Upgrade sagenb to 0.10.x

[kini]

This is a followup to #11080. During the review process of #11080, which stretched for quite a while, at some point we decided to have a feature freeze on the version of sagenb 0.9.x associated with #11080, just to simplify the review process. The purpose of this ticket is to incorporate some new features, bugfixes, code refactoring, etc. into the version of sagenb shipped with Sage, beyond what was reviewed in #11080. sagenb 0.10 contains the following (among other things):

• refactoring of the startup code, uWSGI and Tornado added as possible WSGI servers
• code allowing .sws files to be uploaded by supplying a URL pointing to the .sws as an argument to the upload page's URL
• new dependency on webassets for js/css autominification (not currently used in the master branch)
• the mathjax branch, and a doctest fix in sphinxify.py (#9774 depends on and contributed to this)
• support for uploading .sws files from the local disk via the command line (#8473 basically is this)
• refactoring of sageinspect to not have a duplication of code between the notebook and the Sage library (#11913 depends on this)
• Upgrading Jmol again and allowing for advanced interactive features more easily, solve some memory issues (#12299)
• Remove strict dependency on pyOpenSSL; allow for graceful failure of HTTPS functionality when pyOpenSSL is not installed (#13384 and #13385 coordinate with this)

Changes not in sagenb itself but in how sagenb is incorporated into sage:

• No repository will be installed with sagenb - developers will need to clone sagenb themselves and install the new clone into their Sage installation manually (which is not difficult).

• SPKG: http://wstein.org/home/keshav/files/sagenb-0.10.2.spkg (a comparatively svelte 13 MB)

• Apply attachment: trac_13121-scripts.patch to the scripts repository.

Instructions for installing this and its dependencies into >=sage-5.2.beta0 :

cd $SAGE_ROOT

./sage --hg -R local/bin qimport -P https://github.com/sagemath/sage-prod/files/10650557/trac_9774-scripts-mathjax.patch.gz
./sage --hg -R local/bin qimport -P https://github.com/sagemath/sage-prod/files/10655778/trac_13121-scripts.patch.gz

./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10650563/trac_9774-mathjax-try7.patch.gz
./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10653851/trac_11913-sage.patch.gz
./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10654503/trac_12299-all-in-one.patch.gz
./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10654504/trac_12299_headless_java.patch.gz
./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10654505/trac-12299_java_doctest_opt.patch.gz

./sage -i http://wstein.org/home/keshav/files/sagenb-0.10.2.spkg
./sage -i http://www.uwosh.edu/faculty_staff/gutow/jmol-12.3.27.p2.spkg

./sage -b

Depends on #11080 Depends on #9774 Depends on #11913 Depends on #12299 Depends on #13384

CC: @jhpalmieri @gutow @sagetrac-jyeo @rbeezer

Component: notebook

Keywords: sagenb

Author: Keshav Kini

Reviewer: John Palmieri, Jonathan Gutow

Merged: sage-5.4.beta0

Issue created by migration from https://trac.sagemath.org/ticket/13121

[kini]

Description changed:

--- 
+++ 
@@ -1 +1,8 @@
-This is a followup to #11080. During the review process of #11080, which stretched for quite a while, at some point we decided to have a feature freeze on the version of sagenb 0.9.x associated with #11080, just to simplify the review process. The purpose of this ticket is to incorporate some new features, bugfixes, code refactoring, etc. into the version of sagenb shipped with Sage, beyond what was reviewed in #11080. The exact scope of what will go into this sagenb 0.9.1 release is as yet undecided.
+This is a followup to #11080. During the review process of #11080, which stretched for quite a while, at some point we decided to have a feature freeze on the version of sagenb 0.9.x associated with #11080, just to simplify the review process. The purpose of this ticket is to incorporate some new features, bugfixes, code refactoring, etc. into the version of sagenb shipped with Sage, beyond what was reviewed in #11080. The exact scope of what will go into this sagenb 0.9.1 release is as yet undecided, but so far it contains the following (and possibly more):
+
+* refactoring of the startup code, uWSGI and Tornado added as possible WSGI servers
+* allow .sws files to be uploaded by supplying a URL pointing to the .sws as an argument to the upload page's URL
+* new dependency on webassets for js/css autominification (not currently used in the master branch)
+* the mathjax branch, and a doctest fix in sphinxify.py (#9774 depends on and contributed to this)
+* support for uploading .sws files from the local disk via the command line (#8473 basically is this)
+* refactoring of sageinspect to not have a duplication of code between the notebook and the Sage library (#11913 depends on this)

