Cherry-pick multiple commits to make release/8.2 functional (#2074)

* refactoring: drop java code (#1937) * Update removed_features.rst * Fine tune clang-format and fix CI (#2041) * Delete return statement to avoid ASan error. * CVode.poolshrink(1) deletes unused mechanism pools. (#2033) * Pin bokeh<3, don't pin matplotlib (#2048) * Add list(...) for new matplotlib. Co-authored-by: Alexandru Săvulescu <alexandru.savulescu@epfl.ch> Co-authored-by: Olli Lupton <oliver.lupton@epfl.ch> Co-authored-by: nrnhines <michael.hines@yale.edu>
neuronsimulator · Nov 9, 2022 · eb19ae0 · eb19ae0
1 parent c159069
commit eb19ae0
Show file tree

Hide file tree

Showing 50 changed files with 80 additions and 4,066 deletions.
diff --git a/.clang-format.changes b/.clang-format.changes
@@ -1,3 +1,3 @@
 SortIncludes: false
 Standard: c++11
-StatementMacros: [MKDLL, MKDLLdec, MKDLLif, MKDLLvp, MKDLLvpf]
+StatementMacros: [MKDLL, MKDLLdec, MKDLLif, MKDLLvp, MKDLLvpf, declareList, declarePtrList, implementList, implementPtrList]
diff --git a/cmake/ConfigFileSetting.cmake b/cmake/ConfigFileSetting.cmake
@@ -276,7 +276,6 @@ nrn_configure_file(bbsconf.h src/parallel)
 nrn_configure_file(nrnneosm.h src/nrncvode)
 nrn_configure_file(sundials_config.h src/sundials)
 nrn_configure_file(mos2nrn.h src/uxnrnbbs)
-nrn_configure_file(njconf.h src/nrnjava)
 nrn_configure_dest_src(nrnunits.lib share/nrn/lib nrnunits.lib share/lib)
 nrn_configure_dest_src(nrn.defaults share/nrn/lib nrn.defaults share/lib)
 # NRN_DYNAMIC_UNITS requires nrnunits.lib.in be in same places as nrnunits.lib

diff --git a/cmake/NeuronFileLists.cmake b/cmake/NeuronFileLists.cmake
@@ -31,7 +31,6 @@ set(HEADER_FILES_TO_INSTALL
     nrncvode.h
     nrnisaac.h
     nrniv_mf.h
-    nrnjava.h
     nrnoc_ml.h
     nrnmpi.h
     nrnmpidec.h

diff --git a/docs/docs_requirements.txt b/docs/docs_requirements.txt
@@ -4,7 +4,8 @@ jupyter
 nbconvert
 recommonmark
 matplotlib
-bokeh
+# bokeh 3 seems to break docs notebooks
+bokeh<3
 # do not check import of next line
 ipython
 plotnine

diff --git a/docs/guide/faq.rst b/docs/guide/faq.rst
@@ -30,13 +30,6 @@ To make NEURON read a file called ``foo.hoc`` when it starts :
 
 To exit NEURON : type ``quit()`` or ``^D`` ("control D") at the ``oc>`` or ``>>>`` prompt, or use :menuselection:`File --> Quit` in the NEURON Main Menu toolbar.
 
-
-Installation went smoothly, but every time I bring NEURON up, the interpreter prints this strange message: "jvmdll" not defined in nrn.def JNI_CreateJavaVM returned -1
-++++++++++++++++++++++++++++++++++++
-
-You must be running an old version of NEURON. Warnings about Java, such as "Can't create Java VM" or "Info: optional feature is not present" mean that NEURON can't find a Java run-time environment. This is of interest only to individuals who are using Java to develop new tools. NEURON's computational engine, standard GUI library, etc. don't use Java.
-
-
 What's the best way to learn how to use NEURON?
 -----------------------------------------------
 First be sure to join `The NEURON Forum <https://www.neuron.yale.edu/phpBB/index.php>`_. 

diff --git a/docs/hoc/programming/gui/pwman.rst b/docs/hoc/programming/gui/pwman.rst
@@ -227,23 +227,6 @@ PWManager
         printed to a postscript file with the "filename" or filebrowser selection. 
 
 
-----
-
-
-
-.. hoc:method:: PWManager.jwindow
-
-
-    Syntax:
-        ``index = p.jwindow(hoc_owner, mapORhide, x, y, w, h)``
-
-
-    Description:
-        Manipulate the position and size of a java window frame associated with the 
-        java object referenced by the hoc object. The mapORhide value may be 0 
-        or 1. The index of the window is returned. This is used by session file 
-        statements created by the java object in order to specify window attributes. 
-
 
 ----
 

diff --git a/docs/python/programming/gui/pwman.rst b/docs/python/programming/gui/pwman.rst
@@ -336,24 +336,6 @@ PWManager
 
 
 
-.. method:: PWManager.jwindow
-
-
-    Syntax:
-        ``index = p.jwindow(hoc_owner, mapORhide, x, y, w, h)``
-
-
-    Description:
-        Manipulate the position and size of a java window frame associated with the 
-        java object referenced by the hoc object. The mapORhide value may be 0 
-        or 1. The index of the window is returned. This is used by session file 
-        statements created by the java object in order to specify window attributes. 
-
-
-----
-
-
-
 .. method:: PWManager.scale
 
