update cell census name in docstrings/md files

README.md

@@ -64,7 +64,7 @@ Reference documentation can also be accessed directly from Python or R.
 It is recommended to install the CELLxGENE Census and all of its dependencies in a new virtual environment via `pip`:
 
 ```
-pip install -U cell-census
+pip install -U cellxgene-census
 ```
 
 #### Usage examples

api/python/cellxgene_census/src/cellxgene_census/_open.py

@@ -4,7 +4,7 @@
 
 """Open census and related datasets
 
-Contains methods to open  publicly hosted versions of Cell Census object and access its source datasets.
+Contains methods to open publicly hosted versions of Census object and access its source datasets.
 """
 
 import os.path
@@ -51,7 +51,7 @@ def open_soma(
     uri: Optional[str] = None,
     context: Optional[soma.options.SOMATileDBContext] = None,
 ) -> soma.Collection:
-    """Open the Cell Census by version or URI.
+    """Open the Census by version or URI.
 
     Args:
         census_version:
@@ -74,8 +74,8 @@ def open_soma(
         Experimental.
 
     Examples:
-        Open the default Cell Census version, using a context manager which will automatically
-        close the census upon exit of the context.
+        Open the default Census version, using a context manager which will automatically
+        close the Census upon exit of the context.
 
         >>> with cellxgene_census.open_soma() as census:
                 ...
@@ -86,17 +86,17 @@ def open_soma(
             ...
             census.close()
 
-        Open a specific Cell Census by version:
+        Open a specific Census by version:
 
         >>> with cellxgene_census.open_soma("2022-12-31") as census:
                 ...
 
-        Open a Cell Census by S3 URI, rather than by version.
+        Open a Census by S3 URI, rather than by version.
 
         >>> with cellxgene_census.open_soma(uri="s3://bucket/path") as census:
                 ...
 
-        Open a Cell Census by path (file:// URI), rather than by version.
+        Open a Census by path (file:// URI), rather than by version.
 
         >>> with cellxgene_census.open_soma(uri="/tmp/census") as census:
                 ...
@@ -106,7 +106,7 @@ def open_soma(
         return _open_soma({"uri": uri, "s3_region": None}, context)
 
     if census_version is None:
-        raise ValueError("Must specify either a cell census version or an explicit URI.")
+        raise ValueError("Must specify either a census version or an explicit URI.")
 
     description = get_census_version_description(census_version)  # raises
     return _open_soma(description["soma"], context)

api/python/cellxgene_census/src/cellxgene_census/_release_directory.py

@@ -2,9 +2,9 @@
 #
 # Licensed under the MIT License.
 
-"""Versioning of Cell Census builds
+"""Versioning of Census builds
 
-Methods to retrieve information about versions of the publicly hosted Cell Census object.
+Methods to retrieve information about versions of the publicly hosted Census object.
 """
 
 from typing import Dict, Optional, Union, cast
@@ -13,7 +13,7 @@
 from typing_extensions import TypedDict
 
 """
-The following types describe the expected directory of Cell Census builds, used
+The following types describe the expected directory of Census builds, used
 to bootstrap all data location requests.
 """
 CensusVersionName = str  # census version name, e.g., "release-99", "2022-10-01-test", etc.
@@ -41,8 +41,7 @@
 
 
 def get_census_version_description(census_version: str) -> CensusVersionDescription:
-    """Get release description for given census version, from the Cell
-    Census release directory.
+    """Get release description for given Census version, from the Census release directory.
 
     Args:
         census_version:
@@ -72,13 +71,13 @@ def get_census_version_description(census_version: str) -> CensusVersionDescript
     census_directory = get_census_version_directory()
     description = census_directory.get(census_version, None)
     if description is None:
-        raise KeyError(f"Unable to locate cell census version: {census_version}.")
+        raise KeyError(f"Unable to locate Census version: {census_version}.")
     return description
 
 
 def get_census_version_directory() -> Dict[CensusVersionName, CensusVersionDescription]:
     """
-    Get the directory of cell census releases currently available.
+    Get the directory of Census releases currently available.
 
     Returns:
         A dictionary that contains release names and their corresponding release description.

api/python/cellxgene_census/tests/README.md

@@ -1,22 +1,22 @@
 # Test README
 
-This directory contains tests of the cell-census package API, _and_ the use of the API on the
-live "corpus", i.e., data in the public cell census S3 bucket. The tests use Pytest, and have
+This directory contains tests of the cellxgene-census package API, _and_ the use of the API on the
+live "corpus", i.e., data in the public Census S3 bucket. The tests use Pytest, and have
 Pytest marks to control which tests are run.
 
