Opened 9 years ago

Closed 6 years ago

Last modified 5 years ago

#6495 closed enhancement (fixed)

Build the reference manual incrementally

Reported by: mpatel Owned by: jdemeyer
Priority: major Milestone: sage-5.8
Component: documentation Keywords: days38
Cc: jhpalmieri, leif, niles, hivert, mguaypaq, mhansen Merged in: sage-5.8.beta0
Authors: Mitesh Patel, John Palmieri, Florent Hivert Reviewers: Volker Braun, Florent Hivert
Report Upstream: N/A Work issues:
Branch: Commit:
Dependencies: 5.7.beta2 + #13064, #8327, #13891 Stopgaps:

Description (last modified by jhpalmieri)

Building the Sage reference manual can take a significant amount of time. Decreasing this time could speed up Sage development.

The patch is large, but most of it consists of moving files from one location to another, as described below. A summary of the changes:

Changes in doc/en/reference — this is where the size of the patch comes from, although the changes are pretty simple:

  • rearrange the directory doc/en/reference: for each file like algebras.rst, create a subdirectory algebras and move algebras.rst to algebras/index.rst. Also create a file algebras/conf.py for the build configuration. All of these new conf.py files are identical. Deal with the contents of the directory reference/media similarly, moving the pictures to the appropriate subdirectory.
  • modify reference/index.rst to point to these new files.
  • reorganize reference/index.rst so it is arranged, at least somewhat, by topic.
  • add intersphinx to conf.py — see below. Also add the new subdirectories to the list exclude_trees.
  • new file conf_sub.py, configuration for the pieces of the documentation (as opposed to the main conf.py, which is for building reference/index.rst). This file is imported by each of the files SUBDIRECTORY/conf.py.

Changes to doc/common/builder.py:

  • add code to build the reference manual in sections, and also to build the sections in parallel. The reference manual ought to be built twice to resolve references now, so typing "sage -docbuild all html" will build it twice (along with all of the other documents, of course). "sage -docbuild reference html" will just build it once. You can also run "sage -docbuild reference/combinat html", for example, to just build one part of the manual.
  • the different parts of the manual are separate documents as far as sphinx is concerned, so allow them to reference each other using the "intersphinx" extension. (This is why we need to build it twice: the first pass assembles the intersphinx databases, the second pass uses the databases to create the references correctly.)
  • to accomodate the changes in #11251, which don't seem to be easily compatible with intersphinx, search through the output files looking for "todo" items, and accumulate them in one master "todo" list.
  • for pdf format, since it now produces 30 different pdf files, write an html file which links to each of them.

Other changes:

  • doc/common/conf.py: add the intersphinx extension to the build process.
  • doc/common/themes/sage/layout.html: fix a bug where clicking the Sage logo in the upper left corner of the docs wouldn't take you to the right place, at least in the local documentation.
  • doc/common/themes/sageref/: add a new theme for the pieces of the reference manual. This is almost identical to the "sage" theme, except for a little tinkering to the links along the top and bottom lines.
  • in the main Sage library, change a few pathnames to media files in the reference manual, since those files have been moved.
  • make the necessary changes to .hgignore and MANIFEST.in to deal with the relocated files.

The html docs for Sage 5.4.rc2, html without MathJax, html with MathJax, and pdf, built after applying the patches here.


Apply:


Before building the docs, you should delete the documentation output directory: rm -rf SAGE_ROOT/devel/sage/doc/output. To test this, you should run sage --docbuild all html and sage --docbuild all pdf. (Note: just running sage --docbuild reference html will probably produce many warnings. If you run it a second time, the warnings should go away.)

Attachments (32)

trac_6495_ref_pdf_pieces.patch (2.0 KB) - added by mpatel 9 years ago.
Experimental.
trac_6495-reference_breakup.patch (262.8 KB) - added by mpatel 9 years ago.
Another approach. Depends on #7549. Still experimental. This patch only. sage repo.
trac_6495-reference_breakup_v2.patch (226.8 KB) - added by mpatel 9 years ago.
PDF fixes. This patch only. sage repo.
trac_6495-subdivide-ref-manual.2.patch (281.3 KB) - added by jhpalmieri 7 years ago.
use only this patch
trac_6495-subdivide-ref-manual.patch (283.2 KB) - added by jhpalmieri 7 years ago.
use only this patch
trac_6495-root.patch (1.5 KB) - added by jhpalmieri 7 years ago.
root repo
invbuilder.patch (24.2 KB) - added by hivert 6 years ago.
inventory builder + merge todo list & html / js indexes
trac_6495-part3-the-remaining.patch (34.3 KB) - added by hivert 6 years ago.
trac_6495-part2-everything-else-9774.patch (53.2 KB) - added by jhpalmieri 6 years ago.
apply second (if you've applied the patches at #9774)
trac_6495-part4-interrupts.patch (13.4 KB) - added by jhpalmieri 6 years ago.
trac_6495-part3-the-remaining-vs-5.4.patch (32.5 KB) - added by jhpalmieri 6 years ago.
apply third
trac_6495-redirect_html.patch (3.7 KB) - added by mhansen 6 years ago.
trac-6495_silence_warning-fh.patch (1.7 KB) - added by hivert 6 years ago.
trac_6495-redirect_html.2.patch (3.8 KB) - added by hivert 6 years ago.
trac_6495-docstrings.patch (1.7 KB) - added by jhpalmieri 6 years ago.
trac_6495-other-parts.patch (75.4 KB) - added by jhpalmieri 6 years ago.
everything except "part 1"
trac_6495-script.sh (2.7 KB) - added by jdemeyer 6 years ago.
script used to generate "part 1" patch
trac_6495_output_filter.patch (5.3 KB) - added by vbraun 6 years ago.
Initial patch
trac_6495_separate_inventory.patch (18.7 KB) - added by vbraun 6 years ago.
Initial patch
trac_6495-all-in-one-vb.patch (139.0 KB) - added by vbraun 6 years ago.
Updated patch
trac_6495-all-in-one.patch (139.6 KB) - added by jhpalmieri 6 years ago.
combined patch
trac_6495-filtering.patch (1.9 KB) - added by jhpalmieri 6 years ago.
trac-6495_silence_warning-fh.v2.patch (1.7 KB) - added by jhpalmieri 6 years ago.
trac_6495-part1-moving-files.patch (71.5 KB) - added by jhpalmieri 6 years ago.
apply first
trac_6495-script-jhp.sh (2.7 KB) - added by jhpalmieri 6 years ago.
trac_6495-part3-the-remaining-vs-5.7.beta4.patch (32.1 KB) - added by jhpalmieri 6 years ago.
trac_6495-part1-moving-files-link.patch (46.2 KB) - added by jhpalmieri 6 years ago.
apply first
trac_6495-script-jhp-link.sh (2.2 KB) - added by jhpalmieri 6 years ago.
script used to generate "part 1" patch
dochtml.log (440.2 KB) - added by jdemeyer 6 years ago.
Log file of troublesome build
trac_6495-sphinx-grammar.patch (2.2 KB) - added by jhpalmieri 6 years ago.
patch for Sphinx spkg; for review only
trac_6495-part2-everything-else.patch (53.3 KB) - added by jhpalmieri 6 years ago.
apply second
trac_6495_fixes.patch (3.9 KB) - added by vbraun 6 years ago.
Updated patch

Change History (299)

Changed 9 years ago by mpatel

Experimental.

comment:1 Changed 9 years ago by mpatel

  • Authors set to Mitesh Patel
  • Cc jhpalmieri added
  • Summary changed from Break up the PDF reference manual into smaller pieces to [with patch, needs work] Break up the PDF reference manual into smaller pieces

The attached patch is experimental. Notes:

  • sage -docbuild reference pdf fails to build arithgroup.pdf, apparently because of the math macro \ZZ in the title. Unfortunately, I don't know how to fix this.
  • Since it replaces the top level PDF file with several smaller files, it breaks the patch at #4460.
  • It's not clear what happens to cross-ReST document links. I'll try to investigate.

comment:2 Changed 9 years ago by mpatel

On cross-PDF document links: It seems that Sphinx does not produce these. This may OK, since file:// URLs can break easily.

comment:3 Changed 9 years ago by mpatel

On the \ZZ in arithgroup.tex: It seems the problem stems from \@title in

    \ifsphinxpdfoutput
      \begingroup
      % This \def is required to deal with multi-line authors; it               
      % changes \\ to ', ' (comma-space), making it pass muster for             
      % generating document info in the PDF file.                               
      \def\\{, }
      \pdfinfo{
        /Author (\@author)
        /Title (\@title)
      }
      \endgroup
    \fi

in Sphinx's manual.cls. For some reason, the \math* font commands do not work in this context. I gather that \mathbf is preferred, but one workaround is to use

Arithmetic Subgroups of `{\rm SL}_2({\bf Z})`

in place of

Arithmetic Subgroups of `{\rm SL}_2(\ZZ)`

in arithgroup.rst.

Changed 9 years ago by mpatel

Another approach. Depends on #7549. Still experimental. This patch only. sage repo.

comment:4 Changed 9 years ago by mpatel

  • Priority changed from minor to major
  • Report Upstream set to N/A
  • Summary changed from [with patch, needs work] Break up the PDF reference manual into smaller pieces to Build the reference manual incrementally
  • Type changed from defect to enhancement

The new patch may make it possible to build and update reference manual chapters semi-independently. I think we can use the intersphinx extension to fix the cross-chapter references. But we'll need to build the manual twice, a la LaTeX.

To build just a chapter, try, e.g.,

sage -docbuild reference/algebras html -juiv3

Still to do:

  • Make a combined index page and search page.
  • Check that PDF generation works.
  • Combine chapter PDF files into one large [optional] PDF file (with pdfjam's pdfjoin)?
  • Use a specific LaTeX doc title in each conf.py.
  • Fix the "Arithmetic Subgroups" heading on the top-level page.
  • Use a visual, 2D layout for the top-level page? Group by general area? Add icons?
  • Get a reply from sphinx-dev about making relative paths work.
  • Build docs in parallel (cf. #6255) with multiprocessing?
  • Replace the "website" PDF link?
  • User-friendliness improvements.
  • Encourage more compact chapters? It seems that "Combinatorics" takes the most time and memory.
  • ...

comment:5 Changed 9 years ago by mpatel

Another important item:

  • Use just one _static directory for the manual, not 50+!

comment:6 Changed 9 years ago by mpatel

If this approach is viable, I suggest leaving many (most?) of the "To Do" items for other tickets.

comment:7 Changed 9 years ago by mpatel

While I'm here:

  • Copy PDFs from output/latex/ to output/pdf, so that make all-pdf, at least, doesn't do unnecessary work?

comment:8 Changed 9 years ago by mpatel

  • Description modified (diff)

Changed 9 years ago by mpatel

PDF fixes. This patch only. sage repo.

comment:9 follow-up: Changed 9 years ago by mpatel

Sphinx caches "foreign" object inventories in a document's environment.pickle. These now use a lot of disk space.

comment:10 in reply to: ↑ 9 Changed 9 years ago by mpatel

Replying to mpatel:

Sphinx caches "foreign" object inventories in a document's environment.pickle. These now use a lot of disk space.

Another sphinx-dev query.

comment:11 Changed 8 years ago by leif

  • Cc leif added

comment:12 Changed 7 years ago by jhpalmieri

Here's a new patch, rebased to Sage 4.7.1.alpha4. This implements parallel building, and it provides a great speedup, at least on systems with lots of processors. For example, on sage.math, the time to execute sage -docbuild reference html -j went from about 18 minutes to just under 2 minutes. The main idea is to build each module of the reference manual separately, and use the Sphinx intersphinx extension to handle cross-references (so :class:`blah` will work in the algebras module, even if blah is defined in the rings module).

Remaining issues:

  • The new build uses up more disk space than the old, by about 120 megabytes. I don't know if anything can be done about this, and I also don't think it's a big deal. (With the previous patch, it took about 1 gigabyte more, but the more recent patch manages to cut that down: in the previous patch, the _static subdirectory of the documentation was being copied, once for each module of the reference manual, and with the new version, a symlink is used instead.)
  • There are now some missing bibliographic references: at some point in the past, people have gone through the documentation and unified the references, but this means that references in one module are not seen by any other. This can be fixed just by copying the references to the module where they're used. For example: CMR05 is referenced somewhere in the module on polynomial rings, but the actual item is described in crypto/mq/sr.py.
  • The cross-referencing in intersphinx is not perfect; in particular, it doesn't seem to work after building the documents once, it needs to have the full doctree "inventory" for any module available before resolving references to that module. Since the inventory files are built alongside the documentation, this means it has to be built twice (as far as I can tell) before cross-all of the references work. We could try to figure out dependencies and make sure that if module A is referenced in module B, then A is built first, but that seems complicated, and there is no reason for there not to be circular references. I'm tempted to just allow broken cross-references. For the docs on the web site, we would have to make sure they got built twice.
  • There is a main index for the reference manual, but once you click on any entry (like "Cryptography"), you get to that module's index, and there is no link taking you back to the main index. There ought to be a way to fix this, but I haven't figured it out yet.

comment:13 follow-up: Changed 7 years ago by vbraun

  • Milestone set to sage-4.7.2
  • Reviewers set to Volker Braun

In an ideal world sphinx would be multithreaded, but we probably shouldn't wait for that ;-) The remaining issues about disk space, bibliographic references, and needing two runs seem to be unavoidable. Building parallel gets more and more important, so I think the benefits outweigh the disadvantages.

I tried the patch on Sage-4.7.1.alpha4 without any other patches applied:

  • Only the main page has proper css. For example, html/en/reference/cmd/index.html refers to _static/sage.css but the correct path would be ../_static/sage.css.
  • patch conflicts with #11251 (todo extension). Given that the latter is already positively reviewed, maybe this ticket could be rebased on top of it?
  • During the sage build, I think we should then run the docbuilder twice for the reference manual. Perhaps this should always be done for sage -docbuild all.
  • Can we make output less verbose? The whole intersphinx output scrolled forever off my screen. Ideally, an interspinx failure to find an inventory file would only add one extra line at the end of the build along the lines of "You should re-run docbuild to get references right."

comment:14 in reply to: ↑ 13 Changed 7 years ago by jhpalmieri

  • Authors changed from Mitesh Patel to Mitesh Patel, John Palmieri
  • Dependencies set to 11251

Replying to vbraun:

I tried the patch on Sage-4.7.1.alpha4 without any other patches applied:

  • Only the main page has proper css. For example, html/en/reference/cmd/index.html refers to _static/sage.css but the correct path would be ../_static/sage.css.

This was a mistake in the previous version: it was supposed to create a link from reference/_static to reference/cmd/_static. Now it should work.

  • patch conflicts with #11251 (todo extension). Given that the latter is already positively reviewed, maybe this ticket could be rebased on top of it?

Good point. This raises another problem: intersphinx doesn't easily pass todo lists between different documents, so I don't know how to get a master todo list for the Sage library. Right now, I've put the todolist for each module after its table of contents. I think combinat is the only module with any actual to do elements.

  • During the sage build, I think we should then run the docbuilder twice for the reference manual. Perhaps this should always be done for sage -docbuild all.

Done: sage -docbuild all now builds the reference manual twice. I also added a few print statements to the docbuild process.

  • Can we make output less verbose? The whole intersphinx output scrolled forever off my screen. Ideally, an interspinx failure to find an inventory file would only add one extra line at the end of the build along the lines of "You should re-run docbuild to get references right."

I've tried to do this when doing sage -docbuild all and not in general, but it may be suppressing too much output. (In the first pass, all warnings are suppressed, including intersphinx warnings, and in the second pass, any warnings should be printed. But in the second pass, it's just rewriting output, taking intersphinx links into account -- it's not reading the sources a second time, so it doesn't produce warnings about missing bibliographic references.)

Other issues:

  • In PDF output, this produces one PDF file for each module, but there is no "master" file linking to them. I hope we can create one. Should it be an html file or a PDF file?
  • We could perhaps speed things up more by breaking the combinat module, which is by far the largest, into several pieces. This can happen on another ticket.
  • I've reorganized the main index for the reference manual, grouping modules together by topic. I hope it's easier to find things this way. I wonder if we can get intersphinx to produce a master index for all of the documents...
  • in the old version, at least on my computer, when I clicked on the Sage logo in the top left corner, it wasn't taking me to the right place. I've fixed that. Along the same lines, with the new reorganization, the other links on the top line look a little funny to me in the reference manual. They looked worse before and I've tried to clean them up, but maybe they could use more work?

comment:15 Changed 7 years ago by jhpalmieri

  • Description modified (diff)

comment:16 Changed 7 years ago by jhpalmieri

  • Status changed from needs_work to needs_review

Here's a new version of the patch. This still has the same issue with "todo" items: I don't know a way to accumulate all of them from the different Sage modules, so they are just recorded module-by-module. For PDF output, the main documentation page (in SAGE_ROOT/devel/sage/doc/output/html/en/index.html) has the little PDF icons, and now when you click on the one for the reference manual, it actually opens an html file with links to all of the different PDF files.

I'm marking this for review. If we can come up with a good solution for "todo" items, that would be great, but perhaps we could defer it to another ticket.

comment:17 Changed 7 years ago by jhpalmieri

Okay, so this is not the most elegant solution, but in the most recent patch, in the html version of the reference manual, after everything is built, it searches through all of the output files algebra/index.html, arithgroup/index.html, etc., looking for todo lists. When it finds them, it copies them to todolist/index.html. This only works for the html version; for other formats, the todo list file says "The combined to do list is only available in the html version of the reference manual."

comment:18 Changed 7 years ago by jhpalmieri

Here's a new version; the only difference is this change to SAGE_ROOT/devel/sage/spkg-dist:

  • spkg-dist

    diff --git a/spkg-dist b/spkg-dist
    a b fi 
    3838
    3939# Remove the .cython_hash file, since including this in the bdist will
    4040# completely break "sage -br".
    41 # Also, do not distribute these build files (.os and .os);
     41# Also, do not distribute these build files (.so and .os);
    4242# it wastes space and causes problems!
    4343
    44 rm -f .cython_hash c_lib/*.so c_lib/*.os 
     44rm -f .cython_hash c_lib/*.so c_lib/*.os
    4545
    4646# Delete all the autogenerated files, since they will get created again
    4747# when SAGE is built or upgraded. 
    4848cd sage; "$CUR"/spkg-delauto .; cd ..
    4949
     50# Delete the autogenerated files in the doc directory.
     51rm -rf doc/output
     52rm -rf doc/en/reference/sage
     53rm -rf doc/en/reference/sagenb
     54rm -rf doc/en/reference/static
     55rm -rf doc/en/reference/templates
     56rm -rf doc/en/reference/*/sage sage/doc/en/reference/*/static sage/doc/en/reference/*/templates
     57
    5058# Create the sdist using Python's distutils.
    5159python setup.py sdist

This makes for a slightly smaller sage-....spkg file, and more importantly, if the old autogenerated files are there, they can confuse the docbuild process.

comment:19 Changed 7 years ago by jhpalmieri

Some recent timings on sage.math.

Before the patch:

$ rm -rf SAGE_ROOT/devel/sage/doc/output
$ time sage -docbuild reference html
...
real	17m49.313s
user	16m57.530s
sys	0m45.390s

$ rm -rf SAGE_ROOT/devel/sage/doc/output
$ time sage -docbuild reference pdf
...
real	26m3.623s
user	24m40.290s
sys	0m43.030s

After the patch:

$ rm -rf SAGE_ROOT/devel/sage/doc/output
$ time sage -docbuild reference html
...
real	2m30.092s
user	10m34.900s
sys	1m12.590s

$ rm -rf SAGE_ROOT/devel/sage/doc/output
$ time sage -docbuild reference pdf
...
real	3m35.064s
user	15m49.790s
sys	1m11.070s

comment:20 Changed 7 years ago by jhpalmieri

Question: if you type "sage -docbuild -D" now, it says

$ sage -docbuild -D
DOCUMENTs:
    de/tutorial          a_tour_of_sage       bordeaux_2008        
    constructions        developer            faq                  
    installation         numerical_sage       reference            
    thematic_tutorials   tutorial             website              
    fr/a_tour_of_sage    fr/tutorial          ru/tutorial          
    all  (!)             
(!) Builds everything.

Should we also mention "reference/MODULE" as a valid target?

Changed 7 years ago by jhpalmieri

use only this patch

comment:21 Changed 7 years ago by jhpalmieri

  • Description modified (diff)

Changed 7 years ago by jhpalmieri

use only this patch

comment:22 Changed 7 years ago by jhpalmieri

  • Dependencies changed from 11251 to 11251, 11298
  • Description modified (diff)

Here's a new version, with #11298 as a new dependency. (It may apply without #11298, perhaps with fuzz.) To help with reviewing, I've broken the patch into two pieces, as explained in the ticket description.

comment:23 Changed 7 years ago by jhpalmieri

  • Dependencies changed from 11251, 11298 to #11251, #11298

comment:24 follow-up: Changed 7 years ago by robertwb

Could you post a link to the generated docs so people could browse them?

comment:25 in reply to: ↑ 24 Changed 7 years ago by jhpalmieri

Replying to robertwb:

Could you post a link to the generated docs so people could browse them?

Good idea:

comment:26 Changed 7 years ago by niles

  • Cc niles added

comment:27 Changed 7 years ago by was

  • Keywords sd32 added

comment:28 Changed 7 years ago by jdemeyer

  • Dependencies #11251, #11298 deleted

Testing this against sage-4.8.alpha1 + #10620...

comment:29 Changed 7 years ago by jdemeyer

Against sage-4.8.alpha1:

patching file doc/en/reference/games/index.rst
Hunk #1 FAILED at 6
1 out of 1 hunks FAILED -- saving rejects to file doc/en/reference/games/index.rst.rej
patching file doc/en/reference/graphs/index.rst
Hunk #1 succeeded at 52 with fuzz 1 (offset 2 lines).
abort: patch failed to apply

comment:30 Changed 7 years ago by jdemeyer

Also: I'm not sure whether building totally in parallel should be the default.

comment:31 Changed 7 years ago by jhpalmieri

Here are rebased patches, along with the following change: there is now an environment variable, SAGE_PARALLEL_DOCBUILD, which if set to anything nonempty which doesn't start with "n", causes the reference manual to be built in parallel. I also added "doc-parallel" and "doc-pdf-parallel" targets to the main Makefile with a patch to the root repo.

comment:32 Changed 7 years ago by jhpalmieri

  • Description modified (diff)

Changed 7 years ago by jhpalmieri

root repo

comment:33 Changed 7 years ago by jhpalmieri

By the way, the default in the new patch is to build serially. I've also added a brief description of SAGE_PARALLEL_DOCBUILD to the installation guide.

comment:34 follow-up: Changed 7 years ago by jhpalmieri

  • Description modified (diff)

Some other possible changes: in the parallel-building code (from builder.py)

            from multiprocessing import Pool, cpu_count
            max_cpus = 8 if SAGE_PARALLEL_DOCBUILD else 1
            pool = Pool(min(max_cpus, cpu_count()))

perhaps change "else 1" to "else 2"? As it is, building serially (with max_cpus set to 1) is slower than the current system, because in the new system, the manual has to be built twice to resolve cross-references.

We could also change "pool" to just "Pool(cpu_count())" or "Pool(int(1.5 * cpu_count()))" or something like that, eliminating the minimum of 8 and possibly increasing the maximum.

comment:35 in reply to: ↑ 34 ; follow-up: Changed 7 years ago by jdemeyer

Replying to jhpalmieri:

Some other possible changes: in the parallel-building code (from builder.py)

            from multiprocessing import Pool, cpu_count
            max_cpus = 8 if SAGE_PARALLEL_DOCBUILD else 1
            pool = Pool(min(max_cpus, cpu_count()))

perhaps change "else 1" to "else 2"?

Why? It wouldn't make sense to build with more processes than there are CPUs.

We could also change "pool" to just "Pool(cpu_count())" or "Pool(int(1.5 * cpu_count()))" or something like that, eliminating the minimum of 8 and possibly increasing the maximum.

Why? It wouldn't make sense to build with more processes than there are CPUs.

As I mentioned on sage-devel, I don't like that there is an option to doctest in parallel, a different option to build the docs in parallel, a different option to build in parallel... I would say: let there be one environment variable SAGE_NUM_PROCESSES or something like that and use that for everything.

comment:36 in reply to: ↑ 35 Changed 7 years ago by jhpalmieri

Replying to jdemeyer:

Replying to jhpalmieri:

Some other possible changes: in the parallel-building code (from builder.py)

            from multiprocessing import Pool, cpu_count
            max_cpus = 8 if SAGE_PARALLEL_DOCBUILD else 1
            pool = Pool(min(max_cpus, cpu_count()))

perhaps change "else 1" to "else 2"?

Why? It wouldn't make sense to build with more processes than there are CPUs.

This version still does min(max_cpus, cpu_count()), so it won't use more processes than there are CPUs.

We could also change "pool" to just "Pool(cpu_count())" or "Pool(int(1.5 * cpu_count()))" or something like that, eliminating the minimum of 8 and possibly increasing the maximum.

Why? It wouldn't make sense to build with more processes than there are CPUs.

I see lots of suggestions on the internet to set MAKE=make -jN where N is 1.5 * (the number of cpus), or 1 or 2 more than the number of cpus. Why not here as well?

As I mentioned on sage-devel, I don't like that there is an option to doctest in parallel, a different option to build the docs in parallel, a different option to build in parallel... I would say: let there be one environment variable SAGE_NUM_PROCESSES or something like that and use that for everything.

I think maybe two variables: one (SAGE_PARALLEL) to enable parallel processes, one (SAGE_NUM_THREADS) to determine the maximum number of processes. The first could be "no" by default, and the second could be "0" by default, meaning use cpu_count() or min(8, cpu_count()) or some other variant on this, the way we do with NUM_THREADS in Makefile and sage-ptest. Then it's easy to turn on and off without remembering how many cores your machine has.

comment:37 follow-up: Changed 7 years ago by was

Why not exactly one environment variable "MAKE" which gets set to "make -jN" for some N, and that is it? I suggest this, since that's what I'm used to already for years. I don't claim it is the best solution, but it's in all my .bash* files already, and as John points out above it is documented already all over. Why don't we just stick with it?

comment:38 in reply to: ↑ 37 Changed 7 years ago by jhpalmieri

Replying to was:

Why not exactly one environment variable "MAKE" which gets set to "make -jN" for some N, and that is it?

That's an interesting idea. See #12016.

comment:39 follow-ups: Changed 7 years ago by jhpalmieri

  • Dependencies set to #12016

Here's a new patch which uses the setting of MAKE to build docs in parallel (or not). It's very similar to the code in sage-ptest from #12016, except that when you run sage-ptest, the assumption should be that you want to work in parallel, so the default number of threads (if MAKE is not set) is min(8, #cpus). For doc building, we shouldn't assume parallel building by default, I guess, so the default number of threads is 1.

comment:40 in reply to: ↑ 39 Changed 7 years ago by jdemeyer

Replying to jhpalmieri:

For doc building, we shouldn't assume parallel building by default, I guess, so the default number of threads is 1.

Indeed!

comment:41 in reply to: ↑ 39 Changed 7 years ago by jdemeyer

  • Status changed from needs_review to needs_work

Replying to jhpalmieri:

Here's a new patch which uses the setting of MAKE to build docs in parallel (or not). It's very similar to the code in sage-ptest from #12016, except that when you run sage-ptest, the assumption should be that you want to work in parallel, so the default number of threads (if MAKE is not set) is min(8, #cpus). For doc building, we shouldn't assume parallel building by default, I guess, so the default number of threads is 1.

So then we don't need the environment variable SAGE_PARALLEL_DOCBUILD, nor the Makefile patch, anymore.

comment:42 Changed 7 years ago by jdemeyer

With sage-4.8.alpha1, I get

Building reference manual, first pass.

sphinx-build -b html -d /mnt/usb1/scratch/jdemeyer/merger/sage-4.8.alpha2/devel/sage/doc/output/doctrees/en/reference   -A hide_pdf_links=1 -Q  /mnt/usb1/scratch/jdemeyer/merger/sage-4.8.alpha2/devel/sage/doc/en/reference /mnt/usb1/scratch/jdemeyer/merger/sage-4.8.alpha2/devel/sage/doc/output/html/en/reference
Build finished.  The built documents can be found in /mnt/usb1/scratch/jdemeyer/merger/sage-4.8.alpha2/devel/sage/doc/output/html/en/reference
Traceback (most recent call last):
  File "/mnt/usb1/scratch/jdemeyer/merger/sage-4.8.alpha2/devel/sage/doc/common/builder.py", line 1332, in <module>
    getattr(get_builder(name), type)()
  File "/mnt/usb1/scratch/jdemeyer/merger/sage-4.8.alpha2/devel/sage/doc/common/builder.py", line 288, in _wrapper
    getattr(get_builder(document), 'html')(*args, **kwds)
  File "/mnt/usb1/scratch/jdemeyer/merger/sage-4.8.alpha2/devel/sage/doc/common/builder.py", line 405, in _wrapper
    N = re.search('(-j|--jobs[=]?)\s*([0-9]*)', MAKE).groups()[1]
UnboundLocalError: local variable 're' referenced before assignment
make: *** [doc-html] Error 1

comment:43 Changed 7 years ago by jhpalmieri

  • Description modified (diff)
  • Status changed from needs_work to needs_review

So then we don't need the environment variable SAGE_PARALLEL_DOCBUILD, nor the Makefile patch, anymore.

Right, fixed. Also, I added import re into builder.py; this should fix the other problem as well.

comment:44 Changed 7 years ago by jhpalmieri

This now uses SAGE_NUM_THREADS from #12016.

comment:45 follow-up: Changed 7 years ago by jdemeyer

  • Status changed from needs_review to needs_work

Regarding #12016: you should simply use the value of SAGE_NUM_THREADS, nothing fancier than that.

Regarding spkg-dist: this is essentially a duplicate of #12081 and #12086, so this patch should be removed. In any case, removing the files from MANIFEST.in is the proper way of dealing with this, as opposed to removing the files before packaging the repository. Ideally, sage-sdist should not change the current Sage source tree at all.