[kini]

Description changed:

--- 
+++ 
@@ -1,8 +1,12 @@
 This is a followup to #11080. During the review process of #11080, which stretched for quite a while, at some point we decided to have a feature freeze on the version of sagenb 0.9.x associated with #11080, just to simplify the review process. The purpose of this ticket is to incorporate some new features, bugfixes, code refactoring, etc. into the version of sagenb shipped with Sage, beyond what was reviewed in #11080. The exact scope of what will go into this sagenb 0.9.1 release is as yet undecided, but so far it contains the following (and possibly more):

 * refactoring of the startup code, uWSGI and Tornado added as possible WSGI servers
-* allow .sws files to be uploaded by supplying a URL pointing to the .sws as an argument to the upload page's URL
+* code allowing .sws files to be uploaded by supplying a URL pointing to the .sws as an argument to the upload page's URL
 * new dependency on webassets for js/css autominification (not currently used in the master branch)
 * the mathjax branch, and a doctest fix in sphinxify.py (#9774 depends on and contributed to this)
 * support for uploading .sws files from the local disk via the command line (#8473 basically is this)
 * refactoring of sageinspect to not have a duplication of code between the notebook and the Sage library (#11913 depends on this)
+
+Changes not in sagenb itself but in how sagenb is incorporated into sage:
+
+* No repository will be installed with sagenb - developers will need to clone sagenb themselves and install the new clone into their Sage installation manually (which is not difficult).

[kini]

Changed dependencies from #11080 to #11080, #9774, #8473, #11913

[kini]

Description changed:

--- 
+++ 
@@ -10,3 +10,5 @@
 Changes not in sagenb itself but in how sagenb is incorporated into sage:

 * No repository will be installed with sagenb - developers will need to clone sagenb themselves and install the new clone into their Sage installation manually (which is not difficult).
+
+Preliminary SPKG: http://wstein.org/home/keshav/files/sagenb-0.9.1.spkg (a comparatively svelte 13 MB)

[kcrisman]

Changed dependencies from #11080, #9774, #8473, #11913 to #11080, #9774, #8473, #11913, #12299

[kcrisman]

comment:5

See this comment on github pull request 64 to confirm that #12299 will be in 0.9.1.

[kcrisman]

Description changed:

--- 
+++ 
@@ -6,6 +6,7 @@
 * the mathjax branch, and a doctest fix in sphinxify.py (#9774 depends on and contributed to this)
 * support for uploading .sws files from the local disk via the command line (#8473 basically is this)
 * refactoring of sageinspect to not have a duplication of code between the notebook and the Sage library (#11913 depends on this)
+* Upgrading Jmol again and allowing for advanced interactive features more easily, solve some memory issues (#12299)

 Changes not in sagenb itself but in how sagenb is incorporated into sage:

[kini]

comment:6

I've released 0.9.1. The SPKG is here. Please test and review!

[kini]

Description changed:

--- 
+++ 
@@ -1,4 +1,4 @@
-This is a followup to #11080. During the review process of #11080, which stretched for quite a while, at some point we decided to have a feature freeze on the version of sagenb 0.9.x associated with #11080, just to simplify the review process. The purpose of this ticket is to incorporate some new features, bugfixes, code refactoring, etc. into the version of sagenb shipped with Sage, beyond what was reviewed in #11080. The exact scope of what will go into this sagenb 0.9.1 release is as yet undecided, but so far it contains the following (and possibly more):
+This is a followup to #11080. During the review process of #11080, which stretched for quite a while, at some point we decided to have a feature freeze on the version of sagenb 0.9.x associated with #11080, just to simplify the review process. The purpose of this ticket is to incorporate some new features, bugfixes, code refactoring, etc. into the version of sagenb shipped with Sage, beyond what was reviewed in #11080. sagenb 0.9.1 contains the following (among other things):

 * refactoring of the startup code, uWSGI and Tornado added as possible WSGI servers
 * code allowing .sws files to be uploaded by supplying a URL pointing to the .sws as an argument to the upload page's URL
@@ -12,4 +12,4 @@

 * No repository will be installed with sagenb - developers will need to clone sagenb themselves and install the new clone into their Sage installation manually (which is not difficult).

