Read the Docs build information
Build id: 1664246
Project: institute-for-disease-modeling-emod-hiv
Version: latest
Commit: cd7b42519d875288c6470b5274bd2f1513ee1e68
Date: 2023-08-16T16:58:22.410304Z
State: cancelled
Success: False


[rtd-command-info] start-time: 2023-08-16T16:58:30.129500Z, end-time: 2023-08-16T16:59:05.012789Z, duration: 34, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/EMOD-docs.git .
Cloning into '.'...
Warning: Permanently added 'github.com' (ED25519) to the list of known hosts.

[rtd-command-info] start-time: 2023-08-16T16:59:05.667745Z, end-time: 2023-08-16T16:59:05.842925Z, duration: 0, exit-code: 0
git checkout --force origin/malaria-ongoing
Note: switching to 'origin/malaria-ongoing'.

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 <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at cd7b4251 Merge pull request #1810 from KElsaesser-IDM/1499-migration-filenames

[rtd-command-info] start-time: 2023-08-16T16:59:06.461994Z, end-time: 2023-08-16T16:59:06.538145Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-08-16T16:59:07.015072Z, end-time: 2023-08-16T16:59:07.094982Z, duration: 0, exit-code: 0
cat .readthedocs.yml
# .readthedocs.yml
# Read the Docs configuration file
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

# Required
version: 2

# Build documentation in the docs/ directory with Sphinx
sphinx:
  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:
  version: 3.7
  install:
    - requirements: requirements.txt
        
# Optionally rank topics in search results, between -10 (lower) and 10 (higher).
# 0 is normal rank, not no rank

search:
  ranking:
    install-overview.html: 3
    model-overview.html: 3
    faq.html: 2
    parameter-overview.html: 2
    dev*: -5

[rtd-command-info] start-time: 2023-08-16T16:59:09.853536Z, end-time: 2023-08-16T16:59:14.662011Z, duration: 4, exit-code: 0
python3.7 -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2023-08-16T16:59:15.138867Z, end-time: 2023-08-16T16:59:16.363523Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (23.2.1)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (68.0.0)