What's the rationale for adding all these files to doc/common/themes/sageref?

Instead of always building twice, would it be possible to detect whether the manual has already been built once. For example, if I want both the HTML and PDF documentation, the current patch would do 4 passes, even if 3 would be sufficient.

Last edited 7 years ago by jdemeyer (previous) (diff)

comment:46 Changed 7 years ago by jdemeyer

Last edited 7 years ago by jdemeyer (previous) (diff)

comment:47 in reply to: ↑ 45 Changed 7 years ago by jhpalmieri

  • Cc hivert added
  • Keywords sd32 removed
  • Work issues set to intersphinx

Rebased to 5.0.beta13, but the intersphinx stuff needs fixing (the use of intersphinx here conflicts with the changes in #9128, and I haven't fixed this). Part 1 of the patch was mostly generated automatically using the attached script. After running the script, I removed lines like .. _ch:algebras: (from algebras/index.rst, in this case) by hand.

Replying to jdemeyer:

Regarding #12016: you should simply use the value of SAGE_NUM_THREADS, nothing fancier than that.

Okay, done.

Regarding spkg-dist: this is essentially a duplicate of #12081 and #12086, so this patch should be removed. In any case, removing the files from MANIFEST.in is the proper way of dealing with this, as opposed to removing the files before packaging the repository. Ideally, sage-sdist should not change the current Sage source tree at all.

I removed that part of the patch.

What's the rationale for adding all these files to doc/common/themes/sageref?

The new structure of the reference manual, in particular the new directory structure, means we need new templates for the files coming from reference/algebras/index.rst, as opposed to the old templates, which work for the main file reference/index.rst.

Instead of always building twice, would it be possible to detect whether the manual has already been built once. For example, if I want both the HTML and PDF documentation, the current patch would do 4 passes, even if 3 would be sufficient.

I don't know how to do this.

comment:48 Changed 7 years ago by jhpalmieri

  • Description modified (diff)

comment:49 Changed 7 years ago by jdemeyer

This patch would allow building the reference manual with less memory usage. 1.5GB (still a lot) is sufficient to build the manual, as opposed to more than 2GB without the patch.

comment:50 Changed 7 years ago by jdemeyer

I do get several warnings when building the HTML manual. The following is repeated many times:

sphinx-build -b html -d /fast_scratch/jdemeyer/sage-5.0.beta13/devel/sage/doc/output/doctrees/de/tutorial   -A hide_pdf_links=1  /fast_scr
atch/jdemeyer/sage-5.0.beta13/devel/sage/doc/de/tutorial /fast_scratch/jdemeyer/sage-5.0.beta13/devel/sage/doc/output/html/de/tutorial
Running Sphinx v1.1.2
loading translations [de]... done
loading pickled environment... not yet created
loading intersphinx inventory from /fast_scratch/jdemeyer/sage-5.0.beta13/devel/sage/doc/common/python.inv...
loading intersphinx inventory from /fast_scratch/jdemeyer/sage-5.0.beta13/devel/sage/doc/output/html/en/reference/objects.inv...
WARNING: intersphinx inventory '/fast_scratch/jdemeyer/sage-5.0.beta13/devel/sage/doc/output/html/en/reference/objects.inv' not fetchable
due to <type 'exceptions.IOError'>: [Errno 2] No such file or directory: '/fast_scratch/jdemeyer/sage-5.0.beta13/devel/sage/doc/output/htm
l/en/reference/objects.inv'
building [html]: targets for 22 source files that are out of date
updating environment: 22 added, 0 changed, 0 removed
[...]
Build finished.  The built documents can be found in /fast_scratch/jdemeyer/sage-5.0.beta13/devel/sage/doc/output/html/de/tutorial

There are several of the form:

sphinx-build -b html -d /fast_scratch/jdemeyer/sage-5.0.beta13/devel/sage/doc/output/doctrees/en/reference/schemes   -A hide_pdf_links=1  -q  -a  /fast_scratch/jdemeyer/sage-5.0.beta13/devel/sage/doc/en/reference/schemes /fast_scratch/jdemeyer/sage-5.0.beta13/devel/sage/doc/output/html/en/reference/schemes
None:37: WARNING: citation not found: Fulton
Build finished.  The built documents can be found in /fast_scratch/jdemeyer/sage-5.0.beta13/devel/sage/doc/output/html/en/reference/schemes

comment:51 Changed 7 years ago by jhpalmieri

  • Work issues changed from intersphinx to citations

The intersphinx stuff actually seems to be working, despite my earlier comment. I'll keep testing it to make sure, but I think it's okay.

Regarding the warnings: the missing intersphinx inventories are expected. That's why we have to build everything twice: once to create all of the inventory files, and then a second time to use them. At least for me, if I run sage --docbuild reference html twice in a row, I don't get these warnings the second time through. The citation warnings need to be fixed, though.

comment:52 Changed 6 years ago by hivert

Hi John,

What is the status of this one ? It this robust ?

I'm quite glad that I didn't stomp on your foot with #9128, but I may be right now in the process on jumping high to land on your foot ;-/: I just dived deep inside Sphinx and using @parallel, I managed to have the "writing output..." part of the doc compilation in parallel. I've right now no idea how robust it is. I'll put a log of my experiment on #6255. Also, it seems possible that the read part could also be made parallel.

Florent

comment:53 follow-ups: Changed 6 years ago by jhpalmieri

Hi Florent,

This is in pretty good shape, but it's not perfect. It undoes some of what you did in #9128 (mainly because I haven't tried to rewrite the patch to do it differently), and in particular, I'm not sure that the other parts of the Sage documentation can use intersphinx to access information from the reference manual. Citations may be an issue, in particular if the same reference is cited twice in two different parts of the reference manual: we may just need to add another copy of the citation, or perhaps a master list of citations that gets used by everything. I don't know if that's practical.

There are also issues with having to build the reference manual twice so that all of the references are resolved. This is not ideal.

I think that doing the reading and/or writing in parallel would be good, but given the size of the reference manual, breaking it into pieces seems worthwhile as well. If the parallel reading and writing help to cut down on the memory usage, which seems to be getting out of hand, then maybe that is good enough for now. (At least on sage.math, the writing part seems to take way too long, so doing that in parallel might help significantly.)

So if you have a workable solution which accomplishes some of what is done here, and perhaps does it more simply, go right ahead. I'll take a look at your comments at #6255.

John

comment:54 in reply to: ↑ 53 ; follow-up: Changed 6 years ago by hivert

Hi John,

Thanks for the quick answer.

This is in pretty good shape, but it's not perfect. It undoes some of what you did in #9128 (mainly because I haven't tried to rewrite the patch to do it differently), and in particular, I'm not sure that the other parts of the Sage documentation can use intersphinx to access information from the reference manual.

I'll have a look at it. Please do not hesitate to ask for some more explanation on the hack I did with intersphinx. Is there a specific reason why you doubt intersphinx will work for the other part of the doc ?

There are also issues with having to build the reference manual twice so that all of the references are resolved. This is not ideal.

It doesn't seem to be a huge problem with LaTeX, since this never has been solved since years... Though I never seen a LaTeX compilation as long as Sage's doc.

I think that doing the reading and/or writing in parallel would be good, but given the size of the reference manual, breaking it into pieces seems worthwhile as well.

I agree.

If the parallel reading and writing help to cut down on the memory usage, which seems to be getting out of hand, then maybe that is good enough for now. (At least on sage.math, the writing part seems to take way too long, so doing that in parallel might help significantly.)

I don't think it will cut down memory usage in any way. I'd rather expect the contrary. My solution seems to be working but since I currently for a sage for every single file, a lot of time is wasted in forking. I'll try to improve it tomorrow.

So if you have a workable solution which accomplishes some of what is done here, and perhaps does it more simply, go right ahead. I'll take a look at your comments at #6255.

I don't think I really will. As I said I'll probably trade speed against memory usage... I'll keep you in touch.

Cheers,

Florent

comment:55 in reply to: ↑ 54 ; follow-up: Changed 6 years ago by jdemeyer

Replying to hivert:

I don't think it will cut down memory usage in any way. I'd rather expect the contrary.

Memory usage is already too much, so anything that further increases memory usage is very bad.

comment:56 in reply to: ↑ 55 ; follow-up: Changed 6 years ago by hivert

Replying to jdemeyer:

Replying to hivert:

I don't think it will cut down memory usage in any way. I'd rather expect the contrary.

Memory usage is already too much, so anything that further increases memory usage is very bad.

I respectfully disagree if

  • it is optional
  • it divide by more than 10 the documentation compile time

comment:57 in reply to: ↑ 56 Changed 6 years ago by leif

Replying to hivert:

Replying to jdemeyer:

Replying to hivert:

I don't think it will cut down memory usage in any way. I'd rather expect the contrary.

Memory usage is already too much, so anything that further increases memory usage is very bad.

Like adding more modules and functions to the Sage library, and rising the "doc[test] coverage"... ;-)


I respectfully disagree if

  • it is optional

That would be fine.

  • it divides by more than 10 the documentation compile time

Wow... :P

comment:58 Changed 6 years ago by hivert

This is an extremely useful patch which should go in Sage ASAP. It effectively reduce the compilation time to 10min on my I7 laptop. This is brilliant. It will certainly prove more maintainable in the long term than my parallelization of Sphinx expertiment. Though, I think we should discuss of is with Georges Brandl (the maintainer of Sphinx).

I'm now reviewing the code itself. You'll find below some comments.

Florent

Suggestion of improvement:

  • I think we should get rid of the warning on the first pass, maybe by patching a little bit intersphinx. Also, now the compilation is a lot more verbose. Maybe we should silent the info for loading the bunch of intersphinx load at least in reference/*. If you agree with the idea, I'm Ok to look at this one.
  • Some directories are much longer than the other (eg: combinat) they should be launched first (or maybe in this case broken in even smaller parts). This could wait for another ticket.

Some remaining problems:

  • Interrupting the compilation with ctrl+C doesn't work. I had to kill by hand the master compilation process. I'm not sure what we can do for solving this problem.
  • On the main page, you managed to gather the todos which is great ! Is it possible to do the same for the index (mine is empty). The module index is moreover broken.

comment:59 Changed 6 years ago by hivert

Hi John,

Using your patch I realized that for the first stage, you don't need to get the html file only the pickle and object.inv file. Did you try to do that ? It seems that this is easily feasible with a custom Builder. I'm currently testing this workflow.

Florent

comment:60 Changed 6 years ago by hivert

Another comment: You should start by building the reference manual and then the other component. Currently in class AllBuilder method _wrapper you start by building the other documents.

Florent

comment:61 Changed 6 years ago by hivert

I just attached a new patch which defines a new builder for creating the pickle and object.inv file. It can be called by

sage -docbuild DOCUMENT invpickle

It is automatically called for the first pass when building DOCUMENT=all. As a consequence on my laptop the first pass in only 2 min and a half long.

Florent

comment:62 Changed 6 years ago by hivert

The invpickle builder seem quite efficient here are the timing on my I7 laptop:

  • First stage: 02:36
  • Second Stage: 08:06

Without my patch the first stage is 10:19 long.

Florent

comment:63 Changed 6 years ago by hivert

There is also a failure:

sage -t  builder.py
File "/home/data/Sage-Install/sage-5.0.beta13/devel/sage-doc/doc/common/builder.py", line 862:
    [...]
    sage: builder.ReferenceBuilder("reference").auto_rest_filename("sage.combinat.partition")
      File "/home/data/Sage-Install/sage-5.0.beta13/devel/sage/doc/common/builder.py", line 409, in _wrapper
        getattr(DocBuilder(self.name, lang), format)(*args, **kwds)
    AttributeError: 'DocBuilder' object has no attribute 'auto_rest_filename'

comment:64 Changed 6 years ago by jhpalmieri

Hi Florent,

Your ideas look great; I hope you can keep working on them. I am happy with all of your suggestions. In particular:

  • building the reference manual before the other documents is fine. I think that was your approach in #9128, and the original patch here built the reference manual last. I hadn't gotten around to changing it to build the reference manual first.
  • I'll try to take a look at combining the indices, the way the todo lists are combined.
  • further subdividing combinat (for example) is a good idea, but I also agree that it belongs on another ticket.
  • I've also noticed that ctrl-C doesn't quit the process. Any ideas why? Should we run the parallel processes differently, maybe using the methods you suggested at #6255?

By the way, mpatel should get a lot of the credit for this; he wrote the original patches, which I've just cleaned up and reorganized.

comment:65 Changed 6 years ago by jhpalmieri

I got two doctest failures (after applying your patch), which can be fixed with this patch:

  • doc/common/builder.py

    diff --git a/doc/common/builder.py b/doc/common/builder.py
    a b class DocBuilder(object): 
    200200            sage: import os, sys; sys.path.append(os.environ['SAGE_DOC']+'/common/'); import builder
    201201            sage: b = builder.DocBuilder('tutorial')
    202202            sage: b._output_formats()
    203             ['changes', 'html', 'htmlhelp', 'json', 'latex', 'linkcheck', 'pickle', 'web']
     203            ['changes', 'html', 'htmlhelp', 'invpickle', 'json', 'latex', 'linkcheck', 'pickle', 'web']
    204204
    205205        """
    206206        #Go through all the attributes of self and check to
    class ReferenceSubBuilder(DocBuilder): 
    859859
    860860            sage: import os, sys; sys.path.append(os.environ['SAGE_DOC']+'/common/'); import builder
    861861            sage: import builder
    862             sage: builder.ReferenceBuilder("reference").auto_rest_filename("sage.combinat.partition")
     862            sage: builder.ReferenceSubBuilder("reference").auto_rest_filename("sage.combinat.partition")
    863863            '.../devel/sage/doc/en/reference/sage/combinat/partition.rst'
    864864        """
    865865        return self.dir + os.path.sep + module_name.replace('.',os.path.sep) + '.rst'

comment:66 Changed 6 years ago by jhpalmieri

By the way, searching is broken with these patches. The files searchindex.js (both in reference/ and in its various subdirectories) are all essentially empty. Hmm.

It looks like combining the indices should be doable, but a little annoying: read in the html from each, extract the entries, sort them, and rewrite to a new index file. The same should work for the module index. I think talking to Georg Brandl makes sense: if we wanted Sphinx to support this kind of thing out of the box, what exactly would we be looking for? I guess at the least we want separate Sphinx documents which share indices, searches, and inventories. It would be nice to have a specific "Sphinx Enhancement Proposal", or even some code to contribute.

comment:67 Changed 6 years ago by hivert

Hi John,

Another reason to have this in Sage ASAP: #12878

I'm willing to help on this one but we need to coordinate. I'll be in Montreal for the next Sage days 38 so hopefully will have so time for Sphinx. Do you think you'll have so time on it in the forthcoming weeks ? Please tell me what I can do to help. Here are a few suggestions:

  • avoiding to build the full doc twice: If you agree with the idea of the invpicke builder, I can polish it a little more. Also the name is far from being perfect and I'm open to any suggestion.
  • Intersphinx being too verbose: I don't think we can silence intersphinx a little without patching Sphinx. I can try to do it by some Monkey patch.
  • Parallelizing the rests of the doc: I noticed that the refman is build in parallel but the other documents are build in series. We should build them in parallel too. I'll look for the easiest way.