 

diff --git a/docs/removed_features.rst b/docs/removed_features.rst
@@ -39,3 +39,7 @@ To that end, the following table's columns constitute:
      - Windows versions now use MINGW (more native to WINDOWS).
      - `#1802 <https://github.com/neuronsimulator/nrn/pull/1802>`_
      - 2f90f37
+   * - Java
+     - NEURON Java support.
+     - `#1937 <https://github.com/neuronsimulator/nrn/pull/1937>`_
+     - 5a67957
diff --git a/docs/tutorials/ball-and-stick-2.ipynb b/docs/tutorials/ball-and-stick-2.ipynb
@@ -740,7 +740,7 @@
     "plt.figure()\n",
     "\n",
     "for i, spike_times_vec in enumerate(spike_times):\n",
-    "    plt.vlines(spike_times_vec, i + 0.5, i + 1.5)\n",
+    "    plt.vlines(list(spike_times_vec), i + 0.5, i + 1.5)\n",
     "plt.show()"
    ]
   },

diff --git a/docs/tutorials/ball-and-stick-3.ipynb b/docs/tutorials/ball-and-stick-3.ipynb
@@ -341,7 +341,7 @@
    "source": [
     "plt.figure()\n",
     "for i, cell in enumerate(ring.cells):\n",
-    "    plt.vlines(cell.spike_times, i + 0.5, i + 1.5)\n",
+    "    plt.vlines(list(cell.spike_times), i + 0.5, i + 1.5)\n",
     "plt.show()"
    ]
   },
@@ -371,7 +371,7 @@
     "    h.finitialize(-65 * mV)\n",
     "    h.continuerun(100 * ms)\n",
     "    for i, cell in enumerate(ring.cells):\n",
-    "        plt.vlines(cell.spike_times, i + 0.5, i + 1.5, color=color)\n",
+    "        plt.vlines(list(cell.spike_times), i + 0.5, i + 1.5, color=color)\n",
     "\n",
     "plt.show()"
    ]

diff --git a/nrn_requirements.txt b/nrn_requirements.txt
@@ -2,7 +2,8 @@ wheel
 setuptools<59.7.0
 scikit-build
 matplotlib
-bokeh
+# bokeh 3 seems to break docs notebooks
+bokeh<3
 ipython
 cython
 pytest

diff --git a/share/lib/nrn.defaults.in b/share/lib/nrn.defaults.in
@@ -112,17 +112,6 @@
 // Following useful for one button mouse. Mac has this as 10 by default
 *scene_menu_box_size: 10.
 
-// The full pathname for the Java VM dynamically loadable
-//   library is specified here
-// two examples for mswin on my machines are
-//*jvmdll: c:\Java\jre1.5.0_01\bin\client\jvm.dll
-//*jvmdll: c:\jdk1.3.1\jre\bin\classic\jvm.dll
-// for gnu-linux it should be set as below and the LD_LIBRARY_PATH set
-// so that libjvm.so can itself find other libraries. For example
-// export LD_LIBRARY_PATH=/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server
-@nrndef_unix@*jvmdll: libjvm.so
-@nrndef_mac@*jvmdll: libjvm.dylib
-
 // The default stack size is 1000 and the frame (recursion depth) size is 512 unless explicitly set nonzero below
 // One may also use the -NSTACK stacksize   -NFRAME framesize options at launch.
 *NSTACK: 0

diff --git a/src/ivoc/apwindow.h b/src/ivoc/apwindow.h
@@ -136,7 +136,6 @@ class StandardWindow: public PrintableWindow {
 };
 
 class PWMImpl;
-class JavaWindow;
 
 class PrintableWindowManager: public Observer {
   public:
@@ -149,9 +148,6 @@ class PrintableWindowManager: public Observer {
     void append(PrintableWindow*);
     void remove(PrintableWindow*);
     void reconfigured(PrintableWindow*);
-    void append(JavaWindow*);
-    void remove(JavaWindow*);
-    void reconfigured(JavaWindow*);
     void doprint();
 
     virtual void update(Observable*);

diff --git a/src/ivoc/checkpnt.cpp b/src/ivoc/checkpnt.cpp
@@ -339,9 +339,10 @@ void PortablePointer::set(void* address, int type, unsigned long s) {
 }
 PortablePointer::~PortablePointer() {}
 
-declareList(PPList, PortablePointer) implementList(PPList, PortablePointer)
+declareList(PPList, PortablePointer)
+implementList(PPList, PortablePointer)
 
-    class OcCheckpoint {
+class OcCheckpoint {
   public:
     OcCheckpoint();
     virtual ~OcCheckpoint();

diff --git a/src/ivoc/ivocmain.cpp b/src/ivoc/ivocmain.cpp
@@ -45,12 +45,6 @@ void iv_display_scale(float);
 #undef MAC
 #endif
 
-#if MAC || defined(WIN32)
-#include "njconf.h"
-#else
-#include "../nrnjava/njconf.h"
-#endif
-
 #if 1
 void pr_profile();
 #define PR_PROFILE pr_profile();

diff --git a/src/ivoc/ochelp.cpp b/src/ivoc/ochelp.cpp
@@ -31,9 +31,10 @@ static FILE* help_pipe;
 
 extern const char* hoc_current_xopen();
 
-declareList(CopyStringList, CopyString) implementList(CopyStringList, CopyString)
+declareList(CopyStringList, CopyString)
+implementList(CopyStringList, CopyString)
 
-    static CopyStringList* filequeue;
+static CopyStringList* filequeue;
 
 extern "C" void ivoc_help(const char* s) {
 #if 1