@jadolfbr Much agreed! Ideally those cells were tested before merging, but if I recall correctly those debug statements added in #51 were merely intended as a temporary workaround to permit scheduling 03 PyRosetta unit tests from PRs in RosettaCommons/main (otherwise PyRosetta tests always were failing). Those notebooks cells still need to be addressed.

Those unit test errors were basically saying that this notebook was broken. Without that - I'm not quite understanding why the testing is happening in first place?

I may have added debug statements to cells of certain notebooks that produced unit test errors. If you remove dubug statements, please open a PR in RosettaCommons/main, pull in Pyrosetta.notebooks submodule updates, and schedule the 03 PyRosetta tests to queue PyRosetta4.notebook unit tests.

The function signature has changed for the parser and this needs to be fixed. Also, debug statements should only not run for long components. Not sure where that part changed. I have a branch with this fixed, but for some reason, can't push to the repo.

cdr_selector = CDRResidueSelector()

ERROR: Assertion active( key ) failed. ERROR:: Exit from: /home/benchmark/rosetta/source/build/PyRosetta/linux/clang-3.4.2/python-3.8/release/source/src/utility/keys/SmallKeyVector.hh line: 548 Traceback (most recent call last): File "<stdin>", line 1, in <module> RuntimeError:

File: /home/benchmark/rosetta/source/build/PyRosetta/linux/clang-3.4.2/python-3.8/release/source/src/utility/keys/SmallKeyVector.hh:548 [ ERROR ] UtilityExitException ERROR: Assertion active( key ) failed.

sorry, I forgot run init().

Is this from a notebook you ran as is, or from your own programming?

If the latter, my initial guess is that you forgot to call the init() function prior to calling other PyRosetta functions.

cdr_selector = CDRResidueSelector()

ERROR: Assertion active( key ) failed. ERROR:: Exit from: /home/benchmark/rosetta/source/build/PyRosetta/linux/clang-3.4.2/python-3.8/release/source/src/utility/keys/SmallKeyVector.hh line: 548 Traceback (most recent call last): File "<stdin>", line 1, in <module> RuntimeError:

File: /home/benchmark/rosetta/source/build/PyRosetta/linux/clang-3.4.2/python-3.8/release/source/src/utility/keys/SmallKeyVector.hh:548 [ ERROR ] UtilityExitException ERROR: Assertion active( key ) failed.

Updates the requirements on jwlawson/actions-setup-cmake to permit the latest version. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/jwlawson/actions-setup-cmake/releases">jwlawson/actions-setup-cmake's releases</a>.</em></p> <blockquote> <h2>v1.6</h2> <ul> <li>Fix incorrectly selecting invalid architecture packages</li> <li>Update dependencies</li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li>See full diff in <a href="https://github.com/jwlawson/actions-setup-cmake/commits/0a4250e9746afbf8007d5fc3b26e5b0577e332b9">compare view</a></li> </ul> </details> <br />

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Updates the requirements on jwlawson/actions-setup-cmake to permit the latest version. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/jwlawson/actions-setup-cmake/releases">jwlawson/actions-setup-cmake's releases</a>.</em></p> <blockquote> <h2>v1.5</h2> <ul> <li>Fix handling the new universal macos packages provided in cmake 3.19.2+</li> <li>Improve platform testing</li> <li>Update dependencies</li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li>See full diff in <a href="https://github.com/jwlawson/actions-setup-cmake/commits/b2390a7ca23f349493e575bbb2d838e99b9cb42d">compare view</a></li> </ul> </details> <br />

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Superseded by #2.

Updates the requirements on jwlawson/actions-setup-cmake to permit the latest version. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/jwlawson/actions-setup-cmake/releases">jwlawson/actions-setup-cmake's releases</a>.</em></p> <blockquote> <h2>v1.6</h2> <ul> <li>Fix incorrectly selecting invalid architecture packages</li> <li>Update dependencies</li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li>See full diff in <a href="https://github.com/jwlawson/actions-setup-cmake/commits/0a4250e9746afbf8007d5fc3b26e5b0577e332b9">compare view</a></li> </ul> </details> <br />

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`let obj = new MathMLParser()

obj.parse('<math xmlns="http://www.w3.org/1998/Math/MathML"><mover><mrow><mi>A</mi><mi>B</mi></mrow><mo>→</mo></mover></math>')`

在执行parse后页面卡死 @是因为使用方法有问题吗？麻烦提供测试案例

请提供具体使用测试用例，谢谢

Updates the requirements on jwlawson/actions-setup-cmake to permit the latest version. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/jwlawson/actions-setup-cmake/releases">jwlawson/actions-setup-cmake's releases</a>.</em></p> <blockquote> <h2>v1.5</h2> <ul> <li>Fix handling the new universal macos packages provided in cmake 3.19.2+</li> <li>Improve platform testing</li> <li>Update dependencies</li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li>See full diff in <a href="https://github.com/jwlawson/actions-setup-cmake/commits/b2390a7ca23f349493e575bbb2d838e99b9cb42d">compare view</a></li> </ul> </details> <br />

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The example

+default_pointer_return_value_policy pybind11::return_value_policy::reference

at the bottom of this page https://cppbinder.readthedocs.io/en/latest/config.html#config-file-directives

is not handled in code. Possibly this line should be +default_member_pointer_return_value_policy pybind11::return_value_policy::reference

Thank you for letting me know @MartinKielhornPhilips ! This should be fixed in 3e65a2f0469268e7a87504c4f83866ab62a63edc

The example

+default_pointer_return_value_policy pybind11::return_value_policy::reference

at the bottom of this page https://cppbinder.readthedocs.io/en/latest/config.html#config-file-directives

is not handled in code. Possibly this line should be +default_member_pointer_return_value_policy pybind11::return_value_policy::reference

Hi, I'm thinking about testing this for one of the research projects I participate on and went over the install instructions -- I was just wondering if the release_60 for clang/llvm is a requiremement? Or can I use later/more modern LLVM releases? Thanks for the work on the project -- looks great!

thanks a lot! y.

On Thu, Dec 10, 2020 at 17:16 andriish notifications@github.com wrote:

Hi @jtrmal https://github.com/jtrmal ,

The CI tests binder using versions of LLVM up to 11 (as comes witj Fedora), I think.

Best regards,

Andrii

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/RosettaCommons/binder/issues/148#issuecomment-742622534, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACUKYXZQFP3YJQWTXYDSMGDSUDX7DANCNFSM4UVF3M5A .

Hi @jtrmal ,

The CI tests binder using versions of LLVM up to 11 (as comes witj Fedora), I think.

Best regards,

Andrii

Hi, I'm thinking about testing this for one of the research projects I participate on and went over the install instructions -- I was just wondering if the release_60 for clang/llvm is a requiremement? Or can I use later/more modern LLVM releases? Thanks for the work on the project -- looks great!