Cheers,

Florent

comment:68 Changed 6 years ago by jhpalmieri

I hope I have time to work on it next week, although right now I have other things I need to be doing (like reading my student's PhD thesis).

  • I really like the idea of the invpickle builder, so please continue with that. I don't have any better suggestions for the name.
  • The verbosity of intersphinx is a minor issue. If we can reduce it, that would be fine, but it's not the highest priority, in my opinion.
  • I think it shouldn't be too hard to parallelize building the rest of the docs. We want to do it so that hitting ctrl-c will quit the build. I think we should try using tools from sage.parallel rather than the Python multiprocessing module. If you want to work on that, that would be great.

Also:

  • I can try to work on the indices.
  • I will investigate why the searchindex.js files are empty, but right now I have no idea.

I will try to post any progress that I make, and you should do likewise, so we don't end up duplicating each other's work.

comment:69 follow-up: Changed 6 years ago by jhpalmieri

As far as handling ctrl-c, I found this question. It seems we can replace pool.apply_async(ARGS) with pool.apply_async(ARGS).get(999999). This apparently adds a (very long) timeout to the process, and it apparently works around a bug in Python. In practice, it seems to work for me.

  • doc/common/builder.py

    diff --git a/doc/common/builder.py b/doc/common/builder.py
    a b class ReferenceBuilder(AllBuilder): 
    415415            for doc in self.get_all_documents(refdir):
    416416                pool.apply_async(build_ref_doc,
    417417                                 (doc, lang, format,
    418                                   os.path.split(output_dir)[0]) + args, kwds)
     418                                  os.path.split(output_dir)[0]) + args, kwds).get(999999)
    419419            pool.close()
    420420            pool.join()
    421421            if format == 'html':

comment:70 Changed 6 years ago by leif

Replying to jhpalmieri:

  • I really like the idea of the invpickle builder, so please continue with that. I don't have any better suggestions for the name.

One should perhaps just expand the name to contain "inventory"; "pickle" is IMHO minor (or irrelevant) and won't tell most(?) people much.

  • The verbosity of intersphinx is a minor issue. If we can reduce it, that would be fine, but it's not the highest priority, in my opinion.

Mine, too. Although I hate Sphinx's / Sage's current messages already, especially since "Build succeeded. The built documents can be found in ..." is always printed, so is plain wrong in case of an error. (We tried to fix that once, but then I think Jeroen decided to keep it as is.)

  • I think it shouldn't be too hard to parallelize building the rest of the docs. We want to do it so that hitting ctrl-c will quit the build. I think we should try using tools from sage.parallel rather than the Python multiprocessing module. If you want to work on that, that would be great.

Why not just use make? Either add (and change the) targets in the top-level Makefile, or add one to devel/sage/doc/. To me seems cleanest (preferably the latter), and docbuilding IMHO shouldn't depend [more] on the Sage library [as needed / it already does].

comment:71 Changed 6 years ago by jhpalmieri

The problem with using make is that I want to be able to run sage --docbuild all html, and I don't think that running this should call make. The fix I mentioned above for interrupts (adding a timeout) doesn't make use of the sage.parallel module, just plain Python, by the way. So we should be able to do this for building all of the documents in parallel.

comment:72 in reply to: ↑ 69 Changed 6 years ago by hivert

Replying to jhpalmieri:

As far as handling ctrl-c, I found this question. It seems we can replace pool.apply_async(ARGS) with pool.apply_async(ARGS).get(999999). This apparently adds a (very long) timeout to the process, and it apparently works around a bug in Python. In practice, it seems to work for me.

Does it really work ? For me is seems that ctrl-c is now working but the doc is no more compiling in parallel.

Florent

comment:73 follow-up: Changed 6 years ago by hivert

Concerning todos (and maybe indexes too), I think I've found an alternative: they are pickled in the files environment.pickle. Here is an example, in the directory doc/output/doctrees/en/reference/modules:

sage: import cPickle
sage: f = open('environment.pickle', 'rb')
sage: env = cPickle.load(f)
sage: f.close()
sage: env.todo_all_todos
[{'docname': 'sage/modules/free_module', 'source': u'/home/data/Sage-Install/sage-5.0.beta14/local/lib/python2.7/site-packages/sage/modules/free_module.py:docstring of sage.modules.free_module.FreeModuleFactory', 'todo': <todo_node: <title...><paragraph...>>, 'lineno': 122, 'target': <target: >}]
sage: env.indexentries.keys()
['index', 'sage/modules/free_module_element', 'sage/modules/real_double_vector', 'sage/modules/matrix_morphism', 'sage/modules/fg_pid/fgp_module', 'sage/modules/free_module_homspace', 'sage/modules/vector_space_homspace', 'sage/modules/fg_pid/fgp_element', 'sage/modules/complex_double_vector', 'sage/modules/fg_pid/fgp_morphism', 'sage/modules/vector_callable_symbolic_dense', 'sage/modules/module', 'sage/modules/free_module_morphism', 'sage/modules/vector_space_morphism', 'sage/modules/free_module']

So it seems that we can get them from there from the pickle concatenate them and let sphinx output the todo list and the index.

Florent

Last edited 6 years ago by hivert (previous) (diff)

comment:74 in reply to: ↑ 73 Changed 6 years ago by hivert

Replying to hivert:

So it seems that we can get them from there from the pickle concatenate them and let sphinx output the todo list and the index.

I've a proof of concept which seems to be working upto two problems:

  • The generated links to the "original entry" generated by app.builder.get_relative_uri is missing the subdirectory (ie: "reference/sage/modules/..." instead of "reference/modules/sage/modules/...". This could probably either be fixed by fixing the builder or playing with symlinks.
  • if one recompile the doc twice, all the todos are duplicated. This could probably also be fixed by removing duplicates or clearing the todo-list at the right moment.

I think both problem can be fixed.

comment:75 Changed 6 years ago by hivert

Hi there,

I just uploaded a new invbuilder.patch; you need to apply it after the two mentionned patch in the header of this ticket. It seems to solve the problems of

  • merging todo lists
  • merging the html indexes

It remains to merge the javascript indexes.

Please tests.

Florent

Last edited 6 years ago by hivert (previous) (diff)

comment:76 Changed 6 years ago by hivert

I just uploaded a new patch which merge the javascript indexes as well !!! It was a little more tricky but it seems to work now. The only things that remains to be merged is the list of modules. I'll write a proposal to Sphinx for my merging tool.

Florent

comment:77 Changed 6 years ago by hivert

The new version now also merge modules indexes !!! The obtained doc seems to be in quite a good shape.

Changed 6 years ago by hivert

inventory builder + merge todo list & html / js indexes

comment:78 in reply to: ↑ 53 Changed 6 years ago by hivert

Citations may be an issue, in particular if the same reference is cited twice in two different parts of the reference manual: we may just need to add another copy of the citation, or perhaps a master list of citations that gets used by everything. I don't know if that's practical.

I've probably a way to handle cross-citation as well. They are stored in the environement and I can get them to gather the link in the main reference manual, exactly the way I gather TODO and indexes. It is just a little more tricky because I need to redispatch them to the other documents. I'm experimenting...

Florent

Changed 6 years ago by hivert

comment:79 Changed 6 years ago by hivert

  • Authors changed from Mitesh Patel, John Palmieri to Mitesh Patel, John Palmieri, Florent Hivert
  • Description modified (diff)
  • Status changed from needs_work to needs_review
  • Work issues citations deleted

Hi there,

I just uploaded which seems to solve most of the problems we had here, including merging of

  • the todo list if this extension is activated;
  • the python indexes;
  • the list of python modules;
  • the javascript index;
  • the citations.

I put a need review though I'm quite not sure everything is ready for inclusion into Sage. I do need feedback and people shaking my code to see if it's robust.

Florent

comment:80 Changed 6 years ago by hivert

  • Keywords days38 added

comment:81 follow-up: Changed 6 years ago by jhpalmieri

Hi Florent,

I am quite busy with other things right now, so I hope you can get people at Sage Days 38 to take a good look at this. Maybe you can figure out the ctrl-c issue as well; maybe tinkering with what I had might work; if not, the link I provided had some other ideas, too.

Thanks, John

comment:82 in reply to: ↑ 81 Changed 6 years ago by hivert

Hi John,

Replying to jhpalmieri:

I am quite busy with other things right now, so I hope you can get people at Sage Days 38 to take a good look at this. Maybe you can figure out the ctrl-c issue as well; maybe tinkering with what I had might work; if not, the link I provided had some other ideas, too.

well, they are very few people knowing the documentation building system here and I used quite a few Sphinx internal stuff. I think a good reviewer would be George Brandle himself but I need to sit for a moment to write him an e-mail.

Cheers,

Florent

comment:83 Changed 6 years ago by mguaypaq

I haven't had time yet to read the whole ticket description and discussion, but I will note that this patch has allowed me to build the documentation on my old laptop (with only 1GB of RAM) in a couple of hours, whereas trying to build it without the patch causes my laptop to become unresponsive and eventually crash. (Also, Florent had a look at the output and seemed satisfied that everything was fine.) So, a huge +1 from me!

I will try to do as much as I can to review this ticket, but I know almost nothing about the documentation building process.

comment:84 Changed 6 years ago by mguaypaq

  • Cc mguaypaq added

comment:85 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

After a lot of swearing at my computer, I think I have the ctrl-c situation figured out. We've been using Pool.apply_async, and this didn't handle ctrl-c well. Adding a timeout (using the get method) caused it to handle interrupts, but it no longer build in parallel. If we instead use Pool.map_async together with get to provide a timeout, it seems to work. Please take a look at the new patch.

comment:86 Changed 6 years ago by jhpalmieri

Several quick comments and questions:

  • First, the combined indices and search are great! At first I thought that searching was broken, but that's my browser, not the code. I'm still looking over the patch, but in practice it seems to work.
  • This is an old problem: I object to the use of "type" as a global variable, set by __main__. Then I can't use print type(var) anywhere in the rest of the code (as I tried to do when debugging something). I may change type to something else; any suggestions? Perhaps format (which also has a meaning in Python)?
  • When we're happy about the patches, I'll try to combine them into just one or two chunks. Right now, for example, one of my patches creates the "todolist" directory, and then Florent's patch moves all of the files out of it, so we end up with an empty directory. I don't know if there are other similar things which will need cleaning up.
  • I get some warnings about missing citations. Should we worry about those now?

comment:87 Changed 6 years ago by jhpalmieri

I've modified the part 4 patch to do a little cleanup:

  • I moved the detection of the number of threads to build_options.py, and expanded on the comment about loading build_options.py. This way if someone is reading builder.py and wants to know where NUM_THREADS is defined, at least they'll find a comment pointing them to that file.
  • I modified the mkdir function, making it a bit more secure: the new approach seems to be preferred, as far as I can tell.

comment:88 Changed 6 years ago by jhpalmieri

Another update to part 4: fix the main index.html file for the pdf build of the reference manual.

comment:89 Changed 6 years ago by jhpalmieri

One more update to part 4, to fix a few doctests.

comment:90 follow-up: Changed 6 years ago by jhpalmieri

I think this looks very good. I'm just about ready to give Florent's part a positive review. Two questions: can we reinstate the -Q flag for the first pass on the reference manual, to silence all of the warnings? Also, I see this warning message; do you know if it's important?

preparing documents... WARNING: search index couldn't be loaded, but not all documents will be built: the index will be incomplete.

(This occurs if I do sage --docbuild all html, at the end of the second pass through the reference manual.)

I'm attaching one more version of the part 4 patch, just to fix a few typos and grammar issues in the files Florent added.

comment:91 in reply to: ↑ 90 Changed 6 years ago by hivert

Hi John,

I think this looks very good. I'm just about ready to give Florent's part a positive review.

Wow !!! This is extremely cool. Thanks a lot ! I'm sorry for my current silence. I didn't had the time to look at your part4 code. I'll try to do it shortly.

Two questions: can we reinstate the -Q flag for the first pass on the reference manual, to silence all of the warnings?

No problem. I just wanted to have some idea of the progress and forgot to switch back to a silent mode.

Also, I see this warning message; do you know if it's important?

preparing documents... WARNING: search index couldn't be loaded, but not all documents will be built: the index will be incomplete.

(This occurs if I do sage --docbuild all html, at the end of the second

pass through the reference manual.)

I'm not sure now. I'll though I had silenced this warning. Give me a few day to investigate a little more. It is probably not important as the produced index is correct but I may be missing to merge somme part of it.

I'm attaching one more version of the part 4 patch, just to fix a few typos and grammar issues in the files Florent added.

Thanks for those rereading. I planned to polish more the code and try to get some feedback from Sphinx and didn't find the time. However I now think that we should let the code enter sage as soon as possible because it allows the doc to compile on small machine. At sage days 48, with mguaypaq (see above) we manage to compile the documentation in a seemingly satisfactory way on a 1GB machine. Moreover its a requirement to the feature #12878 which I think is definitely needed at least for huge classes such as graphs...

Thanks a lot,

Florent

comment:92 Changed 6 years ago by jhpalmieri

See #12991 for a peripherally-related ticket: don't doctest the autogenerated rst files.

comment:93 Changed 6 years ago by jdemeyer

  • Status changed from needs_review to needs_work

This needs to be rebased to sage-5.1.beta5:

applying /release/merger/patches/trac_6495-part2-everything-else.patch
patching file doc/en/reference/combinat/index.rst
Hunk #1 FAILED at 3
1 out of 2 hunks FAILED -- saving rejects to file doc/en/reference/combinat/index.rst.rej
patching file doc/en/reference/misc/index.rst
Hunk #1 succeeded at 31 with fuzz 1 (offset 3 lines).
abort: patch failed to apply

comment:94 Changed 6 years ago by jdemeyer

  • Dependencies #12016 deleted

comment:95 Changed 6 years ago by jhpalmieri

  • Status changed from needs_work to needs_review

Okay, this is now rebased.

comment:96 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

I've added a link to the built documents for Sage 5.1.beta5, in case anyone wants to look at it without applying the patches here. The reference manual is organized differently and as a result looks different. The other documents should be unchanged.

comment:97 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

comment:98 Changed 6 years ago by jhpalmieri

  • Dependencies set to #9774
  • Description modified (diff)

This now depends on #9774. If you want to try it without the patches at #9774 (thus using jsMath instead of MathJax), apply trac_6495-part2-everything-else.patch instead of trac_6495-part2-everything-else-9774.patch.

comment:99 Changed 6 years ago by jhpalmieri

A slight issue with the reference manual is that it takes up a little more room, and most of the difference is in devel/sage/doc/output/doctrees. There is some redundancy in the environment.pickle files. I wonder if there is any way to avoid this.

