphinx~=0.9.2 (from -r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a3/a0/ca4aeb2f7f2608a483459a3bb486da250a7eb23eb76c9a0af154395f0cb2/nbsphinx-0.9.3-py3-none-any.whl (31 kB) Collecting jupyterlab~=4.0.2 (from -r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/7b/af/4e8fffc503dc70d3c73328b0421181e3d238f76831769578c4f245130ae9/jupyterlab-4.0.13-py3-none-any.whl (9.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.2/9.2 MB 12.5 MB/s eta 0:00:00 Collecting myst-parser~=2.0.0 (from -r docs/requirements.txt (line 9)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1d/f6/6d61a023d758f488e36638076e8a4ec4447a2cdf86938cf6c60cf1c860e6/myst_parser-2.0.0-py3-none-any.whl (77 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.2/77.2 kB 199.2 MB/s eta 0:00:00 Collecting readthedocs-sphinx-search~=0.3.1 (from -r docs/requirements.txt (line 10)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/04/3c/41bc9d7d4d936a73e380423f23996bee1691e17598d8a03c062be6aac640/readthedocs_sphinx_search-0.3.2-py3-none-any.whl (21 kB) Collecting sphinx-copybutton~=0.5.2 (from -r docs/requirements.txt (line 11)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9e/48/1ea60e74949eecb12cdd6ac43987f9fd331156388dcc2319b45e2ebb81bf/sphinx_copybutton-0.5.2-py3-none-any.whl (13 kB) Collecting pygithub~=1.57 (from -r docs/requirements.txt (line 12)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2c/71/aff5465d9e3d448a5d4beab1dc7c8dec72037e3ae7e0d856ee08538dc934/PyGithub-1.59.1-py3-none-any.whl (342 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 342.2/342.2 kB 15.3 MB/s eta 0:00:00 Collecting sphinxcontrib-jquery~=4.1 (from -r docs/requirements.txt (line 13)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/76/85/749bd22d1a68db7291c89e2ebca53f4306c3f205853cf31e9de279034c3c/sphinxcontrib_jquery-4.1-py2.py3-none-any.whl (121 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.1/121.1 kB 221.7 MB/s eta 0:00:00 Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from sphinxext.remoteliteralinclude~=0.4.0->-r docs/requirements.txt (line 1)) (1.16.0) Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (1.0.8) Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (1.0.6) Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (1.0.1) Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (2.0.5) Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (1.1.10) Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (1.0.7) Requirement already satisfied: Jinja2>=3.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (3.1.3) Requirement already satisfied: Pygments>=2.13 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (2.17.2) Collecting docutils<0.20,>=0.18.1 (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/93/69/e391bd51bc08ed9141ecd899a0ddb61ab6465309f1eb470905c0c8868081/docutils-0.19-py3-none-any.whl (570 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.5/570.5 kB 13.3 MB/s eta 0:00:00 Requirement already satisfied: snowballstemmer>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (2.2.0) Requirement already satisfied: babel>=2.9 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (2.14.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (0.7.16) Requirement already satisfied: imagesize>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (1.4.1) Requirement already satisfied: requests>=2.25.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (2.29.0) Requirement already satisfied: packaging>=21.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (21.3) Requirement already satisfied: importlib-metadata>=4.8 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (7.0.2) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/8d/14/69b4bad34e3f250afe29a854da03acb6747711f3df06c359fa053fae4e76/docutils-0.18.1-py2.py3-none-any.whl (570 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.0/570.0 kB 13.3 MB/s eta 0:00:00 Collecting pockets>=0.3 (from sphinxcontrib-napoleon~=0.7->-r docs/requirements.txt (line 4)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e9/2f/a4583c70fbd8cd04910e2884bcc2bdd670e884061f7b4d70bc13e632a993/pockets-0.9.1-py2.py3-none-any.whl (26 kB) Collecting nbconvert!=5.4 (from nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/4f/90/a522a41247a2c80289f265890d096821698819a15b12f30ff6e51ac00fe6/nbconvert-7.16.2-py3-none-any.whl (257 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 257.3/257.3 kB 21.2 MB/s eta 0:00:00 Collecting traitlets>=5 (from nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/7c/c4/366a09036c07f46eb8c9b2af39c97f502ef24f11f2a6e4d763655d9f2708/traitlets-5.14.2-py3-none-any.whl (85 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 85.4/85.4 kB 182.2 MB/s eta 0:00:00 Collecting nbformat (from nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2f/5c/982c01957e937007fb86f452af5409800bd9b725a0d43c5a4898a6657a10/nbformat-5.10.2-py3-none-any.whl (78 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.4/78.4 kB 199.9 MB/s eta 0:00:00 Collecting async-lru>=1.0.0 (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/fa/9f/3c3503693386c4b0f245eaf5ca6198e3b28879ca0a40bde6b0e319793453/async_lru-2.0.4-py3-none-any.whl (6.1 kB) Collecting ipykernel (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/4b/45/00ceed1948457b6e469e4d44e5ecadc5b0f24fd4f610dd9e7b89f1993128/ipykernel-6.29.3-py3-none-any.whl (117 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 117.1/117.1 kB 213.7 MB/s eta 0:00:00 Collecting jupyter-core (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c9/fb/108ecd1fe961941959ad0ee4e12ee7b8b1477247f30b1fdfd83ceaf017f0/jupyter_core-5.7.2-py3-none-any.whl (28 kB) Collecting jupyter-lsp>=2.0.0 (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/33/1b/9d4925e2afcf66729fbe5d3db2907ebd546a8c5d1e43a41e44bcaa1a19e0/jupyter_lsp-2.2.4-py3-none-any.whl (69 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 69.1/69.1 kB 188.6 MB/s eta 0:00:00 Collecting jupyter-server<3,>=2.4.0 (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/95/85/483b8e09a897d1bc2194646d30d4ce6ae166106e91ecbd11d6b6d9ccfc36/jupyter_server-2.13.0-py3-none-any.whl (383 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 383.2/383.2 kB 16.9 MB/s eta 0:00:00 Collecting jupyterlab-server<3,>=2.19.0 (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/6a/2c/ea4fdd7d4bb72106419fff1fcda7c111bd905b00afed3d8efc1a6d6e4538/jupyterlab_server-2.25.4-py3-none-any.whl (58 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 59.0/59.0 kB 182.7 MB/s eta 0:00:00 Collecting notebook-shim>=0.2 (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f9/33/bd5b9137445ea4b680023eb0469b2bb969d61303dedb2aac6560ff3d14a1/notebook_shim-0.2.4-py3-none-any.whl (13 kB) Collecting tomli (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/97/75/10a9ebee3fd790d20926a90a2547f0bf78f371b2f13aa822c759680ca7b9/tomli-2.0.1-py3-none-any.whl (12 kB) Collecting tornado>=6.2.0 (from jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9f/12/11d0a757bb67278d3380d41955ae98527d5ad18330b2edbdc8de222b569b/tornado-6.4-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (435 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 435.4/435.4 kB 13.4 MB/s eta 0:00:00 Collecting markdown-it-py~=3.0 (from myst-parser~=2.0.0->-r docs/requirements.txt (line 9)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/42/d7/1ec15b46af6af88f19b8e5ffea08fa375d433c998b8a7639e76935c14f1f/markdown_it_py-3.0.0-py3-none-any.whl (87 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.5/87.5 kB 196.2 MB/s eta 0:00:00 Collecting mdit-py-plugins~=0.4 (from myst-parser~=2.0.0->-r docs/requirements.txt (line 9)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e5/3c/fe85f19699a7b40c8f9ce8ecee7e269b9b3c94099306df6f9891bdefeedd/mdit_py_plugins-0.4.0-py3-none-any.whl (54 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.1/54.1 kB 174.4 MB/s eta 0:00:00 Requirement already satisfied: pyyaml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from myst-parser~=2.0.0->-r docs/requirements.txt (line 9)) (6.0.1) Collecting deprecated (from pygithub~=1.57->-r docs/requirements.txt (line 12)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/20/8d/778b7d51b981a96554f29136cd59ca7880bf58094338085bcf2a979a0e6a/Deprecated-1.2.14-py2.py3-none-any.whl (9.6 kB) Collecting pyjwt>=2.4.0 (from pyjwt[crypto]>=2.4.0->pygithub~=1.57->-r docs/requirements.txt (line 12)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2b/4f/e04a8067c7c96c364cef7ef73906504e2f40d690811c021e1a1901473a19/PyJWT-2.8.0-py3-none-any.whl (22 kB) Collecting pynacl>=1.4.0 (from pygithub~=1.57->-r docs/requirements.txt (line 12)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ee/87/f1bb6a595f14a327e8285b9eb54d41fef76c585a0edef0a45f6fc95de125/PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (856 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 856.7/856.7 kB 13.4 MB/s eta 0:00:00 Collecting typing-extensions>=4.0.0 (from async-lru>=1.0.