Read the Docs build information Build id: 893781 Project: mdolab-pygeo Version: latest Commit: fa469afe60dd014132f8039bbf8eb6267be6d424 Date: 2022-03-23T23:56:08.845221Z State: finished Success: True [rtd-command-info] start-time: 2022-03-23T23:56:10.742929Z, end-time: 2022-03-23T23:56:13.607967Z, duration: 2, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/mdolab/pygeo.git . Cloning into '.'... [rtd-command-info] start-time: 2022-03-23T23:56:13.815168Z, end-time: 2022-03-23T23:56:14.106315Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: switching to 'origin/main'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at fa469af fixed exception (#128) [rtd-command-info] start-time: 2022-03-23T23:56:14.285289Z, end-time: 2022-03-23T23:56:14.348288Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-03-23T23:56:15.648127Z, end-time: 2022-03-23T23:56:25.108258Z, duration: 9, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-pygeo/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-pygeo/envs/latest/bin/python Installing setuptools, pip, wheel... done. 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satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-pygeo/envs/latest/lib/python3.7/site-packages (from requests>=2.5.0->sphinx>=1.8->numpydoc->-r doc/requirements.txt (line 1)) (2021.10.8) Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-pygeo/envs/latest/lib/python3.7/site-packages (from packaging->sphinx>=1.8->numpydoc->-r doc/requirements.txt (line 1)) (3.0.7) Installing collected packages: zipp, typing-extensions, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pyyaml, latexcodec, pybtex, importlib-metadata, sphinx, pybtex-docutils, sphinxcontrib-bibtex, sphinxcontrib-autoprogram, sphinx-rtd-theme, sphinx-prompt, sphinx-copybutton, numpydoc, sphinx_mdolab_theme 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 importlib-metadata-4.11.3 latexcodec-2.0.1 numpydoc-1.2 pybtex-0.24.0 pybtex-docutils-1.0.1 pyyaml-6.0 sphinx-4.4.0 sphinx-copybutton-0.5.0 sphinx-prompt-1.5.0 sphinx-rtd-theme-1.0.0 sphinx_mdolab_theme-1.3.9 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-autoprogram-0.1.7 sphinxcontrib-bibtex-2.4.1 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 typing-extensions-4.1.1 zipp-3.7.0 [rtd-command-info] start-time: 2022-03-23T23:56:40.761294Z, end-time: 2022-03-23T23:56:40.822335Z, duration: 0, exit-code: 0 cat doc/conf.py from sphinx_mdolab_theme.config import * # -- Path setup -------------------------------------------------------------- # 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 # documentation root, use os.path.abspath to make it absolute, like shown here. import os import sys sys.path.insert(0, os.path.abspath("../")) sys.path.insert(0, os.path.abspath("../../")) # -- Project information ----------------------------------------------------- project = "pyGeo" # -- General configuration ----------------------------------------------------- # Built-in Sphinx extensions are already contained in the imported variable # here we add external extensions, which must also be added to requirements.txt # so that RTD can import and use them extensions.extend(["numpydoc"]) # mock import for autodoc autodoc_mock_imports = ["numpy", "mpi4py", "scipy", "pyspline", "baseclasses", "pysurf"] ########################################################################### # 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/master/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') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ], 'downloads': [ ("pdf", "//mdolab-pygeo.readthedocs-hosted.com/_/downloads/en/latest/pdf/"), ("html", "//mdolab-pygeo.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ("epub", "//mdolab-pygeo.readthedocs-hosted.com/_/downloads/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'mdolab-pygeo', 'name': u'pygeo', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://mdolab-pygeo.