Nicolas Ochsner

Cannot deepcopy models with gurobipy with BiGG id `st`

3

For some models it is not possible to apply `deepcopy`, because the reaction names may match reserved names of the gurobi LP format—see [gurobi docs](https://www.gurobi.com/documentation/9.1/refman/lp_format.html): > Also, variable names should...

`:%s` does not highlight in editor when using capture groups.

2

**Describe the bug** When using `\(` and `\)` to indicate a group, the matches will not be highlighted in editor. **To Reproduce** For ``` a = "foo" b = "@foo"...

Hi, the following code introduces a racecondition that may trigger when multiple instances of python import ete4 in parallel https://github.com/etetoolkit/ete/blob/254f25643fa59762b10bc1663472d52cfcc2df46/ete4/smartview/renderer/layouts/ncbi_taxonomy_layouts.py#L12-L20 Similar raceconditions apply for `smart2color.json` and `pfam2color.json`.

Hello! I'd like to collapse directories with single entries. Here is a possible implementation, that extends the default formatter. Coloring on this could be improved, to highlight the base of...

Hi I just went through the mildly painful process of trying to input data that includes local tags i.e. `!TagName`. Anyway the way that `dataclass_wizard` handles the loading and dumping...

jblas causes UnsatisfiedLinkError on aarch64 (m1) mac

9

jblas doesn't support m1 (jblas-project/jblas#134 )as @tgvaughan mentioned in CompEvol/beast2#1047 This results in the following errror. ``` java.lang.reflect.InvocationTargetException at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:119) at java.base/java.lang.reflect.Method.invoke(Method.java:577) at beast.app.beastapp.BeastLauncher.run(Unknown Source) at beast.app.beastapp.BeastLauncher.main(Unknown Source) Caused by:...

Hey, I wanted to be able to control which changes are shown from within the `.envrc` file, ideally by annotating commands in some way. This PR adds an environment variable...