From eb75a12a4f4858b0763128b396ad52755306a056 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Fri, 26 Jan 2024 11:49:50 -0500
Subject: [PATCH 01/53] specify PR head commit instead of Jenkins merge commit
 to codecov

---
 Jenkinsfile | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Jenkinsfile b/Jenkinsfile
index 1f6245051..8b80884fb 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -60,7 +60,9 @@ pipeline {
                     shasum -a 256 -c codecov.SHA256SUM
 
                     chmod +x codecov
-                    ./codecov -t ${CODECOV_TOKEN} -f .test_reports/coverage.xml
+                    ./codecov -t ${CODECOV_TOKEN} \
+                        -f .test_reports/coverage.xml \
+                        -C ${GIT_PREVIOUS_COMMIT}
                 '''
             }
         }

From 751a2ff7498d7af563518bbd8dc370ce300636eb Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Sat, 27 Jan 2024 00:22:00 -0500
Subject: [PATCH 02/53] remove inner jenkins coverage reporting. the plugin has
 a vulnerability breach

---
 Jenkinsfile | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/Jenkinsfile b/Jenkinsfile
index 8b80884fb..07cc5a81a 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -45,11 +45,6 @@ pipeline {
                     '''
                 }
                 discoverGitReferenceBuild()
-                recordCoverage(
-                    name: 'Scilpy Coverage Report',
-                    sourceCodeRetention: 'MODIFIED',
-                    tools: [[parser: 'COBERTURA',
-                    pattern: '**/.test_reports/coverage.xml']])
                 sh '''
                     curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --no-default-keyring --import # One-time step
                     curl -Os https://uploader.codecov.io/latest/linux/codecov

From 987b5dbc12896b9d2a47ca02a368f4ead248a3e7 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Sat, 27 Jan 2024 02:26:13 -0500
Subject: [PATCH 03/53] fix jenkins commit in env

---
 Jenkinsfile | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/Jenkinsfile b/Jenkinsfile
index 07cc5a81a..14531517a 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -22,6 +22,7 @@ pipeline {
                                 pip3 install -e .
                             '''
                         }
+
                     }
                 }
             }
@@ -44,6 +45,9 @@ pipeline {
                         pytest --cov-report term-missing:skip-covered
                     '''
                 }
+                script {
+                    GIT_COMMIT = sh(returnStdout: true, script: 'git rev-parse $GIT_BRANCH').trim()
+                }
                 discoverGitReferenceBuild()
                 sh '''
                     curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --no-default-keyring --import # One-time step
@@ -55,9 +59,8 @@ pipeline {
                     shasum -a 256 -c codecov.SHA256SUM
 
                     chmod +x codecov
-                    ./codecov -t ${CODECOV_TOKEN} \
-                        -f .test_reports/coverage.xml \
-                        -C ${GIT_PREVIOUS_COMMIT}
+                    ./codecov -v -t ${CODECOV_TOKEN} \
+                        -f .test_reports/coverage.xml
                 '''
             }
         }

From 7741a93f2f6485845f579dbf086de2e5363482f3 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 29 Jan 2024 12:09:24 -0500
Subject: [PATCH 04/53] force codecov commits to use

---
 Jenkinsfile | 5 ++++-
 codecov.yml | 2 ++
 2 files changed, 6 insertions(+), 1 deletion(-)
 create mode 100644 codecov.yml

diff --git a/Jenkinsfile b/Jenkinsfile
index 14531517a..c31441d8f 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -47,6 +47,7 @@ pipeline {
                 }
                 script {
                     GIT_COMMIT = sh(returnStdout: true, script: 'git rev-parse $GIT_BRANCH').trim()
+                    GIT_PREVIOUS_COMMIT = sh(returnStdout: true, script: 'git merge-base origin/master $GIT_BRANCH').trim()
                 }
                 discoverGitReferenceBuild()
                 sh '''
@@ -60,7 +61,9 @@ pipeline {
 
                     chmod +x codecov
                     ./codecov -v -t ${CODECOV_TOKEN} \
-                        -f .test_reports/coverage.xml
+                        -f .test_reports/coverage.xml \
+                        -C ${GIT_COMMIT} \
+                        -N ${GIT_PREVIOUS_COMMIT}
                 '''
             }
         }
diff --git a/codecov.yml b/codecov.yml
new file mode 100644
index 000000000..6a204f89f
--- /dev/null
+++ b/codecov.yml
@@ -0,0 +1,2 @@
+codecov:
+  allow_coverage_offsets: True
\ No newline at end of file

From 21a439748f1cf5f887de860dae57d2c140ea5567 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 29 Jan 2024 12:38:45 -0500
Subject: [PATCH 05/53] refine codecov config

---
 codecov.yml | 34 +++++++++++++++++++++++++++++++++-
 1 file changed, 33 insertions(+), 1 deletion(-)

diff --git a/codecov.yml b/codecov.yml
index 6a204f89f..42d8ef542 100644
--- a/codecov.yml
+++ b/codecov.yml
@@ -1,2 +1,34 @@
 codecov:
-  allow_coverage_offsets: True
\ No newline at end of file
+  allow_coverage_offsets: True
+  
+  comment:
+    layout: "header, diff, flags, components"
+
+  component_management:
+    individual_components:
+      - component_id: scilpy_scripts
+        name: Scripts
+        paths:
+          - scripts/
+      - component_id: scilpy_library
+        name: Library
+        paths:
+          - scilpy/
+
+  status:
+    project:
+      default:
+        target: 75%
+        threshold: 2%
+        branches: 
+          - master
+        if_ci_failed: error
+        only_pulls: false
+    patch:
+      default:
+        target: 90%
+        branches: 
+          - master
+        if_ci_failed: error
+        only_pulls: false
+

From ea531cd6922473bcd6c08b711fc2ea96a6266382 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 29 Jan 2024 13:58:10 -0500
Subject: [PATCH 06/53] Fix codecov config