-Preliminary SPKG: http://wstein.org/home/keshav/files/sagenb-0.9.1.spkg (a comparatively svelte 13 MB)
+SPKG: http://wstein.org/home/keshav/files/sagenb-0.9.1.spkg (a comparatively svelte 13 MB)

[jhpalmieri]

comment:7

In spkg-install, the check

if [ -n $SAGE64 ]; then

needs to take into account that $SAGE64 may be set to "no". According to SAGE_ROOT/spkg/bin/sage-arch-env, it should be unset, "no", or "yes", so you should test that it's set to "yes".

[jhpalmieri]

comment:8

You should also take this possible change to CPPFLAGS into account. For example:

diff --git a/spkg-install b/spkg-install
--- a/spkg-install
+++ b/spkg-install
@@ -17,10 +17,10 @@ die () {
 export CPATH="$CPATH""$SAGE_LOCAL"/include
 export LIBRARY_PATH="$LIBRARY_PATH""$SAGE_LOCAL"/lib

-export CPPFLAGS="-I$SAGE_LOCAL/include $CPPFLAGS"
+export CPPFLAGS="-I$SAGE_LOCAL/include $CPPFLAGS -D_XOPEN_SOURCE=500"
 export LDFLAGS="-L$SAGE_LOCAL/lib $LDFLAGS"

-if [ -n $SAGE64 ]; then
+if [ $SAGE64 = "yes" ]; then
     echo "Building with extra 64-bit flags for MacOS X and Open Solaris."
     if [ -z $CFLAG64 ]; then
         CFLAG64=-m64

(even better, with a comment explaining why CPPFLAGS has been changed)

[jhpalmieri]

comment:9

With these changes, this spkg builds on OS X Lion, sage.math, hawk, and skynet machines mark (after installing the openssl spkg from #13126), cicero, iras (with openssl), silius (with openssl), and taurus. So it's looking good to me.

[jasongrout]

Description changed:

--- 
+++ 
@@ -13,3 +13,16 @@
 * No repository will be installed with sagenb - developers will need to clone sagenb themselves and install the new clone into their Sage installation manually (which is not difficult).

 SPKG: http://wstein.org/home/keshav/files/sagenb-0.9.1.spkg (a comparatively svelte 13 MB)
+
+
+```
+cd SAGE_ROOT
+cd local/bin
+hg qimport -P https://github.com/sagemath/sage-prod/files/10650557/trac_9774-scripts-mathjax.patch.gz
+cd ../../devel/sage
+hg qimport -P https://github.com/sagemath/sage-prod/files/10650562/trac_9774-mathjax-try6.patch.gz
+hg qimport -P https://github.com/sagemath/sage-prod/files/10653851/trac_11913-sage.patch.gz
+hg qimport -P https://github.com/sagemath/sage-prod/files/10654503/trac_12299-all-in-one.patch.gz
+cd ../../
+./sage -br
+```

[kini]

comment:11

SPKG updated with your changes, more or less:

diff --git a/spkg-install b/spkg-install
--- a/spkg-install
+++ b/spkg-install
@@ -17,10 +17,13 @@
 export CPATH="$CPATH""$SAGE_LOCAL"/include
 export LIBRARY_PATH="$LIBRARY_PATH""$SAGE_LOCAL"/lib

-export CPPFLAGS="-I$SAGE_LOCAL/include $CPPFLAGS"
+# note: the -D_XOPEN_SOURCE=500 is to fix build errors in Twisted 12.1 on
+# Solaris. See ticket:11080#comment:314 and
+# the subsequent few comments.
+export CPPFLAGS="-I$SAGE_LOCAL/include -D_XOPEN_SOURCE=500 $CPPFLAGS"
 export LDFLAGS="-L$SAGE_LOCAL/lib $LDFLAGS"

-if [ -n $SAGE64 ]; then
+if [ $SAGE64 = "yes" ]; then
     echo "Building with extra 64-bit flags for MacOS X and Open Solaris."
     if [ -z $CFLAG64 ]; then
         CFLAG64=-m64

[jhpalmieri]

comment:12

On my Mac (OS X 10.7), I can't get worksheets to actually evaluate anything. With Chrome, Firefox, and Safari, I see an evaluate button, but clicking on it does nothing. Hitting 'shift-enter' either does nothing (Firefox) or gives me a new line in the current cell (Chrome and Safari), and does not evaluate anything. Hitting 'Save & quit' does nothing (Chrome and Safari) or actually quits the current worksheet (Firefox).

