UndefinedError("'meta' is undefined") with Jinja2 version 3

[sebp]

I noticed that CI of https://github.com/sebp/scikit-survival/ was failing when using nbsphinx 0.8.6 in combination with Jinja2 version 3 with the error:

Theme error:
An error happened in rendering the page genindex.
Reason: UndefinedError("'meta' is undefined")

It works fine when using Jinja2 <3

Full log

2021-06-24T19:18:37.1752797Z .package create: /github/workspace/.tox/.package
2021-06-24T19:18:37.6170269Z .package installdeps: setuptools>=42, wheel, setuptools_scm[toml]>=3.4, Cython>=0.29.16, numpy==1.14.5; python_version=='3.7' and platform_system!='AIX', numpy==1.17.3; python_version=='3.8' and platform_system!='AIX', numpy==1.19.3; python_version=='3.9', numpy; python_version>'3.9', scikit-learn==0.24.1; python_version<='3.9', scikit-learn; python_version>'3.9'
2021-06-24T19:18:56.9489657Z py38-docs create: /github/workspace/.tox/py38-docs
2021-06-24T19:18:58.0959674Z py38-docs installdeps: -rdoc/docs_requirements.txt, cython, numpy
2021-06-24T19:19:14.3109970Z py38-docs inst: /github/workspace/.tox/.tmp/package/1/scikit-survival-0.1.dev1+g414f065.tar.gz
2021-06-24T19:20:23.2899456Z py38-docs installed: WARNING: The directory '/github/home/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.,alabaster==0.7.12,async-generator==1.10,attrs==21.2.0,Babel==2.9.1,backcall==0.2.0,bleach==3.3.0,certifi==2021.5.30,chardet==4.0.0,Cython==0.29.23,decorator==5.0.9,defusedxml==0.7.1,docutils==0.16,ecos==2.0.7.post1,entrypoints==0.3,idna==2.10,imagesize==1.2.0,ipython==7.24.1,ipython-genutils==0.2.0,jedi==0.18.0,Jinja2==3.0.1,joblib==1.0.1,jsonschema==3.2.0,jupyter-client==6.1.12,jupyter-core==4.7.1,jupyterlab-pygments==0.1.2,MarkupSafe==2.0.1,matplotlib-inline==0.1.2,mistune==0.8.4,nbclient==0.5.3,nbconvert==6.1.0,nbformat==5.1.3,nbsphinx==0.8.6,nest-asyncio==1.5.1,numexpr==2.7.3,numpy==1.21.0,osqp==0.6.2.post0,packaging==20.9,pandas==1.2.5,pandocfilters==1.4.3,parso==0.8.2,pexpect==4.8.0,pickleshare==0.7.5,prompt-toolkit==3.0.19,ptyprocess==0.7.0,pydata-sphinx-theme==0.4.3,Pygments==2.9.0,pyparsing==2.4.7,pyrsistent==0.17.3,python-dateutil==2.8.1,pytz==2021.1,pyzmq==22.1.0,qdldl==0.1.5.post0,requests==2.25.1,scikit-learn==0.24.2,scikit-survival @ file:///github/workspace/.tox/.tmp/package/1/scikit-survival-0.1.dev1%2Bg414f065.tar.gz,scipy==1.7.0,setuptools-scm==6.0.1,six==1.16.0,snowballstemmer==2.1.0,Sphinx==3.2.1,sphinxcontrib-applehelp==1.0.2,sphinxcontrib-devhelp==1.0.2,sphinxcontrib-htmlhelp==2.0.0,sphinxcontrib-jsmath==1.0.1,sphinxcontrib-qthelp==1.0.3,sphinxcontrib-serializinghtml==1.1.5,testpath==0.5.0,threadpoolctl==2.1.0,tornado==6.1,traitlets==5.0.5,urllib3==1.26.5,wcwidth==0.2.5,webencodings==0.5.1
2021-06-24T19:20:23.2914857Z py38-docs run-test-pre: PYTHONHASHSEED='2426748792'
2021-06-24T19:20:23.2916047Z py38-docs run-test: commands[0] | sphinx-build -d _build/doctrees -E -W -b html . _build/html
2021-06-24T19:20:23.5858749Z Running Sphinx v3.2.1
2021-06-24T19:20:24.2779761Z making output directory... done
