From ea083c753a9253f7ffc9056ba9ed6415abf3df5f Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <imaging@cdcl.ml>
Date: Tue, 14 Sep 2021 02:19:58 +0100
Subject: [PATCH] misc fixes

---
 .github/workflows/test.yml | 4 ++--
 scripts/amypet_gif.py      | 6 +++---
 setup.cfg                  | 3 ++-
 tests/test_gif.py          | 1 +
 tests/test_imtrimup.py     | 1 +
 5 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index dba0d47f..b5395e6c 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -38,7 +38,7 @@ jobs:
     - run: pre-commit run -a --show-diff-on-failure
   test:
     if: github.event_name != 'pull_request' || github.head_ref != 'devel'
-    runs-on: [self-hosted, python]
+    runs-on: [self-hosted, python, cuda]
     timeout-minutes: 4320
     strategy:
       matrix:
@@ -51,7 +51,7 @@ jobs:
     - name: Run setup-python
       run: setup-python -p${{ matrix.python }} miutil scikit-build cmake ninja
     - name: Install
-      run: pip install -U --no-binary nimpa "git+git://github.com/AMYPAD/miutil@devel#egg=miutil" "git+git://github.com/AMYPAD/NiftyPAD@master#egg=niftypad" -e .[dev,gif]
+      run: pip install -U --no-binary nimpa,nipet "git+git://github.com/AMYPAD/NiftyPAD@master#egg=niftypad" "git+git://github.com/NiftyPET/NIMPA@devel#egg=nimpa" "git+git://github.com/NiftyPET/NIPET@devel#egg=nipet" -e .[dev,gif,imtrimup]
     - run: pytest
     - run: codecov
     - name: Post Run setup-python
diff --git a/scripts/amypet_gif.py b/scripts/amypet_gif.py
index a832f8b5..3f66ca4b 100644
--- a/scripts/amypet_gif.py
+++ b/scripts/amypet_gif.py
@@ -67,12 +67,12 @@ def main(argv=None):
                             `pip install SimpleITK`"""
                         )
                     )
-            elif len(fn4b) >= 1:
+            else:
                 if len(fn4b) > 1:
                     log.warning("%d inputs found, selecting latest")
-                fingif = nsort(fn4b)[-1]
+                fingif = nsort(list(map(str, fn4b)))[-1]
                 log.debug("found N4-bias corrected:%s", fingif)
-                if len(fgif) != 0 or not args.overwrite_existing:
+                if fgif and not args.overwrite_existing:
                     log.warning("skipping")
                     continue
 
diff --git a/setup.cfg b/setup.cfg
index bc61e14e..932f0e13 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -61,9 +61,10 @@ niftypet=niftypet>=0.0.1
 niftypad=
 gif=
     argopt
-    miutil>0.8.0
+    miutil>=0.9.0
     nimpa
     SimpleITK>=1.2.0,<2
+imtrimup=nipet
 [options.entry_points]
 console_scripts=
     amypad=amypad.cli:main
diff --git a/tests/test_gif.py b/tests/test_gif.py
index 13cde1e4..0a064b54 100644
--- a/tests/test_gif.py
+++ b/tests/test_gif.py
@@ -20,6 +20,7 @@ def test_gif(fimin):
     else:
         fin = fimin
 
+    print(fin)
     gif.run(fin, outpath=outpath / "GIF")
 
 
diff --git a/tests/test_imtrimup.py b/tests/test_imtrimup.py
index 46b10c45..1aba8030 100644
--- a/tests/test_imtrimup.py
+++ b/tests/test_imtrimup.py
@@ -57,6 +57,7 @@ def dyndir(datain, mMRpars):
     return Path(opth) / "PET" / "multiple-frames"
 
 
+@pytest.mark.timeout(60 * 60)
 def test_rectrim(dyndir):
     rectrim = pytest.importorskip("amypad.rectrim")
     rectrim.run(dyndir)