I think I see some of the same behavior with 0.9.0, but not as severe: it works in Firefox, but not in Chrome or Safari. I'm not sure about that, though; I'm not sure my 0.9.0 install was clean, or whether I corrupted it with 0.9.1 related things.

Does it matter that there is no directory for this version of sagenb in SAGE_LOCAL/lib/python/site-packages/? After installing 0.9.0 and then 0.9.1, I see

  drwxr-xr-x    4 palmieri  admin    136 Jun 19 11:13 sagenb-0.8.29-py2.7.egg
  drwxr-xr-x    4 palmieri  admin    136 Jun 21 16:47 sagenb-0.9.0-py2.7.egg
  -rw-r--r--    1 palmieri  admin     26 Jun 21 16:59 sagenb.egg-link

[kini]

comment:13

I was able to duplicate this on linux. The problem went away when I did a hard refresh of the page, forcing my browser to reload all javascript. The problem is probably caused by this or this.

Does a hard refresh solve the problem on your end too?

[jhpalmieri]

comment:14

A hard refresh helps to get 0.9.0 to work, but not 0.9.1.

By the way, when the notebook is running, how can I tell which version is running? I would suggest having a variable, or displaying it somewhere when the notebook opens.

[kini]

comment:15

Um, wow. Silly typo in this commit. I'll fix this, and actually I think I'm going to call this 0.10. Our version numbers are moving too slowly. Adding mathjax is a lot more substantial of a change than a bump to the patch level should cause a user to expect.

[kini]

Work Issues: fix js typo, make new spkg

[kini]

Description changed:

--- 
+++ 
@@ -1,4 +1,4 @@
-This is a followup to #11080. During the review process of #11080, which stretched for quite a while, at some point we decided to have a feature freeze on the version of sagenb 0.9.x associated with #11080, just to simplify the review process. The purpose of this ticket is to incorporate some new features, bugfixes, code refactoring, etc. into the version of sagenb shipped with Sage, beyond what was reviewed in #11080. sagenb 0.9.1 contains the following (among other things):
+This is a followup to #11080. During the review process of #11080, which stretched for quite a while, at some point we decided to have a feature freeze on the version of sagenb 0.9.x associated with #11080, just to simplify the review process. The purpose of this ticket is to incorporate some new features, bugfixes, code refactoring, etc. into the version of sagenb shipped with Sage, beyond what was reviewed in #11080. sagenb 0.10 contains the following (among other things):

 * refactoring of the startup code, uWSGI and Tornado added as possible WSGI servers
 * code allowing .sws files to be uploaded by supplying a URL pointing to the .sws as an argument to the upload page's URL
@@ -12,17 +12,14 @@

 * No repository will be installed with sagenb - developers will need to clone sagenb themselves and install the new clone into their Sage installation manually (which is not difficult).

-SPKG: http://wstein.org/home/keshav/files/sagenb-0.9.1.spkg (a comparatively svelte 13 MB)
+SPKG: http://wstein.org/home/keshav/files/sagenb-0.10.spkg (a comparatively svelte 13 MB)

cd SAGE_ROOT -cd local/bin -hg qimport -P https://github.com/sagemath/sage-prod/files/10650557/trac_9774-scripts-mathjax.patch.gz -cd ../../devel/sage -hg qimport -P https://github.com/sagemath/sage-prod/files/10650562/trac_9774-mathjax-try6.patch.gz -hg qimport -P https://github.com/sagemath/sage-prod/files/10653851/trac_11913-sage.patch.gz -hg qimport -P https://github.com/sagemath/sage-prod/files/10654503/trac_12299-all-in-one.patch.gz -cd ../../ -./sage -br +hg -R local/bin qimport -P https://github.com/sagemath/sage-prod/files/10650557/trac_9774-scripts-mathjax.patch.gz +hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10650562/trac_9774-mathjax-try6.patch.gz +hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10653851/trac_11913-sage.patch.gz +hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10654503/trac_12299-all-in-one.patch.gz +./sage -b

