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push eventRosettaCommons/PyRosetta.notebooks

Andrew Leaver-Fay

commit sha 311d20c922aaa7bf1d29a402d35e0d1e08230f1f

Updating references to python3.6 to 3.7 following colab's update Google CoLab updated to python3.7 at least as recently as 2021/02/25 Ahead of the next PyRosetta boot camp, this needed to be updated

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Andrew Leaver-Fay

commit sha f187158eb065d60f6a3f2284c7ff560e22250129

Updating student-notebooks

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Andrew Leaver-Fay

commit sha 6dfa37d53631da138a9ae12cfc3bf2e05ade8941

Re-run notebooks to update the embedded .png

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Jared Adolf-Bryfogle

commit sha 76b8a8db49d49eaba982293fcf4c91cf438416a8

fix rabd notebook with recent changes.

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Jared Adolf-Bryfogle

commit sha baa4175a607a61ecae729ff4a4e060b860b36857

Update 12.02-RosettaAntibodyDesign-RAbD.ipynb Manually put back new python version

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Kathy Le

commit sha 53c0f59fc054ac68cbb5c80622a6642d437578c3

Added a link to install Google Colab app for first time users in the instructions.

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Andrew Leaver-Fay

commit sha b10dbb95b0a9a687d58040a40d4fd1f7e9b44195

Merge pull request #64 from branch aleaverfay/update_colab_instructions_to_py37 Updating references to python3.6 to 3.7 following colab's update about a week ago. If you download the 3.6 version, then when you try to run `from pyrosetta import *`, the colab environment throws and error.

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Sergey Lyskov

commit sha 6e8f8acac93f19e9641cc589a926b7467204428c

Merge pull request #62 from RosettaCommons/sergey adding whell-install and PyMOL-Colab demos

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Jared Adolf-Bryfogle

commit sha 3df63f1b3d308d8694aa1f400e6c015d3d703c96

Merge pull request #65 from RosettaCommons/rabd2 Fix rabd notebook with recent changes to master.

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Jared Adolf-Bryfogle

commit sha 66cb994635ab635c7d5e4a4f3c8aaa9a36306331

fix issue with block.

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Jared Adolf-Bryfogle

commit sha 207d46f935fa69aa1272163cc525d6e11e4ac67c

Merge pull request #66 from RosettaCommons/rabd3 Fix RabD issue with block.

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PR opened RosettaCommons/pybind11

chore(deps): bump pre-commit/action from v2.0.0 to v2.0.2

Bumps pre-commit/action from v2.0.0 to v2.0.2. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/pre-commit/action/releases">pre-commit/action's releases</a>.</em></p> <blockquote> <h2>pre-commit/action@v2.0.2</h2> <p>retag of 2.0.1 but on the proper branch</p> <h2>pre-commit/action@v2.0.1</h2> <h3>Fixes</h3> <ul> <li>Avoid failures if cache saving fails <ul> <li><a href="https://github-redirect.dependabot.com/pre-commit/action/issues/54">#54</a> PR by <a href="https://github.com/s-weigand"><code>@​s-weigand</code></a></li> <li><a href="https://github-redirect.dependabot.com/pre-commit/action/issues/53">#53</a> issue by <a href="https://github.com/s-weigand"><code>@​s-weigand</code></a></li> </ul> </li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pre-commit/action/commit/9cf68dc1ace5504cd0e05b9f3df32e6a0822ad89"><code>9cf68dc</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/12c0cbaee9b37d569632139754759021b4dc2ed7"><code>12c0cba</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/686243b93a269e859b827b37c83af97ad125b407"><code>686243b</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/5b6c59a01a99def46b9fd96111c1533e8df334cf"><code>5b6c59a</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/23933a87f57b9d68d9841cef1ca481eac28c9458"><code>23933a8</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/ba03328ac18694cb521a8fcb053db2f07419862b"><code>ba03328</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/055fa4e7efbddb7cdc641d81a40c4497a3f4e39d"><code>055fa4e</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/2fcbdbb9ddd55fb1f15449c82b3e66ffb1320634"><code>2fcbdbb</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/8ba276b2444e938dfc4a7ec990b590b0be4f11e9"><code>8ba276b</code></a> Deployed to github pages</li> <li><a href="https://github.com/pre-commit/action/commit/34072ce8c47fc47e70ba4d94386763155b3c1f8e"><code>34072ce</code></a> Deployed to github pages</li> <li>See full diff in <a href="https://github.com/pre-commit/action/compare/v2.0.0...9cf68dc1ace5504cd0e05b9f3df32e6a0822ad89">compare view</a></li> </ul> </details> <br />

