update cell census name in docstrings/md files #347

bkmartinjr · 2023-04-03T16:36:10Z

Fixes #319

This changes the name of cell census to cellxgene census in all docstrings/md files except the schema spec.

atolopko-czi

Two representative suggestions for casing, which would need to be applied throughout.

atolopko-czi · 2023-04-03T16:49:24Z

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 Cellxgene Census object and access its source datasets.


Suggested change

Contains methods to open publicly hosted versions of Cellxgene Census object and access its source datasets.

Contains methods to open publicly hosted versions of CELLxGENE Census object and access its source datasets.

@atolopko-czi - the motivating GH issue specifically requests the other capitalization. See slack, where I asked if this is actually correct.

atolopko-czi · 2023-04-03T16:50:11Z

tools/cellxgene_census_builder/README.md

@@ -139,10 +139,10 @@ 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")

-#### Mode (a) - creating the full cell census from the entire CELLxGENE (public) corpus:
+#### Mode (a) - creating the full cellxgene census from the entire CELLxGENE (public) corpus:


Suggested change

#### Mode (a) - creating the full cellxgene census from the entire CELLxGENE (public) corpus:

#### Mode (a) - creating the full CELLxGENE Census from the entire CELLxGENE (public) corpus:

or just Census

atolopko-czi

LGTM, with a handful of suggestions for more consistency.

atolopko-czi · 2023-04-03T20:27:48Z

api/python/cellxgene_census/tests/README.md

@@ -16,7 +16,7 @@ Then run the tests:

 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 Cellxgene Census. Enabled by default.


Suggested change

- live_corpus: tests that directly access the `latest` version of the Cellxgene Census. Enabled by default.

- live_corpus: tests that directly access the `latest` version of the CELLxGENE Census. Enabled by default.

atolopko-czi · 2023-04-03T20:28:00Z

api/python/cellxgene_census/tests/README.md

@@ -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 Cellxgene 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')`


Suggested change

- The Cellxgene 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 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')`

atolopko-czi · 2023-04-03T20:30:05Z

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

@@ -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")


Suggested change

subparsers.add_parser("validate", help="Validate an existing census build")

subparsers.add_parser("validate", help="Validate an existing Census build")

atolopko-czi · 2023-04-03T21:25:48Z

tools/cellxgene_census_builder/README.md


 - 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 cellxgene census at `<census_path>`, execute:


Suggested change

- To create a cellxgene census at `<census_path>`, execute:

- To create a census at `<census_path>`, execute:

atolopko-czi · 2023-04-03T21:25:55Z

tools/cellxgene_census_builder/README.md

@@ -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 cellxgene census from a user-provided list of H5AD files:


Suggested change

#### Mode (b) - creating a cellxgene census from a user-provided list of H5AD files:

#### Mode (b) - creating a census from a user-provided list of H5AD files:

atolopko-czi · 2023-04-03T21:26:05Z

tools/cellxgene_census_builder/README.md

@@ -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 cellxgene census at `<census_path>`, execute:


Suggested change

- To create a cellxgene census at `<census_path>`, execute:

- To create a census at `<census_path>`, execute:

atolopko-czi · 2023-04-03T21:26:38Z

tools/cellxgene_census_builder/src/cellxgene_census_builder/census_summary.py

@@ -162,7 +162,7 @@ def create_args_parser() -> argparse.ArgumentParser:
    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")


Suggested change

subparsers.add_parser("summarize", help="Summarize the census")

subparsers.add_parser("summarize", help="Summarize the Census")

pablo-gar

Added a few missed changes and capitalized all "Census".

Can merge after this minor changes.

pablo-gar · 2023-04-03T22:18:52Z

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

@@ -74,7 +74,7 @@ def open_soma(
        Experimental.

    Examples:
-        Open the default Cell Census version, using a context manager which will automatically
+        Open the default Census version, using a context manager which will automatically
        close the census upon exit of the context.


Suggested change

close the census upon exit of the context.

close the Census upon exit of the context.

pablo-gar · 2023-04-03T22:22:37Z

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

@@ -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}.")


Suggested change

raise KeyError(f"Unable to locate census version: {census_version}.")

raise KeyError(f"Unable to locate Census version: {census_version}.")

pablo-gar · 2023-04-03T22:24:45Z

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

@@ -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.


Suggested change

"""Get release description for given census version, from the Census release directory.