-Tests can be run in the usual manner. First, ensure you have cell-census installed, e.g., from the top-level repo directory:
+Tests can be run in the usual manner. First, ensure you have cellxgene-census installed, e.g., from the top-level repo directory:
 
-> pip install -e ./api/python/cell_census/
+> pip install -e ./api/python/cellxgene_census/
 
 Then run the tests:
 
-> pytest ./api/python/cell_census/
+> pytest ./api/python/cellxgene_census/
 
 ## Pytest Marks
 
 There are two Pytest marks you can use from the command line:
 
-- live_corpus: tests that directly access the `latest` version of the Cell Census. Enabled by default.
+- live_corpus: tests that directly access the `latest` version of the Census. Enabled by default.
 - expensive: tests that are expensive (ie., cpu, memory, time). Disabled by default - enable with `--expensive`. Some of these tests are _very_ expensive, ie., require a very large memory host to succeed.
 
 By default, only relatively cheap & fast tests are run. To enable `expensive` tests:
@@ -42,10 +42,10 @@ When run, please record the results in this file (below) and commit the change t
   - EC2 instance type and any system config (i.e., swap)
   - host and OS as reported by `uname -a`
   - Python & package versions and OS - suggest capturing the output of `tiledbsoma.show_package_versions()`
-  - The Cell Census version used for the test (i.e., the version aliased as `latest`). This can be easily captured using `cell_census.get_census_version_description('latest')`
-  - the cell_census package version (ie., `cell_census.__version__`)
+  - The Census version used for the test (i.e., the version aliased as `latest`). This can be easily captured using `cellxgene_census.get_census_version_description('latest')`
+  - the cellxgene_census package version (ie., `cellxgene_census.__version__`)
 - any run notes
-- full output of: `pytest -v --durations=0 --expensive ./api/python/cell_census/tests/`
+- full output of: `pytest -v --durations=0 --expensive ./api/python/cellxgene_census/tests/`
 
 ## 2023-03-29
 

api/python/cellxgene_census/tests/test_acceptance.py

@@ -1,5 +1,5 @@
 """
-Acceptance tests for the CELLxGENE Census.
+Acceptance tests for the Census.
 
 NOTE: those marked `expensive` are not run in the CI as they are, well, expensive...
 

tools/cellxgene_census_builder/README.md

@@ -1,6 +1,6 @@
 # README
 
-This package contains code to build and release the CELLxGENE Census in the SOMA format, as specified in the
+This package contains code to build and release the Census in the SOMA format, as specified in the
 [data schema](https://github.com/chanzuckerberg/cellxgene-census/blob/main/docs/cell_census_schema.md).
 
 This tool is not intended for end-users - it is used by the CELLxGENE team to periodically create and release all
@@ -136,13 +136,13 @@ The build process:
 - (Optional) Validate the entire Census, re-reading from storage.
 
 Modes of operation:
-a) (default) creating the entire "census" using all files currently in the CELLxGENE repository.
-b) creating a smaller "census" from a user-provided list of files (a "manifest")
+a) (default) creating the entire "Census" using all files currently in the CELLxGENE repository.
+b) creating a smaller "Census" from a user-provided list of files (a "manifest")
 
-#### Mode (a) - creating the full cell census from the entire CELLxGENE (public) corpus:
+#### Mode (a) - creating the full Census from the entire CELLxGENE (public) corpus:
 
 - On a large-memory machine with _ample_ free (local) disk (eg, 3/4 TB or more) and swap (1 TB or more)
-- To create a cell census at `<census_path>`, execute:
+- To create a Census at `<census_path>`, execute:
   > $ python -m cellxgene_census_builder -mp --max-workers 12 <census_path> build
 - Tips:
   - `-v` to view info-level logging during run, or `-v -v` for debug-level logging
@@ -151,7 +151,7 @@ b) creating a smaller "census" from a user-provided list of files (a "manifest")
 
 If you run out of memory, reduce `--max-workers`. You can also try a higher number if you have lots of CPU & memory.
 