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/doc/', 'api_host': 'https://readthedocs.com', 'github_user': 'mdolab', 'proxied_api_host': '/_', 'github_repo': 'pygeo', 'github_version': 'main', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'main', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'main', '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': 'fa469afe', } # 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(): html_context.update(context) 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 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/mdolab-pygeo/builds/893781/' 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: 2022-03-23T23:56:41.024577Z, end-time: 2022-03-23T23:56:48.181753Z, duration: 7, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v4.4.0 loading translations [en]... done making output directory... done checking bibtex cache... out of date [autosummary] generating autosummary for: API.rst, DVConstraints.rst, DVGeometry.rst, DVGeometryMulti.rst, geo_utils.rst, index.rst, install.rst, pyBlock.rst, pyGeo.rst, pyNetwork.rst, tutorial.rst, update_pygeo.rst loading intersphinx inventory from https://mdolab-pygeo.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-pyoptsparse.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-baseclasses.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-idwarp.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-adflow.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-pyhyp.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-multipoint.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-pyspline.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-mach-aero.readthedocs-hosted.com/en/latest/objects.inv... building [mo]: targets for 0 po files that are out of date building [html]: targets for 12 source files that are out of date updating environment: [new config] 12 added, 0 changed, 0 removed reading sources... [ 8%] API reading sources... [ 16%] DVConstraints reading sources... [ 25%] DVGeometry reading sources... [ 33%] DVGeometryMulti reading sources... [ 41%] geo_utils reading sources... [ 50%] index reading sources... [ 58%] install reading sources... [ 66%] pyBlock reading sources... [ 75%] pyGeo reading sources... [ 83%] pyNetwork reading sources... [ 91%] tutorial reading sources... [100%] update_pygeo WARNING: error while formatting signature for pygeo.pyBlock.projectPoints: Handler for event 'autodoc-process-signature' threw an exception (exception: Error parsing See Also entry 'See the attachPoints() docstring for the other parameters.' in the docstring of projectPoints in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-pygeo/checkouts/latest/pygeo/pyBlock.py.) looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 8%] API writing output... [ 16%] DVConstraints writing output... 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[100%] images/wingNew.png copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 1 warning. The HTML pages are in _build/html. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2022-03-23T23:56:48.407389Z, end-time: 2022-03-23T23:56:53.921564Z, duration: 5, exit-code: 0 python -m sphinx -T -E -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia Running Sphinx v4.4.0 loading translations [en]... done making output directory... done checking bibtex cache... out of date [autosummary] generating autosummary for: API.rst, DVConstraints.rst, DVGeometry.rst, DVGeometryMulti.rst, geo_utils.rst, index.rst, install.rst, pyBlock.rst, pyGeo.rst, pyNetwork.rst, tutorial.rst, update_pygeo.rst loading intersphinx inventory from https://mdolab-pygeo.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-pyoptsparse.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-baseclasses.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-idwarp.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-adflow.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-pyhyp.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-multipoint.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-pyspline.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-mach-aero.readthedocs-hosted.com/en/latest/objects.inv... building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 12 added, 0 changed, 0 removed reading sources... [ 8%] API reading sources... [ 16%] DVConstraints reading sources... [ 25%] DVGeometry reading sources... [ 33%] DVGeometryMulti reading sources... [ 41%] geo_utils reading sources... [ 50%] index reading sources... [ 58%] install reading sources... [ 66%] pyBlock reading sources... [ 75%] pyGeo reading sources... [ 83%] pyNetwork reading sources... [ 91%] tutorial reading sources... [100%] update_pygeo WARNING: error while formatting signature for pygeo.pyBlock.projectPoints: Handler for event 'autodoc-process-signature' threw an exception (exception: Error parsing See Also entry 'See the attachPoints() docstring for the other parameters.' in the docstring of projectPoints in /home/docs/checkouts/readthedocs.org/user_builds/mdolab-pygeo/checkouts/latest/pygeo/pyBlock.py.) looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... install