From 2cf2020d94454b7804fd53c426000d242e53ef27 Mon Sep 17 00:00:00 2001
From: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
Date: Wed, 29 May 2024 13:58:57 +0100
Subject: [PATCH] Update brainmapper to match cellfinder release candidate
 (#113)

* Update prep_model_weights to match cellfinder

* Set the backend for torch testing

* Fixed linting

* Move keras import inot set_device function

* Set GIHTUB_ACTIONS env variable to true when testing

* Added yield statement to not return set_device_arm until after all tests done

* Switched to using pytest_sessionstart instead of an autouse fixture

* Fixed linting

* Remove any changes relating to fixing macOS latest and PyTorch
---
 .github/workflows/test_and_deploy.yml    | 2 ++
 brainglobe_workflows/brainmapper/main.py | 1 -
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 75c252d..f8e29f0 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -30,6 +30,8 @@ jobs:
     needs: [linting, manifest]
     name: ${{ matrix.os }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
+    env:
+      KERAS_BACKEND: torch
     strategy:
       fail-fast: false
       matrix:
diff --git a/brainglobe_workflows/brainmapper/main.py b/brainglobe_workflows/brainmapper/main.py
index 66e6ef6..89b600f 100644
--- a/brainglobe_workflows/brainmapper/main.py
+++ b/brainglobe_workflows/brainmapper/main.py
@@ -154,7 +154,6 @@ def run_all(args, what_to_run, atlas):
             args.model_weights,
             args.install_path,
             args.model,
-            args.n_free_cpus,
         )
         if what_to_run.classify:
             if points is None: