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Tidy Docs #2702

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ColCarroll opened this issue Nov 10, 2017 · 3 comments
Closed

Tidy Docs #2702

ColCarroll opened this issue Nov 10, 2017 · 3 comments

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@ColCarroll
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Sphinx now builds on travis, and we ignore all of these warnings. Feel free to cherry-pick some and help to fix them!

/home/travis/build/ColCarroll/pymc3/docs/source/api/math.rst:1: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/travis/build/ColCarroll/pymc3/docs/source/api/math.rst:1: WARNING: Inline emphasis start-string without end-string.
<autosummary>:1: WARNING: Undefined substitution referenced: "`a`".
/home/travis/build/ColCarroll/pymc3/pymc3/stats.py:docstring of pymc3.stats.compare:16: WARNING: Unexpected indentation.
/home/travis/build/ColCarroll/pymc3/docs/source/gp.rst:102: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/Diagnosing_biased_Inference_with_Divergences.ipynb:29: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/Diagnosing_biased_Inference_with_Divergences.ipynb:30: WARNING: Line block ends without a blank line.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/Diagnosing_biased_Inference_with_Divergences.ipynb:42: WARNING: Line block ends without a blank line.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/Diagnosing_biased_Inference_with_Divergences.ipynb:47: WARNING: Line block ends without a blank line.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-hierarchical.ipynb:234: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-hierarchical.ipynb:252: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-hierarchical.ipynb:280: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-logistic.ipynb:1968: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-model-selection.ipynb:369: WARNING: Line block ends without a blank line.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-model-selection.ipynb:1342: WARNING: Title level inconsistent:

Evaluate log likelihoods straight from model.logp
'''''''''''''''''''''''''''''''''''''''''''''''''
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-model-selection.ipynb:1365: WARNING: Title level inconsistent:

Plot log-likelihoods
''''''''''''''''''''
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-model-selection.ipynb:1452: WARNING: Title level inconsistent:

Manual calculation, probably error-prone
''''''''''''''''''''''''''''''''''''''''
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-model-selection.ipynb:1507: WARNING: Title level inconsistent:

Or we could use the newly created function in ``stats.py``, much better!
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-model-selection.ipynb:1539: WARNING: Title level inconsistent:

Now loop through all the models and calculate the DIC
'''''''''''''''''''''''''''''''''''''''''''''''''''''
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-model-selection.ipynb:1602: WARNING: Title level inconsistent:

This time we go straight for the implementation in pymc3
''''''''''''''''''''''''''''''''''''''''''''''''''''''''
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-model-selection.ipynb:1624: WARNING: Title level inconsistent:

Now loop through all the models and calculate the BPIC
''''''''''''''''''''''''''''''''''''''''''''''''''''''
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-model-selection.ipynb:1708: WARNING: Title level inconsistent:

Now loop through all the models and calculate the WAIC
''''''''''''''''''''''''''''''''''''''''''''''''''''''
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-model-selection.ipynb:749: WARNING: At least one body element must separate transitions; adjacent transitions are not allowed.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-negative-binomial-regression.ipynb:399: WARNING: Title level inconsistent:

Visualize the Data
~~~~~~~~~~~~~~~~~~
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-robust-with-outlier-detection.ipynb:221: WARNING: Line block ends without a blank line.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-robust-with-outlier-detection.ipynb:549: WARNING: Line block ends without a blank line.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-robust-with-outlier-detection.ipynb:349: WARNING: At least one body element must separate transitions; adjacent transitions are not allowed.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-robust-with-outlier-detection.ipynb:515: WARNING: At least one body element must separate transitions; adjacent transitions are not allowed.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-robust-with-outlier-detection.ipynb:732: WARNING: At least one body element must separate transitions; adjacent transitions are not allowed.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GP-MaunaLoa.ipynb:23: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/PyMC3_tips_and_heuristic.ipynb:95: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/PyMC3_tips_and_heuristic.ipynb:96: WARNING: Line block ends without a blank line.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/bayesian_neural_network_with_sgfs.ipynb.rst: WARNING: file not found: 'notebooks/www.github.com/shkr'
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/bayesian_neural_network_with_sgfs.ipynb:: WARNING: Anonymous hyperlink mismatch: 1 references but 0 targets.
See "backrefs" attribute for IDs.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/multilevel_modeling.ipynb:50: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/multilevel_modeling.ipynb:724: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/multilevel_modeling.ipynb:733: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/rugby_analytics.ipynb.rst: WARNING: file not found: 'notebooks/www.statistica.it/gianluca/Research/BaioBlangiardo.pdf'
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/travis/build/ColCarroll/pymc3/docs/source/notebooks/AR.ipynb: WARNING: document isn't included in any toctree
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/Euler-Maruyama and SDEs.ipynb: WARNING: document isn't included in any toctree
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM.ipynb: WARNING: document isn't included in any toctree
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/GLM-logistic.ipynb: WARNING: document isn't included in any toctree
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/MvGaussianRandomWalk_demo.ipynb: WARNING: document isn't included in any toctree
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/SMC2_gaussians.ipynb: WARNING: document isn't included in any toctree
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/bayesian_neural_network_with_sgfs.ipynb: WARNING: document isn't included in any toctree
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/cox_model.ipynb: WARNING: document isn't included in any toctree
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/gaussian_process.ipynb: WARNING: document isn't included in any toctree
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/lasso_block_update.ipynb: WARNING: document isn't included in any toctree
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/profiling.ipynb: WARNING: document isn't included in any toctree
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/sgfs_simple_optimization.ipynb: WARNING: document isn't included in any toctree
/home/travis/build/ColCarroll/pymc3/docs/source/notebooks/updating_priors.ipynb: WARNING: document isn't included in any toctree
/home/travis/build/ColCarroll/pymc3/docs/source/api/distributions/continuous.rst:63: WARNING: Citation [Tweedie1957812] is not referenced.
/home/travis/build/ColCarroll/pymc3/docs/source/api/distributions/continuous.rst:67: WARNING: Citation [Michael1976812] is not referenced.
/home/travis/build/ColCarroll/pymc3/docs/source/api/distributions/continuous.rst:49: WARNING: Citation [Rigby20051014] is not referenced.
/home/travis/build/ColCarroll/pymc3/docs/source/api/distributions/continuous.rst:53: WARNING: Citation [Lacouture20081014] is not referenced.
/home/travis/build/ColCarroll/pymc3/docs/source/api/distributions/multivariate.rst:33: WARNING: Citation [LKJ20092225] is not referenced.
/home/travis/build/ColCarroll/pymc3/docs/source/api/distributions/multivariate.rst:97: WARNING: Citation [R2426] is not referenced.
/home/travis/build/ColCarroll/pymc3/docs/source/api/distributions/multivariate.rst:102: WARNING: Citation [R2526] is not referenced.
/home/travis/build/ColCarroll/pymc3/docs/source/api/inference.rst:47: WARNING: Citation [R2929] is not referenced.
@ColCarroll
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Oddly, I can't recreate these errors locally -- only a bunch of ones from math.rst...

@sharanry
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sharanry commented Jan 8, 2018

Hey, I am new here. Could I take up some of these?

@springcoil
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springcoil commented Jan 8, 2018 via email

@twiecki twiecki closed this as completed Dec 22, 2018
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