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f9/de/dc04a3ea60b22624b51c703a84bbe0184abcd1d0b9bc8074b5d6b7ab90bb/typing_extensions-4.10.0-py3-none-any.whl (33 kB) Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from importlib-metadata>=4.8->sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (3.17.0) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from Jinja2>=3.0->sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (2.1.5) Collecting anyio>=3.1.0 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/14/fd/2f20c40b45e4fb4324834aea24bd4afdf1143390242c0b33774da0e2e34f/anyio-4.3.0-py3-none-any.whl (85 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 85.6/85.6 kB 203.1 MB/s eta 0:00:00 Collecting argon2-cffi (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a4/6a/e8a041599e78b6b3752da48000b14c8d1e8a04ded09c88c714ba047f34f5/argon2_cffi-23.1.0-py3-none-any.whl (15 kB) Collecting jupyter-client>=7.4.4 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/75/6d/d7b55b9c1ac802ab066b3e5015e90faab1fffbbd67a2af498ffc6cc81c97/jupyter_client-8.6.1-py3-none-any.whl (105 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 105.9/105.9 kB 209.6 MB/s eta 0:00:00 Collecting jupyter-events>=0.9.0 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f2/db/65f23494d5b379cf34ae94a3c2a7ede4829a489bb0a81744609056b36d21/jupyter_events-0.9.1-py3-none-any.whl (18 kB) Collecting jupyter-server-terminals (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/07/2d/2b32cdbe8d2a602f697a649798554e4f072115438e92249624e532e8aca6/jupyter_server_terminals-0.5.3-py3-none-any.whl (13 kB) Collecting overrides (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2c/ab/fc8290c6a4c722e5514d80f62b2dc4c4df1a68a41d1364e625c35990fcf3/overrides-7.7.0-py3-none-any.whl (17 kB) Collecting prometheus-client (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c7/98/745b810d822103adca2df8decd4c0bbe839ba7ad3511af3f0d09692fc0f0/prometheus_client-0.20.0-py3-none-any.whl (54 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.5/54.5 kB 167.6 MB/s eta 0:00:00 Collecting pyzmq>=24 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/76/8b/6fca99e22c6316917de32b17be299dea431544209d619da16b6d9ec85c83/pyzmq-25.1.2-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 13.0 MB/s eta 0:00:00 Collecting send2trash>=1.8.2 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a9/78/e4df1e080ed790acf3a704edf521006dd96b9841bd2e2a462c0d255e0565/Send2Trash-1.8.2-py3-none-any.whl (18 kB) Collecting terminado>=0.8.3 (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/6a/9e/2064975477fdc887e47ad42157e214526dcad8f317a948dee17e1659a62f/terminado-0.18.1-py3-none-any.whl (14 kB) Collecting websocket-client (from jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/1e/70/1e88138a9afbed1d37093b85f0bebc3011623c4f47c166431599fe9d6c93/websocket_client-1.7.0-py3-none-any.whl (58 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.5/58.5 kB 158.8 MB/s eta 0:00:00 Collecting platformdirs>=2.5 (from jupyter-core->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/55/72/4898c44ee9ea6f43396fbc23d9bfaf3d06e01b83698bdf2e4c919deceb7c/platformdirs-4.2.0-py3-none-any.whl (17 kB) Collecting json5>=0.9.0 (from jupyterlab-server<3,>=2.19.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ca/fd/1cffc32cb1c4db0c0aed6c70b4d4cb43c08242bcbf2ac7ff00ba130ac6a5/json5-0.9.22-py3-none-any.whl (29 kB) Collecting jsonschema>=4.18.0 (from jupyterlab-server<3,>=2.19.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/39/9d/b035d024c62c85f2e2d4806a59ca7b8520307f34e0932fbc8cc75fe7b2d9/jsonschema-4.21.1-py3-none-any.whl (85 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 85.5/85.5 kB 172.2 MB/s eta 0:00:00 Collecting requests>=2.25.0 (from sphinx~=6.2.1->-r docs/requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/70/8e/0e2d847013cb52cd35b38c009bb167a1a26b2ce6cd6965bf26b47bc0bf44/requests-2.31.0-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.6/62.6 kB 141.7 MB/s eta 0:00:00 Collecting mdurl~=0.1 (from markdown-it-py~=3.0->myst-parser~=2.0.0->-r docs/requirements.txt (line 9)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/b3/38/89ba8ad64ae25be8de66a6d463314cf1eb366222074cfda9ee839c56a4b4/mdurl-0.1.2-py3-none-any.whl (10.0 kB) Requirement already satisfied: beautifulsoup4 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) (4.12.3) Collecting bleach!=5.0.0 (from nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ea/63/da7237f805089ecc28a3f36bca6a21c31fcbc2eb380f3b8f1be3312abd14/bleach-6.1.0-py3-none-any.whl (162 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 162.8/162.8 kB 10.3 MB/s eta 0:00:00 Collecting defusedxml (from nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/07/6c/aa3f2f849e01cb6a001cd8554a88d4c77c5c1a31c95bdf1cf9301e6d9ef4/defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) Collecting jupyterlab-pygments (from nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/b1/dd/ead9d8ea85bf202d90cc513b533f9c363121c7792674f78e0d8a854b63b4/jupyterlab_pygments-0.3.0-py3-none-any.whl (15 kB) Collecting mistune<4,>=2.0.3 (from nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f0/74/c95adcdf032956d9ef6c89a9b8a5152bf73915f8c633f3e3d88d06bd699c/mistune-3.0.2-py3-none-any.whl (47 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.0/48.0 kB 198.4 MB/s eta 0:00:00 Collecting nbclient>=0.5.0 (from nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ad/41/c3bdff990ded5607321af31e284223eb5fa702e375332fd805f2a9163522/nbclient-0.9.1-py3-none-any.whl (24 kB) Collecting pandocfilters>=1.4.1 (from nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ef/af/4fbc8cab944db5d21b7e2a5b8e9211a03a79852b1157e2c102fcc61ac440/pandocfilters-1.5.1-py2.py3-none-any.whl (8.7 kB) Collecting tinycss2 (from nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/da/99/fd23634d6962c2791fb8cb6ccae1f05dcbfc39bce36bba8b1c9a8d92eae8/tinycss2-1.2.1-py3-none-any.whl (21 kB) Collecting fastjsonschema (from nbformat->nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9c/b9/79691036d4a8f9857e74d1728b23f34f583b81350a27492edda58d5604e1/fastjsonschema-2.19.1-py3-none-any.whl (23 kB) Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from packaging>=21.0->sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (3.1.2) Requirement already satisfied: cryptography>=3.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from pyjwt[crypto]>=2.4.0->pygithub~=1.57->-r docs/requirements.txt (line 12)) (42.0.5) Requirement already satisfied: cffi>=1.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from pynacl>=1.4.0->pygithub~=1.57->-r docs/requirements.txt (line 12)) (1.16.0) Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from requests>=2.25.0->sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (3.3.2) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from requests>=2.25.0->sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (3.6) Requirement already satisfied: urllib3<3,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from requests>=2.25.0->sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (1.26.18) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from requests>=2.25.0->sphinx~=6.2.1->-r docs/requirements.txt (line 2)) (2024.2.2) Collecting wrapt<2,>=1.10 (from deprecated->pygithub~=1.57->-r docs/requirements.txt (line 12)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/b1/e7/459a8a4f40f2fa65eb73cb3f339e6d152957932516d18d0e996c7ae2d7ae/wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (80 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.1/80.1 kB 213.4 MB/s eta 0:00:00 Collecting comm>=0.1.1 (from ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e6/75/49e5bfe642f71f272236b5b2d2691cf915a7283cc0ceda56357b61daa538/comm-0.2.2-py3-none-any.whl (7.2 kB) Collecting debugpy>=1.6.5 (from ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ba/2c/69244a26dc484b37db8fc76ba5af107d501d0e45be27b3042b74aa332aa4/debugpy-1.8.