---
 codecov.yml | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/codecov.yml b/codecov.yml
index 42d8ef542..9f9d97b6f 100644
--- a/codecov.yml
+++ b/codecov.yml
@@ -1,20 +1,7 @@
 codecov:
   allow_coverage_offsets: True
-  
-  comment:
-    layout: "header, diff, flags, components"
-
-  component_management:
-    individual_components:
-      - component_id: scilpy_scripts
-        name: Scripts
-        paths:
-          - scripts/
-      - component_id: scilpy_library
-        name: Library
-        paths:
-          - scilpy/
 
+coverage:
   status:
     project:
       default:
@@ -32,3 +19,16 @@ codecov:
         if_ci_failed: error
         only_pulls: false
 
+component_management:
+  individual_components:
+    - component_id: scilpy_scripts
+      name: Scripts
+      paths:
+        - scripts/
+    - component_id: scilpy_library
+      name: Library
+      paths:
+        - scilpy/
+
+comment:
+  layout: "condensed_header, diff, components"
\ No newline at end of file

From 13b8128a04f2fc9b4422892fc8af959131b821e7 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 29 Jan 2024 14:34:08 -0500
Subject: [PATCH 07/53] set codecov commits in env clause for the stage

---
 Jenkinsfile | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/Jenkinsfile b/Jenkinsfile
index c31441d8f..d13a0e7ef 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -31,6 +31,14 @@ pipeline {
         stage('Test') {
             environment {
                 CODECOV_TOKEN = credentials('scilpy-codecov-token')
+                CODECOV_GIT_COMMIT = """${sh(
+                    returnStdout: true,
+                    script: 'git rev-parse $GIT_BRANCH'
+                ).trim()}"""
+                CODECOV_PARENT_COMMIT = """${sh(
+                    returnStdout: true,
+                    script: 'git merge-base origin/master $GIT_BRANCH'
+                ).trim()}"""
             }
             steps {
                 withPythonEnv('CPython-3.10') {
@@ -45,10 +53,6 @@ pipeline {
                         pytest --cov-report term-missing:skip-covered
                     '''
                 }
-                script {
-                    GIT_COMMIT = sh(returnStdout: true, script: 'git rev-parse $GIT_BRANCH').trim()
-                    GIT_PREVIOUS_COMMIT = sh(returnStdout: true, script: 'git merge-base origin/master $GIT_BRANCH').trim()
-                }
                 discoverGitReferenceBuild()
                 sh '''
                     curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --no-default-keyring --import # One-time step
@@ -62,8 +66,8 @@ pipeline {
                     chmod +x codecov
                     ./codecov -v -t ${CODECOV_TOKEN} \
                         -f .test_reports/coverage.xml \
-                        -C ${GIT_COMMIT} \
-                        -N ${GIT_PREVIOUS_COMMIT}
+                        -C ${CODECOV_GIT_COMMIT} \
+                        -N ${CODECOV_PARENT_COMMIT}
                 '''
             }
         }

From 861b9cced8d76ecc1088689f4634e9e8b24d9c2f Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Fri, 2 Feb 2024 15:54:21 -0500
Subject: [PATCH 08/53] Ensure that we get the right data even if
 ArraySequence's view is not ordered

---
 scripts/scil_tractogram_assign_custom_color.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/scripts/scil_tractogram_assign_custom_color.py b/scripts/scil_tractogram_assign_custom_color.py
index 51b249b54..b49cbbb45 100755
--- a/scripts/scil_tractogram_assign_custom_color.py
+++ b/scripts/scil_tractogram_assign_custom_color.py
@@ -200,7 +200,9 @@ def main():
                 data = np.clip(data, np.quantile(data, 0.05),
                                np.quantile(data, 0.95))
         elif args.use_dpp:
-            data = np.squeeze(sft.data_per_point[args.use_dpp]._data)
+            tmp = [np.squeeze(sft.data_per_point[args.use_dpp][s]) for s in
+                   range(len(sft))]
+            data = np.hstack(tmp)
         elif args.load_dps:
             data = np.squeeze(load_matrix_in_any_format(args.load_dps))
             if len(data) != len(sft):

From 17d7a104a8dc28da7759b557ee7be50512641657 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Fri, 2 Feb 2024 16:00:14 -0500
Subject: [PATCH 09/53] Rename test files

---
 ...o_tractogram.py => test_tractogram_assign_custom_color.py} | 4 ++--
 ...tractograms.py => test_tractogram_assign_uniform_color.py} | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)
 rename scripts/tests/{test_assign_custom_color_to_tractogram.py => test_tractogram_assign_custom_color.py} (85%)
 rename scripts/tests/{test_assign_uniform_color_to_tractograms.py => test_tractogram_assign_uniform_color.py} (83%)

diff --git a/scripts/tests/test_assign_custom_color_to_tractogram.py b/scripts/tests/test_tractogram_assign_custom_color.py
similarity index 85%
rename from scripts/tests/test_assign_custom_color_to_tractogram.py
rename to scripts/tests/test_tractogram_assign_custom_color.py
index 1dc8a4a84..c048d41b7 100644
--- a/scripts/tests/test_assign_custom_color_to_tractogram.py
+++ b/scripts/tests/test_tractogram_assign_custom_color.py
@@ -13,7 +13,7 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_assign_custom_color_to_tractogram.py',
+    ret = script_runner.run('scil_tractogram_assign_custom_color.py',
                             '--help')
     assert ret.success
 
