Scott Gigante

Publish compiled wheels for Windows

4

Thanks for publishing precompiled wheels for Linux and MacOS. Would it be possible to publish wheels for Windows as well? Thanks!

s_gd2 typeerror

13

``` TypeError Traceback (most recent call last) in 1 import phate ----> 2 Y = phate.PHATE(knn_dist='precomputed').fit_transform(A) /mnt/eider_environments/EiderPython/local/apollo/env/EiderPython/python3.7/lib/python3.7/site-packages/phate/phate.py in fit_transform(self, X, **kwargs) 939 with _logger.task("PHATE"): 940 self.fit(X) --> 941 embedding =...

HML 9:57 AM Hello- I first want to say how impressed I am with the PHATE method! I was really excited when I came across the method a few months...

Add optional 7-day smoothing window

2

Here's a simple implementation of a 7-day smoothing window using a checkbox on the package page. I haven't been able to debug this as it's not clear to me how...

Feature request: print read ids of reads supporting variant

2

Is it possible to dump the read ids corresponding to those reads which supported a variant from `nanopolish variants`? I would like to use this for haplotype phasing.

``` Consider removing the 'r-reticulate' environment by running: Error in if (grep("virtualenvs", reticulate::py_config()$python)) { : argument is of length zero ```

C tutorial

1

I am attempting to integrate warp-ctc into an existing C++ project, but can't quite work out the initialisation. Is it possible to give a small-scale example in C of how...

### Minimal code sample ```python import scanpy as sc import rpy2.robjects as ro import rpy2.robjects.numpy2ri import anndata2ri rpy2.robjects.numpy2ri.activate() anndata2ri.activate() pbmc = sc.datasets.pbmc68k_reduced() ro.globalenv['sce'] = pbmc pbmc_converted = ro.globalenv['sce'] pbmc_converted.write_h5ad("test.h5ad") ```...

Taking len of `None` when passing matrices instead of anndata

1

The default value of `var_index` is `None`, but the first thing you do with it if the data is not `AnnData` is take the `len`. https://github.com/chriscainx/mnnpy/blob/master/mnnpy/mnn.py#L148 ``` >>> import numpy...

Current verbosity is hard-coded with `print` statements (e.g. https://github.com/chriscainx/mnnpy/blob/master/mnnpy/mnn.py#L168). Using `logging` and including a `verbose` keyword argument would allow users to turn these off if desired.