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pull request commentRosettaCommons/pybind11

chore(deps): bump pre-commit/action from v2.0.0 to v2.0.1

Superseded by #7.

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PR opened RosettaCommons/pybind11

chore(deps): bump pre-commit/action from v2.0.0 to v2.0.1

Bumps pre-commit/action from v2.0.0 to v2.0.1. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/pre-commit/action/releases">pre-commit/action's releases</a>.</em></p> <blockquote> <h2>pre-commit/action@v2.0.1</h2> <h3>Fixes</h3> <ul> <li>Avoid failures if cache saving fails <ul> <li><a href="https://github-redirect.dependabot.com/pre-commit/action/issues/54">#54</a> PR by <a href="https://github.com/s-weigand"><code>@​s-weigand</code></a></li> <li><a href="https://github-redirect.dependabot.com/pre-commit/action/issues/53">#53</a> issue by <a href="https://github.com/s-weigand"><code>@​s-weigand</code></a></li> </ul> </li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pre-commit/action/commit/b54880c283dfc80a3fc1baf61807e8ae84471361"><code>b54880c</code></a> v2.0.1</li> <li><a href="https://github.com/pre-commit/action/commit/8ac8946854ea5db3be6a2eb8600ba0ac178ad9de"><code>8ac8946</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/pre-commit/action/issues/54">#54</a> from s-weigand/fix-53</li> <li><a href="https://github.com/pre-commit/action/commit/d1027a948b51ee71764d270f9cfeeee2715c01c7"><code>d1027a9</code></a> Wrapped saving pre-commit cache to cache, in a try catch block</li> <li><a href="https://github.com/pre-commit/action/commit/0404b969641801ff99d4cecbfabf14304270b4c9"><code>0404b96</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/pre-commit/action/issues/89">#89</a> from pre-commit/dependabot/npm_and_yarn/y18n-4.0.1</li> <li><a href="https://github.com/pre-commit/action/commit/52ec6e5c9fe15aa1c68925623c0f825e8066e726"><code>52ec6e5</code></a> Bump y18n from 4.0.0 to 4.0.1</li> <li><a href="https://github.com/pre-commit/action/commit/f52f43f850c62e8f2ee58893bf4a7ae42a1e3ece"><code>f52f43f</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/pre-commit/action/issues/87">#87</a> from pre-commit/pre-commit-ci-update-config</li> <li><a href="https://github.com/pre-commit/action/commit/007c7cde5205c83d2fd0b6d36d3c1d0c68bcdadc"><code>007c7cd</code></a> [pre-commit.ci] pre-commit autoupdate</li> <li><a href="https://github.com/pre-commit/action/commit/1365adcff2d9c8606f13644b56e5a5c52fc393c9"><code>1365adc</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/pre-commit/action/issues/86">#86</a> from pre-commit/pre-commit-ci-update-config</li> <li><a href="https://github.com/pre-commit/action/commit/5e4d1b7a22f4f47dfe6cb987ca5e37ba053b3fcf"><code>5e4d1b7</code></a> [pre-commit.ci] pre-commit autoupdate</li> <li><a href="https://github.com/pre-commit/action/commit/ec497e5c4a44eaca8283b84d85d4105e30fb6903"><code>ec497e5</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/pre-commit/action/issues/84">#84</a> from pre-commit/dependabot/npm_and_yarn/elliptic-6.5.4</li> <li>Additional commits viewable in <a href="https://github.com/pre-commit/action/compare/v2.0.0...b54880c283dfc80a3fc1baf61807e8ae84471361">compare view</a></li> </ul> </details> <br />