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 16.1 MB/s eta 0:00:00 Collecting ipython>=7.23.1 (from ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/47/6b/d9fdcdef2eb6a23f391251fde8781c38d42acd82abe84d054cb74f7863b0/ipython-8.18.1-py3-none-any.whl (808 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 808.2/808.2 kB 16.6 MB/s eta 0:00:00 Collecting matplotlib-inline>=0.1 (from ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f2/51/c34d7a1d528efaae3d8ddb18ef45a41f284eacf9e514523b191b7d0872cc/matplotlib_inline-0.1.6-py3-none-any.whl (9.4 kB) Collecting nest-asyncio (from ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/a0/c4/c2971a3ba4c6103a3d10c4b0f24f461ddc027f0f09763220cf35ca1401b3/nest_asyncio-1.6.0-py3-none-any.whl (5.2 kB) Collecting psutil (from ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/c5/4f/0e22aaa246f96d6ac87fe5ebb9c5a693fbe8877f537a1022527c47ca43c5/psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (288 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 288.2/288.2 kB 19.3 MB/s eta 0:00:00 Collecting sniffio>=1.1 (from anyio>=3.1.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e9/44/75a9c9421471a6c4805dbf2356f7c181a29c1879239abab1ea2cc8f38b40/sniffio-1.3.1-py3-none-any.whl (10 kB) Collecting exceptiongroup>=1.0.2 (from anyio>=3.1.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/b8/9a/5028fd52db10e600f1c4674441b968cf2ea4959085bfb5b99fb1250e5f68/exceptiongroup-1.2.0-py3-none-any.whl (16 kB) Collecting webencodings (from bleach!=5.0.0->nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Requirement already satisfied: pycparser in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from cffi>=1.4.1->pynacl>=1.4.0->pygithub~=1.57->-r docs/requirements.txt (line 12)) (2.21) Collecting decorator (from ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d5/50/83c593b07763e1161326b3b8c6686f0f4b0f24d5526546bee538c89837d6/decorator-5.1.1-py3-none-any.whl (9.1 kB) Collecting jedi>=0.16 (from ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/20/9f/bc63f0f0737ad7a60800bfd472a4836661adae21f9c2535f3957b1e54ceb/jedi-0.19.1-py2.py3-none-any.whl (1.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 16.0 MB/s eta 0:00:00 Collecting prompt-toolkit<3.1.0,>=3.0.41 (from ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ee/fd/ca7bf3869e7caa7a037e23078539467b433a4e01eebd93f77180ab927766/prompt_toolkit-3.0.43-py3-none-any.whl (386 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 386.1/386.1 kB 23.5 MB/s eta 0:00:00 Collecting stack-data (from ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f1/7b/ce1eafaf1a76852e2ec9b22edecf1daa58175c090266e9f6c64afcd81d91/stack_data-0.6.3-py3-none-any.whl (24 kB) Collecting pexpect>4.3 (from ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9e/c3/059298687310d527a58bb01f3b1965787ee3b40dce76752eda8b44e9a2c5/pexpect-4.9.0-py2.py3-none-any.whl (63 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.8/63.8 kB 208.5 MB/s eta 0:00:00 Collecting attrs>=22.2.0 (from jsonschema>=4.18.0->jupyterlab-server<3,>=2.19.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e0/44/827b2a91a5816512fcaf3cc4ebc465ccd5d598c45cefa6703fcf4a79018f/attrs-23.2.0-py3-none-any.whl (60 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.8/60.8 kB 213.8 MB/s eta 0:00:00 Collecting jsonschema-specifications>=2023.03.6 (from jsonschema>=4.18.0->jupyterlab-server<3,>=2.19.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ee/07/44bd408781594c4d0a027666ef27fab1e441b109dc3b76b4f836f8fd04fe/jsonschema_specifications-2023.12.1-py3-none-any.whl (18 kB) Collecting referencing>=0.28.4 (from jsonschema>=4.18.0->jupyterlab-server<3,>=2.19.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/90/10/1c92edb0a0a14b67ff825bc338e74bc49ab27d3f3bae3f9a02838cba546f/referencing-0.33.0-py3-none-any.whl (26 kB) Collecting rpds-py>=0.7.1 (from jsonschema>=4.18.0->jupyterlab-server<3,>=2.19.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/fd/ea/92231b62681961812e9fbd8ef9be7137856784406bf6a384976bb7b46472/rpds_py-0.18.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 16.7 MB/s eta 0:00:00 Requirement already satisfied: python-dateutil>=2.8.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from jupyter-client>=7.4.4->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) (2.9.0.post0) Collecting python-json-logger>=2.0.4 (from jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/35/a6/145655273568ee78a581e734cf35beb9e33a370b29c5d3c8fee3744de29f/python_json_logger-2.0.7-py3-none-any.whl (8.1 kB) Collecting rfc3339-validator (from jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/7b/44/4e421b96b67b2daff264473f7465db72fbdf36a07e05494f50300cc7b0c6/rfc3339_validator-0.1.4-py2.py3-none-any.whl (3.5 kB) Collecting rfc3986-validator>=0.1.1 (from jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/9e/51/17023c0f8f1869d8806b979a2bffa3f861f26a3f1a66b094288323fba52f/rfc3986_validator-0.1.1-py2.py3-none-any.whl (4.2 kB) Collecting ptyprocess (from terminado>=0.8.3->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/22/a6/858897256d0deac81a172289110f31629fc4cee19b6f01283303e18c8db3/ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB) Collecting argon2-cffi-bindings (from argon2-cffi->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/ec/f7/378254e6dd7ae6f31fe40c8649eea7d4832a42243acaf0f1fff9083b2bed/argon2_cffi_bindings-21.2.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (86 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.2/86.2 kB 213.5 MB/s eta 0:00:00 Requirement already satisfied: soupsieve>1.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages (from beautifulsoup4->nbconvert!=5.4->nbsphinx~=0.9.2->-r docs/requirements.txt (line 7)) (2.5) Collecting parso<0.9.0,>=0.8.3 (from jedi>=0.16->ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/05/63/8011bd08a4111858f79d2b09aad86638490d62fbf881c44e434a6dfca87b/parso-0.8.3-py2.py3-none-any.whl (100 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.8/100.8 kB 210.0 MB/s eta 0:00:00 Collecting fqdn (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/cf/58/8acf1b3e91c58313ce5cb67df61001fc9dcd21be4fadb76c1a2d540e09ed/fqdn-1.5.1-py3-none-any.whl (9.1 kB) Collecting isoduration (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/7b/55/e5326141505c5d5e34c5e0935d2908a74e4561eca44108fbfb9c13d2911a/isoduration-20.11.0-py3-none-any.whl (11 kB) Collecting jsonpointer>1.13 (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/12/f6/0232cc0c617e195f06f810534d00b74d2f348fe71b2118009ad8ad31f878/jsonpointer-2.4-py2.py3-none-any.whl (7.8 kB) Collecting uri-template (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e7/00/3fca040d7cf8a32776d3d81a00c8ee7457e00f80c649f1e4a863c8321ae9/uri_template-1.3.0-py3-none-any.whl (11 kB) Collecting webcolors>=1.11 (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d5/e1/3e9013159b4cbb71df9bd7611cbf90dc2c621c8aeeb677fc41dad72f2261/webcolors-1.13-py3-none-any.whl (14 kB) Collecting wcwidth (from prompt-toolkit<3.1.0,>=3.0.41->ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/fd/84/fd2ba7aafacbad3c4201d395674fc6348826569da3c0937e75505ead3528/wcwidth-0.2.13-py2.py3-none-any.whl (34 kB) Collecting executing>=1.2.0 (from stack-data->ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/80/03/6ea8b1b2a5ab40a7a60dc464d3daa7aa546e0a74d74a9f8ff551ea7905db/executing-2.0.1-py2.py3-none-any.whl (24 kB) Collecting asttokens>=2.1.0 (from stack-data->ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/45/86/4736ac618d82a20d87d2f92ae19441ebc7ac9e7a581d7e58bbe79233b24a/asttokens-2.4.1-py2.py3-none-any.whl (27 kB) Collecting pure-eval (from stack-data->ipython>=7.23.1->ipykernel->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/2b/27/77f9d5684e6bce929f5cfe18d6cfbe5133013c06cb2fbf5933670e60761d/pure_eval-0.2.2-py3-none-any.whl (11 kB) Collecting arrow>=0.15.0 (from isoduration->jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/f8/ed/e97229a566617f2ae958a6b13e7cc0f585470eac730a73e9e82c32a3cdd2/arrow-1.3.0-py3-none-any.whl (66 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 66.4/66.4 kB 182.5 MB/s eta 0:00:00 Collecting types-python-dateutil>=2.8.10 (from arrow>=0.15.0->isoduration->jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->jupyterlab~=4.0.2->-r docs/requirements.txt (line 8)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/e8/19/e11b8098f5d7864a9950385760f1d8a68abd1e0b8ba89656d94c45cf9f93/types_python_dateutil-2.8.19.20240311-py3-none-any.whl (9.7 kB) Installing collected packages: webencodings, wcwidth, pure-eval, ptyprocess, fastjsonschema, wrapt, websocket-client, webcolors, uri-template, typing-extensions, types-python-dateutil, traitlets, tornado, tomli, tinycss2, sphinxext.remoteliteralinclude, sniffio, send2trash, rpds-py, rfc3986-validator, rfc3339-validator, requests, readthedocs-sphinx-search, pyzmq, python-json-logger, pyjwt, psutil, prompt-toolkit, prometheus-client, pockets, platformdirs, pexpect, parso, pandocfilters, overrides, nest-asyncio, mistune, mdurl, jupyterlab-pygments, jsonpointer, json5, fqdn, executing, exceptiongroup, docutils, defusedxml, decorator, debugpy, bleach, attrs, asttokens, terminado, stack-data, sphinxcontrib-napoleon, sphinx, referencing, pynacl, plantweb, matplotlib-inline, markdown-it-py, jupyter-core, jedi, deprecated, comm, async-lru, arrow, argon2-cffi-bindings, anyio, sphinxcontrib-programoutput, sphinxcontrib-jquery, sphinx-copybutton, mdit-py-plugins, jupyter-server-terminals, jupyter-client, jsonschema-specifications, isoduration, ipython, argon2-cffi, sphinx-rtd-theme, pygithub, myst-parser, jsonschema, ipykernel, nbformat, nbclient, jupyter-events, nbconvert, nbsphinx, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab Attempting uninstall: requests Found existing installation: requests 2.29.0 Uninstalling requests-2.29.0: Successfully uninstalled requests-2.29.0 Attempting uninstall: docutils Found existing installation: docutils 0.20.1 Uninstalling docutils-0.20.1: Successfully uninstalled docutils-0.20.1 Attempting uninstall: sphinx Found existing installation: Sphinx 7.2.6 Uninstalling Sphinx-7.2.6: Successfully uninstalled Sphinx-7.2.6 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. emodpy 1.22.0 requires requests==2.29.0, but you have requests 2.31.0 which is incompatible. Successfully installed anyio-4.3.0 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-2.4.1 async-lru-2.0.4 attrs-23.2.0 bleach-6.1.0 comm-0.2.2 debugpy-1.8.1 decorator-5.1.1 defusedxml-0.7.1 deprecated-1.2.14 docutils-0.18.1 exceptiongroup-1.2.0 executing-2.0.1 fastjsonschema-2.19.1 fqdn-1.5.1 ipykernel-6.29.3 ipython-8.18.1 isoduration-20.11.0 jedi-0.19.1 json5-0.9.22 jsonpointer-2.4 jsonschema-4.21.1 jsonschema-specifications-2023.12.1 jupyter-client-8.6.1 jupyter-core-5.7.2 jupyter-events-0.9.1 jupyter-lsp-2.2.4 jupyter-server-2.13.0 jupyter-server-terminals-0.5.3 jupyterlab-4.0.13 jupyterlab-pygments-0.3.0 jupyterlab-server-2.25.4 markdown-it-py-3.0.0 matplotlib-inline-0.1.6 mdit-py-plugins-0.4.0 mdurl-0.1.2 mistune-3.0.2 myst-parser-2.0.0 nbclient-0.9.1 nbconvert-7.16.2 nbformat-5.10.2 nbsphinx-0.9.3 nest-asyncio-1.6.0 notebook-shim-0.2.4 overrides-7.7.0 pandocfilters-1.5.1 parso-0.8.3 pexpect-4.9.0 plantweb-1.2.1 platformdirs-4.2.0 pockets-0.9.1 prometheus-client-0.20.0 prompt-toolkit-3.0.43 psutil-5.9.8 ptyprocess-0.7.0 pure-eval-0.2.2 pygithub-1.59.1 pyjwt-2.8.0 pynacl-1.5.0 python-json-logger-2.0.7 pyzmq-25.1.2 readthedocs-sphinx-search-0.3.2 referencing-0.33.0 requests-2.31.0 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.18.0 send2trash-1.8.2 sniffio-1.3.1 sphinx-6.2.1 sphinx-copybutton-0.5.2 sphinx-rtd-theme-1.2.2 sphinxcontrib-jquery-4.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.17 sphinxext.remoteliteralinclude-0.4.0 stack-data-0.6.3 terminado-0.18.1 tinycss2-1.2.1 tomli-2.0.1 tornado-6.4 traitlets-5.14.2 types-python-dateutil-2.8.19.20240311 typing-extensions-4.10.0 uri-template-1.3.0 wcwidth-0.2.13 webcolors-1.13 webencodings-0.5.1 websocket-client-1.7.0 wrapt-1.16.0 [rtd-command-info] start-time: 2024-03-12T18:17:04.091542Z, end-time: 2024-03-12T18:17:05.517539Z, duration: 1, exit-code: 0 python ./setup.py install --force /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) running install /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` and ``easy_install``. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://github.com/pypa/setuptools/issues/917 for details. ******************************************************************************** !! self.initialize_options() running bdist_egg running egg_info creating emodpy_hiv.egg-info writing emodpy_hiv.egg-info/PKG-INFO writing dependency_links to emodpy_hiv.egg-info/dependency_links.txt writing requirements to emodpy_hiv.egg-info/requires.txt writing top-level names to emodpy_hiv.egg-info/top_level.txt writing manifest file 'emodpy_hiv.egg-info/SOURCES.txt' reading manifest file 'emodpy_hiv.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'emodpy_hiv.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/tests copying tests/create_auth_token_args.py -> build/lib/tests copying tests/__init__.py -> build/lib/tests creating build/lib/emodpy_hiv copying emodpy_hiv/download.py -> build/lib/emodpy_hiv copying emodpy_hiv/utils.py -> build/lib/emodpy_hiv copying emodpy_hiv/__init__.py -> build/lib/emodpy_hiv creating build/lib/tests/unittests copying tests/unittests/schema_path_file.py -> build/lib/tests/unittests copying tests/unittests/test_hivmuxer.py -> build/lib/tests/unittests copying tests/unittests/test_intervention.py -> build/lib/tests/unittests copying tests/unittests/test_demographics.py -> build/lib/tests/unittests copying tests/unittests/test_import.py -> build/lib/tests/unittests copying tests/unittests/__init__.py -> build/lib/tests/unittests copying tests/unittests/check_coverage.py -> build/lib/tests/unittests copying tests/unittests/test_emod_hiv_package.py -> build/lib/tests/unittests copying tests/unittests/manifest.py -> build/lib/tests/unittests copying tests/unittests/test_nchooser.py -> build/lib/tests/unittests creating build/lib/emodpy_hiv/demographics copying emodpy_hiv/demographics/__init__.py -> build/lib/emodpy_hiv/demographics copying emodpy_hiv/demographics/HIVDemographics.py -> build/lib/emodpy_hiv/demographics copying emodpy_hiv/demographics/DemographicsTemplates.py -> build/lib/emodpy_hiv/demographics creating build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/yearandsexdiag.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/cascade_helpers.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/outbreak.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/stipostdebut.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/setsexualdebut.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/reftrackercoord.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/utils.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/randomchoice.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/artstagingbycd4agnosticdiag.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/hivmuxer.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/rapiddiag.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/pmtct.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/artdropout.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/drawblood.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/nchooser.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/art.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/__init__.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/prep.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/reftracker.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/modcoinf.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/malecirc.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/artstagingbycd4diag.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/sigmoiddiag.py -> build/lib/emodpy_hiv/interventions copying emodpy_hiv/interventions/delay.py -> build/lib/emodpy_hiv/interventions creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/tests copying build/lib/tests/create_auth_token_args.py -> build/bdist.linux-x86_64/egg/tests creating build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/schema_path_file.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_hivmuxer.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_intervention.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_demographics.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_import.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/__init__.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/check_coverage.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_emod_hiv_package.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/manifest.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/unittests/test_nchooser.py -> build/bdist.linux-x86_64/egg/tests/unittests copying build/lib/tests/__init__.py -> build/bdist.linux-x86_64/egg/tests creating build/bdist.linux-x86_64/egg/emodpy_hiv creating build/bdist.linux-x86_64/egg/emodpy_hiv/demographics copying build/lib/emodpy_hiv/demographics/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/demographics copying build/lib/emodpy_hiv/demographics/HIVDemographics.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/demographics copying build/lib/emodpy_hiv/demographics/DemographicsTemplates.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/demographics copying build/lib/emodpy_hiv/download.py -> build/bdist.linux-x86_64/egg/emodpy_hiv copying build/lib/emodpy_hiv/utils.py -> build/bdist.linux-x86_64/egg/emodpy_hiv creating build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/yearandsexdiag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/cascade_helpers.