Merge pull request #12 from gustaveroussy/dev

Dev

.github/workflows/ci.yml

@@ -1,8 +1,12 @@
 name: ci
 on:
   push:
+    branches: [master]
     tags:
       - v*
+  pull_request:
+    branches: [master]
+
 jobs:
   deploy-doc:
     runs-on: ubuntu-latest
@@ -46,6 +50,7 @@ jobs:
         run: poetry run mkdocs gh-deploy --force
   publish:
     needs: [deploy-doc]
+    if: contains(github.ref, 'tags')
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3

.gitignore

@@ -8,7 +8,9 @@ explore
 sandbox
 *.html
 .env
-tuto.*
+*.h5ad
+*.zarr
+*.explorer
 
 # OS related
 .DS_Store
@@ -31,6 +33,7 @@ run.log
 .ipynb_checkpoints
 exploration/*
 *.ipynb
+!docs/tutorials/**.ipynb
 !notebooks/*.ipynb
 
 # pyenv

CHANGELOG.md

@@ -1,11 +1,17 @@
-## [1.0.x] - tbd
+## [1.0.2] - 2024-01-15
 
 ### Fix
 - When geometries are `GeometryCollection`, convert them back to Polygons (#11)
-- Snakemake pipeline fixed when providing `min_area` parameter to Baysor
+- Give `min_area` parameter to the right Baysor function in snakemake
 
 ### Added
+- API tutorial
+- `sopa.spatial` tutorial
 - Docstrings for the snakemake pipeline utils
+- Show right micron scale in the Xenium Explorer
+
+### Changed
+- `sopa.stats` is now called `sopa.spatial`
 
 ## [1.0.1] - 2024-01-10
 

docs/api/spatial.md

@@ -0,0 +1,23 @@
+::: sopa.spatial.mean_distance
+    options:
+      show_root_heading: true
+
+::: sopa.spatial.geometrize_niches
+    options:
+      show_root_heading: true
+
+::: sopa.spatial.niches_geometry_stats
+    options:
+      show_root_heading: true
+
+::: sopa.spatial.cells_to_groups
+    options:
+      show_root_heading: true
+
+::: sopa.spatial.spatial_neighbors
+    options:
+      show_root_heading: true
+
+::: sopa.spatial.prepare_network
+    options:
+      show_root_heading: true

docs/cli.md

@@ -323,6 +323,7 @@ $ sopa explorer write [OPTIONS] SDATA_PATH
 * `--output-path TEXT`: Path to a directory where Xenium Explorer's outputs will be saved. By default, writes to the same path as `sdata_path` but with the `.explorer` suffix
 * `--gene-column TEXT`: Column name of the points dataframe containing the gene names
 * `--shapes-key TEXT`: Sdata key for the boundaries. By default, uses the baysor boundaires, else the cellpose boundaries
+* `--pixelsize FLOAT`: Number of microns in a pixel. Invalid value can lead to inconsistent scales in the Explorer.  [default: 0.2125]
 * `--lazy / --no-lazy`: If `True`, will not load the full images in memory (except if the image memory is below `ram_threshold_gb`)  [default: lazy]
 * `--ram-threshold-gb INTEGER`: Threshold (in gygabytes) from which image can be loaded in memory. If `None`, the image is never loaded in memory  [default: 4]
 * `--mode TEXT`: String that indicated which files should be created. `'-ib'` means everything except images and boundaries, while `'+tocm'` means only transcripts/observations/counts/metadata (each letter corresponds to one explorer file). By default, keeps everything