"""Get release description for given Census version, from the Census release directory.

pablo-gar · 2023-04-03T22:25:41Z

api/python/cellxgene_census/tests/README.md

-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


Suggested change

live "corpus", i.e., data in the public census S3 bucket. The tests use Pytest, and have

live "corpus", i.e., data in the public Census S3 bucket. The tests use Pytest, and have

pablo-gar · 2023-04-03T22:26:08Z

api/python/cellxgene_census/tests/README.md

 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/


Suggested change

> pip install -e ./api/python/cell_census/

> pip install -e ./api/python/cellxgene_census/

pablo-gar · 2023-04-03T22:31:01Z

tools/cellxgene_census_builder/README.md

@@ -139,10 +139,10 @@ 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")


Suggested change

b) creating a smaller "census" from a user-provided list of files (a "manifest")

b) creating a smaller "Census" from a user-provided list of files (a "manifest")

pablo-gar · 2023-04-03T22:31:25Z

tools/cellxgene_census_builder/README.md

@@ -139,10 +139,10 @@ 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")

-#### 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:


Suggested change

#### Mode (a) - creating the full census from the entire CELLxGENE (public) corpus:

#### Mode (a) - creating the full Census from the entire CZ CELLxGENE Discover(public) corpus:

pablo-gar · 2023-04-03T22:31:39Z

tools/cellxgene_census_builder/README.md


 - 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:


Suggested change

- To create a census at `<census_path>`, execute:

- To create a Census at `<census_path>`, execute:

pablo-gar · 2023-04-03T22:32:05Z

tools/cellxgene_census_builder/README.md

@@ -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:


Suggested change

#### Mode (b) - creating a census from a user-provided list of H5AD files:

#### Mode (b) - creating a Census from a user-provided list of H5AD files:

pablo-gar · 2023-04-03T22:32:18Z

tools/cellxgene_census_builder/README.md

@@ -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:


Suggested change

- To create a census at `<census_path>`, execute:

- To create a Census at `<census_path>`, execute:

update cell census name

fa087f5

bkmartinjr changed the title ~~update cell census name~~ update cell census name in docstrings/md files Apr 3, 2023

bkmartinjr requested review from pablo-gar and atolopko-czi April 3, 2023 16:39

bkmartinjr marked this pull request as ready for review April 3, 2023 16:39

atolopko-czi requested changes Apr 3, 2023

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bkmartinjr added 3 commits April 3, 2023 10:30

additional name changes

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bkmartinjr requested a review from atolopko-czi April 3, 2023 20:26

atolopko-czi approved these changes Apr 3, 2023

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bkmartinjr added 5 commits April 3, 2023 14:33

more name changes

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a missed name change

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nit docstring requests

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more errata

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and more

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pablo-gar approved these changes Apr 3, 2023

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bkmartinjr added 2 commits April 3, 2023 16:58

more capitalization fixes

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and some more

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bkmartinjr merged commit e9c57f4 into main Apr 4, 2023

bkmartinjr deleted the bkmartinjr/docstrings-name-update branch April 4, 2023 00:35

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update cell census name in docstrings/md files #347

update cell census name in docstrings/md files #347

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	Contains methods to open publicly hosted versions of Cellxgene Census object and access its source datasets.
	Contains methods to open publicly hosted versions of CELLxGENE Census object and access its source datasets.

	#### Mode (a) - creating the full cellxgene census from the entire CELLxGENE (public) corpus:
	#### Mode (a) - creating the full CELLxGENE Census from the entire CELLxGENE (public) corpus:

	- live_corpus: tests that directly access the `latest` version of the Cellxgene Census. Enabled by default.
	- live_corpus: tests that directly access the `latest` version of the CELLxGENE Census. Enabled by default.

	- The Cellxgene 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 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')`

	subparsers.add_parser("validate", help="Validate an existing census build")
	subparsers.add_parser("validate", help="Validate an existing Census build")

	- To create a cellxgene census at `<census_path>`, execute:
	- To create a census at `<census_path>`, execute:

	#### Mode (b) - creating a cellxgene census from a user-provided list of H5AD files:
	#### Mode (b) - creating a census from a user-provided list of H5AD files:

	subparsers.add_parser("summarize", help="Summarize the census")
	subparsers.add_parser("summarize", help="Summarize the Census")

	close the census upon exit of the context.
	close the Census upon exit of the context.

	raise KeyError(f"Unable to locate census version: {census_version}.")
	raise KeyError(f"Unable to locate Census version: {census_version}.")

	"""Get release description for given census version, from the Census release directory.
	"""Get release description for given Census version, from the Census release directory.

	live "corpus", i.e., data in the public census S3 bucket. The tests use Pytest, and have
	live "corpus", i.e., data in the public Census S3 bucket. The tests use Pytest, and have

	> pip install -e ./api/python/cell_census/
	> pip install -e ./api/python/cellxgene_census/

		@@ -139,10 +139,10 @@ 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")

	#### Mode (a) - creating the full census from the entire CELLxGENE (public) corpus:
	#### Mode (a) - creating the full Census from the entire CZ CELLxGENE Discover(public) corpus:

update cell census name in docstrings/md files #347

update cell census name in docstrings/md files #347

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