Remove markdown handling from the docs by Zaharid · Pull Request #1597 · NNPDF/nnpdf

Zaharid · 2022-09-08T19:17:31Z

Having markdown required more tooling and more documentation and it is not worth it as it ends up being full of eval_rst clauses.

Convert the existing files to markdown and remove the tooling for it.

One problem is that rst has for some reason no obvious way of having markup inside the links, which is something markdown doesn't know about and needs to be cleaned by hand. Also we had explicit references to markdown source files in varios places. Overall there is quite a big chance of things being missed or getting ugly, even though I tried to remove mos of the warnings.

Writing docs in markdown has long been discouraged and supporting it has some costs in terms of tooling, as it requires less tested and developed extensions to sphnx that constitute extra dependencies. Convert exiting files to rst so we can remove markdown processing altogether.

scarlehoff

Thanks for this!

I think I did go through all the files that changed (in the browser, not the source) and I've flagged all the problems I've seen.

scarlehoff · 2022-09-09T07:32:39Z

+[NC] SIA normalized top cross section (electron-proton) -
+SIA_NORM_XSEC_NF4: [NC] SIA normalized total cross section (nf=4)
+(electron-proton) - SIA_NORM_XSEC: [NC] SIA normalized total cross
+section (electron-proton)


The conversion has not quite worked for this list (adding \n before every - should suffice I guess?)

scarlehoff · 2022-09-09T07:35:41Z

+C-factor scaling, copies ``COMPOUND`` files, deletes the subgrids, and
+finally compresses the result into a theory.tgz file ready for upload. -
+``results/upload_theories`` automatically upload to the server all the
+theory.tgz files that have been generated.


It seems to be in general for this file at least that the lists have not been parsed correctly.

scarlehoff · 2022-09-09T07:41:48Z

+Hardware: - Intel(R) Core(TM) i7-6700 CPU @ 4.00GHz - 16 GB RAM 3000 MHz
+DDR4
+
+Timing for a fit: - Walltime: 397s - CPUtime: 1729s


lists again

scarlehoff · 2022-09-09T07:43:32Z

+selectively for specific datasets. To do that, add their names to a list
+called ``do_not_require_similarity_for``. The datasets in the list do
+not need to appear in the ``cuts_intersection_spec`` namespace and will
+be filtered according to the internal cuts unconditionally.


Change now erroneous references to markdown to rst. Prefer removing file extensions from references. Prefer references to links where noticed, adding the corresponding labels. Remove nested markup, particularly inside links, as that is not supported by rst (which makes the output worse, but alternatives don't seem worth it, see https://docutils.sourceforge.io/FAQ.html#is-nested-inline-markup-possible ).

Co-authored-by: Juan M. Cruz-Martinez <juacrumar@lairen.eu> Remove various warnings reported by Shpinx. Fix incorrect conversion of markdown lists to rst wherever encountered.

scarlehoff · 2022-09-12T09:47:04Z

+convergence/stability in the fit. To read more about this, see `How to
+run an iterated fit <run-iterated-fit>`__.


Suggested change

convergence/stability in the fit. To read more about this, see `How to

run an iterated fit <run-iterated-fit>`__.

convergence/stability in the fit. To read more about this, see :ref:`How to

run an iterated fit <run-iterated-fit>`.

I think internal links should be like this instead?

There are a few more than that one (sorry, it wasn't clear)

uh I see this is creating a lot of broken links :(

Co-authored-by: Juan M. Cruz-Martinez <juacrumar@lairen.eu>

scarlehoff · 2022-09-27T11:15:38Z

Are you waiting for me to do #1598 before?

RoyStegeman · 2022-10-06T11:59:04Z

I guess https://github.com/NNPDF/nnpdf/blob/master/doc/README.md should also be updated?

Zaharid · 2023-02-16T15:47:28Z

AFAICT I had started finding and fixing broken links. I think there were a few (also in rst).

