Joel Berendzen

Hi, to help with us users keeping up with developments, please create a release as well as update your tags. pypi lists 4.5.2 as the latest package, but there is...

Request: developers should be able to turn off dependency upper-bound calculations

6

- [x ] I have searched the [issues](https://github.com/python-poetry/poetry/issues) of this repo and believe that this is not a duplicate. - [x] I have searched the [documentation](https://python-poetry.org/docs/) and believe that my...

First, thanks for this project, which I find incredibly useful. This request is about avoiding duplication of work in the face of continuous integration by multiple developers. It's related to...

build fails on include location

1

make fails due to includes not being found. My guess is that the test environment depends on make having been previously run. If I install the bonsai includes directly, then...

please allow builds without recursive cloning

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Recursive cloning results in a mess for distro packagers and can be a headache for both security and functionality. An example is bonsai pulling in sketch, which pulls in a...

compilation fails under gcc > 12

1

Works under gcc-12.3.1_p20230623 First failure under gcc-13.1.1_p20230527 as below: x86_64-pc-linux-gnu-g++ -IlibBigWig -Ibonsai/include -Ibonsai -Ibonsai/hll -Ibonsai/hll/include -Ibonsai -I. -Isrc -Ifmt/include -O3 -march=native -fopenmp -pipe -DD2_CACHE_SIZE=4194304 -std=c++20 -Wall -Wextra -Wno-unused-function -Wno-char-subscripts -pedantic...

Please include license file

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I see no license file. I note that the dependencies (bonsai, fat, libBigWig), which are included by reference, are all MIT-licensed.

<bitset> needs inclusion in src/dp/hmm.cc

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BAli-Phy 3.6.1 gcc 12.2.1 glibc 2.36 Compilation error, bitset undefined. Fixed by this: `diff --git a/src/dp/hmm.cc b/src/dp/hmm.cc index 8be51b5..ea8a15e 100644 --- a/src/dp/hmm.cc +++ b/src/dp/hmm.cc @@ -24,6 +24,7 @@ /// #include...

Please enable deterministic scheduling in the pytest plugin under Trio

4

### Things to check first - [X] I have searched the existing issues and didn't find my feature already requested there ### Feature description I request a pytest plugin feature...

Please allow keyword arguments of deterministic scheduling and random-value generation

2

Deterministic scheduling is a very desirable characteristic for user code testing where external interactions can be mocked-up. In my view, this is one of the major advantages of trio over...