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/outbreak.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/stipostdebut.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/setsexualdebut.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/reftrackercoord.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/utils.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/randomchoice.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/artstagingbycd4agnosticdiag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/hivmuxer.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/rapiddiag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/pmtct.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/artdropout.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/drawblood.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/nchooser.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/art.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/prep.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/reftracker.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/modcoinf.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/malecirc.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/artstagingbycd4diag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/sigmoiddiag.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/interventions/delay.py -> build/bdist.linux-x86_64/egg/emodpy_hiv/interventions copying build/lib/emodpy_hiv/__init__.py -> build/bdist.linux-x86_64/egg/emodpy_hiv byte-compiling build/bdist.linux-x86_64/egg/tests/create_auth_token_args.py to create_auth_token_args.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/schema_path_file.py to schema_path_file.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_hivmuxer.py to test_hivmuxer.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_intervention.py to test_intervention.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_demographics.py to test_demographics.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_import.py to test_import.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/check_coverage.py to check_coverage.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_emod_hiv_package.py to test_emod_hiv_package.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/manifest.py to manifest.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/unittests/test_nchooser.py to test_nchooser.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/demographics/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/demographics/HIVDemographics.py to HIVDemographics.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/demographics/DemographicsTemplates.py to DemographicsTemplates.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/download.py to download.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/utils.py to utils.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/yearandsexdiag.py to yearandsexdiag.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/cascade_helpers.py to cascade_helpers.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/outbreak.py to outbreak.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/stipostdebut.py to stipostdebut.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/setsexualdebut.py to setsexualdebut.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/reftrackercoord.py to reftrackercoord.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/utils.py to utils.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/randomchoice.py to randomchoice.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/artstagingbycd4agnosticdiag.py to artstagingbycd4agnosticdiag.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/hivmuxer.py to hivmuxer.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/rapiddiag.py to rapiddiag.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/pmtct.py to pmtct.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/artdropout.py to artdropout.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/drawblood.py to drawblood.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/nchooser.py to nchooser.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/art.py to art.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/__init__.py to __init__.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/prep.py to prep.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/reftracker.py to reftracker.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/modcoinf.py to modcoinf.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/malecirc.py to malecirc.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/artstagingbycd4diag.py to artstagingbycd4diag.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/sigmoiddiag.py to sigmoiddiag.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/interventions/delay.py to delay.cpython-39.pyc byte-compiling build/bdist.linux-x86_64/egg/emodpy_hiv/__init__.py to __init__.cpython-39.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_hiv.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_hiv.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_hiv.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_hiv.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emodpy_hiv.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... tests.unittests.__pycache__.manifest.cpython-39: module references __file__ tests.unittests.__pycache__.schema_path_file.cpython-39: module references __file__ tests.unittests.__pycache__.test_demographics.cpython-39: module references __file__ tests.unittests.__pycache__.test_intervention.cpython-39: module references __file__ creating dist creating 'dist/emodpy_hiv-1.1.1-py3.9.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing emodpy_hiv-1.1.1-py3.9.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages/emodpy_hiv-1.1.1-py3.9.egg Extracting emodpy_hiv-1.1.1-py3.9.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Adding emodpy-hiv 1.1.1 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages/emodpy_hiv-1.1.1-py3.9.egg Processing dependencies for emodpy-hiv==1.1.1 Searching for requests==2.29.0 Reading https://pypi.org/simple/requests/ Downloading https://files.pythonhosted.org/packages/cf/e1/2aa539876d9ed0ddc95882451deb57cfd7aa8dbf0b8dbce68e045549ba56/requests-2.29.0-py3-none-any.whl#sha256=e8f3c9be120d3333921d213eef078af392fba3933ab7ed2d1cba3b56f2568c3b Best match: requests 2.29.0 Processing requests-2.29.0-py3-none-any.whl Installing requests-2.29.0-py3-none-any.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Adding requests 2.29.0 to easy-install.pth file detected new path './emodpy_hiv-1.1.1-py3.9.egg' Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages/requests-2.29.0-py3.9.egg Searching for emod-hiv==1.0.1 Best match: emod-hiv 1.0.1 Adding emod-hiv 1.0.1 to easy-install.pth file detected new path './requests-2.29.0-py3.9.egg' Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for emodpy==1.22.0 Best match: emodpy 1.22.0 Adding emodpy 1.22.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for pyCOMPS==2.10.0 Best match: pyCOMPS 2.10.0 Adding pyCOMPS 2.10.0 to easy-install.pth file Installing comps-util script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for keyring==24.3.1 Best match: keyring 24.3.1 Adding keyring 24.3.1 to easy-install.pth file Installing keyring script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for bs4==0.0.2 Best match: bs4 0.0.2 Adding bs4 0.0.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for astunparse==1.6.3 Best match: astunparse 1.6.3 Adding astunparse 1.6.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for astor==0.8.1 Best match: astor 0.8.1 Adding astor 0.8.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for matplotlib==3.8.3 Best match: matplotlib 3.8.3 Adding matplotlib 3.8.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for emod-api==1.30.1 Best match: emod-api 1.30.1 Adding emod-api 1.30.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for idmtools-models==1.7.9 Best match: idmtools-models 1.7.9 Adding idmtools-models 1.7.9 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for idmtools-platform-comps==1.7.9 Best match: idmtools-platform-comps 1.7.9 Adding idmtools-platform-comps 1.7.9 to easy-install.pth file Installing comps-cli script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for idmtools==1.7.9 Best match: idmtools 1.7.9 Adding idmtools 1.7.9 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for click==7.1.2 Best match: click 7.1.2 Adding click 7.1.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for certifi==2024.2.2 Best match: certifi 2024.2.2 Adding certifi 2024.2.