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issue closedRosettaCommons/binder

Issue using generated bindings

Hi, I successfully generated and compiled binding for the esmini simulator by calling binder like this and using the config/headers file in the src directory. The generated bindings for each module are accessible in the separated directories under ./src.

However, I noticed the following two issues:

Issue 1: Memory Corruption

import pyesminilib
pyesminilib.SE_Init( '/home/[...]/esmini-pybind11/esmini/resources/xosc/lane_change.xosc',1,1,0,0)

From the log message I can see SE_Init function is called with the correct arguments but the binding introduces a memory corruption as below:

esmini GIT REV: 06f0360
esmini GIT TAG: 
esmini GIT BRANCH: master
esmini BUILD VERSION: N/A - client build
esminiLib.cpp / 104 / ConvertArguments(): Player arguments:  viewer --osc /home/[...]/esmini-pybind11/esmini/resources/xosc/lane_change.xosc --window 60 60 800 400 --disable_controllers
python3: malloc.c:2379: sysmalloc: Assertion `(old_top == initial_top (av) && old_size == 0) || ((unsigned long) (old_size) >= MINSIZE && prev_inuse (old_top) && ((unsigned long) old_end & (pagesize - 1)) == 0)' failed.
Aborted (core dumped)

Issue 2: Missing methods

I noticed that not all methods are included in the generated bindings. As one example one of the constructor methods (ScenarioPlayer(int &argc, char *argv[])) is missing as can be seen in the generated bindings. (note, it is not only the constructors that are missing. SE_InitWithArgs and many other methods are also missing)

closed time in 20 days

ebadi

issue commentRosettaCommons/binder

Issue using generated bindings

I narrowed down the problematic methods to these two methods

-- this quite odd... But overall: this issue is clearly outside the scope of Binder (ie Binder done its work: code was wrapped, results was compiled without the errors) and it should be propagated to Pybind11 team.

If/when you going to submit this to Pybind11 team could you please mention me? I am curious to learn of what might have caused this behavior. Thanks,

ebadi

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issue commentRosettaCommons/binder

Issue using generated bindings

Yes, I didn't push the bindings to the repository. The changes are minor:

~/repositories/esmini-pybind11$ git diff src/playerbase/pyplayerbase.cpp
diff --git a/src/playerbase/pyplayerbase.cpp b/src/playerbase/pyplayerbase.cpp
index d60d314..09fca15 100644
--- a/src/playerbase/pyplayerbase.cpp
+++ b/src/playerbase/pyplayerbase.cpp
@@ -27,9 +27,10 @@ void bind_unknown_unknown(std::function< pybind11::module &(std::string const &n
 {
        { // ScenarioPlayer file: line:35
                pybind11::class_<ScenarioPlayer, std::shared_ptr<ScenarioPlayer>> cl(M(""), "ScenarioPlayer", "");
+               cl.def( pybind11::init( [](){ return new ScenarioPlayer(); } ) );
                cl.def_readwrite("sensor", &ScenarioPlayer::sensor);
-               cl.def_readonly("maxStepSize", &ScenarioPlayer::maxStepSize);
-               cl.def_readonly("minStepSize", &ScenarioPlayer::minStepSize);
+               cl.def_readwrite("maxStepSize", &ScenarioPlayer::maxStepSize);
+               cl.def_readwrite("minStepSize", &ScenarioPlayer::minStepSize);
                cl.def_readwrite("opt", &ScenarioPlayer::opt);
                cl.def_readwrite("callback", &ScenarioPlayer::callback);
                cl.def_readwrite("exe_path_", &ScenarioPlayer::exe_path_);

check if commenting out anything but constructor bindings for ScenarioPlayer makes any difference by commenting out bindings for all member functions and data members here