2021-06-24T19:20:24.2898115Z [autosummary] generating autosummary for: api/compare.rst, api/datasets.rst, api/ensemble.rst, api/functions.rst, api/index.rst, api/io.rst, api/kernels.rst, api/linear_model.rst, api/meta.rst, api/metrics.rst, ..., install.rst, release_notes.rst, user_guide/00-introduction.ipynb, user_guide/boosting.ipynb, user_guide/coxnet.ipynb, user_guide/evaluating-survival-models.ipynb, user_guide/index.rst, user_guide/random-survival-forest.ipynb, user_guide/survival-svm.ipynb, user_guide/understanding_predictions.rst
2021-06-24T19:20:24.8375707Z [autosummary] generating autosummary for: /github/workspace/doc/api/generated/sksurv.column.categorical_to_numeric.rst, /github/workspace/doc/api/generated/sksurv.column.encode_categorical.rst, /github/workspace/doc/api/generated/sksurv.column.standardize.rst, /github/workspace/doc/api/generated/sksurv.compare.compare_survival.rst, /github/workspace/doc/api/generated/sksurv.datasets.get_x_y.rst, /github/workspace/doc/api/generated/sksurv.datasets.load_aids.rst, /github/workspace/doc/api/generated/sksurv.datasets.load_arff_files_standardized.rst, /github/workspace/doc/api/generated/sksurv.datasets.load_breast_cancer.rst, /github/workspace/doc/api/generated/sksurv.datasets.load_flchain.rst, /github/workspace/doc/api/generated/sksurv.datasets.load_gbsg2.rst, ..., /github/workspace/doc/api/generated/sksurv.nonparametric.kaplan_meier_estimator.rst, /github/workspace/doc/api/generated/sksurv.nonparametric.nelson_aalen_estimator.rst, /github/workspace/doc/api/generated/sksurv.preprocessing.OneHotEncoder.rst, /github/workspace/doc/api/generated/sksurv.svm.FastKernelSurvivalSVM.rst, /github/workspace/doc/api/generated/sksurv.svm.FastSurvivalSVM.rst, /github/workspace/doc/api/generated/sksurv.svm.HingeLossSurvivalSVM.rst, /github/workspace/doc/api/generated/sksurv.svm.MinlipSurvivalAnalysis.rst, /github/workspace/doc/api/generated/sksurv.svm.NaiveSurvivalSVM.rst, /github/workspace/doc/api/generated/sksurv.tree.SurvivalTree.rst, /github/workspace/doc/api/generated/sksurv.util.Surv.rst
2021-06-24T19:20:24.8399929Z building [mo]: targets for 0 po files that are out of date
2021-06-24T19:20:24.8411667Z building [html]: targets for 28 source files that are out of date
2021-06-24T19:20:24.8436686Z updating environment: [new config] 73 added, 0 changed, 0 removed
2021-06-24T19:20:24.8437651Z reading sources... [  1%] api/compare
2021-06-24T19:20:24.8949359Z reading sources... [  2%] api/datasets
2021-06-24T19:20:24.9437266Z reading sources... [  4%] api/ensemble
2021-06-24T19:20:25.0571810Z reading sources... [  5%] api/functions
2021-06-24T19:20:25.0695998Z reading sources... [  6%] api/generated/sksurv.column.categorical_to_numeric
2021-06-24T19:20:25.0989703Z reading sources... [  8%] api/generated/sksurv.column.encode_categorical
2021-06-24T19:20:25.1182488Z reading sources... [  9%] api/generated/sksurv.column.standardize
2021-06-24T19:20:25.1338277Z reading sources... [ 10%] api/generated/sksurv.compare.compare_survival
2021-06-24T19:20:25.1625914Z reading sources... [ 12%] api/generated/sksurv.datasets.get_x_y
2021-06-24T19:20:25.1846706Z reading sources... [ 13%] api/generated/sksurv.datasets.load_aids
2021-06-24T19:20:25.2061280Z reading sources... [ 15%] api/generated/sksurv.datasets.load_arff_files_standardized
2021-06-24T19:20:25.2365486Z reading sources... [ 16%] api/generated/sksurv.datasets.load_breast_cancer
2021-06-24T19:20:25.2513164Z reading sources... [ 17%] api/generated/sksurv.datasets.load_flchain