tutorial update_pygeo API DVConstraints DVGeometry DVGeometryMulti pyNetwork pyGeo pyBlock geo_utils done writing... done writing additional files... done copying images... [ 50%] images/wing.png copying images... [100%] images/wingNew.png copying static files... done copying extra files... done dumping object inventory... done build succeeded, 1 warning. The HTML page is in _build/localmedia. Updating searchtools for Read the Docs search... [rtd-command-info] start-time: 2022-03-23T23:56:54.108841Z, end-time: 2022-03-23T23:56:55.707453Z, duration: 1, exit-code: 0 python -m sphinx -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v4.4.0 loading translations [en]... done making output directory... done loading pickled environment... checking bibtex cache... up to date done [autosummary] generating autosummary for: API.rst, DVConstraints.rst, DVGeometry.rst, DVGeometryMulti.rst, geo_utils.rst, index.rst, install.rst, pyBlock.rst, pyGeo.rst, pyNetwork.rst, tutorial.rst, update_pygeo.rst building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 0 added, 0 changed, 0 removed looking for now-outdated files... none found processing pygeo.tex... index install tutorial update_pygeo API DVConstraints DVGeometry DVGeometryMulti pyNetwork pyGeo pyBlock geo_utils resolving references... done writing... done copying images... [ 50%] images/wing.png copying images... [100%] images/wingNew.png copying TeX support files... copying TeX support files... done build succeeded. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/mdolab-pygeo/checkouts/latest/doc/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2022-03-23T23:56:57.508225Z, end-time: 2022-03-23T23:56:57.582185Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2022-03-23T23:56:57.761426Z, end-time: 2022-03-23T23:57:13.350157Z, duration: 15, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=mdolab-pygeo -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="mdolab-pygeo" "pygeo.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./pygeo.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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[3] [4] Chapter 2. [5] [6 <./wing.png>] [7] [8] [9] [10 <./wingNew.png>] Chapter 3. (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) LaTeX Warning: Hyper reference `DVConstraints:pygeo.DVConstraints.addThicknessC onstraints2D' on page 11 undefined on input line 371. LaTeX Warning: Hyper reference `DVConstraints:pygeo.DVConstraints.addThicknessC onstraints1D' on page 11 undefined on input line 373. LaTeX Warning: Hyper reference `DVConstraints:pygeo.DVConstraints.addVolumeCons traint' on page 11 undefined on input line 379. [11] [12] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] ! LaTeX Error: Too deeply nested. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.3331 \item {} \begin{description} [39] [40] [41] [42] [43] [44] [45] LaTeX Warning: Hyper reference `DVGeometry:pygeo.DVGeometry.mapXDictToDVGeo' on page 46 undefined on input line 4187. [46] [47] [48] LaTeX Warning: Hyper reference `DVGeometry:pygeo.DVGeometry.addPointSet' on pag e 49 undefined on input line 4551. [49] [50] [51] [52] [53] LaTeX Warning: Hyper reference `DVGeometryMulti:pygeo.DVGeometryMulti.addPointS et' on page 54 undefined on input line 5164. [54] [55] [56] [57] [58] [59] [60] [61] LaTeX Warning: Hyper reference `geo_utils:pygeo.geo_utils.remove_duplicates.poi ntReduce' on page 62 undefined on input line 6205. LaTeX Warning: Hyper reference `geo_utils:pygeo.geo_utils.remove_duplicates.uni que' on page 62 undefined on input line 6245. [62] LaTeX Warning: Reference `geo_utils:module-pygeo.geo_utils.file_io' on page 63 undefined on input line 6264. LaTeX Warning: Reference `geo_utils:module-pygeo.geo_utils.remove_duplicates' o n page 63 undefined on input line 6265. [63] No file mdolab-pygeo.ind. (./mdolab-pygeo.aux) Package rerunfilecheck Warning: File `mdolab-pygeo.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}{ /usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on mdolab-pygeo.pdf (67 pages, 623496 bytes). Transcript written on mdolab-pygeo.log. Latexmk: Index file 'mdolab-pygeo.idx' was written Latexmk: Missing input file: 'mdolab-pygeo.ind' from line 'No file mdolab-pygeo.