prep for 1.8 release (#852)

* prep for 1.8 release * update stale copyrights * more copyright and name updates to Foundation * Foundation * update tiledbsoma dep to 1.5.1 * Python acceptance tests results * Add R acceptance tests results * Regenerate R docs for release 1.8 (#860) --------- Co-authored-by: Emanuele Bezzi <[email protected]>
chanzuckerberg · Nov 20, 2023 · bba0112 · bba0112
1 parent 6a81cd8
commit bba0112
Show file tree

Hide file tree

Showing 49 changed files with 1,325 additions and 148 deletions.
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022-2023 Chan Zuckerberg Initiative
+Copyright (c) 2022-2023 Chan Zuckerberg Initiative Foundation
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/api/python/cellxgene_census/LICENSE b/api/python/cellxgene_census/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022 Chan Zuckerberg Initiative
+Copyright (c) 2022-2023 Chan Zuckerberg Initiative Foundation
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/api/python/cellxgene_census/pyproject.toml b/api/python/cellxgene_census/pyproject.toml
@@ -7,7 +7,7 @@ name = "cellxgene_census"
 dynamic = ["version"]
 description = "API to facilitate the use of the CZ CELLxGENE Discover Census. For more information about the API and the project visit https://github.com/chanzuckerberg/cellxgene-census/"
 authors = [
-    { name = "Chan Zuckerberg Initiative", email = "[email protected]" }
+    { name = "Chan Zuckerberg Initiative Foundation", email = "[email protected]" }
 ]
 license = { text = "MIT" }
 readme = "README.md"
@@ -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~=1.4.3",
+    "tiledbsoma~=1.5.1",
     "anndata",
     "numpy>=1.21,<1.25",  # numpy is constrained by numba and the old pip solver
     "requests",

diff --git a/api/python/cellxgene_census/src/cellxgene_census/_experiment.py b/api/python/cellxgene_census/src/cellxgene_census/_experiment.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2022-2023 Chan Zuckerberg Initiative
+# Copyright (c) 2022-2023 Chan Zuckerberg Initiative Foundation
 #
 # Licensed under the MIT License.
 

diff --git a/api/python/cellxgene_census/src/cellxgene_census/_get_anndata.py b/api/python/cellxgene_census/src/cellxgene_census/_get_anndata.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2022-2023 Chan Zuckerberg Initiative
+# Copyright (c) 2022-2023 Chan Zuckerberg Initiative Foundation
 #
 # Licensed under the MIT License.
 

diff --git a/api/python/cellxgene_census/src/cellxgene_census/_open.py b/api/python/cellxgene_census/src/cellxgene_census/_open.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2022-2023 Chan Zuckerberg Initiative
+# Copyright (c) 2022-2023 Chan Zuckerberg Initiative Foundation
 #
 # Licensed under the MIT License.
 

diff --git a/api/python/cellxgene_census/src/cellxgene_census/_presence_matrix.py b/api/python/cellxgene_census/src/cellxgene_census/_presence_matrix.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2022-2023 Chan Zuckerberg Initiative
+# Copyright (c) 2022-2023 Chan Zuckerberg Initiative Foundation
 #
 # Licensed under the MIT License.
 

diff --git a/api/python/cellxgene_census/src/cellxgene_census/_release_directory.py b/api/python/cellxgene_census/src/cellxgene_census/_release_directory.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2022-2023 Chan Zuckerberg Initiative
+# Copyright (c) 2022-2023 Chan Zuckerberg Initiative Foundation
 #
 # Licensed under the MIT License.
 

diff --git a/api/python/cellxgene_census/src/cellxgene_census/experimental/util/_csr_iter.py b/api/python/cellxgene_census/src/cellxgene_census/experimental/util/_csr_iter.py
@@ -22,6 +22,9 @@ def X_sparse_iter(
     reindex_sparse_axis: bool = True,
 ) -> Iterator[_RT]:
     """
+    NOTE: this API is deprecated as of version 1.8, and will be removed in version
+    1.9. Please use the `blockwise` iterator support introduced in tiledbsoma version 1.5.
+
     Iterate over rows (or columns) of the query results X matrix, with pagination to
     control peak memory usage for large result sets. Each iteration step yields:
         * obs_coords (coordinates)
@@ -78,7 +81,7 @@ def X_sparse_iter(
         ...             ...
 
     Lifecycle:
-        experimental
+        deprecated
 
     See also: https://github.com/single-cell-data/TileDB-SOMA/issues/1528
     """

diff --git a/api/python/cellxgene_census/tests/README.md b/api/python/cellxgene_census/tests/README.md
diff --git a/api/r/cellxgene.census/DESCRIPTION b/api/r/cellxgene.census/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: cellxgene.census
 Title: CZ CELLxGENE Discover Cell Census
-Version: 1.7.0
+Version: 1.8.0
 Authors@R: 
-    person("Chan Zuckerberg Initiative", email = "[email protected]",
+    person("Chan Zuckerberg Initiative Foundation", email = "[email protected]",
            role = c("aut", "cre", "cph", "fnd"))
 Description: API to facilitate the use of the CZ CELLxGENE Discover 
   Census. For more information about the API and the project visit

diff --git a/api/r/cellxgene.census/LICENSE.md b/api/r/cellxgene.census/LICENSE.md
@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2023 Chan Zuckerberg Initiative
+Copyright (c) 2023 Chan Zuckerberg Initiative Foundation
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

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_compute_over_X.html b/api/r/cellxgene.census/docs/articles/census_compute_over_X.html
diff --git a/api/r/cellxgene.census/docs/articles/census_dataset_presence.html b/api/r/cellxgene.census/docs/articles/census_dataset_presence.html
diff --git a/api/r/cellxgene.census/docs/articles/census_datasets.html b/api/r/cellxgene.census/docs/articles/census_datasets.html
diff --git a/api/r/cellxgene.census/docs/articles/census_query_extract.html b/api/r/cellxgene.census/docs/articles/census_query_extract.html
diff --git a/api/r/cellxgene.census/docs/articles/comp_bio_census_info.html b/api/r/cellxgene.census/docs/articles/comp_bio_census_info.html