| from functools import partial | |
| import math | |
| from typing import Literal | |
| from datashader.mpl_ext import dsshow, alpha_colormap | |
| import datashader as ds | |
| from joblib import parallel_backend | |
| from mpl_toolkits.axes_grid1 import ImageGrid | |
| import matplotlib.pyplot as plt | |
| import pandas as pd | |
| import scanpy as sc |
| def get_bbox(adata, library_id, *, library_key="sample", img_key="hires", margin=50): | |
| adata = adata[adata.obs[library_key] == library_id, :] | |
| coords = adata.obsm["spatial"] | |
| scale_factor = adata.uns["spatial"][library_id]["scalefactors"][f"tissue_{img_key}_scalef"] | |
| return tuple( | |
| np.array( | |
| [ | |
| np.min(coords[:, 0]) - margin, | |
| np.min(coords[:, 1]) - margin, | |
| np.max(coords[:, 0]) + margin, |
| #!/usr/bin/env python | |
| """ | |
| Query GitHub API for the status of the GitHub actions runs associated | |
| with a commit. | |
| Requirements: `pygithub`, the rest is standard lib. | |
| """ | |
| from github import Github |
It would be great to have a tighter integration with jupyter notebooks/Rmd notebooks.
See also Reportsrender v2 / Executable book project Reportsrender v2.
Parametrization with papermill/rmarkdown works, but is quite a bit of overhead. It should be possible to execute the notebooks from outside the pipeline (for development) and from within the pipeline using the results from the previous processes (in production)
It is currently not possible to run multiple instances of Zettlr (Zettlr/Zettlr#243).
As a workaround, I managed to run multiple instances of zettlr side-by-side by running them as different users.
For me this seems to work reasonably well, but this can lead to corruption of your settings or your notes -- Use at own risk.
# create a new user
| import igraph as ig | |
| import numpy as np | |
| from itertools import combinations | |
| def layout_components( | |
| graph: ig.Graph, | |
| component_layout: str = "fr", | |
| arrange_boxes: str = "dense", | |
| pad_x: float = 1.0, | |
| pad_y: float = 1.0, |
| <!DOCTYPE html> | |
| <html xmlns="http://www.w3.org/1999/xhtml" lang="" xml:lang=""> | |
| <head> | |
| <meta charset="utf-8" /> | |
| <meta name="generator" content="pandoc" /> | |
| <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" /> | |
| <title>test</title> | |
| <style> | |
| code{white-space: pre-wrap;} | |
| span.smallcaps{font-variant: small-caps;} |