[kini]

Author: Keshav kini

[kini]

Description changed:

--- 
+++ 
@@ -1,4 +1,4 @@
-This is a followup to #11080. During the review process of #11080, which stretched for quite a while, at some point we decided to have a feature freeze on the version of sagenb 0.9.x associated with #11080, just to simplify the review process. The purpose of this ticket is to incorporate some new features, bugfixes, code refactoring, etc. into the version of sagenb shipped with Sage, beyond what was reviewed in #11080. sagenb 0.10 contains the following (among other things):
+This is a followup to #11080. During the review process of #11080, which stretched for quite a while, at some point we decided to have a feature freeze on the version of sagenb 0.9.x associated with #11080, just to simplify the review process. The purpose of this ticket is to incorporate some new features, bugfixes, code refactoring, etc. into the version of sagenb shipped with Sage, beyond what was reviewed in #11080. sagenb 0.10.0 contains the following (among other things):

 * refactoring of the startup code, uWSGI and Tornado added as possible WSGI servers
 * code allowing .sws files to be uploaded by supplying a URL pointing to the .sws as an argument to the upload page's URL
@@ -12,11 +12,10 @@

 * No repository will be installed with sagenb - developers will need to clone sagenb themselves and install the new clone into their Sage installation manually (which is not difficult).

-SPKG: http://wstein.org/home/keshav/files/sagenb-0.10.spkg (a comparatively svelte 13 MB)
-
+SPKG: http://wstein.org/home/keshav/files/sagenb-0.10.0.spkg (a comparatively svelte 13 MB)

-cd SAGE_ROOT +cd $SAGE_ROOT hg -R local/bin qimport -P https://github.com/sagemath/sage-prod/files/10650557/trac_9774-scripts-mathjax.patch.gz hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10650562/trac_9774-mathjax-try6.patch.gz hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10653851/trac_11913-sage.patch.gz

[kini]

Changed upstream from Fixed upstream, but not in a stable release. to none

[kini]

Changed work issues from fix js typo, make new spkg to none

[kini]

comment:17

OK, new SPKG is up.

By the way, when the notebook is running, how can I tell which version is running? I would suggest having a variable, or displaying it somewhere when the notebook opens.

sagenb.misc.misc.SAGENB_VERSION should tell you that, but it's sort of a hack. I probably could have changed that in the packaging rewrite...

[jhpalmieri]

comment:18

Okay, now a hard refresh is getting everything to work, on all three browsers. Now, is there any way to set it up to avoid the hard refresh? Otherwise users may be frustrated when they first switch to the new notebook.

[jhpalmieri]

Attachment: trac_13121-scripts.patch.gz

scripts repo

[jhpalmieri]

Description changed:

--- 
+++ 
@@ -17,6 +17,7 @@

cd $SAGE_ROOT hg -R local/bin qimport -P https://github.com/sagemath/sage-prod/files/10650557/trac_9774-scripts-mathjax.patch.gz +hg -R local/bin qimport -P https://github.com/sagemath/sage-prod/files/10655778/trac_13121-scripts.patch.gz hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10650562/trac_9774-mathjax-try6.patch.gz hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10653851/trac_11913-sage.patch.gz hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10654503/trac_12299-all-in-one.patch.gz

[jhpalmieri]

comment:19

I've attached a patch to put "webassets" into the .hgignore file.

[kini]

comment:20

Thanks for the .hgignore patch.

As for avoiding hard refreshes, it might be possible to make Flask set some HTTP headers to the date/time when the server was started, to advise client-side caching. I'm not sure of the details, but it's probably not a one-liner like the typo fix I just made was; I'd also consider it more of a feature than a bugfix, so probably it won't go into 0.10.

[kini]

Changed author from Keshav kini to Keshav Kini

[kini]

comment:22

(I've set myself as the author since this ticket is just about making an SPKG - there are many more important contributors to the new version of sagenb than me, for the record.)

[jhpalmieri]

comment:23

This is mostly working for me on OS X Lion, except issues with #8473. Otherwise, the spkg looks good to me. People should test it on other platforms.

[jdemeyer]

comment:24

Any objections to making this a blocker for sage-5.2? It feels to me like sage-0.9.0 is a kind of "beta version" for sage-0.10.0, so I would really prefer to have sage-0.10.0 in the final release.

