From 7493d037d8d9091a8d371412c76862355e5c997f Mon Sep 17 00:00:00 2001
From: Jeremi Levesque <jeremilevesque@hotmail.com>
Date: Fri, 8 Nov 2024 10:09:31 -0500
Subject: [PATCH 1/4] Update version of scilpy to a version with fixed packages
 for HPC

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 7739110b..36423d4e 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -8,7 +8,7 @@
 # -------
 requests==2.28.*
 dipy==1.9.*
-scilpy==2.0.2
+-e git+https://github.com/levje/scilpy@update_scilpy#egg=scilpy
 
 # -------
 # Other important dependencies

From b9d79350e7f34177a1d09812eeab4b5f87aac8f6 Mon Sep 17 00:00:00 2001
From: Jeremi Levesque <jeremilevesque@hotmail.com>
Date: Fri, 8 Nov 2024 10:22:03 -0500
Subject: [PATCH 2/4] fix: dependencies versions and pyproject.toml

---
 pyproject.toml   | 7 +++++++
 requirements.txt | 8 ++++----
 2 files changed, 11 insertions(+), 4 deletions(-)
 create mode 100644 pyproject.toml

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..eb7967b0
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,7 @@
+# Minimal build configuration at detailed here:
+# https://github.com/pypa/pip/issues/11457
+
+[build-system]
+requires = [
+    "setuptools >= 64"
+]
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index 36423d4e..c7df82c1 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -8,7 +8,7 @@
 # -------
 requests==2.28.*
 dipy==1.9.*
--e git+https://github.com/levje/scilpy@update_scilpy#egg=scilpy
+-e git+https://github.com/scilus/scilpy@24435143c507ca018dd7edf3447fd18004c62077#egg=scilpy
 
 # -------
 # Other important dependencies
@@ -28,9 +28,9 @@ pynvml>=11.5.0
 # Necessary but should be installed with scilpy (Last check: 04/2024):
 # -------
 future==0.18.*
-h5py==3.7.*   # h5py must absolutely be >2.4: that's when it became thread-safe
+h5py==3.10.*   # h5py must absolutely be >2.4: that's when it became thread-safe
 matplotlib==3.6.*   # Hint: If matplotlib fails, you may try to install pyQt5.
 nibabel==5.2.*
-numpy==1.23.*
-scipy==1.9.*
+numpy==1.25.*
+scipy==1.11.*
 scikit-image==0.22.*

From dfc44fbc669113aa78055f14014cc7a0692bebaa Mon Sep 17 00:00:00 2001
From: Jeremi Levesque <jeremilevesque@hotmail.com>
Date: Fri, 8 Nov 2024 10:22:58 -0500
Subject: [PATCH 3/4] fix: remove unused requirement

---
 setup.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/setup.py b/setup.py
index 192947b5..2966a59a 100644
--- a/setup.py
+++ b/setup.py
@@ -34,7 +34,6 @@
             version=VERSION,
             packages=find_packages(),
             python_requires=PYTHON_VERSION,
-            setup_requires=['numpy'],
             install_requires=external_dependencies,
             entry_points={
                 'console_scripts': ["{}=scripts_python.{}:main".format(

From 20c76d708244112c0de8695754d39a89689308dd Mon Sep 17 00:00:00 2001
From: Jeremi Levesque <jeremilevesque@hotmail.com>
Date: Fri, 8 Nov 2024 10:28:47 -0500
Subject: [PATCH 4/4] fix: rename package from scilpy's update

---
 dwi_ml/data/processing/streamlines/post_processing.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dwi_ml/data/processing/streamlines/post_processing.py b/dwi_ml/data/processing/streamlines/post_processing.py
index 21356b83..28b15dff 100644
--- a/dwi_ml/data/processing/streamlines/post_processing.py
+++ b/dwi_ml/data/processing/streamlines/post_processing.py
@@ -8,7 +8,7 @@
 from matplotlib.colors import LogNorm
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 
-from scilpy.tractanalysis.tools import \
+from scilpy.tractanalysis.connectivity_segmentation import \
     extract_longest_segments_from_profile as segmenting_func
 from scilpy.tractograms.uncompress import uncompress