As you suggested I removed the extra method and my empty constructor starts working without any memory corruption again! I narrowed down the problematic methods to these two methods :

		cl.def("SetParameterValue", (int (ScenarioPlayer::*)(const char *, const void *)) &ScenarioPlayer::SetParameterValue, "C++: ScenarioPlayer::SetParameterValue(const char *, const void *) --> int", pybind11::arg("name"), pybind11::arg("value"));
		cl.def("GetParameterValue", (int (ScenarioPlayer::*)(const char *, void *)) &ScenarioPlayer::GetParameterValue, "C++: ScenarioPlayer::GetParameterValue(const char *, void *) --> int", pybind11::arg("name"), pybind11::arg("value"));

This is as far as I could go today.

ebadi

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push eventRosettaCommons/binder

Andrii Verbytskyi

commit sha 1c98fce9b0f9f2fea810f384d3001d3c8035d3e6

Remove semicolons in module_header to prevent gcc warnings when compiling with -pedantic

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Sergey Lyskov

commit sha 664499d47a8a96c5a9793337ee405ad61f035c17

Merge pull request #152 from andriish/fix_pedandic_warnings remove semicolons in module_header

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PR merged RosettaCommons/binder

Remove semicolons in module_header

Hi @lyskov ,

here is a tiny, completely non-urgent pull request.

The idea is to remove semicolons in "module_header" to prevent gcc warnings when compiling with -Wpedantic.

The messages I see look like this:

 warning: extra ‘;’ [-Wpedantic]
  PYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr<T>);
                                                     ^
 warning: extra ‘;’ [-Wpedantic]
  PYBIND11_DECLARE_HOLDER_TYPE(T, T*);
                                     ^
 warning: extra ‘;’ [-Wpedantic]
  PYBIND11_MAKE_OPAQUE(std::shared_ptr<void>);
                                             ^

There are two other warnings:

 warning: ISO C++11 requires at least one argument for the "..." in a variadic macro
  PYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr<T>);
                                                    ^
 warning: ISO C++11 requires at least one argument for the "..." in a variadic macro
  PYBIND11_DECLARE_HOLDER_TYPE(T, T*);

however these are inside the pybind11 code.

Best regards,

Andrii

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andriish

pr closed time in 24 days

issue commentRosettaCommons/binder

Issue using generated bindings

@ebadi could you please point me to where source code generated by Binder is located? I found this https://github.com/ebadi/esmini-pybind11/blob/master/src/playerbase/pyplayerbase.cpp but it lack bindings for constructor so i am guessing you might have a newer version?

On issue itself: i looked at the code here https://github.com/ebadi/esmini-pybind11/blob/master/src/playerbase/pyplayerbase.cpp#L28 and everything seems to be in order. I would recommend to investigate the following:

  • check if commenting out anything but constructor bindings for ScenarioPlayer makes any difference by commenting out bindings for all member functions and data members here: https://github.com/ebadi/esmini-pybind11/blob/master/src/playerbase/pyplayerbase.cpp#L30
  • if above make no difference then check if compiling/linking work as expected by adding dummy struct into you original C++ code (say struct Dummy {};) and then running Binder on this code base and trying to import Dummy in python.
  • if above works then issue have to be in how ScenarioPlayer class initiate it members (i see some custom classes in it: https://github.com/ebadi/esmini/commit/6913ab193807ff0fc8004b408938a2e392efa86f#diff-7b24101d5a5cf8ec18012f762c597a8d10d39876a01cf6b40a103a926989addcR109 ). try to create a minimal C++ executable with main function creating ScenarioPlayer object, - see if that works
  • if minimal C++ excitable works then propagate this to Pybind11 team

Hope that helps,

ebadi

comment created time in 24 days

IssuesEvent

issue commentRosettaCommons/binder

Issue using generated bindings

I created a minimal example and I still get memory corruption errors when I run the this simple test script:

BTW, I dockerized the build process as documented here.