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for urllib3==1.26.18 Best match: urllib3 1.26.18 Adding urllib3 1.26.18 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for idna==3.6 Best match: idna 3.6 Adding idna 3.6 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for charset-normalizer==3.3.2 Best match: charset-normalizer 3.3.2 Adding charset-normalizer 3.3.2 to easy-install.pth file Installing normalizer script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for xdg==6.0.0 Best match: xdg 6.0.0 Adding xdg 6.0.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for future==1.0.0 Best match: future 1.0.0 Adding future 1.0.0 to easy-install.pth file Installing futurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Installing pasteurize script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for pytz==2024.1 Best match: pytz 2024.1 Adding pytz 2024.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for jeepney==0.8.0 Best match: jeepney 0.8.0 Adding jeepney 0.8.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for SecretStorage==3.3.3 Best match: SecretStorage 3.3.3 Adding SecretStorage 3.3.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for importlib-metadata==7.0.2 Best match: importlib-metadata 7.0.2 Adding importlib-metadata 7.0.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for jaraco.classes==3.3.1 Best match: jaraco.classes 3.3.1 Adding jaraco.classes 3.3.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for beautifulsoup4==4.12.3 Best match: beautifulsoup4 4.12.3 Adding beautifulsoup4 4.12.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for six==1.16.0 Best match: six 1.16.0 Adding six 1.16.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for wheel==0.40.0 Best match: wheel 0.40.0 Adding wheel 0.40.0 to easy-install.pth file Installing wheel script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for importlib-resources==6.1.3 Best match: importlib-resources 6.1.3 Adding importlib-resources 6.1.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for python-dateutil==2.9.0.post0 Best match: python-dateutil 2.9.0.post0 Adding python-dateutil 2.9.0.post0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for pyparsing==3.1.2 Best match: pyparsing 3.1.2 Adding pyparsing 3.1.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for pillow==10.2.0 Best match: pillow 10.2.0 Adding pillow 10.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for packaging==21.3 Best match: packaging 21.3 Adding packaging 21.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for numpy==1.26.4 Best match: numpy 1.26.4 Adding numpy 1.26.4 to easy-install.pth file Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for kiwisolver==1.4.5 Best match: kiwisolver 1.4.5 Adding kiwisolver 1.4.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for fonttools==4.49.0 Best match: fonttools 4.49.0 Adding fonttools 4.49.0 to easy-install.pth file Installing fonttools script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Installing pyftmerge script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Installing pyftsubset script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Installing ttx script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for cycler==0.12.1 Best match: cycler 0.12.1 Adding cycler 0.12.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for contourpy==1.2.0 Best match: contourpy 1.2.0 Adding contourpy 1.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for parse==1.20.1 Best match: parse 1.20.1 Adding parse 1.20.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for graphviz==0.20.1 Best match: graphviz 0.20.1 Adding graphviz 0.20.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for prodict==0.8.18 Best match: prodict 0.8.18 Adding prodict 0.8.18 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for lz4==4.3.3 Best match: lz4 4.3.3 Adding lz4 4.3.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for scikit-learn==1.4.1.post1 Best match: scikit-learn 1.4.1.post1 Adding scikit-learn 1.4.1.post1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for geographiclib==2.0 Best match: geographiclib 2.0 Adding geographiclib 2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for pyproj==3.6.1 Best match: pyproj 3.6.1 Adding pyproj 3.6.1 to easy-install.pth file Installing pyproj script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for shapely==2.0.3 Best match: shapely 2.0.3 Adding shapely 2.0.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for scipy==1.12.0 Best match: scipy 1.12.0 Adding scipy 1.12.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for pandas==2.2.1 Best match: pandas 2.2.1 Adding pandas 2.2.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for PyYAML==6.0.1 Best match: PyYAML 6.0.1 Adding PyYAML 6.0.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for Jinja2==3.1.3 Best match: Jinja2 3.1.3 Adding Jinja2 3.1.3 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for natsort==8.4.0 Best match: natsort 8.4.0 Adding natsort 8.4.0 to easy-install.pth file Installing natsort script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for tqdm==4.66.2 Best match: tqdm 4.66.2 Adding tqdm 4.66.2 to easy-install.pth file Installing tqdm script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for pygit2==1.10.1 Best match: pygit2 1.10.1 Adding pygit2 1.10.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for tabulate==0.9.0 Best match: tabulate 0.9.0 Adding tabulate 0.9.0 to easy-install.pth file Installing tabulate script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for pluggy==1.2.0 Best match: pluggy 1.2.0 Adding pluggy 1.2.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for pipreqs==0.4.13 Best match: pipreqs 0.4.13 Adding pipreqs 0.4.13 to easy-install.pth file Installing pipreqs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for more-itertools==9.1.0 Best match: more-itertools 9.1.0 Adding more-itertools 9.1.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for filelock==3.13.1 Best match: filelock 3.13.1 Adding filelock 3.13.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for diskcache==5.4.0 Best match: diskcache 5.4.0 Adding diskcache 5.4.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for coloredlogs==15.0.1 Best match: coloredlogs 15.0.1 Adding coloredlogs 15.0.1 to easy-install.pth file Installing coloredlogs script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for backoff==2.2.1 Best match: backoff 2.2.1 Adding backoff 2.2.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for cryptography==42.0.5 Best match: cryptography 42.0.5 Adding cryptography 42.0.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for zipp==3.17.0 Best match: zipp 3.17.0 Adding zipp 3.17.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for soupsieve==2.5 Best match: soupsieve 2.5 Adding soupsieve 2.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for threadpoolctl==3.3.0 Best match: threadpoolctl 3.3.0 Adding threadpoolctl 3.3.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for joblib==1.3.2 Best match: joblib 1.3.2 Adding joblib 1.3.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for tzdata==2024.1 Best match: tzdata 2024.1 Adding tzdata 2024.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for MarkupSafe==2.1.5 Best match: MarkupSafe 2.1.5 Adding MarkupSafe 2.1.5 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for cffi==1.16.0 Best match: cffi 1.16.0 Adding cffi 1.16.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for yarg==0.1.9 Best match: yarg 0.1.9 Adding yarg 0.1.9 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for docopt==0.6.2 Best match: docopt 0.6.2 Adding docopt 0.6.2 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for humanfriendly==10.0 Best match: humanfriendly 10.0 Adding humanfriendly 10.0 to easy-install.pth file Installing humanfriendly script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/bin Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Searching for pycparser==2.21 Best match: pycparser 2.21 Adding pycparser 2.21 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/199/lib/python3.9/site-packages Finished processing dependencies for emodpy-hiv==1.1.1 [rtd-command-info] start-time: 2024-03-12T18:17:06.221408Z, end-time: 2024-03-12T18:17:06.283215Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Sphinx Demo docs build configuration file, created by # sphinx-quickstart on Fri Aug 26 16:52:16 2016. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # docs root, use os.path.abspath to make it absolute, like shown here. # import os import subprocess import sys import sphinx_rtd_theme import configparser from datetime import datetime if sys.platform in ["linux", "darwin"]: subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) else: subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) # Rename "emodpy-hiv" to "API reference" filename = 'modules.rst' # This must match the Makefile with open(filename) as f: # Read existing file lines = f.readlines() lines[0] = "API reference\n" # Blast away the existing heading and replace with this lines[1] = "=============\n" # Ensure the heading is the right length with open(filename, "w") as f: # Write new file f.writelines(lines) # -- General configuration ------------------------------------------------ tags.add('emodpyhiv') # If your docs needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.mathjax', 'sphinx.ext.githubpages', 'sphinx.ext.autodoc', 'sphinxcontrib.napoleon', 'sphinx.ext.todo', 'plantweb.directive', 'sphinxcontrib.programoutput', 'sphinx.ext.intersphinx', 'sphinxext.remoteliteralinclude', 'sphinx_copybutton', 'myst_parser', 'sphinx_search.extension', # search across multiple docsets in domain 'sphinx.ext.viewcode', # link to view source code 'myst_parser', # source files written in MD or RST ] myst_enable_extensions = [ "amsmath", "attrs_inline", "colon_fence", "deflist", "dollarmath", "fieldlist", "html_admonition", "html_image", "linkify", "replacements", "smartquotes", "strikethrough", "substitution", "tasklist", ] plantuml = 'plantweb' autodoc_default_options = { 'member-order': 'bysource', 'members': None, 'exclude-members': '__all__' } autodoc_mock_imports = [] napoleon_google_docstring = True # napoleon_numpy_docstring = True # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # source_suffix = ['.rst', '.md'] # The encoding of source files. # # source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'emodpy-hiv' copyright = f'1999 - {datetime.today().year}, Bill & Melinda Gates Foundation. All rights reserved.' author = u'Institute for Disease Modeling' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. #current_path = os.path.dirname(__file__) #version_path = os.path.join(current_path, '..', '.bumpversion.cfg') #config = configparser.ConfigParser() #config.read(version_path) #version = config['bumpversion']['current_version'] # The full version, including alpha/beta/rc tags. # release = u'1.0' # The language for content autogenerated by Sphinx. Refer to docs # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = 'en' # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: # # today = '' # # Else, today_fmt is used as the format for a strftime call. # # today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # The reST default role (used for this markup: `text`) to use for all # documents. # # default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. # # add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). # # add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. # # show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. # keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # RST epilog is added to the end of every topic. Useful for replace # directives to use across the docset. rst_epilog = "\n.. include:: /variables.txt" # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the docs for # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # docs. # # # html_theme_options = { # } # Add any paths that contain custom themes here, relative to this directory. html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] # The name for this set of Sphinx documents. # " v docs" by default. # # html_title = u'Sphinx Demo v1.0' # A shorter title for the navigation bar. Default is the same as html_title. # # html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. # html_logo = "images/IDM_white.png" # The name of an image file (relative to this directory) to use as a favicon of # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. # html_favicon = "images/favicon.ico" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] html_css_files = ['theme_overrides.css'] html_js_files = ['show_block_by_os.js'] # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the docs. # # html_extra_path = [] # If not None, a 'Last updated on:' timestamp is inserted at every page # bottom, using the given strftime format. # The empty string is equivalent to '%b %d, %Y'. # # html_last_updated_fmt = None # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. # # html_use_smartypants = True # Custom sidebar templates, maps document names to template names. # # html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. # # html_additional_pages = {} # If false, no module index is generated. # # html_domain_indices = True # If false, no index is generated. # # html_use_index = True # If true, the index is split into individual pages for each letter. # # html_split_index = False # If true, links to the reST sources are added to the pages. # html_show_sourcelink = False # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. # html_show_sphinx = False # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. # # html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. # html_use_opensearch = 'www.idmod.org/docs/' # -- RTD Sphinx search for searching across the entire domain, default parent ------------- if os.environ.get('READTHEDOCS') == 'True': search_project_parent = "institute-for-disease-modeling-idm" search_project = os.environ["READTHEDOCS_PROJECT"] search_version = os.environ["READTHEDOCS_VERSION"] rtd_sphinx_search_default_filter = f"subprojects:{search_project}/{search_version}" rtd_sphinx_search_filters = { "Search this project": f"project:{search_project}/{search_version}", "Search all IDM docs": f"subprojects:{search_project_parent}/{search_version}", } # This is the file name suffix for HTML files (e.g. ".xhtml"). # html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh' # # html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # 'ja' uses this config value. # 'zh' user can custom change `jieba` dictionary path. # # html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. # # html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. htmlhelp_basename = 'emodpy-hiv' # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'emodpy-hiv-docs.tex', u'emodpy-hiv', u'Institute for Disease Modeling', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. # # latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. # # latex_use_parts = False # If true, show page references after internal links. # # latex_show_pagerefs = False # If true, show URL addresses after external links. # # latex_show_urls = False # Documents to append as an appendix to all manuals. # # latex_appendices = [] # It false, will not define \strong, \code, itleref, \crossref ... but only # \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added # packages. # # latex_keep_old_macro_names = True # If false, no module index is generated. # # latex_domain_indices = True # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'emodpy-hiv-docs', u'emodpy-hiv', [author], 1) ] # If true, show URL addresses after external links. # man_show_urls = True # -- Options for Texinfo output ------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'emodpy-hiv-docs', u'emodpy-hiv', author, 'Institute for Disease Modeling', 'How to use emodpy for HIV simulations.', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. # # texinfo_appendices = [] # If false, no module index is generated. # # texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. # # texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. # # texinfo_no_detailmenu = False # Example configuration for intersphinx: refer to the Python standard library. intersphinx_mapping = {'python': ('https://docs.python.org/3', None), 'emod_api': ('https://docs.idmod.org/projects/emod-api/en/latest/', None), 'emodpy': ('https://docs.idmod.org/projects/emodpy/en/latest/', None), 'emodpy_generic': ('https://docs.idmod.org/projects/emodpy-generic/en/latest/', None), 'idmtools': ('https://docs.idmod.org/projects/idmtools/en/latest/', None), 'calibra': ('https://docs.idmod.org/projects/idmtools_calibra/en/latest/', None), 'emod-hiv': ('https://docs.idmod.org/projects/emod-hiv/en/latest/', None), 'emod-generic': ('https://docs.idmod.org/projects/emod-generic/en/latest/', None), 'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None) } ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Define this variable in case it's not defined by the user. # It defaults to `alabaster` which is the default from Sphinx. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme html_theme = globals().get('html_theme', 'alabaster') #Add project information to the template context. context = { 'html_theme': html_theme, 'current_version': "199", 'version_slug': "199", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ("v1.0.2", "/en/v1.0.2/"), ("v1.0.1", "/en/v1.0.1/"), ("v0.0.41", "/en/v0.0.41/"), ("v0.0.38", "/en/v0.0.38/"), ("v0.0.37", "/en/v0.0.37/"), ("v0.0.35", "/en/v0.0.35/"), ("v0.0.22", "/en/v0.0.22/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-emodpy-hiv', 'name': u'emodpy-hiv', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': '', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'emodpy-hiv', 'github_version': '1d761ace739da60657255f96481ad79aa56914b2', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '1d761ace739da60657255f96481ad79aa56914b2', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '1d761ace739da60657255f96481ad79aa56914b2', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '1d761ace', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): for key in context: if key not in html_context: html_context[key] = context[key] else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'external' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'https://github.com/InstituteforDiseaseModeling/emodpy-hiv/pull/199' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-emodpy-hiv/builds/2079085/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2024-03-12T18:17:06.361009Z, end-time: 2024-03-12T18:17:13.811383Z, duration: 7, exit-code: 0 python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v6.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [Makefile:58: generate-api] Error 1 (ignored) making output directory... done loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-api/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emodpy-generic/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/idmtools/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/idmtools_calibra/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-hiv/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/emod-generic/en/latest/objects.inv... loading intersphinx inventory from https://docs.idmod.org/projects/pycomps/en/latest/objects.inv... myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'substitution', 'html_image', 'colon_fence', 'dollarmath', 'tasklist', 'smartquotes', 'linkify', 'replacements', 'deflist', 'strikethrough', 'fieldlist', 'html_admonition', 'attrs_inline', 'amsmath'}, disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 34 source files that are out of date updating environment: [new config] 34 added, 0 changed, 0 removed reading sources... [ 2%] emodpy_hiv reading sources... [ 5%] emodpy_hiv.demographics reading sources... [ 8%] emodpy_hiv.demographics.DemographicsTemplates reading sources... [ 11%] emodpy_hiv.demographics.HIVDemographics reading sources... [ 14%] emodpy_hiv.download reading sources... [ 17%] emodpy_hiv.interventions reading sources... [ 20%] emodpy_hiv.interventions.art reading sources... [ 23%] emodpy_hiv.interventions.artdropout reading sources... [ 26%] emodpy_hiv.interventions.artstagingbycd4agnosticdiag reading sources... [ 29%] emodpy_hiv.interventions.artstagingbycd4diag reading sources... [ 32%] emodpy_hiv.interventions.cascade_helpers reading sources... [ 35%] emodpy_hiv.interventions.delay reading sources... [ 38%] emodpy_hiv.interventions.drawblood reading sources... [ 41%] emodpy_hiv.interventions.hivmuxer reading sources... [ 44%] emodpy_hiv.interventions.malecirc reading sources... [ 47%] emodpy_hiv.interventions.modcoinf reading sources... [ 50%] emodpy_hiv.interventions.nchooser reading sources... [ 52%] emodpy_hiv.interventions.outbreak reading sources... [ 55%] emodpy_hiv.interventions.pmtct reading sources... [ 58%] emodpy_hiv.interventions.prep reading sources... [ 61%] emodpy_hiv.interventions.randomchoice reading sources... [ 64%] emodpy_hiv.interventions.rapiddiag reading sources... [ 67%] emodpy_hiv.interventions.reftracker reading sources... [ 70%] emodpy_hiv.interventions.reftrackercoord reading sources... [ 73%] emodpy_hiv.interventions.setsexualdebut reading sources... [ 76%] emodpy_hiv.interventions.sigmoiddiag reading sources... [ 79%] emodpy_hiv.interventions.stipostdebut reading sources... [ 82%] emodpy_hiv.interventions.utils reading sources... [ 85%] emodpy_hiv.interventions.yearandsexdiag reading sources... [ 88%] emodpy_hiv.utils reading sources... [ 91%] faq reading sources... [ 94%] index reading sources... [ 97%] installation reading sources... [100%] modules looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 2%] emodpy_hiv writing output... [ 5%] emodpy_hiv.demographics writing output... [ 8%] emodpy_hiv.demographics.DemographicsTemplates writing output... [ 11%] emodpy_hiv.demographics.HIVDemographics writing output... [ 14%] emodpy_hiv.download writing output... [ 17%] emodpy_hiv.interventions writing output... [ 20%] emodpy_hiv.interventions.art writing output... [ 23%] emodpy_hiv.interventions.artdropout writing output... [ 26%] emodpy_hiv.interventions.artstagingbycd4agnosticdiag writing output... [ 29%] emodpy_hiv.interventions.artstagingbycd4diag writing output... [ 32%] emodpy_hiv.interventions.cascade_helpers writing output... [ 35%] emodpy_hiv.interventions.delay writing output... [ 38%] emodpy_hiv.interventions.drawblood writing output... [ 41%] emodpy_hiv.interventions.hivmuxer writing output... [ 44%] emodpy_hiv.interventions.malecirc writing output... [ 47%] emodpy_hiv.interventions.modcoinf writing output... [ 50%] emodpy_hiv.interventions.nchooser writing output... [ 52%] emodpy_hiv.interventions.outbreak writing output... [ 55%] emodpy_hiv.interventions.pmtct writing output... [ 58%] emodpy_hiv.interventions.prep writing output... [ 61%] emodpy_hiv.interventions.randomchoice writing output... [ 64%] emodpy_hiv.interventions.rapiddiag writing output... [ 67%] emodpy_hiv.interventions.reftracker writing output... [ 70%] emodpy_hiv.interventions.reftrackercoord writing output... [ 73%] emodpy_hiv.interventions.setsexualdebut writing output... [ 76%] emodpy_hiv.interventions.sigmoiddiag writing output... [ 79%] emodpy_hiv.interventions.stipostdebut writing output... [ 82%] emodpy_hiv.interventions.utils writing output... [ 85%] emodpy_hiv.interventions.yearandsexdiag writing output... [ 88%] emodpy_hiv.utils writing output... [ 91%] faq writing output... [ 94%] index writing output... [ 97%] installation writing output... [100%] modules generating indices... genindex py-modindex done highlighting module code... [ 3%] emodpy_hiv.demographics.DemographicsTemplates highlighting module code... [ 7%] emodpy_hiv.demographics.HIVDemographics highlighting module code... [ 11%] emodpy_hiv.download highlighting module code... [ 14%] emodpy_hiv.interventions.art highlighting module code... [ 18%] emodpy_hiv.interventions.artdropout highlighting module code... [ 22%] emodpy_hiv.interventions.artstagingbycd4agnosticdiag highlighting module code... [ 25%] emodpy_hiv.interventions.artstagingbycd4diag highlighting module code... [ 29%] emodpy_hiv.interventions.cascade_helpers highlighting module code... [ 33%] emodpy_hiv.interventions.delay highlighting module code... [ 37%] emodpy_hiv.interventions.drawblood highlighting module code... [ 40%] emodpy_hiv.interventions.hivmuxer highlighting module code... [ 44%] emodpy_hiv.interventions.malecirc highlighting module code... [ 48%] emodpy_hiv.interventions.modcoinf highlighting module code... [ 51%] emodpy_hiv.interventions.nchooser highlighting module code... [ 55%] emodpy_hiv.interventions.outbreak highlighting module code... [ 59%] emodpy_hiv.interventions.pmtct highlighting module code... [ 62%] emodpy_hiv.interventions.prep highlighting module code... [ 66%] emodpy_hiv.interventions.randomchoice highlighting module code... [ 70%] emodpy_hiv.interventions.rapiddiag highlighting module code... [ 74%] emodpy_hiv.interventions.reftracker highlighting module code... [ 77%] emodpy_hiv.interventions.reftrackercoord highlighting module code... [ 81%] emodpy_hiv.interventions.setsexualdebut highlighting module code... [ 85%] emodpy_hiv.interventions.sigmoiddiag highlighting module code... [ 88%] emodpy_hiv.interventions.stipostdebut highlighting module code... [ 92%] emodpy_hiv.interventions.utils highlighting module code... [ 96%] emodpy_hiv.interventions.yearandsexdiag highlighting module code... [100%] emodpy_hiv.utils writing additional pages... search opensearch done copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done Updating searchtools for Read the Docs search... build succeeded. The HTML pages are in ../_readthedocs/html.