diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 0da743b..0e6ba20 100755 --- a/.github/workflows/CI.yml +++ b/.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 diff --git a/docs/commands/create-screen.md b/docs/commands/create-screen.md index 4cf6964..d9200b7 100644 --- a/docs/commands/create-screen.md +++ b/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. \ No newline at end of file +`gRNA_library.csv` and `sample_list.csv` should be formatted as :ref:`input`. \ No newline at end of file diff --git a/docs/qc.rst b/docs/qc.rst index e0fbb94..604e77a 100644 --- a/docs/qc.rst +++ b/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 \ No newline at end of file diff --git a/docs/run.rst b/docs/run.rst index aea11a9..a6dc1fc 100644 --- a/docs/run.rst +++ b/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 \ No newline at end of file diff --git a/docs/subcommands.rst b/docs/subcommands.rst index 2feb03d..56319ca 100644 --- a/docs/subcommands.rst +++ b/docs/subcommands.rst @@ -11,3 +11,4 @@ Subcommands qc filter run + create_screen \ No newline at end of file