In more detail: using MathJax instead of jsMath saves room in the directory doc/output/html: with the old version, jsMath and non-parallel, that directory takes about 325M, while the new version, MathJax and parallel, takes about 200M, saving 125M. Unfortunately, the doctree directory has increased by about 150M, so the whole thing has gone up by 25M. Not a big difference, but if there were a way to improve it, it would be nice. Maybe on another ticket...

comment:100 Changed 6 years ago by jdemeyer

  • Dependencies changed from #9774 to #13126, #11078, #11874, #12229, #11503, #12327, #11080, #9774, #8473, #11913, #12299, #13121
  • Milestone changed from sage-5.1 to sage-pending

Clarified recursive dependencies.

comment:101 Changed 6 years ago by jdemeyer

  • Status changed from needs_review to needs_work
  • Work issues set to too many WARNINGs

I get tons of warnings (1043 to be precise) when building the manuals. I don't like this, because it's hard to distinguish warnings due to this ticket with true warnings about bad formatting. Is there a way not to produce any warnings during the first run (I assume the warnings should only appear in the first run)?

comment:102 Changed 6 years ago by jhpalmieri

Rebased because of #12299. I'll try to work on the warnings. I think it might be best to only suppress the warnings when you run sage --docbuild all html, because that is when both passes of the reference manual are actually run, and the first pass is designed to be fast: it just produces the inventory files, not html output. If you run sage --docbuild reference html, then it will just do one pass, html format.

Edit: actually, the warnings are easy to get rid of. Florent intentionally left them there while working on the ticket: see these lines in builder.py:

        global ALLSPHINXOPTS
        # ALLSPHINXOPTS += ' -Q -D multidoc_first_pass=1'
        ALLSPHINXOPTS += ' -D multidoc_first_pass=1'

If we uncomment the second line and remove the third, the warnings will go away. I'll incorporate this change into the 4th patch.

Last edited 6 years ago by jhpalmieri (previous) (diff)

comment:103 Changed 6 years ago by jhpalmieri

  • Status changed from needs_work to needs_review

comment:104 Changed 6 years ago by jhpalmieri

  • Work issues too many WARNINGs deleted

comment:105 Changed 6 years ago by jhpalmieri

I see one warning now:

WARNING: search index couldn't be loaded, but not all documents will be built: the index will be incomplete.

I don't know what this means. The search index looks pretty good to me. Florent might have some idea, when he has a chance to look at this.

comment:106 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

comment:107 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

comment:108 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

comment:109 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

comment:110 Changed 6 years ago by jhpalmieri

In addition to the warning mentioned in comment #105, I have a question about .buildinfo files. It seems that on the first pass through the reference manual, these files contain lines like

config: 6a23e6beb735e39dc46994bfb813cf55
tags: fbb0d17656682115ca4d033fb2f83ba1

On the second pass, these files get overwritten, and the new files have

config:
tags:

Then running sage --docbuild reference all produces warnings like

WARNING: unsupported build info format in '.../devel/sage/doc/output/html/en/reference/libs/.buildinfo', building all

and then everything is rebuilt again. I propose this change, which seems to fix this issue:

  • doc/common/builder.py

    diff --git a/doc/common/builder.py b/doc/common/builder.py
    a b class AllBuilder(object): 
    300300        logger.warning("Building reference manual, second pass.\n")
    301301        ALLSPHINXOPTS = ALLSPHINXOPTS.replace(
    302302            'multidoc_first_pass=1', 'multidoc_first_pass=0')
    303         ALLSPHINXOPTS = ALLSPHINXOPTS.replace('-Q', '-q') + ' -a '
     303        ALLSPHINXOPTS = ALLSPHINXOPTS.replace('-Q', '-q') + ' '
    304304        for document in refs:
    305305            getattr(get_builder(document), name)(*args, **kwds)
    306306
Last edited 6 years ago by jhpalmieri (previous) (diff)

Changed 6 years ago by jhpalmieri

apply second (if you've applied the patches at #9774)

comment:111 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

comment:112 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

comment:113 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

comment:114 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

comment:115 Changed 6 years ago by jhpalmieri

Rebased to Sage 5.4.beta0.

comment:116 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

comment:117 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

comment:118 follow-up: Changed 6 years ago by jhpalmieri

Florent: any chance you can work on this? I think that the only thing needed reviewing is the part 4 patch. (There is also the warning at comment 105, but I think that the actual output is good, so suppressing the warning would be nice but not absolutely necessary. You might also look at comment 110, but I can't reproduce that issue right now.)

Last edited 6 years ago by jhpalmieri (previous) (diff)

comment:119 in reply to: ↑ 118 Changed 6 years ago by hivert

Hi John,

Replying to jhpalmieri:

Florent: any chance you can work on this? I think that the only thing needed reviewing is the part 4 patch. (There is also the warning at comment 105, but I think that the actual output is good, so suppressing the warning would be nice but not absolutely necessary. You might also look at comment 110, but I can't reproduce that issue right now.)

Yes ! And thanks for your work and your patience. This is very high on my priority list, but it has to remain after the list "things that must be done right now" (such as teaching or meeting the dead-line to get money for Sage-Combinat) or even "thing that should have been done yesterday". Unfortunately, until the end of September, I will still be moving a flat, so I definitely won't be able to work during the Week-End. I definitely want to do this done ASAP. So I didn't give-up, but the summer didn't went as expected and I had to stop working on sage for a few month. Please ping me in the first week of October if I didn't manage to do it .

Cheers,

Florent

comment:120 Changed 6 years ago by jhpalmieri

Rebased to Sage 5.4.beta1.

comment:121 follow-up: Changed 6 years ago by jhpalmieri

  • Dependencies changed from #13126, #11078, #11874, #12229, #11503, #12327, #11080, #9774, #8473, #11913, #12299, #13121 to #13143

Made #13143 a dependency and rebased to that.

comment:122 in reply to: ↑ 121 Changed 6 years ago by hivert

Hi John,

Replying to jhpalmieri:

Made #13143 a dependency and rebased to that.

Consider me as pinged. And don't hesitate to email me more aggressively if nothing come up before the end of the week.

Florent

Changed 6 years ago by jhpalmieri

comment:123 Changed 6 years ago by jhpalmieri

Rebased to #13143 and Sage 5.4.rc2 (because of changes to builder.py in #13579).

comment:124 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

comment:125 Changed 6 years ago by kcrisman

  • Status changed from needs_review to needs_work
  • Work issues set to rebase

John, I've tried to use this on an existing Sage installation (well, previous versions of this) a few different times, and it always ends up causing problems, even when I delete the whole output directory. Is there something to do other than apply the all-in-one patch, delete output, do sage -b, and start building docs? For instance, is there an env var (e.g. SAGE_NUM_THREADS) to set or something? I feel like I must have done something obvious wrong...

On a related note, this no longer applies :-(

comment:126 follow-up: Changed 6 years ago by jhpalmieri

What sort of problems do you see? As far as environment variables, setting MAKE is the right thing to do: export MAKE='make -j2' for example.

I just rebased the patches on top of 5.5.rc0.

comment:127 Changed 6 years ago by jhpalmieri

  • Status changed from needs_work to needs_review

comment:128 Changed 6 years ago by jhpalmieri

  • Work issues rebase deleted

comment:129 in reply to: ↑ 126 Changed 6 years ago by kcrisman

What sort of problems do you see? As far as environment variables, setting MAKE is the right thing to do: export MAKE='make -j2' for example.

Lots of

WARNING: intersphinx inventory '/Users/.../sage-5.5.rc0/devel/sage/doc/output/html/en/reference/monoids/objects.inv' not fetchable due to <type 'exceptions.IOError'>: [Errno 2] No such file or directory: '/Users/.../sage-5.5.rc0/devel/sage/doc/output/html/en/reference/monoids/objects.inv'

stuff.

build succeeded, 1074 warnings.

That's while building reference html, and now I see upon careful reading of the ticket description that perhaps that's implicitly expected. When I build the whole documentation as a target, I don't get this problem, though I do get one warning:

WARNING: search index couldn't be loaded, but not all documents will be built: the index will be incomplete.

comment:130 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

Yes, the warnings are somewhat expected. Those are like what happens when you run LaTeX on a file for the first time: all of the unknown reference warnings which get resolved the second time through. I think typically people will do the following:

  • either build Sage from scratch or download a binary. In the first case, sage --docbuild all html will get run and so the intersphinx warnings have been turned off explicitly in this case. I also get the one about "search index couldn't be loaded...". I don't know the cause of that; Florent might be able to help.
  • then modify parts of the Sage library and do sage --docbuild reference html or sage --docbuild reference/combinat html or .... At this point, the various parts of the reference manual have been built along with their intersphinx inventories, so there shouldn't be any intersphinx warnings.

That is, I hope that most users/developers won't see all of these warnings. I've updated the ticket description so it mentions the warnings. (We could turn off all of the warnings all of the time, but I don't think that's a good idea.)

comment:131 follow-up: Changed 6 years ago by jdemeyer

I consider it a requirement that there are no visible warnings/errors when building the documentation from scratch. Otherwise, it becomes difficult to differentiate warnings caused by this ticket from true warnings.

comment:132 Changed 6 years ago by jdemeyer

Does this patch enable links like :func:`plot()` from other manuals (e.g. the developer manual) to the reference manual?

comment:133 in reply to: ↑ 131 ; follow-up: Changed 6 years ago by kcrisman

I consider it a requirement that there are no visible warnings/errors when building the documentation from scratch. Otherwise, it becomes difficult to differentiate warnings caused by this ticket from true warnings.

John, is this even possible under this setup? It would really be a shame to hold this up but Jeroen makes a good point as well.

comment:134 in reply to: ↑ 133 ; follow-up: Changed 6 years ago by jhpalmieri

Replying to jdemeyer:

Does this patch enable links like :func:`plot()` from other manuals (e.g. the developer manual) to the reference manual?

I think so, but it ought to be tested. You might need to specify the cross-reference more explicitly, the way you might if you want to reference the Python docs, for instance.

Replying to kcrisman:

I consider it a requirement that there are no visible warnings/errors when building the documentation from scratch. Otherwise, it becomes difficult to differentiate warnings caused by this ticket from true warnings.

John, is this even possible under this setup? It would really be a shame to hold this up but Jeroen makes a good point as well.

I thought that Florent had ideas about how to get rid of the one remaining warning. (As I said before, the intersphinx warnings are turned off on the first pass through the reference manual when you do sage --docbuild all html, and I think this is appropriate.)

I'll try to look into both of these. Anyone else is welcome, also. Florent, do you have any time these days?

comment:135 Changed 6 years ago by dimpase

please rebase for 5.6.beta3:

$sage-5.6.beta3/devel/sage$ ../../sage -hg qpushapplying trac_6495-all-in-one.patch
patching file doc/en/reference/combinat/index.rst
Hunk #1 FAILED at 3
1 out of 3 hunks FAILED -- saving rejects to file doc/en/reference/combinat/index.rst.rej
patch failed, unable to continue (try -v)
patch failed, rejects left in working dir
errors during apply, please fix and refresh trac_6495-all-in-one.patch

comment:136 in reply to: ↑ 134 Changed 6 years ago by hivert

Replying to jhpalmieri:

I thought that Florent had ideas about how to get rid of the one remaining warning. (As I said before, the intersphinx warnings are turned off on the first pass through the reference manual when you do sage --docbuild all html, and I think this is appropriate.)

I'll try to look into both of these. Anyone else is welcome, also. Florent, do you have any time these days?

I'm deeply sorry for letting time pass and not finishing this one... I'll be in Sage-Days in Edimbourg in two weeks so I hopefully will finish this one.

Florent

comment:137 Changed 6 years ago by Snark

I did the following:

  • Apply the patch against 5.5 - there was fuzz
  • Run sage -b - ok
  • Run sage -docbuild all html - ok
  • Run sage -docbuild all pdf - error at the ru/tutorial stage, because I don't have cyrillic encoding definitions available for babel

Does that help?

comment:138 Changed 6 years ago by jhpalmieri

Snark: is that specific to this ticket, or does sage --docbuild ru/tutorial pdf fail before applying these patches?

comment:139 Changed 6 years ago by jhpalmieri

Rebased for 5.6.beta3.

comment:140 Changed 6 years ago by Snark

I installed the needed cyrillic support and it went through without problem.

comment:141 follow-up: Changed 6 years ago by jhpalmieri

Another approach to parallel building (not that we want to throw away all of this work): a proposed patch to Sphinx. I don't know if using this proposal would affect Sphinx's memory usage, though, which is another issue that is helped by breaking up the reference manual.

comment:142 in reply to: ↑ 141 ; follow-up: Changed 6 years ago by jdemeyer

Replying to jhpalmieri:

Another approach to parallel building (not that we want to throw away all of this work): a proposed patch to Sphinx.

It only parallelizes the "writing output" phase, not the "reading" phase, so it cannot be that useful.

I don't know if using this proposal would affect Sphinx's memory usage, though

Most likely not.

comment:143 Changed 6 years ago by jdemeyer

Just for fun, I packaged it: http://boxen.math.washington.edu/home/jdemeyer/spkg/sphinx-parallel.spkg and made it support the Sage standard MAKE="-j20" mechanism.

comment:144 in reply to: ↑ 142 Changed 6 years ago by hivert

Replying to jdemeyer:

It only parallelizes the "writing output" phase, not the "reading" phase, so it cannot be that useful.

This is more or less what I did when experimenting on #6255. At that time, since I was building the whole documentation it increased the memory usage. By the way, we probably should close #6255 at some point as a duplicate of this one.

Florent

comment:145 Changed 6 years ago by jdemeyer

With the parallel Sphinx package I get lots of errors, some might be due to the "upgrade" to the devleopment version of Sphinx 1.2, but some also to the parallel code.

comment:146 follow-up: Changed 6 years ago by jhpalmieri

I think our Sphinx package needs some work. In particular, the file SAGE_ROOT/devel/sage/common/sage-autodoc.py should be part of the Sphinx package, built by patching Sphinx's autodoc.py. This would make it easier to incorporate modifications to autodoc.py. I don't know if this has to do with the problems with using Sphinx 1.2, but it might.

It's probably also not a good idea to use Sphinx's parallel building at the same time as ours, or else we'll be using more threads than we intended: maybe building 8 pieces of documentation at the same time, and then writing each of those using 8 processes. That sounds like a bad idea to me.

Having said all of that, do the errors you get suggest problems with our parallel code?

comment:147 in reply to: ↑ 146 Changed 6 years ago by jdemeyer

Replying to jhpalmieri:

Having said all of that, do the errors you get suggest problems with our parallel code?

I didn't use any code from this ticket, I only used the patch you linked to for parallel Sphinx writing.

Changed 6 years ago by jhpalmieri

apply third

comment:148 Changed 6 years ago by jhpalmieri

Rebased to 5.6.rc0 (among other things, dealing with the addition of doc/en/reference/sat.rst).

comment:149 follow-up: Changed 6 years ago by hivert

This is an answer to Mike Hansen:

He asked if the page url are kept or not. The answer is that they moved: For example:

doc/output/html/en/reference/sage/symbolic/expression.html

is now

doc/output/html/en/reference/calculus/sage/symbolic/expression.html

So the location is not kept.