@@ -24,7 +24,7 @@ def test_execution_tractometry(script_runner):
                              'IFGWM.trk')
     in_anat = os.path.join(get_home(), 'tractometry',
                            'IFGWM_labels_map.nii.gz')
-    ret = script_runner.run('scil_assign_custom_color_to_tractogram.py',
+    ret = script_runner.run('scil_tractogram_assign_custom_color.py',
                             in_bundle, 'colored.trk', '--from_anatomy',
                             in_anat)
     assert ret.success
diff --git a/scripts/tests/test_assign_uniform_color_to_tractograms.py b/scripts/tests/test_tractogram_assign_uniform_color.py
similarity index 83%
rename from scripts/tests/test_assign_uniform_color_to_tractograms.py
rename to scripts/tests/test_tractogram_assign_uniform_color.py
index 7caf221bf..20147b069 100644
--- a/scripts/tests/test_assign_uniform_color_to_tractograms.py
+++ b/scripts/tests/test_tractogram_assign_uniform_color.py
@@ -13,7 +13,7 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_assign_uniform_color_to_tractograms.py',
+    ret = script_runner.run('scil_tractogram_assign_uniform_color.py',
                             '--help')
     assert ret.success
 
@@ -22,7 +22,7 @@ def test_execution_tractometry(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_bundle = os.path.join(get_home(), 'tractometry',
                              'IFGWM.trk')
-    ret = script_runner.run('scil_assign_uniform_color_to_tractograms.py',
+    ret = script_runner.run('scil_tractogram_assign_uniform_color.py',
                             in_bundle, '--fill_color', '0x000000',
                             '--out_tractogram', 'colored.trk')
     assert ret.success

From 8b5de45b6f32411da85351ca726fbd46a02ff72f Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Wed, 31 Jan 2024 23:30:47 -0500
Subject: [PATCH 10/53] simple hello world workflow

---
 .github/workflows/hello_world.yml | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 .github/workflows/hello_world.yml

diff --git a/.github/workflows/hello_world.yml b/.github/workflows/hello_world.yml
new file mode 100644
index 000000000..c540c0f5f
--- /dev/null
+++ b/.github/workflows/hello_world.yml
@@ -0,0 +1,10 @@
+name: Actions Runner Controller Demo
+on:
+  workflow_dispatch:
+
+jobs:
+  Explore-GitHub-Actions:
+    # You need to use the INSTALLATION_NAME from the previous step
+    runs-on: scilus-runners
+    steps:
+    - run: echo "🎉 This job uses runner scale set runners!"

From a8aa4a83fbf9976e7fcc500b67b4e872fec9d933 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 1 Feb 2024 14:56:32 -0500
Subject: [PATCH 11/53] add simpletest pipeline

---
 .github/workflows/test.yml | 64 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 000000000..a2048a6e6
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,64 @@
+name: Scilpy test suite
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: action/checkout@v4
+
+      - name: Fetch python version from repository
+        id: python-selector
+        run: echo ::set-output name=python-version::$(cat .python-version)
+
+      - name: Set up Python for Scilpy
+        uses: actions/setup-python@v5.0.0
+        with:
+          python-version: python${{ steps.python-selector.outputs.python-version }}
+
+      - name: Install non-python dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            python${{ steps.python-selector.outputs.python-version }}-dev \
+            python${{ steps.python-selector.outputs.python-version }}-venv \
+            python${{ steps.python-selector.outputs.python-version }}-minimal \
+            python${{ steps.python-selector.outputs.python-version }}-tk \
+            libblas-dev \
+            liblapack-dev \
+            libfreetype6-dev
+
+      - name: Install Scilpy
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .
+
+      - name: Run tests
+        run: |
+          export MPLBACKEND="agg"
+          export OPENBLAS_NUM_THREADS=1
+          pytest --cov-report term-missing:skip-covered
+
+      - name: Upload test reports and coverage to artifacts
+        uses: echapmanFromBunnings/upload-artifact@3.0.0
+        with:
+          name: test-reports
+          path: |
+            .test_reports/*
+
+      - name: Upload coverage to codecov
+        uses: codecov/codecov-action@v4.0.0
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: .test_reports/coverage.xml
+          flags: unittests
+          fail_ci_if_error: true

From 592a728a5844c02e3c56b515bd57df58f4c27d72 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 1 Feb 2024 14:57:41 -0500
Subject: [PATCH 12/53] fix checkout

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a2048a6e6..1f8b7e6a5 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: action/checkout@v4
+        uses: actions/checkout@v4.1.1
 
       - name: Fetch python version from repository
         id: python-selector

From 9b7c4a285845a333db11184bee290e61c541be3c Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 1 Feb 2024 15:00:20 -0500
Subject: [PATCH 13/53] bad python version

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 1f8b7e6a5..1c3256714 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -23,7 +23,7 @@ jobs:
       - name: Set up Python for Scilpy
         uses: actions/setup-python@v5.0.0
         with:
-          python-version: python${{ steps.python-selector.outputs.python-version }}
+          python-version: ${{ steps.python-selector.outputs.python-version }}
 
       - name: Install non-python dependencies
         run: |

From f503d40725600c45b9f8065aebc190ee2dc07ab8 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 1 Feb 2024 15:09:50 -0500
Subject: [PATCH 14/53] run on scilus-runners

---
 .github/workflows/test.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 1c3256714..8fecb38ce 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -9,9 +9,13 @@ on:
       - master
   workflow_dispatch:
 
+env:
+  MPLBACKEND: agg
+  OPENBLAS_NUM_THREADS: 1
+
 jobs:
   test:
-    runs-on: ubuntu-latest
+    runs-on: scilus-runners
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4.1.1
@@ -44,8 +48,6 @@ jobs:
 
       - name: Run tests
         run: |
-          export MPLBACKEND="agg"
-          export OPENBLAS_NUM_THREADS=1
           pytest --cov-report term-missing:skip-covered
 
       - name: Upload test reports and coverage to artifacts

From ef656e8fe1aae7b9991bf77a89328899b6f1671e Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 1 Feb 2024 15:13:38 -0500
Subject: [PATCH 15/53] Add build-essentials for gcc