2021-06-24T19:20:25.2696114Z reading sources... [ 19%] api/generated/sksurv.datasets.load_gbsg2
2021-06-24T19:20:25.2841883Z reading sources... [ 20%] api/generated/sksurv.datasets.load_veterans_lung_cancer
2021-06-24T19:20:25.2991198Z reading sources... [ 21%] api/generated/sksurv.datasets.load_whas500
2021-06-24T19:20:25.3140397Z reading sources... [ 23%] api/generated/sksurv.ensemble.ComponentwiseGradientBoostingSurvivalAnalysis
2021-06-24T19:20:25.5850683Z reading sources... [ 24%] api/generated/sksurv.ensemble.ExtraSurvivalTrees
2021-06-24T19:20:25.8831373Z reading sources... [ 26%] api/generated/sksurv.ensemble.GradientBoostingSurvivalAnalysis
2021-06-24T19:20:26.2104384Z reading sources... [ 27%] api/generated/sksurv.ensemble.RandomSurvivalForest
2021-06-24T19:20:26.5059921Z reading sources... [ 28%] api/generated/sksurv.functions.StepFunction
2021-06-24T19:20:26.5360515Z reading sources... [ 30%] api/generated/sksurv.io.loadarff
2021-06-24T19:20:26.5516840Z reading sources... [ 31%] api/generated/sksurv.io.writearff
2021-06-24T19:20:26.5785220Z reading sources... [ 32%] api/generated/sksurv.kernels.ClinicalKernelTransform
2021-06-24T19:20:26.7245057Z reading sources... [ 34%] api/generated/sksurv.kernels.clinical_kernel
2021-06-24T19:20:26.7439134Z reading sources... [ 35%] api/generated/sksurv.linear_model.CoxPHSurvivalAnalysis
2021-06-24T19:20:26.9311761Z reading sources... [ 36%] api/generated/sksurv.linear_model.CoxnetSurvivalAnalysis
2021-06-24T19:20:27.1417579Z reading sources... [ 38%] api/generated/sksurv.linear_model.IPCRidge
2021-06-24T19:20:27.2526281Z reading sources... [ 39%] api/generated/sksurv.meta.EnsembleSelection
2021-06-24T19:20:27.5186666Z reading sources... [ 41%] api/generated/sksurv.meta.EnsembleSelectionRegressor
2021-06-24T19:20:27.6651476Z reading sources... [ 42%] api/generated/sksurv.meta.Stacking
2021-06-24T19:20:27.7906970Z reading sources... [ 43%] api/generated/sksurv.metrics.brier_score
2021-06-24T19:20:27.8485097Z reading sources... [ 45%] api/generated/sksurv.metrics.concordance_index_censored
2021-06-24T19:20:27.8754152Z reading sources... [ 46%] api/generated/sksurv.metrics.concordance_index_ipcw
2021-06-24T19:20:27.9096173Z reading sources... [ 47%] api/generated/sksurv.metrics.cumulative_dynamic_auc
2021-06-24T19:20:27.9524755Z reading sources... [ 49%] api/generated/sksurv.metrics.integrated_brier_score
2021-06-24T19:20:27.9804549Z reading sources... [ 50%] api/generated/sksurv.nonparametric.CensoringDistributionEstimator
2021-06-24T19:20:28.0837451Z reading sources... [ 52%] api/generated/sksurv.nonparametric.SurvivalFunctionEstimator
2021-06-24T19:20:28.1522167Z reading sources... [ 53%] api/generated/sksurv.nonparametric.ipc_weights
2021-06-24T19:20:28.1701049Z reading sources... [ 54%] api/generated/sksurv.nonparametric.kaplan_meier_estimator
2021-06-24T19:20:28.2727617Z reading sources... [ 56%] api/generated/sksurv.nonparametric.nelson_aalen_estimator
2021-06-24T19:20:28.2908860Z reading sources... [ 57%] api/generated/sksurv.preprocessing.OneHotEncoder
2021-06-24T19:20:28.3821925Z reading sources... [ 58%] api/generated/sksurv.svm.FastKernelSurvivalSVM
2021-06-24T19:20:28.5955784Z reading sources... [ 60%] api/generated/sksurv.svm.FastSurvivalSVM
