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**Is your feature request related to a problem? Please describe.**
To keep this plugin as optimized as possible, it would be useful to do a run through and cache some queries/methods.
We should u…
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Hello,
I'm currently running `OrthoFinder` on a cluster with `2000` species. Besides using the `-op` option for `BLAST`, are there any other commands or methods for distributing the tasks?
Addit…
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It has been noted that the current implementation of GUI windows lacks comprehensive exception handling. This can lead to application instability if exceptions occur during the window's loading or ini…
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The current implementation of the `req.accepts`, `req.acceptsEncodings`, and `req.acceptsEncoding` methods in _lib/request.js_ creates a new `accepts` instance for each call.
Am I correct to think…
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`LevenbergMarquardt` currently accepts `xtol` and `gtol` arguments in the constructor. These are passed as the respective arguments into the `MINPACK::lmdif()` call. These appear to be duplicates of `…
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Methods that are mentioned in the literature are
- Binary Segmentation, currently implemented via `segmentation="BS"` and `optimizer="line_search"`.
- naive Optimistic Binary Segmentation, current…
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Currently, the default for LevMar, NelderMead, etc. is set to epsilon for single precision float `'epsfcn': 1.1920928955078125e-07`. Why was it chosen this way?
I don't think anyone still uses mac…
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# Feature: Gradients and geometry optimization.
## Summary
Implement convenience methods to utilize existing integrals for gradient calculations, streamlining their use e.g. geometry optimization …
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At the moment, our only optimized decompression is for `SparseMatrixCSC` in `:direct` mode: we store a vector of `compressed_indices` such that `nonzeros(A) = vec(B)[compressed_indices]`.
We can prob…
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I tried to optimize some of the program by implementing multiprocessing with the parse_links method, but on some templates the program still takes several minutes to run. Any work on code optimization…