---
 .github/workflows/test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 8fecb38ce..e0eb42844 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -33,6 +33,7 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install -y \
+            build-essentials \
             python${{ steps.python-selector.outputs.python-version }}-dev \
             python${{ steps.python-selector.outputs.python-version }}-venv \
             python${{ steps.python-selector.outputs.python-version }}-minimal \

From a6e738d6e17c2404d9d8fe66af9feed53ead0467 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 1 Feb 2024 15:15:02 -0500
Subject: [PATCH 16/53] typo

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index e0eb42844..7e3c5df34 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -33,7 +33,7 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install -y \
-            build-essentials \
+            build-essential \
             python${{ steps.python-selector.outputs.python-version }}-dev \
             python${{ steps.python-selector.outputs.python-version }}-venv \
             python${{ steps.python-selector.outputs.python-version }}-minimal \

From c35d3e5cafb0eb87af85a87ccffaa23643941d08 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 1 Feb 2024 15:28:43 -0500
Subject: [PATCH 17/53] add libgl

---
 .github/workflows/test.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 7e3c5df34..a8f329ec7 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -40,7 +40,9 @@ jobs:
             python${{ steps.python-selector.outputs.python-version }}-tk \
             libblas-dev \
             liblapack-dev \
-            libfreetype6-dev
+            libfreetype6-dev \
+            libgl1-mesa-dev \
+            libgl1-mesa-dri
 
       - name: Install Scilpy
         run: |

From a6e376496f4a498b4683fe353b79eb4cad28ee22 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 1 Feb 2024 16:06:02 -0500
Subject: [PATCH 18/53] install git

---
 .github/workflows/test.yml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a8f329ec7..662b1075e 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -34,15 +34,16 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y \
             build-essential \
-            python${{ steps.python-selector.outputs.python-version }}-dev \
-            python${{ steps.python-selector.outputs.python-version }}-venv \
-            python${{ steps.python-selector.outputs.python-version }}-minimal \
-            python${{ steps.python-selector.outputs.python-version }}-tk \
+            git \
             libblas-dev \
             liblapack-dev \
             libfreetype6-dev \
             libgl1-mesa-dev \
-            libgl1-mesa-dri
+            libgl1-mesa-dri \
+            python${{ steps.python-selector.outputs.python-version }}-dev \
+            python${{ steps.python-selector.outputs.python-version }}-venv \
+            python${{ steps.python-selector.outputs.python-version }}-minimal \
+            python${{ steps.python-selector.outputs.python-version }}-tk
 
       - name: Install Scilpy
         run: |

From 180aed1135c614e85b449fc5c236d5d20c5bcecb Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 1 Feb 2024 22:54:56 -0500
Subject: [PATCH 19/53] remove python install, should be handled by the
 setup-python action

---
 .github/workflows/test.yml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 662b1075e..d34100933 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -39,11 +39,7 @@ jobs:
             liblapack-dev \
             libfreetype6-dev \
             libgl1-mesa-dev \
-            libgl1-mesa-dri \
-            python${{ steps.python-selector.outputs.python-version }}-dev \
-            python${{ steps.python-selector.outputs.python-version }}-venv \
-            python${{ steps.python-selector.outputs.python-version }}-minimal \
-            python${{ steps.python-selector.outputs.python-version }}-tk
+            libgl1-mesa-dri
 
       - name: Install Scilpy
         run: |

From 13b54d325ece697f68d50947625c388bb0dd362a Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 1 Feb 2024 23:26:01 -0500
Subject: [PATCH 20/53] remove mesa-dri

---
 .github/workflows/test.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index d34100933..6f93dea11 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -38,8 +38,7 @@ jobs:
             libblas-dev \
             liblapack-dev \
             libfreetype6-dev \
-            libgl1-mesa-dev \
-            libgl1-mesa-dri
+            libgl1-mesa-dev
 
       - name: Install Scilpy
         run: |

From 6dd408bae61a4cef0a2c87986a294e0b293f97bc Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Thu, 1 Feb 2024 23:36:01 -0500
Subject: [PATCH 21/53] add missing lib

---
 .github/workflows/test.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 6f93dea11..fc346997f 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -38,7 +38,8 @@ jobs:
             libblas-dev \
             liblapack-dev \
             libfreetype6-dev \
-            libgl1-mesa-dev
+            libgl1-mesa-dev \
+            libxrender1
 
       - name: Install Scilpy
         run: |

From b27527ed000661d6eb25c1572aa0d996f7a4d1e1 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Fri, 2 Feb 2024 16:34:22 -0500
Subject: [PATCH 22/53] try custom image (no need to set rendering)

---
 .github/workflows/test.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index fc346997f..b363f369c 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -37,9 +37,7 @@ jobs:
             git \
             libblas-dev \
             liblapack-dev \
-            libfreetype6-dev \
-            libgl1-mesa-dev \
-            libxrender1
+            libfreetype6-dev
 
       - name: Install Scilpy
         run: |

From ce209343e6fb30d334ebb7b2aaf17aa6d39fbe96 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Sun, 4 Feb 2024 00:30:10 -0500
Subject: [PATCH 23/53] re-add python headers

---
 .github/workflows/test.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index b363f369c..c1d95185e 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -37,7 +37,8 @@ jobs:
             git \
             libblas-dev \
             liblapack-dev \
-            libfreetype6-dev
+            libfreetype6-dev \
+            python${{ steps.python-selector.outputs.python-version }}-dev
 
       - name: Install Scilpy
         run: |

From d486a03ba907edc8d5c8c9309f3a574ffc5d62dd Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 5 Feb 2024 14:01:36 -0500
Subject: [PATCH 24/53] fixes

---
 .github/workflows/test.yml | 7 ++++---
 MANIFEST.in                | 1 +
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index c1d95185e..116413b06 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -31,22 +31,23 @@ jobs:
 
