From 03653a1fcfca528768235dcb4ec8286cd18d2a01 Mon Sep 17 00:00:00 2001 From: Matthias Koeppe Date: Sun, 4 Aug 2024 15:58:37 -0700 Subject: [PATCH 1/7] build/pkgs/jmol: Change to optional --- build/pkgs/jmol/type | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build/pkgs/jmol/type b/build/pkgs/jmol/type index a6a7b9cd726..134d9bc32d5 100644 --- a/build/pkgs/jmol/type +++ b/build/pkgs/jmol/type @@ -1 +1 @@ -standard +optional From 40f7b7f339919eb712fe631af0196f20a2fa0207 Mon Sep 17 00:00:00 2001 From: Matthias Koeppe Date: Tue, 3 Sep 2024 16:52:51 -0700 Subject: [PATCH 2/7] build/pkgs/sagemath_doc_html/dependencies: Remove jmol --- build/pkgs/sagemath_doc_html/dependencies | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build/pkgs/sagemath_doc_html/dependencies b/build/pkgs/sagemath_doc_html/dependencies index 801c36fcd9e..40717629a77 100644 --- a/build/pkgs/sagemath_doc_html/dependencies +++ b/build/pkgs/sagemath_doc_html/dependencies @@ -1,4 +1,4 @@ -sagelib sphinx sphinx_copybutton sphinx_inline_tabs pplpy_doc | $(SAGERUNTIME) maxima networkx scipy sympy matplotlib pillow mathjax mpmath ipykernel jupyter_client conway_polynomials tachyon jmol ipywidgets sage_docbuild elliptic_curves furo fpylll graphs +sagelib sphinx sphinx_copybutton sphinx_inline_tabs pplpy_doc | $(SAGERUNTIME) maxima networkx scipy sympy matplotlib pillow mathjax mpmath ipykernel jupyter_client conway_polynomials tachyon ipywidgets sage_docbuild elliptic_curves furo fpylll graphs # Building the documentation has many dependencies, because all # documented modules are imported and because we use matplotlib to From d4fba8097d322a472efea09a191a56c6ab37b004 Mon Sep 17 00:00:00 2001 From: Matthias Koeppe Date: Mon, 12 Aug 2024 11:57:45 -0700 Subject: [PATCH 3/7] src/sage/features/jmol.py: Make it optional --- src/sage/features/jmol.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sage/features/jmol.py b/src/sage/features/jmol.py index 52104202a40..cf5780094bd 100644 --- a/src/sage/features/jmol.py +++ b/src/sage/features/jmol.py @@ -36,7 +36,7 @@ def __init__(self): filename='JmolData.jar', search_path=jmol_search_path, spkg='jmol', - type='standard', + type='optional', description="Java viewer for chemical structures in 3D") From 6d852ccd50a05682440db2f339c460982d70bd97 Mon Sep 17 00:00:00 2001 From: Matthias Koeppe Date: Mon, 12 Aug 2024 12:17:35 -0700 Subject: [PATCH 4/7] build/pkgs/sagetex/dependencies_check: Remove jmol --- build/pkgs/sagetex/dependencies_check | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build/pkgs/sagetex/dependencies_check b/build/pkgs/sagetex/dependencies_check index d24e23242d4..ff812202db7 100644 --- a/build/pkgs/sagetex/dependencies_check +++ b/build/pkgs/sagetex/dependencies_check @@ -1,4 +1,4 @@ -$(SAGERUNTIME) sympy elliptic_curves jmol +$(SAGERUNTIME) sympy elliptic_curves To build SageTeX, you just need Python, but to test (SAGE_CHECK=yes) SageTeX, you actually need to run Sage, produce plots,... From b5557539b6e4ef44638cc8f14cfa04b705508329 Mon Sep 17 00:00:00 2001 From: Matthias Koeppe Date: Mon, 12 Aug 2024 12:43:24 -0700 Subject: [PATCH 5/7] src/doc/{en,it}/faq/faq-usage.rst: Remove ancient jmol/java-related troubleshooting advice --- src/doc/en/faq/faq-usage.rst | 29 ----------------------------- src/doc/it/faq/faq-usage.rst | 31 ------------------------------- 2 files changed, 60 deletions(-) diff --git a/src/doc/en/faq/faq-usage.rst b/src/doc/en/faq/faq-usage.rst index d03881c36a2..393a9c369e5 100644 --- a/src/doc/en/faq/faq-usage.rst +++ b/src/doc/en/faq/faq-usage.rst @@ -479,35 +479,6 @@ How do I run sage in daemon mode, i.e. as a service? There are several possibilities. Use ``screen``, ``nohup`` or ``disown``. -The show command for plotting 3-D objects does not work. -"""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -The default live 3-D plotting for Sage 6.4+ uses -`Jmol/JSmol `_ -for viewing. From the command line the Jmol Java application is used, -and for in browser viewing either pure javascript or a Java applet -is used. By default in browsers pure javascript is used to avoid -the problems with some browsers that do not support java applet -plugins (namely Chrome). On each browser worksheet there is a -checkbox which must be checked before a 3-D plot is generated if -the user wants to use the Java applet (the applet is a little faster -with complex plots). - -The most likely reason for a malfunction is that you do not have -a