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'mdolab-pygeo.pdf' Latexmk: List of undefined refs and citations: Reference `geo_utils:module-pygeo.geo_utils.file_io' on page 63 undefined on input line 6264 Reference `geo_utils:module-pygeo.geo_utils.remove_duplicates' on page 63 undefined on input line 6265 Latexmk: Summary of warnings: Latex failed to resolve 2 reference(s) Rule 'makeindex mdolab-pygeo.idx': File changes, etc: Non-existent destination files: 'mdolab-pygeo.ind' ------------ Run number 1 of rule 'makeindex mdolab-pygeo.idx' ------------ ------------ Running 'makeindex -s python.ist -o "mdolab-pygeo.ind" "mdolab-pygeo.idx"' ------------ Latexmk: applying rule 'makeindex mdolab-pygeo.idx'... This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file mdolab-pygeo.idx....done (137 entries accepted, 0 rejected). Sorting entries....done (1061 comparisons). Generating output file mdolab-pygeo.ind....done (200 lines written, 0 warnings). Output written in mdolab-pygeo.ind. Transcript written in mdolab-pygeo.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'mdolab-pygeo.aux' 'mdolab-pygeo.ind' ------------ Run number 2 of rule 'pdflatex' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="mdolab-pygeo" "pygeo.tex"' ------------ This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./pygeo.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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[3] [4] Chapter 2. [5] [6 <./wing.png>] [7] [8] [9] [10 <./wingNew.png>] Chapter 3. (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) [11] [12] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] ! LaTeX Error: Too deeply nested. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.3331 \item {} \begin{description} [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] (./mdolab-pygeo.ind [64] Underfull \hbox (badness 10000) in paragraph at lines 13--15 []\T1/txtt/m/n/10 addCompositeVolumeConstraint() \T1/qtm/m/n/10 (\T1/qtm/m/it/1 0 py- Underfull \hbox (badness 10000) in paragraph at lines 15--16 []\T1/txtt/m/n/10 addConstraintsPyOpt() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 py-geo. 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DVConstraints [67]) (./mdolab-pygeo.aux) Package rerunfilecheck Warning: File `mdolab-pygeo.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}{ /usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on mdolab-pygeo.pdf (71 pages, 651973 bytes). Transcript written on mdolab-pygeo.log. Latexmk: Index file 'mdolab-pygeo.idx' was written Latexmk: References changed. 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[3] [4] Chapter 2. [5] [6 <./wing.png>] [7] [8] [9] [10 <./wingNew.png>] Chapter 3. (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) [11] [12] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] ! LaTeX Error: Too deeply nested. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.3331 \item {} \begin{description} [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] (./mdolab-pygeo.ind [64] Underfull \hbox (badness 10000) in paragraph at lines 13--15 []\T1/txtt/m/n/10 addCompositeVolumeConstraint() \T1/qtm/m/n/10 (\T1/qtm/m/it/1 0 py- Underfull \hbox (badness 10000) in paragraph at lines 15--16 []\T1/txtt/m/n/10 addConstraintsPyOpt() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 py-geo. 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DVConstraints Underfull \hbox (badness 10000) in paragraph at lines 58--59 []\T1/txtt/m/n/10 computeTotalJacobian() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 py-geo .DVGeometry Underfull \hbox (badness 10000) in paragraph at lines 59--60 []\T1/txtt/m/n/10 computeTotalJacobianCS() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 py-g eo.DVGeometry Underfull \hbox (badness 10000) in paragraph at lines 60--61 []\T1/txtt/m/n/10 computeTotalJacobianFD() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 py-g eo.DVGeometry Underfull \hbox (badness 10000) in paragraph at lines 61--62 []\T1/txtt/m/n/10 convertDictToSensitivity() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 py -geo.DVGeometry Underfull \hbox (badness 10000) in paragraph at lines 62--63 []\T1/txtt/m/n/10 convertSensitivityToDict() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 py -geo.DVGeometry [65] Underfull \hbox (badness 10000) in paragraph at lines 91--93 []\T1/txtt/m/n/10 getCoordinatesFromFile() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in m od-ule py- Underfull \hbox (badness 10000) in paragraph at lines 94--95 []\T1/txtt/m/n/10 getFlattenedChildren() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 py-geo .DVGeometry Underfull \hbox (badness 10000) in paragraph at lines 99--100 []\T1/txtt/m/n/10 