[rtd-command-info] start-time: 2023-08-16T16:59:16.842537Z, end-time: 2023-08-16T16:59:24.115188Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir pillow==5.4.1 mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0
Collecting pillow==5.4.1
  Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 37.3 MB/s eta 0:00:00
Collecting mock==1.0.1
  Downloading mock-1.0.1.zip (861 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 219.6 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting alabaster!=0.7.5,<0.8,>=0.7
  Downloading alabaster-0.7.13-py3-none-any.whl (13 kB)
Collecting commonmark==0.9.1
  Downloading commonmark-0.9.1-py2.py3-none-any.whl (51 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.1/51.1 kB 158.9 MB/s eta 0:00:00
Collecting recommonmark==0.5.0
  Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB)
Collecting sphinx<2
  Downloading Sphinx-1.8.6-py2.py3-none-any.whl (3.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 189.1 MB/s eta 0:00:00
Collecting sphinx-rtd-theme<0.5
  Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.4/6.4 MB 171.4 MB/s eta 0:00:00
Collecting readthedocs-sphinx-ext<2.3
  Obtaining dependency information for readthedocs-sphinx-ext<2.3 from https://files.pythonhosted.org/packages/8c/f1/3d783ebfc084a9d556123d54669116101760e5e0dbb894b006745bcb59ea/readthedocs_sphinx_ext-2.2.2-py2.py3-none-any.whl.metadata
  Downloading readthedocs_sphinx_ext-2.2.2-py2.py3-none-any.whl.metadata (1.5 kB)
Collecting jinja2<3.1.0
  Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.6/133.6 kB 184.1 MB/s eta 0:00:00
Collecting docutils>=0.11 (from recommonmark==0.5.0)
  Obtaining dependency information for docutils>=0.11 from https://files.pythonhosted.org/packages/26/87/f238c0670b94533ac0353a4e2a1a771a0cc73277b88bff23d3ae35a256c1/docutils-0.20.1-py3-none-any.whl.metadata
  Downloading docutils-0.20.1-py3-none-any.whl.metadata (2.8 kB)
Collecting six>=1.5 (from sphinx<2)
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting Pygments>=2.0 (from sphinx<2)
  Obtaining dependency information for Pygments>=2.0 from https://files.pythonhosted.org/packages/43/88/29adf0b44ba6ac85045e63734ae0997d3c58d8b1a91c914d240828d0d73d/Pygments-2.16.1-py3-none-any.whl.metadata
  Downloading Pygments-2.16.1-py3-none-any.whl.metadata (2.5 kB)
Collecting docutils>=0.11 (from recommonmark==0.5.0)
  Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 223.1 MB/s eta 0:00:00
Collecting snowballstemmer>=1.1 (from sphinx<2)
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 183.0 MB/s eta 0:00:00
Collecting babel!=2.0,>=1.3 (from sphinx<2)
  Downloading Babel-2.12.1-py3-none-any.whl (10.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.1/10.1 MB 155.0 MB/s eta 0:00:00
Collecting imagesize (from sphinx<2)
  Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Collecting requests>=2.0.0 (from sphinx<2)
  Obtaining dependency information for requests>=2.0.0 from https://files.pythonhosted.org/packages/70/8e/0e2d847013cb52cd35b38c009bb167a1a26b2ce6cd6965bf26b47bc0bf44/requests-2.31.0-py3-none-any.whl.metadata
  Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx<2) (68.0.0)
Collecting packaging (from sphinx<2)
  Downloading packaging-23.1-py3-none-any.whl (48 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.9/48.9 kB 156.7 MB/s eta 0:00:00
Collecting sphinxcontrib-websupport (from sphinx<2)
  Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB)
Collecting MarkupSafe>=2.0 (from jinja2<3.1.0)
  Obtaining dependency information for MarkupSafe>=2.0 from https://files.pythonhosted.org/packages/e5/dd/49576e803c0d974671e44fa78049217fcc68af3662a24f831525ed30e6c7/MarkupSafe-2.1.3-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading MarkupSafe-2.1.3-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Collecting pytz>=2015.7 (from babel!=2.0,>=1.3->sphinx<2)
  Downloading pytz-2023.3-py2.py3-none-any.whl (502 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 502.3/502.3 kB 213.2 MB/s eta 0:00:00
Collecting charset-normalizer<4,>=2 (from requests>=2.0.0->sphinx<2)
  Obtaining dependency information for charset-normalizer<4,>=2 from https://files.pythonhosted.org/packages/89/f5/88e9dd454756fea555198ddbe6fa40d6408ec4f10ad4f0a911e0b7e471e4/charset_normalizer-3.2.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading charset_normalizer-3.2.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (31 kB)
Collecting idna<4,>=2.5 (from requests>=2.0.0->sphinx<2)
  Downloading idna-3.4-py3-none-any.whl (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.5/61.5 kB 149.0 MB/s eta 0:00:00
Collecting urllib3<3,>=1.21.1 (from requests>=2.0.0->sphinx<2)
  Obtaining dependency information for urllib3<3,>=1.21.1 from https://files.pythonhosted.org/packages/9b/81/62fd61001fa4b9d0df6e31d47ff49cfa9de4af03adecf339c7bc30656b37/urllib3-2.0.4-py3-none-any.whl.metadata
  Downloading urllib3-2.0.4-py3-none-any.whl.metadata (6.6 kB)
Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx<2)
  Obtaining dependency information for certifi>=2017.4.17 from https://files.pythonhosted.org/packages/4c/dd/2234eab22353ffc7d94e8d13177aaa050113286e93e7b40eae01fbf7c3d9/certifi-2023.7.22-py3-none-any.whl.metadata
  Downloading certifi-2023.7.22-py3-none-any.whl.metadata (2.2 kB)
Collecting sphinxcontrib-serializinghtml (from sphinxcontrib-websupport->sphinx<2)
  Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.0/94.0 kB 188.8 MB/s eta 0:00:00
Downloading readthedocs_sphinx_ext-2.2.2-py2.py3-none-any.whl (11 kB)
Downloading MarkupSafe-2.1.3-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Downloading Pygments-2.16.1-py3-none-any.whl (1.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 220.3 MB/s eta 0:00:00
Downloading requests-2.31.0-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.6/62.6 kB 178.5 MB/s eta 0:00:00
Downloading certifi-2023.7.22-py3-none-any.whl (158 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 158.3/158.3 kB 204.6 MB/s eta 0:00:00
Downloading charset_normalizer-3.2.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (175 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 175.8/175.8 kB 206.2 MB/s eta 0:00:00
Downloading urllib3-2.0.4-py3-none-any.whl (123 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 123.9/123.9 kB 201.4 MB/s eta 0:00:00
Building wheels for collected packages: mock
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23753 sha256=2079151c8fe9333f43359e703ddf21a96949265afa22b3109d11eecb0a852300
  Stored in directory: /tmp/pip-ephem-wheel-cache-3fbgzuvk/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1
Successfully built mock
Installing collected packages: snowballstemmer, pytz, mock, commonmark, urllib3, sphinxcontrib-serializinghtml, six, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed MarkupSafe-2.1.3 Pygments-2.16.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.7.22 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.1 pillow-5.4.1 pytz-2023.3 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-2.0.4