       - name: Install non-python dependencies
         run: |
+
           sudo apt-get update
           sudo apt-get install -y \
             build-essential \
             git \
             libblas-dev \
             liblapack-dev \
-            libfreetype6-dev \
-            python${{ steps.python-selector.outputs.python-version }}-dev
+            libfreetype6-dev
 
       - name: Install Scilpy
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -e .
+          python -m pip install -e . -vvvvv
 
       - name: Run tests
         run: |
+          export C_INCLUDE_PATH=$pythonLocation/include/python${{ steps.python-selector.outputs.python-version }}:$C_INCLUDE_PATH
           pytest --cov-report term-missing:skip-covered
 
       - name: Upload test reports and coverage to artifacts
diff --git a/MANIFEST.in b/MANIFEST.in
index beea28192..2a51044ad 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -2,6 +2,7 @@ include README.md
 include LICENSE
 include requirements.txt
 include .python-version
+include data/
 
 recursive-include scilpy *.c
 recursive-include scilpy *.cpp

From dcc2b4a8f60417eef3c1b4830d161955edbe6bed Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 5 Feb 2024 14:31:23 -0500
Subject: [PATCH 25/53] downgrade action/setup-python

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 116413b06..f99e918d7 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -25,7 +25,7 @@ jobs:
         run: echo ::set-output name=python-version::$(cat .python-version)
 
       - name: Set up Python for Scilpy
-        uses: actions/setup-python@v5.0.0
+        uses: actions/setup-python@v4.8.0
         with:
           python-version: ${{ steps.python-selector.outputs.python-version }}
 

From 3b9b4043e8266d54121fdf4cc79afa4ee3b397f5 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 5 Feb 2024 14:41:45 -0500
Subject: [PATCH 26/53] run failing test only

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index f99e918d7..14dc9c3fd 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -48,7 +48,7 @@ jobs:
       - name: Run tests
         run: |
           export C_INCLUDE_PATH=$pythonLocation/include/python${{ steps.python-selector.outputs.python-version }}:$C_INCLUDE_PATH
-          pytest --cov-report term-missing:skip-covered
+          pytest --cov-report term-missing:skip-covered scilpy/scripts/tests/test_tractogram_filter_by_anatomy.py
 
       - name: Upload test reports and coverage to artifacts
         uses: echapmanFromBunnings/upload-artifact@3.0.0

From f29e6ab57098dc1ab78ff8b57173f1d17eccdfee Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 5 Feb 2024 14:48:53 -0500
Subject: [PATCH 27/53] fix

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 14dc9c3fd..93eda74a1 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -48,7 +48,7 @@ jobs:
       - name: Run tests
         run: |
           export C_INCLUDE_PATH=$pythonLocation/include/python${{ steps.python-selector.outputs.python-version }}:$C_INCLUDE_PATH
-          pytest --cov-report term-missing:skip-covered scilpy/scripts/tests/test_tractogram_filter_by_anatomy.py
+          pytest --cov-report term-missing:skip-covered scripts/tests/test_tractogram_filter_by_anatomy.py
 
       - name: Upload test reports and coverage to artifacts
         uses: echapmanFromBunnings/upload-artifact@3.0.0

From 35420f20a35c0ac19a4098716ecc00842627901b Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 5 Feb 2024 15:10:20 -0500
Subject: [PATCH 28/53] include package data via manifest, as should be

---
 MANIFEST.in | 2 +-
 setup.py    | 4 ----
 2 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/MANIFEST.in b/MANIFEST.in
index 2a51044ad..a685197b6 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -2,8 +2,8 @@ include README.md
 include LICENSE
 include requirements.txt
 include .python-version
-include data/
 
+recursive-include data *
 recursive-include scilpy *.c
 recursive-include scilpy *.cpp
 recursive-include scilpy *.pyx
diff --git a/setup.py b/setup.py
index f8127082b..ffaad9614 100644
--- a/setup.py
+++ b/setup.py
@@ -103,10 +103,6 @@ def run(self):
                     os.path.basename(s).split(".")[0]) for s in SCRIPTS] +
                 entry_point_legacy
             },
-            data_files=[('data/LUT',
-                         ["data/LUT/freesurfer_desikan_killiany.json",
-                          "data/LUT/freesurfer_subcortical.json",
-                          "data/LUT/dk_aggregate_structures.json"])],
             include_package_data=True)
 
 setup(**opts)

From 5c70a47c8738fc9fb5af3171b445c5cc99722364 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 5 Feb 2024 15:10:41 -0500
Subject: [PATCH 29/53] remove verbose install

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 93eda74a1..6c6033d47 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -43,7 +43,7 @@ jobs:
       - name: Install Scilpy
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -e . -vvvvv
+          python -m pip install -e .
 
       - name: Run tests
         run: |

From 283b33eeb9c04098c1e433f753415362fde8219d Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 5 Feb 2024 15:16:03 -0500
Subject: [PATCH 30/53] use importlib

---
 scripts/scil_tractogram_filter_by_anatomy.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/scil_tractogram_filter_by_anatomy.py b/scripts/scil_tractogram_filter_by_anatomy.py
index b9c5bfeb0..3a8080381 100755
--- a/scripts/scil_tractogram_filter_by_anatomy.py
+++ b/scripts/scil_tractogram_filter_by_anatomy.py
@@ -49,7 +49,7 @@
 import json
 import logging
 import os
-import pkg_resources
+import importlib.resources as resources
 
 from dipy.io.streamline import save_tractogram
 from dipy.io.utils import is_header_compatible
@@ -142,9 +142,9 @@ def load_wmparc_labels():
     Load labels dictionary of different parcellations from the
     Desikan-Killiany atlas
     """
-    resource_package = pkg_resources.get_distribution('scilpy').location
+    resource_package = resources.path('scilpy', 'data')
     labels_path = os.path.join(
-        resource_package, 'data/LUT/dk_aggregate_structures.json')
+        resource_package, 'LUT/dk_aggregate_structures.json')
     with open(labels_path) as labels_file:
         labels = json.load(labels_file)
     return labels

From c7d9904bc39e83e67bb54288809f90cbc56f1f0f Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 5 Feb 2024 15:24:17 -0500
Subject: [PATCH 31/53] update setuptools and wheel

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 6c6033d47..8590dd9c7 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -42,7 +42,7 @@ jobs:
 
       - name: Install Scilpy
         run: |
-          python -m pip install --upgrade pip
+          python -m pip install --upgrade pip setuptools wheel
           python -m pip install -e .
 
