[misc] release 1.10 PR (#969)

* bump versions in prep for 1.10 release * relax dependency pins * Regenerate R docs * More R docs stuff * try codecov fix * fix code cov config --------- Co-authored-by: Emanuele Bezzi <[email protected]>
chanzuckerberg · Feb 2, 2024 · bc6e773 · bc6e773
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diff --git a/.coveragerc b/.coveragerc
@@ -1,2 +1,7 @@
 [run]
 relative_files = True
+
+[report]
+omit =
+    # torch-generated JIT files
+    _remote_module_non_scriptable.py
diff --git a/api/python/cellxgene_census/pyproject.toml b/api/python/cellxgene_census/pyproject.toml
@@ -31,7 +31,7 @@ dependencies= [
     # NOTE: the tiledbsoma version must be >= to the version used in the Census builder, to
     # ensure that the assets are readable (tiledbsoma supports backward compatible reading).
     # Make sure this version does not fall behind the builder's tiledbsoma version.
-    "tiledbsoma~=1.6.0",
+    "tiledbsoma~=1.7.0",
     "anndata",
     "numpy>=1.21,<1.25",  # numpy is constrained by numba and the old pip solver
     "requests",

diff --git a/api/r/cellxgene.census/DESCRIPTION b/api/r/cellxgene.census/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: cellxgene.census
 Title: CZ CELLxGENE Discover Cell Census
-Version: 1.9.1
+Version: 1.10.0
 Authors@R: 
     person("Chan Zuckerberg Initiative Foundation", email = "[email protected]",
            role = c("aut", "cre", "cph", "fnd"))

diff --git a/api/r/cellxgene.census/_pkgdown.yml b/api/r/cellxgene.census/_pkgdown.yml
@@ -41,6 +41,10 @@ reference:
   contents:
     - get_census_version_description
     - get_census_version_directory
+- title: Census mirrors
+  contents:
+    - get_census_mirror
+    - get_census_mirror_directory
 
 articles:
 - title: Embeddings

diff --git a/api/r/cellxgene.census/docs/404.html b/api/r/cellxgene.census/docs/404.html
diff --git a/api/r/cellxgene.census/docs/LICENSE-text.html b/api/r/cellxgene.census/docs/LICENSE-text.html
diff --git a/api/r/cellxgene.census/docs/LICENSE.html b/api/r/cellxgene.census/docs/LICENSE.html
diff --git a/api/r/cellxgene.census/docs/articles/census_access_maintained_embeddings.html b/api/r/cellxgene.census/docs/articles/census_access_maintained_embeddings.html
diff --git a/...les/census_access_maintained_embeddings_files/figure-html/unnamed-chunk-4-1.png b/...les/census_access_maintained_embeddings_files/figure-html/unnamed-chunk-4-1.png
diff --git a/...les/census_access_maintained_embeddings_files/figure-html/unnamed-chunk-6-1.png b/...les/census_access_maintained_embeddings_files/figure-html/unnamed-chunk-6-1.png