Open CameronFRWatson opened 6 months ago
Working branch
https://github.com/goeckslab/tools-mti/tree/scimap-update-1.3.10
Goals
scimap 1.3.10
which will bring anndata
up to 0.10.5
Current status
quay.io/goeckslab/scimap:1.3.10
), pinned scimap and anndata versions, pushed to quay.io mcmicro_to_anndata.xml
tutorial_data.h5ad
to accommodate file size of h5ad files output by anndata >0.10
(file size differs substantially from previous anndata versions due to different default float type being used and addition of layers attribute) scimap_spatial.xml
PARC
option for clustering, so removed related params from the Galaxy wrapper xml scimap_phenotyping.xml
rescale_plots
from XML to reflect tool change random_state
param to Galaxylog
boolean param to wrapper To-do
build.sh
and meta.yml
) to reflect changes in the Docker image Working branch
No working branch yet
Goals
anndata
to at least 0.8.0
, maybe need to be higher? Current status
--platform linux/amd64
in build command
ImportError: Error importing numpy: you should not try to import numpy from
its source directory; please exit the numpy source tree, and relaunch
your python interpreter from there.
To-do
Working branch
No working branch yet
Goals
Squidpy
to 1.4.1
and bring anndata
to 0.10
Current status
1.1.2
to 1.4.1
and have prioritized changes that may need to be addressedTo-do
ax
keyword can now be passed to squidpy.pl.nhood_enrichment
functionlibrary_key
in squidpy.gr.spatial_neighbors
to support building graphs across multiple slidespercentile
option to squidpy.gr.spatial_neighbors
to filter neighbor graph using percentile of distances threshold.attr
option to squidpy.gr.spatial_autocorr
to select values from anndata.AnnData.obs
or anndata.AnnData.obsm.
squidpy.gr.ligrec
use_raw
in squidpy.gr.spatial_autocorr
pandas
inf squidpy.pl.ligrec
sq.gr.nhood_enrichment
Breaking change between
anndata 0.10
and prior versions means that some of our tools runninganndata 0.7-0.8
are incompatible with tool suites that runanndata 0.10
, resulting in the following error when trying to read h5ad files from the newer version:This impacts tools in the following suites:
Scimap
(Requires version upgrade to1.3.3
)Squidpy
(Requires version upgrade to>=1.3
)Vitessce
(May require version upgrade, but maybe be able to just re-pin anndata version in Dockerfile and conda build files)Short term fix:
Longer term:
scimap
,squidpy
, andvitessce
(This will become its own issue)