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Looks like all major functionality of `TransformVariables` is available as optics/lenses, as defined in `Accessors`. Optics are very general and composable, so maybe it's worth looking into "replacing…
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I'm trying to calculate the pairwise alignment scores between a query protein sequence and a set of target protein sequences for all possible substitutions and indels of the query sequence. Currently …
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Hello bio python people,
Thank you so much for this module! It's really great and has helped us a lot. My issue is the following, I keep getting the message:
```
Bio.pairwise2 has been deprecat…
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```-> % python
Python 3.9.12 | packaged by conda-forge | (main, Mar 24 2022, 23:22:55)
[GCC 10.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import prod…
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#1296 introduced a new setting for lambda indentation, however I think it's inconsistent.
My uncrustify version is:
```bash
$uncrustify --version
Uncrustify-0.72.0
```
Say I have two lambd…
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`KanesMethod` uses and [`LUsolve` ](https://github.com/sympy/sympy/blob/4fb6b42dd0941f05178aa570edf9ef61162ce960/sympy/physics/mechanics/kane.py#L252) to solve the velocity constraints. While this mat…
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### Describe the bug
When passing `precisions_init` to a `GaussianMixture` model, a user expects to resume training the model from the provided precision matrices, which is done by calculating the …
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Hi,
While introducing biopython 1.80 in Debian experimental, I noticed in [Debian Bug#1024835] that pauvre fails when trying to run test suites with:
```
$ python3 -m unittest discover -v
```
…
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Hello,
I am trying to mutate a fasta sequence using a GTR model, but I can not figure out the abcdef parameter order. The vignette("sub-models") gives an indication but I am not familiar with the not…
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_Feature request_
In addition to the options to save graphical representations (PNG and SVG), it would be great to be able to save the configuration of tiles in an easy-to-parse text file, e.g. csv…