Zaharid · 2023-02-16T15:51:29Z

FWIW a subset of the "broken" stuff below is indeed broken. I think the first few are introduced by incorrect conversion to rst.

Details

~/n/n/d/sphinx (nomddocs %) $ sphinx-build source/ build/ -b linkcheck

preparing documents... done
writing output... [100%] vp/upload                                                                                                                                                                                                            

(tutorials/apfelcomb: line  308) broken    ../data/th-data-files.rst#compound-file-format - 
(       vp/upload: line   28) broken    ../get-started/access - 
(external-code/grids: line   32) ok        ../theory/FastInterface.rst
(    vp/datthcomp: line    6) broken    ../tutorials/datthcomp.html - 
(tutorials/compare-fits: line    6) broken    ../vp/index.html - 
(theory/theoryparamsinfo: line  145) broken    ./theoryparamsdefinitions - 
(tutorials/list-resources: line   36) broken    NNPDF-server - 
(        ci/index: line    6) broken    conda - 
(         vp/cuts: line  111) broken    data-theory-comp - 
(external-code/apfelcomb: line   20) broken    ../data/exp-data-files.rst#exp-data-files - 
(        ci/index: line    6) broken    git - 
(     buildmaster: line   15) broken    exp_data_files - 
(tutorials/apfelcomb: line  315) broken    ../data/th-data-files.rst#cfactor-file-format - 
(serverconf/index: line   68) broken    download - 
(tutorials/APPLgrids: line   38) ok        http://fastjet.fr/
(tutorials/buildmaster: line   28) redirect  http://lhcbproject.web.cern.ch/lhcbproject/Publications/LHCbProjectPublic/Summary_all.html - with Found to https://lhcbproject.web.cern.ch/lhcbproject/Publications/LHCbProjectPublic/Summary_all.html
(  n3fit/hyperopt: line   51) redirect  http://n3pdf.mi.infn.it/wp-content/uploads/2019/10/JCruz-Martinez_Mexico_102019.pdf - with Found to https://n3pdf.mi.infn.it/wp-content/uploads/2019/10/JCruz-Martinez_Mexico_102019.pdf
(contributing/git: line   20) ok        http://rogerdudler.github.io/git-guide/
(       vp/upload: line   83) redirect  http://pandoc.org/MANUAL.html#metadata-blocks - permanently to https://pandoc.org/MANUAL.html#metadata-blocks
(      vp/reports: line   11) redirect  http://pandoc.org/MANUAL.html#pandocs-markdown - permanently to https://pandoc.org/MANUAL.html#pandocs-markdown
(external-code/cross-secs: line   36) redirect  http://www.desy.de/~znagy/Site/NLOJet++.html - with Found to https://www.desy.de/~znagy/Site/NLOJet++.html
(external-code/cross-secs: line   42) redirect  http://www.precision.hep.phy.cam.ac.uk/top-plus-plus/ - permanently to https://www.precision.hep.phy.cam.ac.uk/top-plus-plus/
(external-code/cross-secs: line   17) ok        https://amcfast.hepforge.org/
(contributing/sphinx-documentation: line    6) redirect  http://www.sphinx-doc.org/en/master/ - with Found to https://www.sphinx-doc.org/en/master/
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(external-code/pdf-codes: line   22) ok        https://apfel.hepforge.org/
(external-code/grids: line   17) ok        https://applgrid.hepforge.org/
(tutorials/run-fit: line  218) ok        https://anaconda.org/anaconda/tensorflow-eigen
(           index: line  151) ok        https://arxiv.org/abs/0912.2276
(external-code/cross-secs: line   32) ok        https://arxiv.org/abs/1011.3540
(           index: line  151) ok        https://arxiv.org/abs/1103.0914
(           index: line  151) ok        https://arxiv.org/abs/1303.6254
(tutorials/closuretest: line   14) ok        https://arxiv.org/abs/1410.8849
(external-code/pdf-codes: line    6) ok        https://arxiv.org/abs/1412.7420
(           index: line  151) ok        https://arxiv.org/abs/1504.02540
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(           index: line  151) ok        https://arxiv.org/abs/1505.04794
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(external-code/apfelcomb: line    6) ok        https://arxiv.org/abs/1605.02070
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(           index: line  151) ok        https://arxiv.org/abs/2001.04986
(           index: line  151) ok        https://arxiv.org/abs/2005.11327
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(           index: line  151) ok        https://arxiv.org/abs/2103.08606
(           index: line  151) ok        https://arxiv.org/abs/2109.02671
(           index: line  151) ok        https://arxiv.org/abs/2110.08274
(           index: line  151) ok        https://arxiv.org/abs/2109.02653
(           index: line  151) ok        https://arxiv.org/abs/2111.02954
(contributing/python-tools: line  140) ok        https://black.readthedocs.io/en/stable/
(contributing/python-tools: line   16) ok        https://code.visualstudio.com/