[rtd-command-info] start-time: 2023-08-16T16:59:24.575667Z, end-time: 2023-08-16T16:59:31.719103Z, duration: 7, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
Collecting sphinx-rtd-theme~=0.5.2 (from -r requirements.txt (line 1))
  Downloading sphinx_rtd_theme-0.5.2-py2.py3-none-any.whl (9.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.1/9.1 MB 86.1 MB/s eta 0:00:00
Collecting sphinxcontrib-napoleon~=0.7 (from -r requirements.txt (line 2))
  Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB)
Collecting sphinx~=4.4.0 (from -r requirements.txt (line 3))
  Downloading Sphinx-4.4.0-py3-none-any.whl (3.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 188.0 MB/s eta 0:00:00
Collecting plantweb~=1.2.1 (from -r requirements.txt (line 4))
  Downloading plantweb-1.2.1-py3-none-any.whl (20 kB)
Collecting numpy~=1.19.1 (from -r requirements.txt (line 5))
  Downloading numpy-1.19.5-cp37-cp37m-manylinux2010_x86_64.whl (14.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.8/14.8 MB 154.4 MB/s eta 0:00:00
Collecting numpydoc~=1.0.0 (from -r requirements.txt (line 6))
  Downloading numpydoc-1.0.0-py3-none-any.whl (47 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.4/47.4 kB 131.1 MB/s eta 0:00:00
Collecting myst-parser (from -r requirements.txt (line 7))
  Downloading myst_parser-1.0.0-py3-none-any.whl (77 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.3/77.3 kB 182.4 MB/s eta 0:00:00
Collecting readthedocs-sphinx-search (from -r requirements.txt (line 8))
  Downloading readthedocs_sphinx_search-0.3.1-py3-none-any.whl (21 kB)
Collecting docutils<0.17 (from sphinx-rtd-theme~=0.5.2->-r requirements.txt (line 1))
  Downloading docutils-0.16-py2.py3-none-any.whl (548 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 548.2/548.2 kB 211.6 MB/s eta 0:00:00
Requirement already satisfied: six>=1.5.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-napoleon~=0.7->-r requirements.txt (line 2)) (1.16.0)
Collecting pockets>=0.3 (from sphinxcontrib-napoleon~=0.7->-r requirements.txt (line 2))
  Downloading pockets-0.9.1-py2.py3-none-any.whl (26 kB)
Collecting sphinxcontrib-applehelp (from sphinx~=4.4.0->-r requirements.txt (line 3))
  Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.2/121.2 kB 193.5 MB/s eta 0:00:00
Collecting sphinxcontrib-devhelp (from sphinx~=4.4.0->-r requirements.txt (line 3))
  Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.7/84.7 kB 188.7 MB/s eta 0:00:00
Collecting sphinxcontrib-jsmath (from sphinx~=4.4.0->-r requirements.txt (line 3))
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting sphinxcontrib-htmlhelp>=2.0.0 (from sphinx~=4.4.0->-r requirements.txt (line 3))
  Downloading sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl (100 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.5/100.5 kB 191.7 MB/s eta 0:00:00
Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r requirements.txt (line 3)) (1.1.5)
Collecting sphinxcontrib-qthelp (from sphinx~=4.4.0->-r requirements.txt (line 3))
  Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 90.6/90.6 kB 188.2 MB/s eta 0:00:00
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r requirements.txt (line 3)) (3.0.3)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r requirements.txt (line 3)) (2.16.1)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r requirements.txt (line 3)) (2.2.0)
Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r requirements.txt (line 3)) (2.12.1)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r requirements.txt (line 3)) (0.7.13)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r requirements.txt (line 3)) (1.4.1)
Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r requirements.txt (line 3)) (2.31.0)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from sphinx~=4.4.0->-r requirements.txt (line 3)) (23.1)
Collecting importlib-metadata>=4.4 (from sphinx~=4.4.0->-r requirements.txt (line 3))
  Obtaining dependency information for importlib-metadata>=4.4 from https://files.pythonhosted.org/packages/ff/94/64287b38c7de4c90683630338cf28f129decbba0a44f0c6db35a873c73c4/importlib_metadata-6.7.0-py3-none-any.whl.metadata
  Downloading importlib_metadata-6.7.0-py3-none-any.whl.metadata (4.9 kB)
Collecting markdown-it-py<3.0.0,>=1.0.0 (from myst-parser->-r requirements.txt (line 7))
  Downloading markdown_it_py-2.2.0-py3-none-any.whl (84 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.5/84.5 kB 165.7 MB/s eta 0:00:00
Collecting mdit-py-plugins~=0.3.4 (from myst-parser->-r requirements.txt (line 7))
  Downloading mdit_py_plugins-0.3.5-py3-none-any.whl (52 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 52.1/52.1 kB 157.7 MB/s eta 0:00:00
Collecting pyyaml (from myst-parser->-r requirements.txt (line 7))
  Obtaining dependency information for pyyaml from https://files.pythonhosted.org/packages/d7/8f/db62b0df635b9008fe90aa68424e99cee05e68b398740c8a666a98455589/PyYAML-6.0.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading PyYAML-6.0.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
INFO: pip is looking at multiple versions of myst-parser to determine which version is compatible with other requirements. This could take a while.
Collecting myst-parser (from -r requirements.txt (line 7))
  Downloading myst_parser-0.19.2-py3-none-any.whl (77 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.3/77.3 kB 184.1 MB/s eta 0:00:00
  Downloading myst_parser-0.19.1-py3-none-any.whl (76 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 76.8/76.8 kB 170.0 MB/s eta 0:00:00
  Downloading myst_parser-0.19.0-py3-none-any.whl (76 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 76.8/76.8 kB 181.3 MB/s eta 0:00:00
  Downloading myst_parser-0.18.1-py3-none-any.whl (58 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.2/58.2 kB 141.7 MB/s eta 0:00:00
Collecting typing-extensions (from myst-parser->-r requirements.txt (line 7))
  Obtaining dependency information for typing-extensions from https://files.pythonhosted.org/packages/ec/6b/63cc3df74987c36fe26157ee12e09e8f9db4de771e0f3404263117e75b95/typing_extensions-4.7.1-py3-none-any.whl.metadata
  Downloading typing_extensions-4.7.1-py3-none-any.whl.metadata (3.1 kB)
Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from babel>=1.3->sphinx~=4.4.0->-r requirements.txt (line 3)) (2023.3)
Collecting zipp>=0.5 (from importlib-metadata>=4.4->sphinx~=4.4.0->-r requirements.txt (line 3))
  Downloading zipp-3.15.0-py3-none-any.whl (6.8 kB)
Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx~=4.4.0->-r requirements.txt (line 3)) (2.1.3)
Collecting mdurl~=0.1 (from markdown-it-py<3.0.0,>=1.0.0->myst-parser->-r requirements.txt (line 7))
  Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=4.4.0->-r requirements.txt (line 3)) (3.2.0)
Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=4.4.0->-r requirements.txt (line 3)) (3.4)
Requirement already satisfied: urllib3<3,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=4.4.0->-r requirements.txt (line 3)) (2.0.4)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-hiv/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx~=4.4.0->-r requirements.txt (line 3)) (2023.7.22)
Downloading importlib_metadata-6.7.0-py3-none-any.whl (22 kB)
Downloading typing_extensions-4.7.1-py3-none-any.whl (33 kB)
Downloading PyYAML-6.0.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (670 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 670.1/670.1 kB 210.6 MB/s eta 0:00:00
Installing collected packages: zipp, typing-extensions, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, readthedocs-sphinx-search, pyyaml, pockets, numpy, mdurl, docutils, sphinxcontrib-napoleon, plantweb, markdown-it-py, importlib-metadata, sphinx, mdit-py-plugins, sphinx-rtd-theme, numpydoc, myst-parser
  Attempting uninstall: docutils
    Found existing installation: docutils 0.17.1
    Uninstalling docutils-0.17.1:
      Successfully uninstalled docutils-0.17.1
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 1.8.6
    Uninstalling Sphinx-1.8.6:
      Successfully uninstalled Sphinx-1.8.6
  Attempting uninstall: sphinx-rtd-theme
    Found existing installation: sphinx-rtd-theme 0.4.3
    Uninstalling sphinx-rtd-theme-0.4.3:
      Successfully uninstalled sphinx-rtd-theme-0.4.3
Successfully installed docutils-0.16 importlib-metadata-6.7.0 markdown-it-py-2.2.0 mdit-py-plugins-0.3.5 mdurl-0.1.2 myst-parser-0.18.1 numpy-1.19.5 numpydoc-1.0.0 plantweb-1.2.1 pockets-0.9.1 pyyaml-6.0.1 readthedocs-sphinx-search-0.3.1 sphinx-4.4.0 sphinx-rtd-theme-0.5.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-qthelp-1.0.3 typing-extensions-4.7.1 zipp-3.15.0