2021-06-24T19:20:28.7203488Z reading sources... [ 61%] api/generated/sksurv.svm.HingeLossSurvivalSVM
2021-06-24T19:20:28.8713521Z reading sources... [ 63%] api/generated/sksurv.svm.MinlipSurvivalAnalysis
2021-06-24T19:20:28.9941660Z reading sources... [ 64%] api/generated/sksurv.svm.NaiveSurvivalSVM
2021-06-24T19:20:29.2618409Z reading sources... [ 65%] api/generated/sksurv.tree.SurvivalTree
2021-06-24T19:20:29.4809019Z reading sources... [ 67%] api/generated/sksurv.util.Surv
2021-06-24T19:20:29.5456855Z reading sources... [ 68%] api/index
2021-06-24T19:20:29.5504457Z reading sources... [ 69%] api/io
2021-06-24T19:20:29.5618463Z reading sources... [ 71%] api/kernels
2021-06-24T19:20:29.5723916Z reading sources... [ 72%] api/linear_model
2021-06-24T19:20:29.5883668Z reading sources... [ 73%] api/meta
2021-06-24T19:20:29.6048906Z reading sources... [ 75%] api/metrics
2021-06-24T19:20:29.6339765Z reading sources... [ 76%] api/nonparametric
2021-06-24T19:20:29.6539130Z reading sources... [ 78%] api/preprocessing
2021-06-24T19:20:29.6727201Z reading sources... [ 79%] api/svm
2021-06-24T19:20:29.6981053Z reading sources... [ 80%] api/tree
2021-06-24T19:20:29.7074710Z reading sources... [ 82%] api/util
2021-06-24T19:20:29.7175917Z reading sources... [ 83%] cite
2021-06-24T19:20:29.7225086Z reading sources... [ 84%] contributing
2021-06-24T19:20:29.7486149Z reading sources... [ 86%] index
2021-06-24T19:20:29.7583464Z reading sources... [ 87%] install
2021-06-24T19:20:29.7775299Z reading sources... [ 89%] release_notes
2021-06-24T19:20:29.9058850Z reading sources... [ 90%] user_guide/00-introduction
2021-06-24T19:20:31.9985035Z reading sources... [ 91%] user_guide/boosting
2021-06-24T19:20:33.0007155Z reading sources... [ 93%] user_guide/coxnet
2021-06-24T19:20:34.2256016Z reading sources... [ 94%] user_guide/evaluating-survival-models
2021-06-24T19:20:35.6987967Z reading sources... [ 95%] user_guide/index
2021-06-24T19:20:35.7117033Z reading sources... [ 97%] user_guide/random-survival-forest
2021-06-24T19:20:36.6116979Z reading sources... [ 98%] user_guide/survival-svm
2021-06-24T19:20:38.2927171Z reading sources... [100%] user_guide/understanding_predictions
2021-06-24T19:20:38.3146490Z 
2021-06-24T19:20:38.3152836Z looking for now-outdated files... none found
2021-06-24T19:20:38.3210083Z pickling environment... done
2021-06-24T19:20:38.3215608Z checking consistency... done
2021-06-24T19:20:38.3231160Z preparing documents... done
2021-06-24T19:20:38.3234908Z writing output... [  1%] api/compare
2021-06-24T19:20:38.4351255Z writing output... [  2%] api/datasets
2021-06-24T19:20:38.4659790Z writing output... [  4%] api/ensemble
2021-06-24T19:20:38.4929904Z writing output... [  5%] api/functions
2021-06-24T19:20:38.5168597Z writing output... [  6%] api/generated/sksurv.column.categorical_to_numeric
2021-06-24T19:20:38.5450356Z writing output... [  8%] api/generated/sksurv.column.encode_categorical
2021-06-24T19:20:38.5756701Z writing output... [  9%] api/generated/sksurv.column.standardize
2021-06-24T19:20:38.6062949Z writing output... [ 10%] api/generated/sksurv.compare.compare_survival
2021-06-24T19:20:38.6392920Z writing output... [ 12%] api/generated/sksurv.datasets.get_x_y
