From a75e06790705e91b72f2a2ba0b5f46fb58b5c1d8 Mon Sep 17 00:00:00 2001
From: Jason Kai <tkai@uwo.ca>
Date: Sat, 24 Feb 2024 10:08:22 -0500
Subject: [PATCH] Update run.py and config for snakebids 0.12.x

- Remove standard bids-app options from config (no longer necessary)
- Refactor run.py to work with new version
---
 docs/usage/cli.md           |  7 ++++---
 scattr/config/snakebids.yml | 31 -------------------------------
 scattr/run.py               | 21 +++++++++++----------
 3 files changed, 15 insertions(+), 44 deletions(-)

diff --git a/docs/usage/cli.md b/docs/usage/cli.md
index 134b2bb5..4b27ec7b 100644
--- a/docs/usage/cli.md
+++ b/docs/usage/cli.md
@@ -9,8 +9,9 @@ cases, only the required arguments are needed.
 
 ```{argparse}
 ---
-filename: ../scattr/run.py
-func: get_parser
+ref: scattr.run.get_parser
+#filename: ../scattr/run.py
+#func: get_parser
 prog: scattr
 ---
 ```
@@ -34,4 +35,4 @@ module: snakemake
 func: get_argument_parser
 prog: snakemake
 ---
-```
\ No newline at end of file
+```
diff --git a/scattr/config/snakebids.yml b/scattr/config/snakebids.yml
index b5b8c802..e3940dad 100644
--- a/scattr/config/snakebids.yml
+++ b/scattr/config/snakebids.yml
@@ -56,37 +56,6 @@ pybids_inputs_dwi:
 # Configuration for the command-line parameters to make available
 # passed on the argparse add_argument()
 parse_args:
-  #--- core BIDS-app options --- (do not modify below) ---#
-  bids_dir:
-    help: The directory with the input dataset formatted according to the
-      BIDS standard.
-
-  output_dir:
-    help: The directory where the output files should be stored. If you are
-      running group level analysis, this folder should be prepopulated
-      with the results of the participant level analysis.
-
-  analysis_level:
-    help: Level of the analysis that will be performed
-    choices: *analysis_levels
-
-  --participant_label:
-    help: The label(s) of the participant(s) that should be analyzed. The label
-      corresponds to sub-<participant_label> from the BIDS spec (so it does
-      not include "sub-"). If this parameter is not provided, all subjects
-      will be analyzed. Multiple participants can be specified with a space
-      seperated list.
-    nargs: "+"
-
-  --exclude_participant_label:
-    help: The label(s) of the participant(s) that should be excluded. The label
-      corresponds to sub-<participant_label> from the BIDS spec (so it does
-      not include "sub-"). If this parameter is not provided, all subjects
-      will be analyzed. Multiple participants can be specified with a space
-      sepearated list.
-    nargs: "+"
-  #-----------------------------------------------------#
-
   #--- additional BIDS-app options --- (add in below) --#
   --slurm_tmpdir:
     help: "Flag to indicate use of SLURM temporary directory. A temporary
diff --git a/scattr/run.py b/scattr/run.py
index 0d15d63d..9794a819 100644
--- a/scattr/run.py
+++ b/scattr/run.py
@@ -1,22 +1,23 @@
 #!/usr/bin/env python
-import os
+from pathlib import Path
 
-from snakebids.app import SnakeBidsApp
-from snakebids.cli import add_dynamic_args
+from snakebids import bidsapp, plugins
+
+app = bidsapp.app(
+    [
+        plugins.SnakemakeBidsApp(Path(__file__).resolve().parent),
+        plugins.Version(distribution="scattr"),
+    ]
+)
 
 
 def get_parser():
     """Exposes parser for sphinx doc generation, cwd is the docs dir"""
-    app = SnakeBidsApp("../scattr", skip_parse_args=True)
-    add_dynamic_args(
-        app.parser, app.config["parse_args"], app.config["pybids_inputs"]
-    )
-    return app.parser
+    return app.build_parser().parser
 
 
 def main():
-    app = SnakeBidsApp(os.path.abspath(os.path.dirname(__file__)))
-    app.run_snakemake()
+    app.run()
 
 
 if __name__ == "__main__":