Florent

comment:150 in reply to: ↑ 149 ; follow-up: Changed 6 years ago by kcrisman

Replying to hivert:

This is an answer to Mike Hansen:

He asked if the page url are kept or not. The answer is that they moved:

Hmm, I was dimly aware of this but didn't think it through. That will break a loooot of links (e.g., on ask.sagemath.org). Is there any way to auto-generate forwarding or 'mirrors' from the old pages?

comment:151 Changed 6 years ago by hivert

  • Description modified (diff)

comment:152 in reply to: ↑ 150 Changed 6 years ago by dimpase

Replying to kcrisman:

Replying to hivert:

This is an answer to Mike Hansen:

He asked if the page url are kept or not. The answer is that they moved:

Hmm, I was dimly aware of this but didn't think it through. That will break a loooot of links (e.g., on ask.sagemath.org). Is there any way to auto-generate forwarding or 'mirrors' from the old pages?

there are several options:

  1. use .htaccess thing to fix this on any particular website;

  1. write a script to look through all href targets in each file with changed location, and create for it a file with forwards;
  1. maybe sphinx can help in this business, I don't know.

In any event we do not want to keep the old links around forever, I think, so there should be some kind of deprecation being turned on.

comment:153 Changed 6 years ago by hivert

He asked if the page url are kept or not. The answer is that they moved:

Hmm, I was dimly aware of this but didn't think it through. That will break a loooot of links (e.g., on ask.sagemath.org). Is there any way to auto-generate forwarding or 'mirrors' from the old pages?

there are several options:

  1. use .htaccess thing to fix this on any particular website;

  1. write a script to look through all href targets in each file with changed location, and create for it a file with forwards;
  1. maybe sphinx can help in this business, I don't know.

I don't thinks it does. On the contrary, it makes it a nightmare (at least to me). Sphinx made the assumption that creating a new document needs creating a new directory (storing html, markup, indexes...). Since we splitting the reference manual in different documents we had to move files around.

Mike Hansen was considering implementing something which is close to option 2, because it it seems that option 1 is not easily doable (whereas I'm starting to now more than a little about Sphinx, I shamefully admitting that I don't know how to write/configure a website).

Florent

comment:154 Changed 6 years ago by vbraun

We should just have versioned documentation on sagemath.org, just like Singular:

The "latest" manual would then never be stable; independent of this ticket in particular there is always the danger of a module being renamed or moved around.

Having said that, Apache mod_rewrite could be used to dull some of the pain and automatically guess the new location.

comment:155 Changed 6 years ago by hivert

  • Cc mhansen added

comment:156 Changed 6 years ago by mhansen

Replying to vbraun:

Having said that, Apache mod_rewrite could be used to dull some of the pain and automatically guess the new location.

Can you really use mod_rewrite to do this? You have to turn a request like reference/sage/symbolic/expression.html to something like reference/calculus/sage/symbolic/expression.html . So, you'd have to walk to filesystem in order to find out the analog of "calculus".

comment:157 follow-up: Changed 6 years ago by vbraun

Yes and no... its not beautiful but you can just add a rule for each sage/ subdirectory that does the equivalent of

sed s-sage/symbolic-calculus/sage/symbolic-

Changed 6 years ago by mhansen

comment:158 in reply to: ↑ 157 ; follow-up: Changed 6 years ago by mhansen

Replying to vbraun:

Yes and no... its not beautiful but you can just add a rule for each sage/ subdirectory that does the equivalent of

sed s-sage/symbolic-calculus/sage/symbolic-

I don't think that you can really do this since it isn't guaranteed that all of the files that are in say sage/misc/ will all go to the same document.

I wrote a patch which adds small HTML files to do the redirect. I've looked through Florent's code as well, and things seem fine to me -- trac_6495-all-in-one.patch and trac-6495_silence_warning-fh.patch .

If someone reviews trac_6495-redirect_html.patch , we can mark this as positive_review.

comment:159 Changed 6 years ago by mhansen

  • Description modified (diff)

comment:160 in reply to: ↑ 158 Changed 6 years ago by kcrisman

I wrote a patch which adds small HTML files to do the redirect. I've looked through Florent's code as well, and things seem fine to me -- trac_6495-all-in-one.patch and trac-6495_silence_warning-fh.patch .

If someone reviews trac_6495-redirect_html.patch , we can mark this as positive_review.

Thank you so much for adding this, Mike - I hope to try it out tonight and see if it works fine, but I doubt I'll be competent to give positive review.

Here is a question about all the patches. There are a lot of functions (esp. underscore ones) in doc/... that have no doctests. Problem? (This includes Mike's new function, but is not limited to it.) Hope this isn't evil to ask.

comment:161 Changed 6 years ago by jhpalmieri

I have yet to test trac_6495-redirect_html.patch, but the docstring for html ends rather abruptly.

comment:162 Changed 6 years ago by jhpalmieri

If I run sage --docbuild all html, at the end of the second pass for the reference manual, I see

*******************SKIPPING Load indexer call*******************
WARNING: search index couldn't be loaded, but not all documents will be built: the index will be incomplete.
Build finished.  The built documents can be found in /scratch/palmieri/6495/sage-5.7.beta0/devel/sage/doc/output/html/en/reference

So the warning isn't gone.

comment:163 Changed 6 years ago by jhpalmieri

Addendum: if I delete documentation output and run sage --docbuild reference html twice, I don't see the warning message. So perhaps something can be tweaked to make it go away on the second pass when running sage --docbuild all html.

comment:164 Changed 6 years ago by jhpalmieri

Rebased to 5.7.beta0.

comment:165 Changed 6 years ago by jhpalmieri

trac_6495-redirect_html.patch doesn't quite work, because os.path.split(path) always returns a list of length 2. With this change, it works for me:

  • doc/common/builder.py

    diff --git a/doc/common/builder.py b/doc/common/builder.py
    a b class WebsiteBuilder(DocBuilder): 
    391391                    redirect_filename = os.path.join(reference_dir, shorter_path, filename)
    392392
    393393                    # the number of levels up we need to use in the relative url
    394                     levels_up = len(os.path.split(shorter_path))
     394                    levels_up = len(shorter_path.split(os.sep))
    395395
    396396                    # the relative url that we will redirect to
    397397                    redirect_url = "/".join(['..']*levels_up + [document_name, shorter_path, filename])

Fix that, and fix the docstring for the html method, and I think this part is good.

The warning is still an issue, and I don't know why it still shows up during the second pass for the reference manual when doing sage --docbuild all html but not when running sage --docbuild reference html twice. Florent, any ideas? Does anyone else see this?

kcrisman, I don't know about doctests for all of these methods.

comment:166 Changed 6 years ago by hivert

Strange, It's working for me. Can you post the log of the docbuild which shows the warning, please

Florent

Changed 6 years ago by hivert

comment:167 Changed 6 years ago by hivert

Sorry, I ended up uploading the wrong version of my patch. I uploaded a new version.

Florent

comment:168 Changed 6 years ago by hivert

Hi there

I'm at the point where everything seems to work for me. I'd like to test this automatically it I can't see how. So provided someone testify that the new version of trac-6495_silence_warning-fh.patch works for him, I'm ready to put a positive review here.

Cheers,

Florent

comment:169 follow-up: Changed 6 years ago by jdemeyer

  • Reviewers changed from Volker Braun to Volker Braun, Florent Hivert
  • Status changed from needs_review to positive_review

comment:170 follow-up: Changed 6 years ago by jdemeyer

  • Dependencies changed from #13143 to #13143, #12719

This conflicts with #12719 and should be rebased.

comment:171 in reply to: ↑ 169 Changed 6 years ago by leif

Replying to jdemeyer:

Positive review without the HTML redirection patch? (Cf. John's comments above.)

Changed 6 years ago by hivert

comment:172 Changed 6 years ago by hivert

  • Description modified (diff)

comment:173 Changed 6 years ago by hivert

  • Description modified (diff)

comment:174 Changed 6 years ago by hivert

When I Said "I'm ready to put a positive review" that was including John's modification. I uploaded a new version of patch with it. Jeroen, do we need to go in a re-review process (except of rebasing) ? Or should I leave a positive review ?

Florent

comment:175 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

Well, the docstrings are still a bit of a mess. Here's a patch; maybe the last one?

Changed 6 years ago by jhpalmieri

comment:176 Changed 6 years ago by hivert

Replying to jhpalmieri:

Well, the docstrings are still a bit of a mess. Here's a patch; maybe the last one?

Thanks for this cleanup. I'm positive reviewing these new changes.

Florent

comment:177 in reply to: ↑ 170 Changed 6 years ago by jhpalmieri

Replying to jdemeyer:

This conflicts with #12719 and should be rebased.

I don't see any conflicts: starting with 5.7.beta0, I applied the patches from #12719 and then the patches here with no problem. Can you clarify?

comment:178 Changed 6 years ago by jdemeyer

  • Status changed from positive_review to needs_work

This is totally a pain w.r.t. rebasing. For example, there are again conflicts with #11641 and #13077. If this is mostly the automatic scripted part which needs to be rebased, could you please split off the scripted part again such that I could simply run the script instead of applying the patch?

comment:179 Changed 6 years ago by jhpalmieri

  • Description modified (diff)
  • Status changed from needs_work to positive_review

Changed 6 years ago by jhpalmieri

everything except "part 1"

comment:180 Changed 6 years ago by hivert

This is definitely the most painful patch I've ever put into Sage. It would be a huge relief to have it integrated into sage. So I hope nothing more is blocking it. Is the rebase done with your script ?

Florent

comment:181 follow-up: Changed 6 years ago by jhpalmieri

Yes, the script does the main work of moving all of the MODULE.rst files around. That is the part that change the most (as people add files to the reference manual), so that's where the rebasing happens.

Florent, thank you for all of your help with this; your contributions have made this much better. And much of the thanks goes to Mitesh Patel, wherever he is, who put in most of the original work on the patch.

comment:182 in reply to: ↑ 181 Changed 6 years ago by hivert

Replying to jhpalmieri:

Florent, thank you for all of your help with this; your contributions have made this much better. And much of the thanks goes to Mitesh Patel, wherever he is, who put in most of the original work on the patch.

And thanks a lot for your patience, awaiting for me, not giving up, keeping trying to have this patch moving forward and constantly rebasing it.

comment:183 Changed 6 years ago by jdemeyer

  • Milestone changed from sage-pending to sage-5.7

comment:184 Changed 6 years ago by jdemeyer

  • Description modified (diff)

Updated script.

comment:185 follow-up: Changed 6 years ago by jdemeyer

  • Status changed from positive_review to needs_work
WARNING: intersphinx inventory '/release/merger/sage-5.7.beta2/devel/sage/doc/output/html/en/reference/combinat/objects.inv' not readable due to AssertionError:

and

/release/merger/sage-5.7.beta2/devel/sage/doc/en/reference/sat/index.rst:77: WARNING: toctree contains reference to nonexisting document 'sat/sage/sat/solvers/dimacs'
/release/merger/sage-5.7.beta2/devel/sage/doc/en/reference/sat/index.rst:104: WARNING: toctree contains reference to nonexisting document 'sat/sage/sat/converters/polybori'
/release/merger/sage-5.7.beta2/devel/sage/doc/en/reference/sat/index.rst:124: WARNING: toctree contains reference to nonexisting document 'sat/sage/sat/boolean_polynomials'

comment:186 in reply to: ↑ 185 Changed 6 years ago by hivert

First of all, let me express my frustration: #%)&^@$(&%#^#%

/release/merger/sage-5.7.beta2/devel/sage/doc/en/reference/sat/index.rst:77: WARNING: toctree contains reference to nonexisting document 'sat/sage/sat/solvers/dimacs'
/release/merger/sage-5.7.beta2/devel/sage/doc/en/reference/sat/index.rst:104: WARNING: toctree contains reference to nonexisting document 'sat/sage/sat/converters/polybori'
/release/merger/sage-5.7.beta2/devel/sage/doc/en/reference/sat/index.rst:124: WARNING: toctree contains reference to nonexisting document 'sat/sage/sat/boolean_polynomials'

Though I don't yet fully understand why, looking at the other doc suggest that replacing the three :maxdepth: 1 by :maxdepth: 2 should solve this particular problem. I don't have time to propose a patch now.

Replying to jdemeyer:

WARNING: intersphinx inventory '/release/merger/sage-5.7.beta2/devel/sage/doc/output/html/en/reference/combinat/objects.inv' not readable due to AssertionError:

To investigate this one I need to install sage-5.7.beta2 which takes time. Jeroen, could you give a some context for this second error. I've never seen it but I only used sage-5.6.rc1.

Cheers,

Florent

comment:187 Changed 6 years ago by jhpalmieri

I don't understand these problems, either. I've never seen the one about the intersphinx inventory. For the other one, aside from maxdepth: 1, the other difference is that sage.sat is not imported anywhere:

sage: sage.sat
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/Users/palmieri/Desktop/Sage_stuff/sage_builds/6495/sage-5.7.beta0/<ipython console> in <module>()

AttributeError: 'module' object has no attribute 'sat'

Could that be related? Should that be fixed in any case?

comment:188 follow-up: Changed 6 years ago by jdemeyer

  • Owner changed from tba to jdemeyer

See the logfile dochtml.log (this is from a second build, note the error message is slightly different).

comment:189 in reply to: ↑ 188 Changed 6 years ago by hivert

Replying to jdemeyer:

See the logfile dochtml.log (this is from a second build, note the error message is slightly different).

I'm seriously scared that it could come from a race condition, an nightmare to debug. Is it deterministic ?

comment:190 follow-up: Changed 6 years ago by jhpalmieri

On what platforms, and how reliably, do you see the WARNING: intersphinx inventory ...?

For the other problem, this patch fixes it for me:

  • doc/common/builder.py

    diff --git a/doc/common/builder.py b/doc/common/builder.py
    a b class AllBuilder(object): 
    274274        global ALLSPHINXOPTS
    275275        ALLSPHINXOPTS += ' -Q -D multidoc_first_pass=1'
    276276        for document in refs:
    277             getattr(get_builder(document), 'inventory')(*args, **kwds)
     277            getattr(get_builder(document), name)(*args, **kwds)
    278278        logger.warning("Building reference manual, second pass.\n")
    279279        ALLSPHINXOPTS = ALLSPHINXOPTS.replace(
    280280            'multidoc_first_pass=1', 'multidoc_first_pass=0')

Or perhaps we should use this one:

  • doc/common/builder.py

    diff --git a/doc/common/builder.py b/doc/common/builder.py
    a b class AllBuilder(object): 
    274274        global ALLSPHINXOPTS
    275275        ALLSPHINXOPTS += ' -Q -D multidoc_first_pass=1'
    276276        for document in refs:
    277             getattr(get_builder(document), 'inventory')(*args, **kwds)
     277            if name == 'pdf':
     278                getattr(get_builder(document), 'inventory')(*args, **kwds)
     279            else:
     280                getattr(get_builder(document), name)(*args, **kwds)
    278281        logger.warning("Building reference manual, second pass.\n")
    279282        ALLSPHINXOPTS = ALLSPHINXOPTS.replace(
    280283            'multidoc_first_pass=1', 'multidoc_first_pass=0')

With an html build, building with this patch does not take any more time. Opinions?

comment:191 Changed 6 years ago by jhpalmieri

By the way, the new version of the script doesn't work on OS X, because OS X uses a BSD version of sed which is not completely compatible with the linux version. To get it to work, you have to make these changes:

  • trac_6495-script.sh

    a b  
    1616do
    1717    hg rename $f.rst $f/index.rst
    1818    # delete lines of the form ".. _ch:blah"
    19     sed -e 's|^\.\. _ch:.*$||' -i $f/index.rst
     19    sed -e 's|^\.\. _ch:.*$||' -i '' $f/index.rst
    2020    # remove resulting blank lines from top of file
    21     sed -e '/./,$!d' -i $f/index.rst
     21    sed -e '/./,$!d' -i '' $f/index.rst
    2222    cat >$f/conf.py <<EOF
    2323# -*- coding: utf-8 -*-
    2424# This file is execfile()d with the current directory set to its
     
    4747cp cmd/conf.py combinat/conf.py
    4848hg add combinat/conf.py
    4949# in combinat/index.rst: change "../sage/combinat/blah" to "sage/combinat/blah"
    50 sed -e "s|\.\./||" -i combinat/index.rst
     50sed -e "s|\.\./||" -i '' combinat/index.rst
    5151
    5252cat >> combinat/index.rst <<EOF
    5353

comment:192 in reply to: ↑ 190 Changed 6 years ago by jdemeyer

Replying to jhpalmieri:

On what platforms

Only tried sage.math so far.

and how reliably, do you see the WARNING: intersphinx inventory ...?