2021-06-24T19:20:38.6723445Z writing output... [ 13%] api/generated/sksurv.datasets.load_aids
2021-06-24T19:20:38.7036031Z writing output... [ 15%] api/generated/sksurv.datasets.load_arff_files_standardized
2021-06-24T19:20:38.7402542Z writing output... [ 16%] api/generated/sksurv.datasets.load_breast_cancer
2021-06-24T19:20:38.7708623Z writing output... [ 17%] api/generated/sksurv.datasets.load_flchain
2021-06-24T19:20:38.8008228Z writing output... [ 19%] api/generated/sksurv.datasets.load_gbsg2
2021-06-24T19:20:38.8292854Z writing output... [ 20%] api/generated/sksurv.datasets.load_veterans_lung_cancer
2021-06-24T19:20:38.9293509Z writing output... [ 21%] api/generated/sksurv.datasets.load_whas500
2021-06-24T19:20:38.9584634Z writing output... [ 23%] api/generated/sksurv.ensemble.ComponentwiseGradientBoostingSurvivalAnalysis
2021-06-24T19:20:39.0910300Z writing output... [ 24%] api/generated/sksurv.ensemble.ExtraSurvivalTrees
2021-06-24T19:20:39.1902541Z writing output... [ 26%] api/generated/sksurv.ensemble.GradientBoostingSurvivalAnalysis
2021-06-24T19:20:39.3002706Z writing output... [ 27%] api/generated/sksurv.ensemble.RandomSurvivalForest
2021-06-24T19:20:39.4894771Z writing output... [ 28%] api/generated/sksurv.functions.StepFunction
2021-06-24T19:20:39.5233428Z writing output... [ 30%] api/generated/sksurv.io.loadarff
2021-06-24T19:20:39.5502663Z writing output... [ 31%] api/generated/sksurv.io.writearff
2021-06-24T19:20:39.5790217Z writing output... [ 32%] api/generated/sksurv.kernels.ClinicalKernelTransform
2021-06-24T19:20:39.6344557Z writing output... [ 34%] api/generated/sksurv.kernels.clinical_kernel
2021-06-24T19:20:39.6655125Z writing output... [ 35%] api/generated/sksurv.linear_model.CoxPHSurvivalAnalysis
2021-06-24T19:20:39.7391862Z writing output... [ 36%] api/generated/sksurv.linear_model.CoxnetSurvivalAnalysis
2021-06-24T19:20:39.9180869Z writing output... [ 38%] api/generated/sksurv.linear_model.IPCRidge
2021-06-24T19:20:39.9751459Z writing output... [ 39%] api/generated/sksurv.meta.EnsembleSelection
2021-06-24T19:20:40.0400519Z writing output... [ 41%] api/generated/sksurv.meta.EnsembleSelectionRegressor
2021-06-24T19:20:40.1045651Z writing output... [ 42%] api/generated/sksurv.meta.Stacking
2021-06-24T19:20:40.1574295Z writing output... [ 43%] api/generated/sksurv.metrics.brier_score
2021-06-24T19:20:40.1975523Z writing output... [ 45%] api/generated/sksurv.metrics.concordance_index_censored
2021-06-24T19:20:40.2321648Z writing output... [ 46%] api/generated/sksurv.metrics.concordance_index_ipcw
2021-06-24T19:20:40.2686505Z writing output... [ 47%] api/generated/sksurv.metrics.cumulative_dynamic_auc
2021-06-24T19:20:40.3069504Z writing output... [ 49%] api/generated/sksurv.metrics.integrated_brier_score
2021-06-24T19:20:40.3459162Z writing output... [ 50%] api/generated/sksurv.nonparametric.CensoringDistributionEstimator
2021-06-24T19:20:40.4761738Z writing output... [ 52%] api/generated/sksurv.nonparametric.SurvivalFunctionEstimator
2021-06-24T19:20:40.5135572Z writing output... [ 53%] api/generated/sksurv.nonparametric.ipc_weights
2021-06-24T19:20:40.5433275Z writing output... [ 54%] api/generated/sksurv.nonparametric.kaplan_meier_estimator