[jasongrout]

comment:25

Actually, I think of 0.9.0 as sort of the stable, LTS release where we had a long feature freeze and concentrated on stability. 0.10.0 is like the release just after LTS stable release, where we merged in a bunch of new functionality that was put off during the long feature freeze. There are some important bugfixes in 0.10.0 (IIRC), but there is a lot of new functionality in 0.10 too.

[jasongrout]

comment:26

That said, I would prefer 0.10 to be in 5.2, but I think it's probably more important to have 0.9 out by the time school starts.

There is still one or two rather frustrating known bugs in 0.9 (and 0.10): some sort of leak where worker processes don't get killed, and sometimes creating a new worksheet actually just gets an old worksheet. If we solve those in 0.10.1 or something, it would be great to have that as our before-semester release.

[kcrisman]

comment:27

That said, I would prefer 0.10 to be in 5.2, but I think it's probably more important to have 0.9 out by the time school starts.

Correct.

[kcrisman]

comment:28

Replying to @jhpalmieri:

This is mostly working for me on OS X Lion, except issues with #8473. Otherwise, the spkg looks good to me. People should test it on other platforms.

Just for reference, this was (or will be, when it's merged) dealt with - see this pull request on sagenb.

[jhpalmieri]

comment:29

Replying to @kcrisman:

Replying to @jhpalmieri:

This is mostly working for me on OS X Lion, except issues with #8473. Otherwise, the spkg looks good to me. People should test it on other platforms.

Just for reference, this was (or will be, when it's merged) dealt with - see this pull request on sagenb.

Right. Keshav, when you have a chance, could you make a new 0.10.0 spkg for us to test? Any notebook fans: can you positively review the last change at #11080 (the one which allows building on Solaris)?

[kcrisman]

comment:30

To clarify for whoever makes the "final" spkg here - to make sure #8473 is a-ok, we would need this pull request and this one to fix the minor issues John mentioned.

[jhpalmieri]

comment:31

I'm confused about the location of JMOL. It used to be (before #11080) part of sagenb. Now it isn't (or at least I don't see it anywhere). Does it need to be distributed as a separate spkg, and thus included in spkg/standard/deps? Or should the new JMOL spkg from #12299 be part of this spkg?

Oh, I see: it is now in spkg/standard/deps, and it needs to be included as a separate spkg.

[kini]

comment:32

See #11503, where the deps file is patched to require the new JMOL spkg from #11503. For some reason #12299 seems to require a newer version of the SPKG, a version which is not on #11503 or anywhere else. I posted a comment on #11503 about it.

[jhpalmieri]

comment:33

The spkg here needs work: when it gets installed, SAGE_ROOT/devel may not yet exist. So something like this:

diff --git a/spkg-install b/spkg-install
--- a/spkg-install
+++ b/spkg-install
@@ -53,6 +53,7 @@ BASENAME=${BASENAME%.tar.gz}
 #easy_install -H None -f src "sagenb" || die "Error installing sagenb !"

 # Extract sagenb into $SAGE_ROOT/devel and set up the symlink
+mkdir -p "$SAGE_ROOT/devel"
 cd "$SAGE_ROOT/devel"
 if [ -d "$SAGE_ROOT/devel/sagenb-main" ]; then
     echo "Moving old SageNB package to '$SAGE_ROOT/devel/sagenb-main-old'..."

[kcrisman]

comment:34

See #11503, where the deps file is patched to require the new JMOL spkg from #11503. For some reason #12299 seems to require a newer version of the SPKG, a version which is not on #11503 or anywhere else. I posted a comment on #11503 about it.

As far as I know, this is on purpose, because the newest Jmol at #12299 needs the many updates to Jmol there. In that sense #11503 is a 'hard' prereq for #11080 and hence this ticket. I am pretty sure Jonathan was careful about exactly which version of Jmol needed to be with which other patches.

[kini]

comment:35

OK, I see, thanks.

[kcrisman]

comment:36

jhpalmieri or others:

When you ran into the problem with the evaluate button not working, did you find that other buttons also stopped working? For instance, the Stop and Archive buttons on the main worksheet list page. I must have done something wrong because even a hard refresh isn't getting things to work for me, but I wanted to ask if anyone had tried those.

