update dependency

.github/workflows/CI.yml

@@ -27,7 +27,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install torch==1.12.1+cpu torchvision==0.13.1+cpu torchaudio==0.12.1 --extra-index-url https://download.pytorch.org/whl/cpu
+        pip install torch torchvision torchaudio
         pip install -r requirements.txt
         pip install -e .
     - name: Test with pytest

docs/commands/create-screen.md

@@ -1,12 +1,9 @@
-## `bean create-screen`: Create ReporterScreen object from flat files
+# `bean create-screen`: Create ReporterScreen object from flat files
 ```bash
 bean create-screen gRNA_library.csv sample_list.csv gRNA_counts_table.csv
 ```
-### Input
-  * [gRNA_library.csv](#1-gRNA_librarycsv)
-  * [sample_list.csv](#2-sample_listcsv)
+## Input
+  * gRNA_library.csv
+  * sample_list.csv
   * gRNA_counts_table.csv: Table with gRNA ID in the first column and sample IDs as the column names (first row)
-
-### Full Parameters
-  * `-e`, `--edits` (default: `None`): Path to edit counts .csv table, with index at first column and column names at the first row.
-  * `-o`, `--output-prefix` (default: `None`): Output file prefix (output will be saved as `output_prefix.h5ad`). If not provided, `gRNA_counts_table_csv` file prefix is used.
+`gRNA_library.csv` and `sample_list.csv` should be formatted as :ref:`input`.

docs/qc.rst

@@ -6,6 +6,6 @@
 Full parameters
 ==================
 .. argparse::
-   :filename: ../bean/qc/utils.py
+   :filename: ../bean/qc/parser.py
    :func: parse_args
    :prog: bean qc

docs/run.rst

@@ -6,6 +6,6 @@
 Full parameters
 ==================
 .. argparse::
-   :filename: ../bean/model/run.py
+   :filename: ../bean/model/parser.py
    :func: parse_args
    :prog: bean run

docs/subcommands.rst

@@ -11,3 +11,4 @@ Subcommands
     qc
     filter
     run
+    create_screen