       - name: Run tests

From 5f8252e5f89be2e94996eb98d52ac52998bbf359 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 5 Feb 2024 15:42:31 -0500
Subject: [PATCH 32/53] fix manifest

---
 .github/workflows/test.yml | 2 +-
 MANIFEST.in                | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 8590dd9c7..f9b55ef97 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -25,7 +25,7 @@ jobs:
         run: echo ::set-output name=python-version::$(cat .python-version)
 
       - name: Set up Python for Scilpy
-        uses: actions/setup-python@v4.8.0
+        uses: actions/setup-python@v5.0.0
         with:
           python-version: ${{ steps.python-selector.outputs.python-version }}
 
diff --git a/MANIFEST.in b/MANIFEST.in
index a685197b6..e16edd8b0 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -3,7 +3,7 @@ include LICENSE
 include requirements.txt
 include .python-version
 
-recursive-include data *
+recursive-include data/LUT *
 recursive-include scilpy *.c
 recursive-include scilpy *.cpp
 recursive-include scilpy *.pyx

From f595d2064ea35141df5abd8d4d3ddaf214ca4172 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 5 Feb 2024 16:32:18 -0500
Subject: [PATCH 33/53] debug messages

---
 .github/workflows/test.yml | 4 +++-
 setup.py                   | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index f9b55ef97..4bc13422d 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -42,8 +42,10 @@ jobs:
 
       - name: Install Scilpy
         run: |
+          python --version
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install -e .
+          python -m pip install -e . -v
+          python -m pip list
 
       - name: Run tests
         run: |
diff --git a/setup.py b/setup.py
index ffaad9614..68d63c4a6 100644
--- a/setup.py
+++ b/setup.py
@@ -103,6 +103,7 @@ def run(self):
                     os.path.basename(s).split(".")[0]) for s in SCRIPTS] +
                 entry_point_legacy
             },
+            package_data={'': ['*.json', 'data/LUT/*.json']},
             include_package_data=True)
 
 setup(**opts)

From 0ec747d83f40ad56edb8c73320ad03c2752b6005 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 5 Feb 2024 21:48:57 -0500
Subject: [PATCH 34/53] revert and debug

---
 .github/workflows/test.yml | 1 +
 setup.py                   | 5 ++++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4bc13422d..2936d0208 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -43,6 +43,7 @@ jobs:
       - name: Install Scilpy
         run: |
           python --version
+          python -m pip list
           python -m pip install --upgrade pip setuptools wheel
           python -m pip install -e . -v
           python -m pip list
diff --git a/setup.py b/setup.py
index 68d63c4a6..f8127082b 100644
--- a/setup.py
+++ b/setup.py
@@ -103,7 +103,10 @@ def run(self):
                     os.path.basename(s).split(".")[0]) for s in SCRIPTS] +
                 entry_point_legacy
             },
-            package_data={'': ['*.json', 'data/LUT/*.json']},
+            data_files=[('data/LUT',
+                         ["data/LUT/freesurfer_desikan_killiany.json",
+                          "data/LUT/freesurfer_subcortical.json",
+                          "data/LUT/dk_aggregate_structures.json"])],
             include_package_data=True)
 
 setup(**opts)

From 25669e26acce59bc67b65f377dd605cd5ac0dea7 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 5 Feb 2024 22:47:08 -0500
Subject: [PATCH 35/53] sleepfor debug purposes

---
 .github/workflows/test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 2936d0208..2b12c2424 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -47,6 +47,7 @@ jobs:
           python -m pip install --upgrade pip setuptools wheel
           python -m pip install -e . -v
           python -m pip list
+          sleep infinite
 
       - name: Run tests
         run: |

From 9d58df54cf7910bb0f55f271e0f086488bb5c3de Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 5 Feb 2024 23:09:48 -0500
Subject: [PATCH 36/53] typo

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 2b12c2424..65fa8df0e 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -47,7 +47,7 @@ jobs:
           python -m pip install --upgrade pip setuptools wheel
           python -m pip install -e . -v
           python -m pip list
-          sleep infinite
+          sleep infinity
 
       - name: Run tests
         run: |

From d6924f59fd6710b6d657f70ff51215422bc5e7d1 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Mon, 5 Feb 2024 23:18:36 -0500
Subject: [PATCH 37/53] move sleep for debug

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 65fa8df0e..fab10d239 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -47,11 +47,11 @@ jobs:
           python -m pip install --upgrade pip setuptools wheel
           python -m pip install -e . -v
           python -m pip list
-          sleep infinity
 
       - name: Run tests
         run: |
           export C_INCLUDE_PATH=$pythonLocation/include/python${{ steps.python-selector.outputs.python-version }}:$C_INCLUDE_PATH
+          sleep infinity
           pytest --cov-report term-missing:skip-covered scripts/tests/test_tractogram_filter_by_anatomy.py
 
       - name: Upload test reports and coverage to artifacts

From 316397073598a2f7c178f002f2464e378ea93713 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Tue, 6 Feb 2024 00:09:05 -0500
Subject: [PATCH 38/53] put sleep after pytest to investiguate

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index fab10d239..7f10a26f7 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -51,8 +51,8 @@ jobs:
       - name: Run tests
         run: |
           export C_INCLUDE_PATH=$pythonLocation/include/python${{ steps.python-selector.outputs.python-version }}:$C_INCLUDE_PATH
-          sleep infinity
           pytest --cov-report term-missing:skip-covered scripts/tests/test_tractogram_filter_by_anatomy.py
+          sleep infinity
 