$python3 tests/scenarioplayer.py

malloc(): corrupted top size
Aborted (core dumped)

in gdb :

~/r/esmini-pybind11 (master) [127]> gdb python3 
GNU gdb (Ubuntu 9.2-0ubuntu1~20.04) 9.2
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Reading symbols from python3...
(No debugging symbols found in python3)
(gdb) r tests/scenarioplayer.py
Starting program: /usr/bin/python3 tests/scenarioplayer.py
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
malloc(): corrupted top size

Program received signal SIGABRT, Aborted.
__GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:50
50	../sysdeps/unix/sysv/linux/raise.c: No such file or directory.
(gdb) bt
#0  __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:50
#1  0x00007ffff7dd2859 in __GI_abort () at abort.c:79
#2  0x00007ffff7e3d3ee in __libc_message (action=action@entry=do_abort, fmt=fmt@entry=0x7ffff7f67285 "%s\n") at ../sysdeps/posix/libc_fatal.c:155
#3  0x00007ffff7e4547c in malloc_printerr (str=str@entry=0x7ffff7f65556 "malloc(): corrupted top size") at malloc.c:5347
#4  0x00007ffff7e4883a in _int_malloc (av=av@entry=0x7ffff7f98b80 <main_arena>, bytes=bytes@entry=104) at malloc.c:4107
#5  0x00007ffff7e4a2d4 in __GI___libc_malloc (bytes=104) at malloc.c:3058
#6  0x00007ffff512fc29 in operator new(unsigned long) () from /lib/x86_64-linux-gnu/libstdc++.so.6
#7  0x00007ffff6e93694 in ?? () from /home/wave/.local/lib/python3.8/site-packages/pyplayerbase.cpython-38-x86_64-linux-gnu.so
#8  0x00007ffff6ea25ae in ?? () from /home/wave/.local/lib/python3.8/site-packages/pyplayerbase.cpython-38-x86_64-linux-gnu.so
#9  0x00000000005f2fb9 in PyCFunction_Call ()
#10 0x00000000005f3446 in _PyObject_MakeTpCall ()
#11 0x000000000050aa4a in ?? ()
#12 0x00000000005f2b87 in PyObject_Call ()
#13 0x000000000059bc1c in ?? ()
#14 0x00000000005a6867 in ?? ()
#15 0x00007ffff6e9f02d in ?? () from /home/wave/.local/lib/python3.8/site-packages/pyplayerbase.cpython-38-x86_64-linux-gnu.so
#16 0x00000000005f3446 in _PyObject_MakeTpCall ()
#17 0x000000000056f1ca in _PyEval_EvalFrameDefault ()
#18 0x000000000056822a in _PyEval_EvalCodeWithName ()
#19 0x000000000068c1e7 in PyEval_EvalCode ()
#20 0x000000000067d5a1 in ?? ()
#21 0x000000000067d61f in ?? ()
#22 0x000000000067d6db in PyRun_FileExFlags ()
#23 0x000000000067da6e in PyRun_SimpleFileExFlags ()
#24 0x00000000006b6132 in Py_RunMain ()
#25 0x00000000006b64bd in Py_BytesMain ()
#26 0x00007ffff7dd40b3 in __libc_start_main (main=0x4eec80 <main>, argc=2, argv=0x7fffffffdf38, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffdf28)
    at ../csu/libc-start.c:308
#27 0x00000000005f927e in _start ()
(gdb) 
ebadi

comment created time in 25 days

PR opened RosettaCommons/binder

Remove semicolons in module_header

Hi @lyskov ,

here is a tiny, completely non-urgent pull request.

The idea is to remove semicolons in "module_header" to prevent gcc warnings when compiling with -Wpedantic.

