Jeffrey Hsu

The `n_test_samplers parameter` for `evalute_model` seems to be required in the config even though IntervalsSampler is specified in the config as well. The docstring for EvaluateModel makes it seem like...

I can paste the full config if you want, but it is the basic the Deeperdeepsea config with only the ops: [evaluate] set. The train_model and evaulate_model are both specified....

Have a similar issue getting a zero division error, but not quite the same: ```INFO @ Tue, 29 Nov 2022 11:03:12: 47534495 fragments have been read. INFO @ Tue, 29...

For blending I'm doing something like: ```python from stitching.blender import Blender blender = Blender() bsizes = [(img.shape[1], img.shape[0]) for img in ic_conv] result_df["y_pos2"] = result_df["y_pos"] - result_df["y_pos"].min() result_df["x_pos2"] = result_df["x_pos"]...

Matt Loose has some data from his Read Until paper: https://github.com/mattloose/RUscripts . Seems pretty small and all the scripts seem to work on it.

If brentp's pull request is accepted I would recommend using mpld3. http://mpld3.github.io/

The model itself takes one-hot encodings.

Thanks! The design matrix isn't affected, but the obs df is. ```python print(adf.obs.time.dtype) # Output: dtype('int64') # After creating DeseqDataSet dds = DeseqDataSet( adata=adf, design_factors=["treatment", "time"], continuous_factors=["time"], ref_level=["treatment", "CTRL"], )...

Snakemake version: 7.32.3 Snakemake wrapper: 2.6.0 I am getting a similar issue where logs for rules that use snakemake wrappers aren't getting written to logs if they error out. Running...

The rule: ``` rule STAR_multi: input: fq1 = input_reads, fq2 = input_reads_2, idx = config["star_index"], output: aln = f"{bp}STAR/{{sample}}/{{sample}}.bam", log = f"{bp}STAR/{{sample}}/{{sample}}.log", log_final = f"{bp}STAR/{{sample}}/Log.final.out", sj = f"{bp}STAR/{{sample}}/SJ.out.tab" log: f"{bp}logs/STAR/{{sample}}.log"...