getSymmetricCoefList() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 py-geo .DVGeometry Underfull \hbox (badness 10000) in paragraph at lines 118--120 []\T1/txtt/m/n/10 pointReduce() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule py- Underfull \hbox (badness 10000) in paragraph at lines 120--122 []\T1/txtt/m/n/10 pointReduceBruteForce() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mo d-ule py- Underfull \hbox (badness 10000) in paragraph at lines 123--124 []\T1/txtt/m/n/10 pointSetUpToDate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 py-geo.DVG eometryMulti Underfull \hbox (badness 10000) in paragraph at lines 126--127 []\T1/txtt/m/n/10 printDesignVariables() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 py-geo .DVGeometry Underfull \hbox (badness 10000) in paragraph at lines 141--142 []\T1/txtt/m/n/10 readAirfoilFile() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule py- Underfull \hbox (badness 10000) in paragraph at lines 143--145 []\T1/txtt/m/n/10 readPlot3DSurfFile() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le py- Underfull \hbox (badness 10000) in paragraph at lines 160--161 []\T1/txtt/m/n/10 totalSensitivity() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 py-geo.DVG eometryMulti Underfull \hbox (badness 10000) in paragraph at lines 161--162 []\T1/txtt/m/n/10 totalSensitivityProd() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 py-geo .DVGeometry Underfull \hbox (badness 10000) in paragraph at lines 166--167 []\T1/txtt/m/n/10 unique() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule py- Underfull \hbox (badness 10000) in paragraph at lines 167--169 []\T1/txtt/m/n/10 uniqueIndex() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule py- [66] Underfull \hbox (badness 10000) in paragraph at lines 176--178 []\T1/txtt/m/n/10 write_wing_FFD_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule py- Underfull \hbox (badness 10000) in paragraph at lines 178--179 []\T1/txtt/m/n/10 writeAirfoilFile() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule py- Underfull \hbox (badness 10000) in paragraph at lines 187--188 []\T1/txtt/m/n/10 writeSurfaceTecplot() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 py-geo. DVConstraints [67]) (./mdolab-pygeo.aux) ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}{ /usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on mdolab-pygeo.pdf (71 pages, 652095 bytes). Transcript written on mdolab-pygeo.log. Latexmk: Index file 'mdolab-pygeo.idx' was written Latexmk: Log file says output to 'mdolab-pygeo.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 Latexmk: Errors, in force_mode: so I tried finishing targets [rtd-command-info] start-time: 2022-03-23T23:57:13.539365Z, end-time: 2022-03-23T23:57:13.624889Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/mdolab-pygeo/checkouts/latest/doc/_build/latex/mdolab-pygeo.pdf /home/docs/checkouts/readthedocs.org/user_builds/mdolab-pygeo/artifacts/latest/sphinx_pdf/mdolab-pygeo.pdf [rtd-command-info] start-time: 2022-03-23T23:57:13.807026Z, end-time: 2022-03-23T23:57:19.243578Z, duration: 5, exit-code: 0 python -m sphinx -T -E -b epub -d _build/doctrees -D language=en . _build/epub Running Sphinx v4.4.0 loading translations [en]... done making output directory... done checking bibtex cache... out of date WARNING: conf value "version" should not be empty for EPUB3 [autosummary] generating autosummary for: API.rst, DVConstraints.rst, DVGeometry.rst, DVGeometryMulti.rst, geo_utils.rst, index.rst, install.rst, pyBlock.rst, pyGeo.rst, pyNetwork.rst, tutorial.rst, update_pygeo.rst loading intersphinx inventory from https://mdolab-pygeo.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-pyoptsparse.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-baseclasses.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-idwarp.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-adflow.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-pyhyp.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-multipoint.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-pyspline.readthedocs-hosted.com/en/latest/objects.inv... loading intersphinx inventory from https://mdolab-mach-aero.readthedocs-hosted.com/en/latest/objects.inv... building [mo]: targets for 0 po files that are out of date building [epub]: targets for 12 source files that are out of date updating environment: [new config] 12 added, 0 changed, 0 removed reading sources... 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