       - name: Upload test reports and coverage to artifacts
         uses: echapmanFromBunnings/upload-artifact@3.0.0

From f9f0e2f4ea1bd71d96aea1b63028bfbbf0d5b36d Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Tue, 6 Feb 2024 00:30:14 -0500
Subject: [PATCH 39/53] final try

---
 scripts/scil_tractogram_filter_by_anatomy.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/scripts/scil_tractogram_filter_by_anatomy.py b/scripts/scil_tractogram_filter_by_anatomy.py
index 3a8080381..5accd0c94 100755
--- a/scripts/scil_tractogram_filter_by_anatomy.py
+++ b/scripts/scil_tractogram_filter_by_anatomy.py
@@ -142,9 +142,8 @@ def load_wmparc_labels():
     Load labels dictionary of different parcellations from the
     Desikan-Killiany atlas
     """
-    resource_package = resources.path('scilpy', 'data')
-    labels_path = os.path.join(
-        resource_package, 'LUT/dk_aggregate_structures.json')
+    lut_package = os.path.join(resources.files('data'), 'LUT')
+    labels_path = os.path.join(lut_package, 'dk_aggregate_structures.json')
     with open(labels_path) as labels_file:
         labels = json.load(labels_file)
     return labels

From b22b800910b8e10ed65e482705a3715e7e8c1231 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Tue, 6 Feb 2024 09:08:15 -0500
Subject: [PATCH 40/53] set pip cache + fix

---
 .github/workflows/test.yml                   | 3 ++-
 scripts/scil_tractogram_filter_by_anatomy.py | 4 ++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 7f10a26f7..6d97906ab 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -28,6 +28,7 @@ jobs:
         uses: actions/setup-python@v5.0.0
         with:
           python-version: ${{ steps.python-selector.outputs.python-version }}
+          cache: 'pip'
 
       - name: Install non-python dependencies
         run: |
@@ -45,7 +46,7 @@ jobs:
           python --version
           python -m pip list
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install -e . -v
+          python -m pip install -e .
           python -m pip list
 
       - name: Run tests
diff --git a/scripts/scil_tractogram_filter_by_anatomy.py b/scripts/scil_tractogram_filter_by_anatomy.py
index 5accd0c94..d2e2625f1 100755
--- a/scripts/scil_tractogram_filter_by_anatomy.py
+++ b/scripts/scil_tractogram_filter_by_anatomy.py
@@ -142,8 +142,8 @@ def load_wmparc_labels():
     Load labels dictionary of different parcellations from the
     Desikan-Killiany atlas
     """
-    lut_package = os.path.join(resources.files('data'), 'LUT')
-    labels_path = os.path.join(lut_package, 'dk_aggregate_structures.json')
+    lut_package = resources.files('data').joinpath('LUT')
+    labels_path = lut_package.joinpath('dk_aggregate_structures.json')
     with open(labels_path) as labels_file:
         labels = json.load(labels_file)
     return labels

From e81424bd6b4edb96c2cb14ccaa933190038e9a5e Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Tue, 6 Feb 2024 09:50:23 -0500
Subject: [PATCH 41/53] remove debug

---
 .github/workflows/test.yml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 6d97906ab..390f92110 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -43,17 +43,13 @@ jobs:
 
       - name: Install Scilpy
         run: |
-          python --version
-          python -m pip list
           python -m pip install --upgrade pip setuptools wheel
           python -m pip install -e .
-          python -m pip list
 
       - name: Run tests
         run: |
           export C_INCLUDE_PATH=$pythonLocation/include/python${{ steps.python-selector.outputs.python-version }}:$C_INCLUDE_PATH
-          pytest --cov-report term-missing:skip-covered scripts/tests/test_tractogram_filter_by_anatomy.py
-          sleep infinity
+          pytest --cov-report term-missing:skip-covered
 
       - name: Upload test reports and coverage to artifacts
         uses: echapmanFromBunnings/upload-artifact@3.0.0

From 8745547a2ad6bca002ad866e135cbce5c7abc4a1 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Tue, 6 Feb 2024 11:14:08 -0500
Subject: [PATCH 42/53] codecov fix

---
 .github/workflows/test.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 390f92110..e9c0b8392 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -62,6 +62,8 @@ jobs:
         uses: codecov/codecov-action@v4.0.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          file: .test_reports/coverage.xml
+          directory: .test_reports/
+          file: ./coverage.xml
           flags: unittests
           fail_ci_if_error: true
+          verbose: true

From dcbc09434ef5ef688cf72c9010dc0522542bb889 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Tue, 6 Feb 2024 11:19:07 -0500
Subject: [PATCH 43/53] update deprecated workflow components

---
 .github/workflows/test.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index e9c0b8392..f2393b62c 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -22,7 +22,7 @@ jobs:
 
       - name: Fetch python version from repository
         id: python-selector
-        run: echo ::set-output name=python-version::$(cat .python-version)
+        run: echo "python-version=$(cat .python-version)" >> $GITHUB_OUTPUT
 
       - name: Set up Python for Scilpy
         uses: actions/setup-python@v5.0.0
@@ -32,7 +32,6 @@ jobs:
 
       - name: Install non-python dependencies
         run: |
-
           sudo apt-get update
           sudo apt-get install -y \
             build-essential \
@@ -52,7 +51,7 @@ jobs:
           pytest --cov-report term-missing:skip-covered
 
       - name: Upload test reports and coverage to artifacts
-        uses: echapmanFromBunnings/upload-artifact@3.0.0
+        uses: actions/upload-artifact@v4.3.1
         with:
           name: test-reports
           path: |

From 9031dfcca9952963f6b960bfd711ecf9ed9a7af9 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Tue, 6 Feb 2024 13:18:52 -0500
Subject: [PATCH 44/53] fix ownership