-#### Mode (b) - creating a cell census from a user-provided list of H5AD files:
+#### Mode (b) - creating a Census from a user-provided list of H5AD files:
 
 - Create a manifest file, in CSV format, containing two columns: dataset_id, h5ad_uri. Example:
   ```csv
@@ -160,5 +160,5 @@ If you run out of memory, reduce `--max-workers`. You can also try a higher numb
   5b93b8fc-7c9a-45bd-ad3f-dc883137de30, /files/5b93b8fc-7c9a-45bd-ad3f-dc883137de30.h5ad
   ```
   You can specify a file system path or a URI in the second field
-- To create a cell census at `<census_path>`, execute:
+- To create a Census at `<census_path>`, execute:
   > $ python -m cellxgene_census_builder <census_path> build --manifest <the_manifest_file.csv>

tools/cellxgene_census_builder/src/cellxgene_census_builder/__main__.py

@@ -145,7 +145,7 @@ def do_create_reports(args: CensusBuildArgs) -> bool:
 
 
 def create_args_parser() -> argparse.ArgumentParser:
-    parser = argparse.ArgumentParser(prog="cellxgene_census_builder", description="Build the official cell census.")
+    parser = argparse.ArgumentParser(prog="cellxgene_census_builder", description="Build the official Census.")
     parser.add_argument("working_dir", type=str, help="Working directory for the build")
     parser.add_argument(
         "--test-resume",

tools/cellxgene_census_builder/src/cellxgene_census_builder/build_soma/__main__.py

@@ -50,7 +50,7 @@ def create_args_parser() -> argparse.ArgumentParser:
     subparsers = parser.add_subparsers(required=True, dest="subcommand")
 
     # BUILD
-    build_parser = subparsers.add_parser("build", help="Build Cell Census")
+    build_parser = subparsers.add_parser("build", help="Build the Census")
     build_parser.add_argument(
         "--manifest",
         type=argparse.FileType("r"),
@@ -71,7 +71,7 @@ def create_args_parser() -> argparse.ArgumentParser:
     build_parser.add_argument("--test-disable-dirty-git-check", action=argparse.BooleanOptionalAction)
 
     # VALIDATE
-    subparsers.add_parser("validate", help="Validate an existing cell census build")
+    subparsers.add_parser("validate", help="Validate an existing Census build")
 
     return parser
 

tools/cellxgene_census_builder/src/cellxgene_census_builder/build_soma/datasets.py

@@ -64,7 +64,7 @@ def assign_dataset_soma_joinids(datasets: List[Dataset]) -> None:
 
 def create_dataset_manifest(info_collection: soma.Collection, datasets: List[Dataset]) -> None:
     """
-    Write the Cell Census `census_datasets` dataframe
+    Write the Census `census_datasets` dataframe
     """
     logging.info("Creating dataset_manifest")
     manifest_df = Dataset.to_dataframe(datasets)

tools/cellxgene_census_builder/src/cellxgene_census_builder/census_summary.py

@@ -158,15 +158,15 @@ def display_diff(
 
 def create_args_parser() -> argparse.ArgumentParser:
     parser = argparse.ArgumentParser(prog="cellxgene_census_summary")
-    parser.add_argument("-c", "--census-version", default="latest", help="Version of the census. Defaults to latest")
+    parser.add_argument("-c", "--census-version", default="latest", help="Version of the Census. Defaults to latest")
     subparsers = parser.add_subparsers(required=True, dest="subcommand")
 
     # BUILD
-    subparsers.add_parser("summarize", help="Summarize the cell census")
+    subparsers.add_parser("summarize", help="Summarize the Census")
 
     # VALIDATE
-    diff_parser = subparsers.add_parser("diff", help="Shows the diff with a previous census version")
-    diff_parser.add_argument("-p", "--previous-version", help="Version of the census to diff")
+    diff_parser = subparsers.add_parser("diff", help="Shows the diff with a previous Census version")
+    diff_parser.add_argument("-p", "--previous-version", help="Version of the Census to diff")
 
     return parser
 

tools/cellxgene_census_builder/tests/test_builder.py

@@ -111,7 +111,7 @@ def test_base_builder_creation(
 def test_unicode_support(tmp_path: pathlib.Path) -> None:
     """
     Regression test that unicode is supported correctly in tiledbsoma.
-    This test is not strictly necessary, but it validates the requirements that Cell Census
+    This test is not strictly necessary, but it validates the requirements that Census
     support unicode in DataFrame columns.
     """
     pd_df = pd.DataFrame(data={"value": ["Ünicode", "S̈upport"]}, columns=["value"])