(           index: line  151) ok        https://arxiv.org/abs/2111.05787
(           index: line  151) ok        https://arxiv.org/abs/2208.08372
(tutorials/buildmaster: line  125) ok        https://arxiv.org/abs/physics/0403086
(serverconf/index: line   10) ok        https://data.nnpdf.science
(tutorials/datthcomp: line   61) ok        https://data.nnpdf.science/validphys-docs/guide.html#development-installs
(   vp/pydataobjs: line   56) redirect  https://dask.org/ - permanently to https://www.dask.org/
(serverconf/index: line  132) ok        https://datatables.net/
(contributing/python-tools: line   51) ok        https://coverage.readthedocs.io/en/coverage-5.2.1/
(n3fit/runcard_detailed: line  411) broken    https://arxiv.org/pdf/1410.8849.pdf#page=29 - 'utf-8' codec can't decode byte 0xc7 in position 10: invalid continuation byte
(serverconf/index: line   16) ok        https://docs.nnpdf.science/
(   vp/pydataobjs: line  150) ok        https://docs.python.org/3/library/dataclasses.html
(contributing/python-tools: line   91) ok        https://docs.python.org/3/library/pdb.html
(contributing/python-tools: line   91) ok        https://docs.python.org/3/library/pdb.html#pdbcommand-!
(contributing/python-tools: line   43) ok        https://docs.pytest.org/en/latest/
(        ci/index: line   40) ok        https://docs.conda.io/projects/conda-build/en/latest/
(serverconf/index: line  160) ok        https://docs.conda.io/projects/conda-build/en/latest/resources/commands/conda-index.html
(get-started/installation: line  111) ok        https://docs.conda.io/projects/conda-build/en/latest/resources/compiler-tools.html#macos-sdk
(n3fit/methodology: line  285) ok        https://docs.scipy.org/doc/scipy/reference/generated/scipy.interpolate.PchipInterpolator.html
(           index: line  151) redirect  https://doi.org/10.1007/JHEP02(2018)026 - with Found to https://link.springer.com/article/10.1007/JHEP02(2018)026
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(       vp/design: line  126) ok        https://en.wikipedia.org/wiki/Design_by_contract
(  n3fit/hyperopt: line  157) ok        https://en.wikipedia.org/wiki/Hyperparameter_optimization
(           index: line  151) redirect  https://doi.org/10.1140/epjc/s10052-022-10297-x - with Found to https://link.springer.com/article/10.1140/epjc/s10052-022-10297-x
(        releases: line   73) ok        https://en.wikipedia.org/wiki/Linux_kernel_interfaces#In-kernel_APIs
(       vp/design: line  132) ok        https://en.wikipedia.org/wiki/YAML
(tutorials/APPLgrids: line  571) ok        https://fastnlo.hepforge.org/code/other/nlojet++-4.1.3-patched.tar.gz
(external-code/grids: line   42) ok        https://fastnlo.hepforge.org/
(tutorials/APPLgrids: line  643) ok        https://fastnlo.hepforge.org/code/v23/fastnlo_interface_nlojet-2.3.1pre-2411.tar.gz
(tutorials/APPLgrids: line  643) ok        https://fastnlo.hepforge.org/code/v23/fastnlo_toolkit-2.3.1pre-2411.tar.gz
(contributing/git: line    9) ok        https://git-scm.com/
( get-started/git: line   36) redirect  https://git-lfs.github.com/ - permanently to https://git-lfs.com/
(contributing/git: line   20) ok        https://git-scm.com/docs
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(           index: line  151) redirect  https://doi.org/10.5281/zenodo.2571601 - with Found to https://zenodo.org/record/2571601
(external-code/apfelcomb: line   30) ok        https://github.com/NNPDF/applgrids
(tutorials/APPLgrids: line   92) ok        https://github.com/J-M-Moore/applgrid_docker
(tutorials/reproduce: line  133) ok        https://github.com/N3PDF/pycompressor
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(n3fit/runcard_detailed: line  185) ok        https://github.com/NNPDF/nnpdf/blob/master/n3fit/src/n3fit/backends/keras_backend/MetaModel.py
(vp/custom_pipelines: line   27) ok        https://github.com/NNPDF/nnpdf/blob/master/validphys2/src/validphys/config.py
(     vp/examples: line   46) ok        https://github.com/NNPDF/nnpdf/blob/master/validphys2/src/validphys/tests/conftest.py#L23
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(vp/dataspecification: line   75) ok        https://github.com/NNPDF/nnpdf/issues/226
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(tutorials/plot_pdfs: line    6) ok        https://github.com/NNPDF/nnpdf/tree/master/validphys2/examples
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(get-started/nnpdfmodules: line   74) ok        https://github.com/NNPDF/reportengine/
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(vp/dataspecification: line  417) ok        https://github.com/NNPDF/reportengine/issues/38
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scarlehoff and others added 3 commits September 8, 2022 16:45

