doc does not compile

[smasson]

Context

In the trunk the doc fails to compile with the following bug:

bash-3.2$ ./manual_build.sh NEMO
NEMO
        ¤ Generation of the PDF format
Latexmk: RC file [./latex/global/latexmk.pl] does not exist

        ¤ End of building run

Analysis

The compilation of the v4-HEAD works.
the file release-4.0-HEAD/doc/latex/global/latexmk.pl does exist whereas there is no such a file in trunk/doc/latex/global
I don't know why...

Fix

copying release-4.0-HEAD/doc/latex/global/latexmk.pl into trunk/doc/latex/global seems to do the job...
but I don't know if it is the good solution...

[smasson]

Some additional informations:

From Simon:

1) latexmk.pl in the trunk seems to have appeared with [11591] and to have disappeared with [12182] upstream of the trunk update of the 2019 merge; the commit message suggests that [12182] "merges in dev_ASINTER-01-05_merge" (presumably source:/NEMO/branches/2019/dev_ASINTER-01-05_merged).
2) Apparently :
source:/NEMO/branches/2019/dev_ASINTER-01-05_merged started from
source:NEMO/branches/2019/dev_r11265_ASINTER-01_Guillaume_ABL1D@11945, which started from
source:/NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization@11268, which started from
source:/NEMO/trunk@10996

[12182] merge source:/NEMO/branches/2019/dev_ASINTER-01-05_merged@12165

[12165] 2019/dev_ASINTER-01-05_merged: Update to r12072 of trunk. merge source:/NEMO/trunk@12072
source:NEMO/branches/2019/dev_ASINTER-01-05_merged/doc/latex/global@12164 does not contain latexmk.pl
source:/NEMO/trunk/doc/latex/global@12072 contains the file latexmk.pl
source:NEMO/branches/2019/dev_ASINTER-01-05_merged/doc/latex/global@12165 still does not contain latexmk.pl

-> why?
-> Was the merge properly done (with svn merge and not "by hand")?
-> With which version of the trunk was merged source:NEMO/branches/2019/dev_ASINTER-01-05_merged/doc/latex/global@12164 ?
-> Which version of svn was used? With the release of Subversion 1.7 the svn merge subcommand disables merges into mixed-revision working copies by default. It gives an error like:

svn: E195020: Cannot merge into mixed-revision working copy 

see ​http://svnbook.red-bean.com/en/1.7/svn.branchmerge.basicmerging.html

if we look at the revision log of source:/NEMO/branches/2019/dev_ASINTER-01-05_merged@12165:
https://forge.ipsl.jussieu.fr/nemo/log/NEMO/branches/2019/dev_ASINTER-01-05_merged
We see some "multiple merge" in a single commit:
[12063] dev_ASINTER-01-05_merged: update branch with dev_r11085_ASINTER-05_Brodeau_Advanced_Bulk@r12061 and trunk@r12055
but still no latexmk.pl... copying from the trunk
[12015] dev_ASINTER-01-05_merged: merge dev_r11085_ASINTER-05_Brodeau_Advanced_Bulk branch @rev11988 with dev_r11265_ASINTER-01_Guillaume_ABL1D branch @rev11937
-> how was this done?

if we look at [12015] nothing is done on the doc directory but:
source:NEMO/branches/2019/dev_r11085_ASINTER-05_Brodeau_Advanced_Bulk/doc/latex/global@11988 does contain latexmk.pl
because of [11831] dev_r11085_ASINTER-05_Brodeau_Advanced_Bulk: Update the branch to r11830 of the trunk!

If we look at dev_r11265_ASINTER-01_Guillaume_ABL1D revision log:
https://forge.ipsl.jussieu.fr/nemo/log/NEMO/branches/2019/dev_r11265_ASINTER-01_Guillaume_ABL1D
The last merge of this branch with the trunk seems to be:
[11587] dev_r11265_ASINTER-01_Guillaume_ABL1D: merge trunk @ r11584 with dev_r11265_ABL … so before the addition of latexmk.pl in the trunk.

[smasson]

clearly we have to remove most of the modifications done on the doc/latex in [12182]
https://forge.ipsl.jussieu.fr/nemo/changeset/12182/NEMO/branches/2019/dev_r11943_MERGE_2019/doc/latex
or in [12063] which looks very similar
https://forge.ipsl.jussieu.fr/nemo/changeset/12063/NEMO/branches/2019/dev_ASINTER-01-05_merged/doc

but we have to keep some of these changes...

