egourgoulhon commented 7 years ago

Now that #22389 (Make Three.js work offline) and #22261 (Three.js: Default lighting) have been merged, it is time to make threejs the default 3d viewer, in replacement of jmol.

A discussion about this started in #22389. In addition, one may note the following:

pros:

three.js offers functionality absent in Jmol, notably axis labels
three.js works better with Jupyter than Jmol, see e.g. this report)
Jmol is a nightmare for packagers (for Debian, Windows, ...), see e.g. this discussion on debian-science-sagemath; in particular jsmol, which is invoked in Jupyter notebooks, is not packaged for Debian (see comment:49)
Jmol, as currently shipped with Sage, is broken with recent version of Java runtime environment, e.g. on Debian Buster and Ubuntu 18.04, see this ask.sagemath question

cons:

some features are still missing in three.js, like
- converting the view to a png image in non-interactive mode (e.g. when generating the reference manual, cf. comment:66); NB: thanks to #27910 (merged in Sage 8.8.rc0), the png conversion is now possible in interactive mode; see this discussion
- ~~mesh plots~~ ==> fixed by #28343 (merged in Sage 8.9.beta8)
- ~~vector field plots~~ ==> fixed by #27932 (merged in Sage 8.9.beta0)
three.js has some issues:
- ~~faces of polytopes look rounded~~ ==> fixed by #27836 (merged in Sage 8.8.beta7)
- some opacity issues: cf. comment:75 and below

CC: @paulmasson @novoselt @sagetrac-tmonteil @kcrisman @slel @williamstein @embray @infinity0 @kiwifb @egourgoulhon @strogdon @timokau @jplab

Component: graphics

Keywords: 3D, plot3d, threejs, three.js, jmol

Author: Paul Masson, Eric Gourgoulhon

Branch: fcac479

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/22408

jhpalmieri commented 4 years ago

comment:98

Then it's due to #25026, I think. Would this be the right fix?

diff --git a/build/pkgs/jmol/spkg-install b/build/pkgs/jmol/spkg-install
index 27798e6232..65dfa6df44 100644
--- a/build/pkgs/jmol/spkg-install
+++ b/build/pkgs/jmol/spkg-install
@@ -6,6 +6,7 @@ rm -f "${SAGE_LOCAL}/bin/jmol"
 # jsmol goes in a dedicated directory
 sdh_install src/jsmol "${SAGE_SHARE}/"
 rm -rf src/jsmol
+chmod a+rx src

 sdh_install -T src "${SAGE_SHARE}/jmol"
 sdh_install jmol "${SAGE_LOCAL}/bin/"

jhpalmieri commented 4 years ago

comment:99

Is there a trac ticket open for the jmol permissions issue?

novoselt commented 4 years ago

comment:100

I don't think so, at least I didn't open one.

jhpalmieri commented 4 years ago

comment:101

Replying to @novoselt:

I don't think so, at least I didn't open one.

28596. In my opinion, you should have opened a ticket the same time you reported the problem on sage-devel: sage-devel threads can get lost pretty easily.

jhpalmieri commented 4 years ago

comment:102

Replying to @fchapoton:

This seems to have broken the doc building on some python3 sage:

see https://patchbot.sagemath.org/log/0/Ubuntu/16.04/x86_64/4.4.0-161-generic/atlas/2019-10-10%2016:18:22?plugin=docbuild

Could you try #28596 to see if Andrey's guess is right? With that branch, do sage -f jmol and see if it fixes your problems.

sagemath / sage

Make threejs / three.js the default 3d viewer instead of jmol #22408

28596. In my opinion, you should have opened a ticket the same time you reported the problem on sage-devel: sage-devel threads can get lost pretty easily.