[jhpalmieri]

comment:37

For me, on some browsers, everything stopped working. A hard refresh did fix it (Firefox or Chrome: cmd-shift-r. Safari: hold the option key down while hitting the little "refresh" symbol at the right end of the address box).

[kcrisman]

comment:38

For me, on some browsers, everything stopped working.

Ok.

A hard refresh did fix it (Firefox or Chrome: cmd-shift-r. Safari: hold the option key down while hitting the little "refresh" symbol at the right end of the address box).

Yup, that's what I tried, and that didn't work. But like I said on those commits in sagenb, maybe I just destroyed my installation anyway.

Edit: I did finally manage to get the upstream commit of the parenthesis fix in to make it work with the "hard refresh". That definitely needs some big warning somewhere... Strange that doing it "by hand" didn't work, but getting from upstream did.

[kini]

Description changed:

--- 
+++ 
@@ -14,12 +14,50 @@

 SPKG: http://wstein.org/home/keshav/files/sagenb-0.10.0.spkg (a comparatively svelte 13 MB)

+Instructions after following the ones at #11080:
+

cd $SAGE_ROOT -hg -R local/bin qimport -P https://github.com/sagemath/sage-prod/files/10650557/trac_9774-scripts-mathjax.patch.gz -hg -R local/bin qimport -P https://github.com/sagemath/sage-prod/files/10655778/trac_13121-scripts.patch.gz -hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10650562/trac_9774-mathjax-try6.patch.gz -hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10653851/trac_11913-sage.patch.gz -hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10654503/trac_12299-all-in-one.patch.gz + +./sage --hg -R local/bin qimport -P https://github.com/sagemath/sage-prod/files/10650557/trac_9774-scripts-mathjax.patch.gz +./sage --hg -R local/bin qimport -P https://github.com/sagemath/sage-prod/files/10655778/trac_13121-scripts.patch.gz + +./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10650562/trac_9774-mathjax-try6.patch.gz +./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10653851/trac_11913-sage.patch.gz +./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10654503/trac_12299-all-in-one.patch.gz + +./sage -i http://wstein.org/home/keshav/files/sagenb-0.10.0.spkg +./sage -i http://www.uwosh.edu/faculty_staff/gutow/jmol-12.3.27.p0.spkg + ./sage -b

+
+Or, instructions without #11080:
+
+```
+cd $SAGE_ROOT
+
+./sage --hg -R . qimport -P https://github.com/sagemath/sage-prod/files/10653764/trac-11874-remove-twisted.patch.gz
+./sage --hg -R . qimport -P https://github.com/sagemath/sage-prod/files/10653164/trac-11503-jmol-spkg.2.patch.gz
+
+./sage --hg -R local/bin qimport -P https://github.com/sagemath/sage-prod/files/10650557/trac_9774-scripts-mathjax.patch.gz
+./sage --hg -R local/bin qimport -P https://github.com/sagemath/sage-prod/files/10652518/trac_11080-scripts-hgignore-dulwich.patch.gz
+./sage --hg -R local/bin qimport -P https://github.com/sagemath/sage-prod/files/10655778/trac_13121-scripts.patch.gz
+
+./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10653765/sage-spkg-11874.patch.gz
+./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10652514/trac_11078.patch.gz
+./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10653161/trac-11503-jmol-commandline.patch.gz
+./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10654419/trac_12229-sagenb-developer-doc.3.patch.gz
+./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10654418/trac-12229-manifest.patch.gz
+./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10652516/trac-11080-notebook-docs.patch.gz
+./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10652517/trac_11080-openssl-in-installation-docs.patch.gz
+./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10650562/trac_9774-mathjax-try6.patch.gz
+./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10653851/trac_11913-sage.patch.gz
+./sage --hg -R devel/sage qimport -P https://github.com/sagemath/sage-prod/files/10654503/trac_12299-all-in-one.patch.gz
+
+./sage -i openssl # optional if you have systemwide SSL dev headers installed
+./sage -i http://wstein.org/home/keshav/files/sagenb-0.10.0.spkg
+./sage -i http://www.uwosh.edu/faculty_staff/gutow/jmol-12.3.27.p0.spkg
+
+./sage -b
+```

[jhpalmieri]

Work Issues: create SAGE_ROOT/devel