I propose to take the changes done "intentionally" in the following branches and modified by [12063] or [12182]

• dev_ASINTER-01-05_merged :
  based on https://forge.ipsl.jussieu.fr/nemo/log/NEMO/branches/2019/dev_ASINTER-01-05_merged/doc?rev=12182 https://forge.ipsl.jussieu.fr/nemo/changeset/12157/NEMO/branches/2019/dev_ASINTER-01-05_merged/doc https://forge.ipsl.jussieu.fr/nemo/changeset/12126/NEMO/branches/2019/dev_ASINTER-01-05_merged/doc https://forge.ipsl.jussieu.fr/nemo/changeset/12081/NEMO/branches/2019/dev_ASINTER-01-05_merged/doc
• dev_r11085_ASINTER-05_Brodeau_Advanced_Bulk :
  based on https://forge.ipsl.jussieu.fr/nemo/log/NEMO/branches/2019/dev_r11085_ASINTER-05_Brodeau_Advanced_Bulk/doc?rev=12182 https://forge.ipsl.jussieu.fr/nemo/changeset/12051/NEMO/branches/2019/dev_r11085_ASINTER-05_Brodeau_Advanced_Bulk/doc https://forge.ipsl.jussieu.fr/nemo/changeset/12046/NEMO/branches/2019/dev_r11085_ASINTER-05_Brodeau_Advanced_Bulk/doc https://forge.ipsl.jussieu.fr/nemo/changeset/12031/NEMO/branches/2019/dev_r11085_ASINTER-05_Brodeau_Advanced_Bulk/doc https://forge.ipsl.jussieu.fr/nemo/changeset/12019/NEMO/branches/2019/dev_r11085_ASINTER-05_Brodeau_Advanced_Bulk/doc
• dev_r11265_ASINTER-01_Guillaume_ABL1D :
  based on https://forge.ipsl.jussieu.fr/nemo/log/NEMO/branches/2019/dev_r11265_ASINTER-01_Guillaume_ABL1D/doc?rev=12182 I see nothing to do...
• dev_r10984_HPC-13_IRRMANN_BDY_optimization :
  based on https://forge.ipsl.jussieu.fr/nemo/log/NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc?rev=12182 many?

[mathiot]

I am also struggling to compile the doc (even with your suggested fix)

===========Latexmk: Missing input file: '../../global/epilogue.tex' from line
  '! LaTeX Error: File `../../global/epilogue.tex' not found.'

I am surprised it compile at all. In the head of the trunk, appendices.tex has some links to annex_[A-E] but they are not there (this is still the old filename), chap_misc.tex need to access epilogue.tex but this file has been removed since (during the big merge) and probably other.

I am wondering if we should simply revert doc to the state before the big merge and let people re-introduced there changes one by one.

[smasson]

I agree the fix is not working. It is only a small part of the problem.
As we found with Simon, there was a problem in the merge of the different branches.
Yes, we have to find the simplest way to kind of "revert" this corrupted merge... Maybe your proposition is the good one.

[nicolasmartin]

I guess I'm the most relevant for looking at the case.

As far as I remember, the LaTeX documentation was compiling successfully when I committed my last changes to the trunk in 2019 ([11711]), or at least with few missing uncommitted changes.
I will get back to this revision as the starting point and I think I would be able to identify in the different branches merged the updates done in the LaTeX sources, because the modifications will be contain either in the chapters or in the bibliography.

[nicolasmartin]

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[nicolasmartin]

For the moment, I manage to recover the state of the ./doc/latex folder (up to r11711), just before the merging commit in the mid 2020, regarding the files used to configure the latex compilation and not the ones containing the text sources.

From the log in order to determine my last commit, I undo the changes with the cherry-picking option of the svn merge cmd and made fixes if needed

$ svn merge -c -12377 .