remove recommonmark

ae63cb2

Remove eval-rst

317a898

Zaharid requested review from andreab1997 and scarlehoff September 8, 2022 19:17

scarlehoff reviewed Sep 9, 2022

View reviewed changes

Zaharid added 4 commits September 9, 2022 10:19

Remove markdown configuration

10f3218

Remove mentions of markdown from the sphinx doc

352d36a

Fix markup

4e06c48

Co-authored-by: Juan M. Cruz-Martinez <juacrumar@lairen.eu> Remove various warnings reported by Shpinx. Fix incorrect conversion of markdown lists to rst wherever encountered.

Zaharid force-pushed the nomddocs branch from b90c66b to 4e06c48 Compare September 9, 2022 15:39

scarlehoff reviewed Sep 12, 2022

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Comment thread doc/sphinx/source/tutorials/run-fit.rst Outdated

scarlehoff reviewed Sep 12, 2022

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Apply suggestions from code review

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Co-authored-by: Juan M. Cruz-Martinez <juacrumar@lairen.eu>

scarlehoff mentioned this pull request Sep 14, 2022

Change recommonmark for myst #1596

Closed

scarlehoff mentioned this pull request Oct 6, 2022

Fix warnings in n3fit documentation #1598

Open

Zaharid mentioned this pull request Feb 16, 2023

Build for Python 3.10 #1628

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Zaharid force-pushed the nomddocs branch 2 times, most recently from 50cd35c to 64befe2 Compare February 16, 2023 15:45

Fix some broken links

a684cda

Zaharid force-pushed the nomddocs branch from 64befe2 to a684cda Compare February 16, 2023 15:46

RoyStegeman closed this Oct 10, 2023

RoyStegeman mentioned this pull request Mar 4, 2024

Get rid of recommonmark dependency #1978

Closed

scarlehoff deleted the nomddocs branch November 14, 2024 10:25

		convergence/stability in the fit. To read more about this, see `How to
		run an iterated fit <run-iterated-fit>`__.

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