Two out of two builds so far.

Changed 6 years ago by jdemeyer

script used to generate "part 1" patch

comment:193 follow-up: Changed 6 years ago by jdemeyer

Third attempt, now it's the notebook which gives problems:

WARNING: intersphinx inventory '/release/merger/sage-5.7.beta3/devel/sage/doc/output/html/en/reference/notebook/objects.inv' not readable due to ValueError: unknown or unsupported inventory version

So it's certainly not deterministic, but quite likely that something goes wrong.

comment:194 in reply to: ↑ 193 Changed 6 years ago by hivert

Hi there,

Replying to jdemeyer:

Third attempt, now it's the notebook which gives problems:

WARNING: intersphinx inventory '/release/merger/sage-5.7.beta3/devel/sage/doc/output/html/en/reference/notebook/objects.inv' not readable due to ValueError: unknown or unsupported inventory version

So it's certainly not deterministic, but quite likely that something goes wrong.

Unfortunately the one week window for sage days I had is over. I didn't had time to make any experiment, and I don't expect to find much time to work on this in the forthcoming days (the new semester is starting and I'm moving from one house to another in two weeks).

Anyway, I have a guess one what could be happening. The first pass of compilation is designed to build the intersphinx inventory. However, they are rewritten during the second phase. Due to parallelism, it is fairly possible that one process is trying to read the inventory just at the time another one is writing it. The more process you have, the larger the probability of this happening. This explain why we don't see this on small laptop. I'm not sure how to test that this is precisely what's happening. But if it's the case, the solution should be easy: similarly to what I did recently for indexes, we should deactivate the output of the inventory for a second pass compilation of a sub-document.

Does anyone have time to experiment more ?

comment:195 follow-up: Changed 6 years ago by jhpalmieri

I have not been able to reproduce this on sage.math. I've tried building in /scratch and in /home. Could there be something about /release that's contributing to this? Jeroen, what do you have MAKE set to?

comment:196 in reply to: ↑ 195 Changed 6 years ago by jdemeyer

Replying to jhpalmieri:

Could there be something about /release that's contributing to this?

It's quite a fast disk, could that play a role?

Jeroen, what do you have MAKE set to?

MAKE=make -j6

comment:197 follow-up: Changed 6 years ago by vbraun

You just have to strace -o logfile -ff the build process, then you'll see who is writing to the offending file. Also, can we have a beta with this ticket? Too many patches ;-)

comment:198 in reply to: ↑ 197 Changed 6 years ago by kcrisman

You just have to strace -o logfile -ff the build process, then you'll see who is writing to the offending file. Also, can we have a beta with this ticket? Too many patches ;-)

+1

comment:199 Changed 6 years ago by jhpalmieri

Here's a tar file, based on 5.7.beta1.

comment:200 Changed 6 years ago by kcrisman

Wow, going fast already.

Elapsed time: 284.1 seconds.

Just a slight improvement.

I couldn't find (i.e., browser says it's not there)

file:///Users/.../sage-5.7.beta1_6495/devel/sage-main/doc/output/html/en/reference/functions.html

and the like, but most redirection of actual pages of content seem to be working fine - it's the old ones corresponding to

file:///Users/.../sage-5.7.beta1_6495/devel/sage-main/doc/output/html/en/reference/functions/index.html

that seem to have not been "translated" properly.

Changed 6 years ago by vbraun

Initial patch

comment:201 Changed 6 years ago by vbraun

I can totally reproduce the issue, works every time.

I've started by adding a framework to suppress unwanted messages and print the ones that we do intact (that is, line buffered). Now I can at least start to see what is going on...

comment:202 Changed 6 years ago by vbraun

The issue was indeed that the object inventory was written to and read from parallel processes. Sphinx makes no attempt to update the object.inv atomically.

I've changed things such that

  • the inventory build process outputs to output/inventory and does not read inventory
  • the second pass then reads the object inventory from output/inventory and writes to output/html

Now I don't see any races any more. The first stage still warns erroneously about a few missing citations, but thats not a big deal.

Also, the whole thing runs just shy of 200 seconds on my desktop (i7-3770K)

sage -docbuild all html
...
Elapsed time: 196.5 seconds.
Done building the documentation!

Changed 6 years ago by vbraun

Initial patch

comment:203 Changed 6 years ago by vbraun

  • Description modified (diff)
  • Status changed from needs_work to needs_review

comment:204 Changed 6 years ago by jdemeyer

Not sure why you removed the script, because the patches still fail to apply:

patching file doc/en/reference/combinat/index.rst
Hunk #1 FAILED at 3
Hunk #3 FAILED at 66
2 out of 3 hunks FAILED -- saving rejects to file doc/en/reference/combinat/index.rst.rej
patching file doc/en/reference/groups/index.rst
Hunk #2 succeeded at 39 with fuzz 1 (offset 9 lines).
abort: patch failed to apply

comment:205 Changed 6 years ago by vbraun

I removed the "apply" script since I based my patch on top of John's source dist tar file at comment:199.

comment:206 Changed 6 years ago by jdemeyer

But in the end the patch will need to be rebased to the latest development version. Do you want to wait with that until after positive_review?

comment:207 Changed 6 years ago by vbraun

  • Description modified (diff)

Ok I've rebased the first patch on top of sage-5.7.beta2. All apply cleanly now.

comment:208 Changed 6 years ago by vbraun

Ok some more fixes needed as more documentation was changed

Changed 6 years ago by vbraun

Updated patch

comment:209 Changed 6 years ago by vbraun

Ok I've now correctly resolved the merge conflict ;-) Just a minor change in the combinat docs, its all fine now.

The only thing left to review would be my final patch. I made all changes that I wanted, so I'm fine with anything else thats in this ticket.

comment:210 Changed 6 years ago by jhpalmieri

I haven't verified that the intersphinx warning is gone, but I see two other possible problems: I get a warning

[reference] .../sage-5.7.beta2/devel/sage/doc/en/reference/sat/index.rst:: WARNING: document isn't included in any toctree

along with some citations not being found. Also with trac_6495_separate_inventory.patch, the build is a bit slower than without: on my OS X box (with only two threads), the fastest time with the patch was 858 seconds, and more typical (5 out of 6 runs) was 885 seconds or more. Without the patch, the slowest time was 813 seconds. On sage.math, with MAKE="make -j12": with the patch, 450 seconds, without the patch, 390 seconds.

comment:211 Changed 6 years ago by vbraun

Are you always nuking the output directory for timings? Also, I'm always adding all inventory files to the intersphinx-mapping whereas before Sphinx would only add them as needed. But there Sphinx assumes that the inventory is in the html directory, so its not good if you want to avoid races.

As I said already, the first stage still warns erroneously about a few missing cross-document citations. We could hide them, but I don't think its a big deal.

The sat/index.rst isn't included warning is correct. The sat subdoc was not listed in multidocs_subdoc_list (en/reference/conf.py).

comment:212 Changed 6 years ago by vbraun

  • Description modified (diff)

The last patch fixes the unlisted sat subdoc and moves the citations pickle to the inventory dir. Also, write the citation pickle atomically to avoid another potential race. Now everything builds without any warnings.

comment:213 Changed 6 years ago by jhpalmieri

Are you always nuking the output directory for timings?

Yes. Good catch on finding sat not being listed in multidocs_subdoc_list, by the way.

comment:214 Changed 6 years ago by jhpalmieri

I'm pretty happy with the latest patches, but I'm not quite ready to give a positive review. In my testing, I'm not seeing the intersphinx warning any more, but I was only sporadically able to reproduce it in the first place.

With the current useless_chatter settings, on the first pass through the reference manual, I see two summaries

[polynomia] build succeeded, 1 warning.
[geometry ] build succeeded, 3 warnings.

The actual warnings are suppressed, though. Should these message be suppressed (or modified), also? Otherwise, someone might wonder what the warnings actually were.

comment:215 Changed 6 years ago by jhpalmieri

Another thing: if I have built the documentation already and then run ./sage --docbuild reference html, then all of the output from building the individual parts of the reference manual is suppressed, so there is a long pause (several minutes, enough to wonder whether it's hung), and then finally

[reference] Compiling the master document
[reference] updating environment: 0 added, 0 changed, 1098 removed
[reference] Merging environment/index files...

comment:216 Changed 6 years ago by jhpalmieri

Maybe just removing one line from useless_chatter would address my last point:

  • doc/common/custom-sphinx-build.py

    diff --git a/doc/common/custom-sphinx-build.py b/doc/common/custom-sphinx-build.py
    a b  
    3131    re.compile('^Compiling a sub-document'),
    3232    re.compile('^updating environment: 0 added, 0 changed, 0 removed'),
    3333    re.compile('^looking for now-outdated files... none found'),
    34     re.compile('^no targets are out of date.'),
    3534    re.compile('^building \[.*\]: targets for 0 source files that are out of date'),
    3635    re.compile('^loading pickled environment... done'),
    3736    re.compile('^loading cross citations... done \([0-9]* citations\).')

doesn't look too bad: if you change one file in homology then rebuild the docs, then you get

[polynomia] no targets are out of date.
[combinat ] no targets are out of date.
[cmd      ] no targets are out of date.
[arithgrou] no targets are out of date.
[graphs   ] no targets are out of date.
[misc     ] no targets are out of date.
...

until it finally gets to something which has changed.

Changed 6 years ago by jhpalmieri

combined patch

Changed 6 years ago by jhpalmieri

Changed 6 years ago by jhpalmieri

comment:217 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

I rebased the patches to 5.7.beta3. The only change of substance: in the "part2" patch:

  • sage/graphs/graph_plot.py

    diff --git a/sage/graphs/graph_plot.py b/sage/graphs/graph_plot.py
    a b  
    106106      settings from ``DEFAULT_SHOW_OPTIONS`` only affects ``G.show()``.
    107107
    108108    * In order to define a default value permanently, you can add a couple of
    109       lines to :doc:`Sage's startup scripts <../../startup>`. Example ::
     109      lines to `Sage's startup scripts <../../../cmd/startup.html>`_. Example ::
    110110
    111111       sage: import sage.graphs.graph_plot
    112112       sage: sage.graphs.graph_plot.DEFAULT_SHOW_OPTIONS['figsize'] = [4,4]

(The only change to the "part3" patch was to change the commit message.) With the newest patch (trac_6495-filtering.patch), all superfluous warnings are suppressed. I'm happy with this now.

I think it might be best to include every single patch, or else credit will not get assigned appropriately; for example, the old "all in one" patch combined my work (which is really based on mpatel's, but I don't know how to get his name back in here...) with Florent's.

Changed 6 years ago by jhpalmieri

apply first

Changed 6 years ago by jhpalmieri

comment:218 Changed 6 years ago by SimonKing

Are you sure that the first patch applies? At least with sage-5.7.beta2, I get a mismatch in doc/en /reference/rings_standard/index.rst, which is not surprising as this file does not seem to exist.

But I suppose it is better anyway to run the sript?

comment:219 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

Rebased to Sage 5.7.beta4 (because of the recently added file doc/en/reference/finite_rings.rst).

Changed 6 years ago by jhpalmieri

comment:220 Changed 6 years ago by SimonKing

Aha, now I understand! It starts with doc/en/reference/rings_standard.rst, adds one line and moves the result to doc/en/reference/rings_standard/index.rst.

Problem: The line

sage/rings/universal_cyclotomic_field/universal_cyclotomic_field

does not exist in sage-5.7.beta2.

In what ticket has this line been introduced? That would be a new dependency.

comment:221 follow-up: Changed 6 years ago by jhpalmieri

Simon: the patches should apply to 5.7.beta4, and probably only to this version. The script also may only work on this version (or any later version, I hope). This patch is very sensitive to changes, so it needs to be rebased frequently. I'm sorry I haven't kept track of the dependencies -- I just keep rebasing to the latest beta.

Here's a tar file for 5.7.beta4 source with these patches applied.

comment:222 in reply to: ↑ 221 Changed 6 years ago by SimonKing

Bad. It seems that I managed to destroy my sage-5.7.beta2 by this patch. No idea how that happened. Could it be that popping the patch does not revert all changes?

Replying to jhpalmieri:

Here's a tar file for 5.7.beta4 source with these patches applied.

I currently don't have the bandwith to download a Sage tarball.

comment:223 follow-up: Changed 6 years ago by jhpalmieri

How about downloading just the sage library spkg (which is 57M)?

Again, I apologize for not keeping track of the dependencies. My general reaction when a new beta comes out is to try to apply the patches, find that they don't apply, swear a bit, and then rebase them. If someone does something minor (say, modify doc/en/reference/algebras.rst), then running the script instead of applying the "part1" patch should take care of things. But if someone adds a new file to doc/en/reference/, then several of the patch files will need to be rebased. This happened between 5.7.beta3 and 5.7.beta4.

Is there a good way with mercurial to find out all of the recent changes to files in a certain directory? Then I could identify the dependencies easily.

comment:224 in reply to: ↑ 223 Changed 6 years ago by SimonKing

Replying to jhpalmieri:

How about downloading just the sage library spkg (which is 57M)?

That could be a good idea.

comment:225 Changed 6 years ago by jhpalmieri

  • Dependencies changed from #13143, #12719 to 5.7.beta2 + #13064, #8327, #13891

comment:226 Changed 6 years ago by SimonKing

Hooray, the patches apply cleanly! Thank you for naming the additional dependencies!

By the way, I still don't understand why seemingly my hg repository became dysfunctional, but now it seems to be fine again (which I don't understand either...).

comment:227 Changed 6 years ago by jhpalmieri

I don't understand it either. I occasionally have seen this, too, but not at all reproducibly, and not recently. Maybe mercurial is just more likely get confused if it moves lot of files around and creates a lot of directories, and then the patch is popped? Or maybe it also requires the patch not to apply cleanly first?

comment:228 Changed 6 years ago by SimonKing

In the ticket description, it is said: "Also create a file algebras/conf.py for the build configuration. All of these new conf.py files are identical."