• global my last commit was 11702, output of diff

     $ svn diff http://forge.ipsl.jussieu.fr/nemo/svn/NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/global http://forge.ipsl.jussieu.fr/nemo/svn/NEMO/trunk/doc/latex/global@11702
  

  packages.tex

  @@ -42 +42 @@
   
   %% Missing utmr8a font
   \usepackage{times}
  -
  -\usepackage{hyperref}   %% links
  - No newline at end of file

• NEMO/main: my last commit was 11711, output of diff

     $ svn diff http://forge.ipsl.jussieu.fr/nemo/svn/NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/main http://forge.ipsl.jussieu.fr/nemo/svn/NEMO/trunk/doc/latex/NEMO/main@11711
  

  bibliography.bib

  @@ -3133 +3133 @@
     issn          = "0148-0227",
     doi           = "10.1029/92jc00911"
   }
  -
  -@article{large.yeager_CD09,
  -author="Large, W. G. and Yeager, S. G.",
  -title="The Global Climatology of an Interannually Varying Air-Sea Flux Data Set",
  -pages = "341--364",
  -journal="Climate Dynamics",
  -volume = "33",
  -number = "2-3",
  -year="2009",
  -month = "aug",
  -publisher = "Springer Science and Business Media LLC",
  -doi="10.1007/s00382-008-0441-3"
  -}
  -
  -@book{sverdrup.johnson.ea_1942,
  -author = {H. U. Sverdrup and Martin W. Johnson and Richard H. Fleming},
  -title = {The Oceans, Their Physics, Chemistry, and General Biology},
  -publisher = {Prentice-Hall},
  -address = {New York},
  -year = {1942},
  -pages = {1087},
  -}
  -
  -@article{kraus.businger_QJRMS96,
  -author = "E. B. Kraus and J. A. Businger",
  -title = "Atmosphere-ocean interaction.",
  -journal="Quarterly Journal of the Royal Meteorological Society",
  -year = "1996",
  -volume = "122",
  -number = "529",
  -pages = "324-325",
  -publisher = "John Wiley & Sons, Ltd",
  -issn = "1477-870X",
  -doi = "10.1002/qj.49712252914"
  -}
  -
  -@article{josey.gulev.ea_2013,
  -title = "Exchanges through the ocean surface",
  -journal = "Ocean Circulation and Climate - A 21st Century Perspective, Int. Geophys. Ser.",
  -year = "2013",
  -author = "S. A. Josey and S. Gulev and L. Yu",
  -pages = "115-140, edited by G. Siedler et al., Academic Press, Oxford",
  -volume = "103",
  -doi = "10.1016/B978-0-12-391851-2.00005-2"
  -}
  -
  -@article{fairall.bradley.ea_JGR96,
  -  year = "1996",
  - journal = "Journal of Geophysical Research: Oceans",
  -  month = "jan",
  -  publisher = "American Geophysical Union",
  -  volume = "101",
  -  number = "C1",
  -  pages = "1295-1308",
  -  author = "C. W. Fairall and E. F. Bradley and J. S. Godfrey and G. A. Wick and J. B. Edson and G. S. Young",
  -  title = "Cool-skin and warm-layer effects on sea surface temperature",
  -  doi = "10.1029/95jc03190"
  -}
  -
  -@article{zeng.beljaars_GRL05,
  -  year = "2005",
  -  month = "jul",
  -  publisher = "American Geophysical Union",
  -  volume = "32",
  -  number = "14",
  -  author = "Xubin Zeng and Anton Beljaars",
  -  title = "A prognostic scheme of sea surface skin temperature for modeling and data assimilation",
  -  journal = "Geophysical Research Letters",
  -  doi = "10.1029/2005gl023030"
  -}

• SI3/main: my last commit was 11711, no diff output

     $ svn diff http://forge.ipsl.jussieu.fr/nemo/svn/NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/SI3/main http://forge.ipsl.jussieu.fr/nemo/svn/NEMO/trunk/doc/latex/SI3/main@11711
  

• TOP/main: my last commit was 11711, no diff output

     $ svn diff http://forge.ipsl.jussieu.fr/nemo/svn/NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/TOP/main http://forge.ipsl.jussieu.fr/nemo/svn/NEMO/trunk/doc/latex/TOP/main@11711
  

Some particular files required some modifications to build the manuals

• NEMO/subfiles/chap_misc.tex : change verbatim for fortran envs to avoid error with % in the code snippets
• NEMO/subfiles/apdx_triads.tex : move \newcommand after \begin{document}
• NEMO/subfiles/chap_ZDF.tex : move \newcommand after \begin{document}
• TOP/subfiles/model_description.tex: move \newcommand after \begin{document}

Still to check in details what was introduced in the latex subfiles with the big merge...

[nicolasmartin]

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