The messages I see look like this:

 warning: extra ‘;’ [-Wpedantic]
  PYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr<T>);
                                                     ^
 warning: extra ‘;’ [-Wpedantic]
  PYBIND11_DECLARE_HOLDER_TYPE(T, T*);
                                     ^
 warning: extra ‘;’ [-Wpedantic]
  PYBIND11_MAKE_OPAQUE(std::shared_ptr<void>);
                                             ^

There are two other warnings:

 warning: ISO C++11 requires at least one argument for the "..." in a variadic macro
  PYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr<T>);
                                                    ^
 warning: ISO C++11 requires at least one argument for the "..." in a variadic macro
  PYBIND11_DECLARE_HOLDER_TYPE(T, T*);

however these are inside the pybind11 code.

Best regards,

Andrii

+3 -3

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1 changed file

pr created time in a month

issue closedRosettaCommons/binder

Issue using generated bindings

Hi, I successfully generated and compiled binding for the esmini simulator by calling binder like this and using the config/headers file in the src directory. The generated bindings for each module are accessible in the separated directories under ./src.

However, I noticed the following two issues:

Issue 1: Memory Corruption

import pyesminilib
pyesminilib.SE_Init( '/home/[...]/esmini-pybind11/esmini/resources/xosc/lane_change.xosc',1,1,0,0)

From the log message I can see SE_Init function is called with the correct arguments but the binding introduces a memory corruption as below:

esmini GIT REV: 06f0360
esmini GIT TAG: 
esmini GIT BRANCH: master
esmini BUILD VERSION: N/A - client build
esminiLib.cpp / 104 / ConvertArguments(): Player arguments:  viewer --osc /home/[...]/esmini-pybind11/esmini/resources/xosc/lane_change.xosc --window 60 60 800 400 --disable_controllers
python3: malloc.c:2379: sysmalloc: Assertion `(old_top == initial_top (av) && old_size == 0) || ((unsigned long) (old_size) >= MINSIZE && prev_inuse (old_top) && ((unsigned long) old_end & (pagesize - 1)) == 0)' failed.
Aborted (core dumped)

Issue 2: Missing methods

I noticed that not all methods are included in the generated bindings. As one example one of the constructor methods (ScenarioPlayer(int &argc, char *argv[])) is missing as can be seen in the generated bindings. (note, it is not only the constructors that are missing. SE_InitWithArgs and many other methods are also missing)

closed time in a month

ebadi

issue commentRosettaCommons/binder

Issue using generated bindings

Thanks @lyskov and @eknabevcc Issue 1: I will investigate this further and come back with more details. Issue 2: Right, it makes sense. I only expected to receive a warning message instead of the tool silently skipping/ignoring these methods.

Thanks again, I close this issue for now.

ebadi

comment created time in a month

delete branch RosettaCommons/PyRosetta.notebooks

delete branch : rabd3

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push eventRosettaCommons/PyRosetta.notebooks

Jared Adolf-Bryfogle

commit sha 66cb994635ab635c7d5e4a4f3c8aaa9a36306331

fix issue with block.

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Jared Adolf-Bryfogle

commit sha 207d46f935fa69aa1272163cc525d6e11e4ac67c

Merge pull request #66 from RosettaCommons/rabd3 Fix RabD issue with block.

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create barnchRosettaCommons/PyRosetta.notebooks

branch : rabd3

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issue commentRosettaCommons/binder

Issue using generated bindings

Re issue 1: Try initialize esmini without viewer: pyesminilib.SE_Init( '/home/[...]/esmini-pybind11/esmini/resources/xosc/lane_change.xosc',1,0,0,0) The viewer is quite complex and it would be interesting to see if the issue is related to it or not - a way to narrow down the scope.

Re issue 2: We've tried to stick with basic C data types to simplify DLL usage. Maybe it would be possible to use C++ std-types as well, but would need some investigation and testing on a few platforms.

ebadi

comment created time in a month