If they are all identical, why is there not just a single conf.py, to which all other locations refer by a soft link? In that way, it would be easier to maintain changes.

comment:229 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

Good question. The files conf.py are pretty minimal, and most of the content is in en/reference/conf_sub.py, which is imported by each conf.py file. So the idea is that to maintain it, you would just need to modify conf_sub.py. But here's a new version of the part 1 patch and the script which creates links directly from en/reference/MODULE/conf.py pointing to en/reference/conf_sub.py. This seems to work. I'll check on OpenSolaris to make sure there's nothing strange going on there.

Changed 6 years ago by jhpalmieri

apply first

comment:230 follow-up: Changed 6 years ago by jhpalmieri

trac_6495-script-jhp.2.sh is identical to the old script; it can be deleted. (Why can't I delete my own attachments?)

Changed 6 years ago by jhpalmieri

script used to generate "part 1" patch

comment:231 in reply to: ↑ 230 Changed 6 years ago by kcrisman

trac_6495-script-jhp.2.sh is identical to the old script; it can be deleted. (Why can't I delete my own attachments?)

I suppose so that the history is preserved. That said, it would be helpful to have that ability for at least some users.

Given your post at this sage-support thread, now it's really exciting to think about this getting in.

comment:232 Changed 6 years ago by SimonKing

For the record: Documentation builds for me, at least with the old patches. And now I am really curious what will happen if I add a thematic tutorial and try to link to the reference manual, via :class:`sage.structure.parent.Parent`

comment:233 Changed 6 years ago by SimonKing

That said: I am not totally sure, but my impression is that building the documentation took longer than in the old way. Also, it surprises me that sage --docbuild all pdf takes more than three minutes after previously doing sage --docbuild all html.

Last edited 6 years ago by SimonKing (previous) (diff)

comment:234 Changed 6 years ago by SimonKing

OK, processing the LaTeX files seems less trivial than I thought, and does take time.

Currently, I am seeing a lot of unresolved references, and one fatal error:

...

! LaTeX Error: Too deeply nested.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.26942 \begin{Verbatim}[commandchars=\\\{\}]
                                             
? 
! Emergency stop.
 ...                                              
                                                  
l.26942 \begin{Verbatim}[commandchars=\\\{\}]
                                             
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on categories.log.
make: *** [categories.pdf] Fehler 1
Build finished.  The built documents can be found in /home/simon/SAGE/debug/sage-5.7.beta2/devel/sage/doc/output/pdf/en/reference/categories
[coding   ] building [latex]: all documents
[coding   ] updating environment: [config changed] 6 added, 0 changed, 0 removed
[coding   ] reading sources... [ 16%] index
...

I suppose there will automatically be a second run, which resolves the cross-references. And we will see about the fatal error.

comment:235 follow-up: Changed 6 years ago by SimonKing

OK, the links in the pdf and the mathematics in the html do not seem to work.

For example, I am looking at the documentation of sage.structure.coerce, The Coercion Model.

I see

Coercions are canonical (possibly modulo a finite number of deterministic choices) morphisms, and the set of all coercions between all parents forms a commuting diagram (modulo possibly rounding issues). [Math Processing Error] is an example of a coercion. These are invoked implicitly by the coercion model.

in the html. It is fine in the pdf.

Both in pdf and html, I read

For more information on how to specify coercions, conversions, and actions, see the documentation for Parent.

class sage.structure.coerce.CoercionModel_cache_maps

    Bases: sage.structure.element.CoercionModel

    See also sage.categories.pushout

I would expect the "see the documentation for Parent" and "See also sage.categories.pushout" come with a link, but apparently that has been forgotten (bug in the documentation).

In the html, Bases: sage.structure.element.CoercionModel is a link. In the pdf, it is not a link. I guess it should be a link in pdf, too, isn't it?

comment:236 Changed 6 years ago by SimonKing

And now the good news: When I added my (not yet completed) thematic tutorial on categories and coercion, both the mathematical type-setting and the links to the reference manual (!) work fine.

comment:237 in reply to: ↑ 235 ; follow-up: Changed 6 years ago by jhpalmieri

Replying to SimonKing:

OK, the links in the pdf and the mathematics in the html do not seem to work.

For the links in the pdf, I don't know what to do about that. Intersphinx seems to work only in html, not pdf, or at least that's what I gather from its documentation. I don't even know if it's possible to put relative links into a PDF file.

For mathematics in the html, I don't see this at all, either on OS X (with any of the browsers I've tried) or on sage.math. See the coercion model page on sage.math, for instance -- this renders fine for me with my browser.

Did you delete the directory devel/sage/doc/output before the first attempt at a parallel build? If not, maybe there were artifacts there which caused problems. Otherwise, I don't know what's causing it. What is your OS and what is your browser?

Replying to SimonKing:

And now the good news: When I added my (not yet completed) thematic tutorial on categories and coercion, both the mathematical type-setting and the links to the reference manual (!) work fine.

Great.

comment:238 in reply to: ↑ 237 Changed 6 years ago by SimonKing

Replying to jhpalmieri:

Did you delete the directory devel/sage/doc/output before the first attempt at a parallel build?

I deleted it, and I think I did not do a parallel build (or at least, I did not define MAKE to be make -j2).

If not, maybe there were artifacts there which caused problems. Otherwise, I don't know what's causing it. What is your OS and what is your browser?

openSuse 12.1 Asparagus, and Firefox 18.0

Replying to SimonKing:

And now the good news: When I added my (not yet completed) thematic tutorial on categories and coercion, both the mathematical type-setting and the links to the reference manual (!) work fine.

And that's why I wonder: The maths is fine in the tutorial, but not in the reference manual.

I just observed: When I load a page from the reference manual, there is a message on the lower left corner of my browser, Loading [MathJax]/jax/output/HTML-CSS/imageFonts.js, and a bit later there is a message "File failed to load" (but too quickly disappearing, I didn't manage to copy the message).

comment:239 follow-up: Changed 6 years ago by vbraun

To debug Firefox issues: Tools->Web Developer->Web Console.

Simon's issue sounds a lot like http://docs.mathjax.org/en/v1.1-latest/installation.html#firefox-and-local-fonts. Either use a different browser or install the stix fonts. Should be fine if served over http instead of a local dir.

comment:240 in reply to: ↑ 239 ; follow-up: Changed 6 years ago by SimonKing

Replying to vbraun:

To debug Firefox issues: Tools->Web Developer->Web Console.

Simon's issue sounds a lot like http://docs.mathjax.org/en/v1.1-latest/installation.html#firefox-and-local-fonts. Either use a different browser or install the stix fonts.

Would this explain why the maths typesetting is fine in one document and broken in another document?

comment:241 in reply to: ↑ 240 ; follow-up: Changed 6 years ago by vbraun

Replying to SimonKing:

Would this explain why the maths typesetting is fine in one document and broken in another document?

Yes. It depends on whether or not mathjax is loaded from the same directory as the document. And we don't plaster a copy of mathjax into every subdirectory.

comment:242 in reply to: ↑ 241 Changed 6 years ago by SimonKing

Replying to vbraun:

Replying to SimonKing:

Would this explain why the maths typesetting is fine in one document and broken in another document?

Yes. It depends on whether or not mathjax is loaded from the same directory as the document. And we don't plaster a copy of mathjax into every subdirectory.

OK, by installing the fonts as suggested on the link you provided, I can now see the reference manual in all its beauty.

comment:243 follow-up: Changed 6 years ago by vbraun

Is there anything left to review?

There are no inter-document links to specific anchors in the PDF reference manual. Its not a big loss since it your pdf viewer probably doesn't support them anyways (e.g. the PDF viewer in Chrome does not). If you want hyperlinks just use the html version.

comment:244 in reply to: ↑ 243 Changed 6 years ago by jhpalmieri

Replying to vbraun:

Is there anything left to review?

The only unreviewed parts are trac_6495-filtering.patch and the change to trac_6495-part1-moving-files-link.patch to use symbolic links for reference/MODULE/conf.py (see 229).

comment:245 Changed 6 years ago by vbraun

  • Status changed from needs_review to positive_review

Looks reasonable to me.

comment:246 Changed 6 years ago by jdemeyer

  • Milestone changed from sage-5.7 to sage-5.8

Changed 6 years ago by jdemeyer

Log file of troublesome build

comment:247 Changed 6 years ago by jdemeyer

  • Status changed from positive_review to needs_work

It still doesn't quite work completely. During one build, I got

Building reference manual, first pass.

[polynomia] Exception occurred:
[polynomia] File "/release/merger/sage-5.8.beta0/local/lib/python/pickle.py", line 880, in load_eof
[polynomia] raise EOFError
[polynomia] EOFError
[polynomia] The full traceback has been saved in /tmp/release/sphinx-err-2hqEZ_.log, if you want to report the issue to the developers.
[polynomia] Please also report this if it was a user error, so that a better error message can be provided next time.
[polynomia] Either send bugs to the mailing list at <http://groups.google.com/group/sphinx-dev/>,
[polynomia] or report them in the tracker at <http://bitbucket.org/birkenfeld/sphinx/issues/>. Thanks!

where the "full traceback" reads

# Sphinx version: 1.1.2
# Python version: 2.7.3
# Docutils version: 0.7 release
# Jinja2 version: 2.5.5
Traceback (most recent call last):
  File "/release/merger/sage-5.8.beta0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/cmdline.py", line 188, in main
    warningiserror, tags)
  File "/release/merger/sage-5.8.beta0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/application.py", line 114, in __init__
    self.setup_extension(extension)
  File "/release/merger/sage-5.8.beta0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/application.py", line 247, in setup_extension
    mod = __import__(extension, None, None, ['setup'])
  File "/release/merger/sage-5.8.beta0/devel/sage-main/doc/common/sage_autodoc.py", line 35, in <module>
    from sphinx.pycode import ModuleAnalyzer, PycodeError
  File "/release/merger/sage-5.8.beta0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/pycode/__init__.py", line 25, in <module>
    pygrammar = driver.load_grammar(_grammarfile)
  File "/release/merger/sage-5.8.beta0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/pycode/pgen2/driver.py", line 135, in load_grammar
    g.load(gp)
  File "/release/merger/sage-5.8.beta0/local/lib/python2.7/site-packages/Sphinx-1.1.2-py2.7.egg/sphinx/pycode/pgen2/grammar.py", line 96, in load
    d = pickle.load(f)
  File "/release/merger/sage-5.8.beta0/local/lib/python/pickle.py", line 1378, in load
    return Unpickler(file).load()
  File "/release/merger/sage-5.8.beta0/local/lib/python/pickle.py", line 858, in load
    dispatch[key](self)
  File "/release/merger/sage-5.8.beta0/local/lib/python/pickle.py", line 880, in load_eof
    raise EOFError
EOFError

The second pass of this build starts with:

Building reference manual, second pass.

[polynomia] loading pickled environment... not yet created
[homology ] loading pickled environment... not yet created
[polynomia] WARNING: intersphinx inventory '/release/merger/sage-5.8.beta0/devel/sage/doc/output/inventory/en/reference/polynomial_rings/objects.inv' not fetchable due to <type 'exceptions.IOError'>: [Errno 2] No such file or directory: '/release/merger/sage-5.8.beta0/devel/sage/doc/output/inventory/en/reference/polynomial_rings/objects.inv'

See dochtml.log

comment:248 Changed 6 years ago by vbraun

Upon first use, Sphinx apparenty saves a cached pickle of its grammar under site-packages/ (!) non-atomically (!). Thats just peachy...

comment:249 Changed 6 years ago by jdemeyer

I think the best place to solve this would be in the Sphinx installer: generate the grammar pickle at install time. It's completely normal to put files in site-packages/ during install and you won't need to worry about non-atomic accesses.

comment:250 Changed 6 years ago by jhpalmieri

So I don't know exactly what to do. We could create a script like this in the Sphinx spkg, and then run it as part of the installation. How does that sound?

# Code taken from sphinx/pycode/__init__.py to generate the grammar pickle.

from os import path
from sphinx import package_dir
from sphinx.pycode.pgen2 import driver

# load the Python grammar
_grammarfile = path.join(package_dir, 'pycode', 'Grammar.txt')
pygrammar = driver.load_grammar(_grammarfile)
Last edited 6 years ago by jhpalmieri (previous) (diff)

Changed 6 years ago by jhpalmieri

patch for Sphinx spkg; for review only

comment:252 Changed 6 years ago by vbraun

  • Status changed from needs_work to positive_review

Thanks, looks good and works for me. Hopefully that was the last race in Sphinx, fingers crossed ;-)

comment:253 Changed 6 years ago by jhpalmieri

  • Description modified (diff)

comment:254 Changed 6 years ago by jdemeyer

  • Status changed from positive_review to needs_work

The spkg is not clean:

$ hg status
? create_grammar_pickle.py~

comment:255 Changed 6 years ago by jhpalmieri

  • Status changed from needs_work to positive_review

Fixed. Sorry about that.

comment:256 Changed 6 years ago by jdemeyer

  • Status changed from positive_review to needs_work

In devel/sage/doc/common/custom-sphinx-build.py, you write

    def write(self, str):
        try:
            self._write(str)
        except:
            import traceback
            traceback.print_exc(file=self._stream)

One should never use bare except: statements, because these usually catch too much, for example KeyboardInterrupts. Use except StandardError if you want to catch all errors, or catch a specific exception instead.

And in devel/sage/doc/common/themes/sageref/layout.html, indentation is done mostly with spaces but there are a few TABs. You should use spaces consistently.

But most importantly: the code actually seems to work now! It still needs buildbot testing though.

comment:257 Changed 6 years ago by jhpalmieri

I got rid of the tabs in layout.html.

Changed 6 years ago by jhpalmieri

apply second

Changed 6 years ago by vbraun

Updated patch

comment:258 Changed 6 years ago by vbraun

  • Status changed from needs_work to positive_review

I've replaced the bare except:.

comment:259 Changed 6 years ago by jdemeyer

  • Merged in set to sage-5.8.beta0
  • Resolution set to fixed
  • Status changed from positive_review to closed

comment:260 follow-up: Changed 6 years ago by hivert

Hurrah !!!

comment:261 in reply to: ↑ 260 ; follow-up: Changed 6 years ago by aschilling

Could I make one suggestion (perhaps for a later ticket)? Compiling the docs does not say any longer where to look on one's machine for the compiled docs. This was a very useful feature beforehand!

Thanks for your work on this!

Anne

comment:262 in reply to: ↑ 261 Changed 6 years ago by jhpalmieri

Replying to aschilling:

Could I make one suggestion (perhaps for a later ticket)? Compiling the docs does not say any longer where to look on one's machine for the compiled docs. This was a very useful feature beforehand!

See #14148.

comment:263 Changed 6 years ago by jdemeyer

See #14156 for a blocker follow-up.

comment:264 Changed 6 years ago by jdemeyer

See #14199 for another follow-up.

comment:265 Changed 6 years ago by jdemeyer

Can somebody here please review blocker ticket #14199?

comment:266 Changed 6 years ago by hivert

Another followup #14245: cloning is broken.

comment:267 Changed 5 years ago by jdemeyer

Followup #14626: docbuilder hangs if latex fails.

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