Java Run Time Environment (JRE) installed or you have one older than -version 1.7. If things work from the command line another possibility -is that your browser does not have the proper plugin to support Java -applets (at present, 2014, plugins do not work with most versions of -Chrome). Make sure you have installed either the IcedTea browser -plugin (for linux see your package manager), see: -`IcedTea `_, -or the Oracle Java plugin see: -`Java `_. - -If you are using a Sage server over the web and even javascript rendering -does not work, you may have a problem with your browser's javascript -engine or have it turned off. - May I use Sage tools in a commercial environment? """"""""""""""""""""""""""""""""""""""""""""""""" diff --git a/src/doc/it/faq/faq-usage.rst b/src/doc/it/faq/faq-usage.rst index 5d3183769f7..677d1a24bc2 100644 --- a/src/doc/it/faq/faq-usage.rst +++ b/src/doc/it/faq/faq-usage.rst @@ -469,37 +469,6 @@ Ci sono parecchie possibilità. Puoi usare i programmi a riga di comando ``screen``, ``nohup`` o ``disown``. -Il comando show (mostra) per la visualizzazione di oggetti 3D non funziona. -""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -La visualizzazione 3D in tempo reale per Sage dalla versione 6.4 in -avanti usa il pacchetto `Jmol/JSmol `_. -Dalla linea di comando viene utilizzata l'applicazione Java Jmol, -mentre per la visualizzazione dal browser viene usato puro javascript -oppure una Java applet. In genere nei browser è usato javascript puro -per evitare problemi con quei browser che non supportano i plugin per -le applet Java (ad esempio Chrome). In ogni worksheet su browser c'è -una casella da spuntare prima di generare una vista tridimensionale -qualora l'utente voglia usare l'applet Java (essa è un po' più veloce -con viste complicate). - -La ragione più probabile di un malfunzionamento è che non hai -installato l'ambiente runtime di Java (JRE) o che è più vecchio della -versione 1.7. Se le cose funzionano dalla riga di comando, -un'altra possibilità è che il tuo browser non abbia il plugin giusto -per supportare le Java applet (al momento, nel 2014, tali plugin non -lavorano con la maggior parte delle versioni di Chrome). Assicurati di -aver installato il plugin IcedTea (su Linux vedi il tuo gestore dei -pacchetti) o il plugin di Oracle Java -(vedi: `IcedTea `_ -e `Java `_). - -Se stai usando un server Sage sul web e anche la visualizzazione -tramite javascript non funziona, potresti avere un problema con la -funzionalità javascript del tuo browser, o potresti aver disabilitato -javascript. - - Posso usare gli strumenti di Sage in un ambiente commerciale? """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" From 513efbf027170d3075116166a86bb65efc66ec00 Mon Sep 17 00:00:00 2001 From: Matthias Koeppe Date: Mon, 12 Aug 2024 12:45:29 -0700 Subject: [PATCH 6/7] src/doc/en/prep/Symbolics-and-Basic-Plotting.rst: Remove outdated comment on 3d graphics backends --- src/doc/en/prep/Symbolics-and-Basic-Plotting.rst | 5 ----- 1 file changed, 5 deletions(-) diff --git a/src/doc/en/prep/Symbolics-and-Basic-Plotting.rst b/src/doc/en/prep/Symbolics-and-Basic-Plotting.rst index 3bc9308669b..c97efdecee4 100644 --- a/src/doc/en/prep/Symbolics-and-Basic-Plotting.rst +++ b/src/doc/en/prep/Symbolics-and-Basic-Plotting.rst @@ -384,11 +384,6 @@ Below, you can experiment with several of the plotting options. Basic 3D Plotting ----------------- -There are several mechanisms for viewing three\-dimensional plots in -Sage, but we will stick to the default option in the notebook interface, -which is via javascript applets from the program `Jmol/JSmol -`_ . - Plotting a 3D plot is similar to plotting a 2D plot, but we need to specify ranges for two variables instead of one. From 4d1c2d74fd9d9b1c6fcdb819b332d49f1a49e17d Mon Sep 17 00:00:00 2001 From: Matthias Koeppe Date: Mon, 12 Aug 2024 12:47:19 -0700 Subject: [PATCH 7/7] src/sage/graphs/graph.py: Remove outdated reference to jmol in docstring --- src/sage/graphs/graph.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sage/graphs/graph.py b/src/sage/graphs/graph.py index 4b0b43e5adb..6e5a6680662 100644 --- a/src/sage/graphs/graph.py +++ b/src/sage/graphs/graph.py @@ -362,7 +362,7 @@ sage: G = graphs.RandomGNP(15,.3) sage: G.show() # needs sage.plot -And you can view it in three dimensions via jmol with ``show3d()``. :: +And you can view it in three dimensions with ``show3d()``. :: sage: G.show3d() # needs sage.plot