From 8c87bccb413e88102fda119d58c7d7fe5fa52c3b Mon Sep 17 00:00:00 2001 From: shntnu Date: Thu, 21 Mar 2024 10:17:00 +0000 Subject: [PATCH] deploy: d8a3b6963a81bcfe3b7b1bd69776e8e47c7f72e9 --- 05-create-profiles.html | 2 +- _sources/05-create-profiles.md | 2 +- searchindex.js | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/05-create-profiles.html b/05-create-profiles.html index 8759484..03c1c04 100644 --- a/05-create-profiles.html +++ b/05-create-profiles.html @@ -475,7 +475,7 @@

5.3. Create Database Backendcytominer-database installed, you can install it at the same time as pycytominer by changing the final command above to python3 -m pip install -e .[collate]

The command below first calls cytominer-database ingest to create the SQLite backend, and then pycytominer’s aggregate_profiles to create per-well profiles. Once complete, all files are uploaded to S3 and the local cache are deleted. This step takes several hours, but metadata creation and GitHub setup can be done in this time.

-

collate_cmd.py ingests and indexes the database.

+

collate.py ingests and indexes the database. collate_command.py exposes this functionality to the command line.

pyenv shell 3.8.10
 
 mkdir -p  ../../log/${BATCH_ID}/
diff --git a/_sources/05-create-profiles.md b/_sources/05-create-profiles.md
index a86ffda..fd397b7 100644
--- a/_sources/05-create-profiles.md
+++ b/_sources/05-create-profiles.md
@@ -77,7 +77,7 @@ Note that if your system does not already have `cytominer-database` installed, y
 
 The command below first calls `cytominer-database ingest` to create the SQLite backend, and then pycytominer's `aggregate_profiles` to create per-well profiles. Once complete, all files are uploaded to S3 and the local cache are deleted. This step takes several hours, but metadata creation and GitHub setup can be done in this time.
 
-[collate_cmd.py](https://github.com/cytomining/pycytominer/blob/master/pycytominer/cyto_utils/collate_cmd.py) ingests and indexes the database.
+[collate.py](https://github.com/cytomining/pycytominer/blob/master/pycytominer/cyto_utils/collate.py) ingests and indexes the database. [collate_command.py](https://github.com/cytomining/pycytominer/blob/master/pycytominer/cyto_utils/collate_cmd.py) exposes this functionality to the command line. 
 
 ```sh
 pyenv shell 3.8.10
diff --git a/searchindex.js b/searchindex.js
index 38ca8e6..623bd18 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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