2021-06-24T19:20:40.5778432Z writing output... [ 56%] api/generated/sksurv.nonparametric.nelson_aalen_estimator
2021-06-24T19:20:40.6077104Z writing output... [ 57%] api/generated/sksurv.preprocessing.OneHotEncoder
2021-06-24T19:20:40.6537186Z writing output... [ 58%] api/generated/sksurv.svm.FastKernelSurvivalSVM
2021-06-24T19:20:40.7175161Z writing output... [ 60%] api/generated/sksurv.svm.FastSurvivalSVM
2021-06-24T19:20:40.7757667Z writing output... [ 61%] api/generated/sksurv.svm.HingeLossSurvivalSVM
2021-06-24T19:20:40.8357815Z writing output... [ 63%] api/generated/sksurv.svm.MinlipSurvivalAnalysis
2021-06-24T19:20:40.9750198Z writing output... [ 64%] api/generated/sksurv.svm.NaiveSurvivalSVM
2021-06-24T19:20:41.0384353Z writing output... [ 65%] api/generated/sksurv.tree.SurvivalTree
2021-06-24T19:20:41.1237373Z writing output... [ 67%] api/generated/sksurv.util.Surv
2021-06-24T19:20:41.1579554Z writing output... [ 68%] api/index
2021-06-24T19:20:41.1878594Z writing output... [ 69%] api/io
2021-06-24T19:20:41.2124119Z writing output... [ 71%] api/kernels
2021-06-24T19:20:41.2371295Z writing output... [ 72%] api/linear_model
2021-06-24T19:20:41.2632481Z writing output... [ 73%] api/meta
2021-06-24T19:20:41.2887818Z writing output... [ 75%] api/metrics
2021-06-24T19:20:41.3153146Z writing output... [ 76%] api/nonparametric
2021-06-24T19:20:41.3418708Z writing output... [ 78%] api/preprocessing
2021-06-24T19:20:41.3693490Z writing output... [ 79%] api/svm
2021-06-24T19:20:41.3958402Z writing output... [ 80%] api/tree
2021-06-24T19:20:41.4198296Z writing output... [ 82%] api/util
2021-06-24T19:20:41.5261133Z writing output... [ 83%] cite
2021-06-24T19:20:41.5446628Z writing output... [ 84%] contributing
2021-06-24T19:20:41.5787485Z writing output... [ 86%] index
2021-06-24T19:20:41.5984800Z writing output... [ 87%] install
2021-06-24T19:20:41.6256433Z writing output... [ 89%] release_notes
2021-06-24T19:20:41.7027049Z writing output... [ 90%] user_guide/00-introduction
2021-06-24T19:20:42.1779388Z writing output... [ 91%] user_guide/boosting
2021-06-24T19:20:42.2867386Z writing output... [ 93%] user_guide/coxnet
2021-06-24T19:20:42.4059253Z writing output... [ 94%] user_guide/evaluating-survival-models
2021-06-24T19:20:42.5462128Z writing output... [ 95%] user_guide/index
2021-06-24T19:20:42.5730854Z writing output... [ 97%] user_guide/random-survival-forest
2021-06-24T19:20:42.6525423Z writing output... [ 98%] user_guide/survival-svm
2021-06-24T19:20:42.7785960Z writing output... [100%] user_guide/understanding_predictions
2021-06-24T19:20:42.8101748Z 
2021-06-24T19:20:42.8371374Z generating indices...  genindexfailed
2021-06-24T19:20:42.8371922Z 
2021-06-24T19:20:42.8372291Z Theme error:
2021-06-24T19:20:42.8372905Z An error happened in rendering the page genindex.
2021-06-24T19:20:42.8377050Z Reason: UndefinedError("'meta' is undefined")
2021-06-24T19:20:43.1594853Z ERROR: InvocationError for command /github/workspace/.tox/py38-docs/bin/sphinx-build -d _build/doctrees -E -W -b html . _build/html (exited with code 2)

[mgeier]

Theme error suggests that this has something to do with the HTML theme, it sounds kinda like pydata/pydata-sphinx-theme#395.

[sebp]

You are right, updating pydata-sphinx-theme fixed the problem. Thanks for the help!