Constructing spatial neighborhood with custom parameters

[Qirongmao97]

No description provided.

[niklasmueboe]

I think this should rather be multiple scripts, one per methodology; radius, delaunay, ... rather than having all as one script just because squidpy decided to have them represented by a single function. This would make tracking differently generated neighborhoods easier.

[niklasmueboe]

General comment for all cases;

I think arguments such as radius, n_neighbors should be moved to the config rather than in the CLI

[niklasmueboe]

Are the spatial_distances matrices actually needed at all?

[Qirongmao97]

General comment for all cases;

I think arguments such as radius, n_neighbors should be moved to the config rather than in the CLI

Just wondering if it is still necessary to separate them into different files based on different functions since the parameters could be set up all at once in the config file now.

[Qirongmao97]

Are the spatial_distances matrices actually needed at all?

I will then remove them from the script.

[niklasmueboe]

General comment for all cases;
I think arguments such as radius, n_neighbors should be moved to the config rather than in the CLI

Just wondering if it is still necessary to separate them into different files based on different functions since the parameters could be set up all at once in the config file now.

I would still keep it separate because it is easier to track that you have e.g. neighbors defined using a radius if there is a specific script for that rather than having to parse the json file and then looking into the logic that is actually implemented when using these parameters

[niklasmueboe]

ContextManager will automatically close the file. This line is not needed

[Qirongmao97]

Removed in all scripts

[niklasmueboe]

You should also use a config file for the other scripts to pass radius etc. Make sure that the scripts and the yaml files have the same name so it is clear which ones belong together

[Qirongmao97]

You should also use a config file for the other scripts to pass radius etc. Make sure that the scripts and the yaml files have the same name so it is clear which ones belong together

Config file added

[Qirongmao97]

I noticed that in #154 spatial distance metric is needed as input.

[niklasmueboe]

Configs should be per script not for all at the same time. Laso I think now that we expanded this we should move each script with its yaml and config into a subdirectory. Should be an easy change. Maake sure to put each config also into a subdirectory called config.

[niklasmueboe]

Why delaunay: false. I think for this one we won't need a config at all. And delaunay should always be true