---
 .github/workflows/test.yml | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index f2393b62c..2045e0da3 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -48,15 +48,9 @@ jobs:
       - name: Run tests
         run: |
           export C_INCLUDE_PATH=$pythonLocation/include/python${{ steps.python-selector.outputs.python-version }}:$C_INCLUDE_PATH
+          git config --global --add safe.directory "$GITHUB_WORKSPACE"
           pytest --cov-report term-missing:skip-covered
 
-      - name: Upload test reports and coverage to artifacts
-        uses: actions/upload-artifact@v4.3.1
-        with:
-          name: test-reports
-          path: |
-            .test_reports/*
-
       - name: Upload coverage to codecov
         uses: codecov/codecov-action@v4.0.0
         with:
@@ -66,3 +60,10 @@ jobs:
           flags: unittests
           fail_ci_if_error: true
           verbose: true
+
+      - name: Upload test reports and coverage to artifacts
+        uses: actions/upload-artifact@v4.3.1
+        with:
+          name: test-reports
+          path: |
+            .test_reports/*

From 6aaab8c89c3b9be15598335b6466343071ac0be6 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Tue, 6 Feb 2024 14:33:37 -0500
Subject: [PATCH 45/53] bump codecov-action

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 2045e0da3..116c731f7 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -52,7 +52,7 @@ jobs:
           pytest --cov-report term-missing:skip-covered
 
       - name: Upload coverage to codecov
-        uses: codecov/codecov-action@v4.0.0
+        uses: codecov/codecov-action@v4.0.1
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           directory: .test_reports/

From 865e562c4c4075d0adb908790ff79b76200da3b4 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Tue, 6 Feb 2024 16:17:40 -0500
Subject: [PATCH 46/53] use codecov-cli instead of action until its working

---
 .github/workflows/test.yml | 25 ++++++++++++++++---------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 116c731f7..8e1f418c2 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -4,7 +4,7 @@ on:
   push:
     branches:
       - master
-  pull_request:
+  pull_request_target:
     branches:
       - master
   workflow_dispatch:
@@ -52,14 +52,21 @@ jobs:
           pytest --cov-report term-missing:skip-covered
 
       - name: Upload coverage to codecov
-        uses: codecov/codecov-action@v4.0.1
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          directory: .test_reports/
-          file: ./coverage.xml
-          flags: unittests
-          fail_ci_if_error: true
-          verbose: true
+        run: |
+          curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --no-default-keyring --keyring trustedkeys.gpg --import
+          curl -Os https://cli.codecov.io/latest/linux/codecov
+          curl -Os https://cli.codecov.io/latest/linux/codecov.SHA256SUM
+          curl -Os https://cli.codecov.io/latest/linux/codecov.SHA256SUM.sig
+          gpgv codecov.SHA256SUM.sig codecov.SHA256SUM
+
+          shasum -a 256 -c codecov.SHA256SUM
+          chmod +x codecov
+          ./codecov --verbose upload-process \
+            --fail-on-error \
+            -t ${{ secrets.CODECOV_TOKEN }} \
+            -n 'scilpy-unittests'-${{ github.run_id }} \
+            -F scilpy-unittests -f .test_reports/coverage.xml
+
 
       - name: Upload test reports and coverage to artifacts
         uses: actions/upload-artifact@v4.3.1

From cd5d9d3d818aef19a8f11f0fea99e045c445c1a6 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Tue, 6 Feb 2024 17:04:40 -0500
Subject: [PATCH 47/53] add curl

---
 .github/workflows/test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 8e1f418c2..14c892159 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -35,6 +35,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y \
             build-essential \
+            curl \
             git \
             libblas-dev \
             liblapack-dev \

From cb9380101e63b3022bdbf7ddf48354fe7405b38f Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Tue, 6 Feb 2024 19:45:49 -0500
Subject: [PATCH 48/53] add service

---
 .github/workflows/test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 14c892159..d3bcb872e 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -64,6 +64,7 @@ jobs:
           chmod +x codecov
           ./codecov --verbose upload-process \
             --fail-on-error \
+            --git-service github \
             -t ${{ secrets.CODECOV_TOKEN }} \
             -n 'scilpy-unittests'-${{ github.run_id }} \
             -F scilpy-unittests -f .test_reports/coverage.xml

From 7098dfb97eca1467bd9381840013ae4a0346dc03 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Tue, 6 Feb 2024 22:20:23 -0500
Subject: [PATCH 49/53] back at codecov action

---
 .github/workflows/test.yml | 32 ++++++++++++++------------------
 1 file changed, 14 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index d3bcb872e..2e5ce5665 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -50,25 +50,21 @@ jobs:
         run: |
           export C_INCLUDE_PATH=$pythonLocation/include/python${{ steps.python-selector.outputs.python-version }}:$C_INCLUDE_PATH
           git config --global --add safe.directory "$GITHUB_WORKSPACE"
-          pytest --cov-report term-missing:skip-covered
-
-      - name: Upload coverage to codecov
-        run: |
-          curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --no-default-keyring --keyring trustedkeys.gpg --import
-          curl -Os https://cli.codecov.io/latest/linux/codecov
-          curl -Os https://cli.codecov.io/latest/linux/codecov.SHA256SUM
-          curl -Os https://cli.codecov.io/latest/linux/codecov.SHA256SUM.sig
-          gpgv codecov.SHA256SUM.sig codecov.SHA256SUM
-
-          shasum -a 256 -c codecov.SHA256SUM
-          chmod +x codecov
-          ./codecov --verbose upload-process \
-            --fail-on-error \
-            --git-service github \
-            -t ${{ secrets.CODECOV_TOKEN }} \
-            -n 'scilpy-unittests'-${{ github.run_id }} \
-            -F scilpy-unittests -f .test_reports/coverage.xml
+          pytest --cov-report term-missing:skip-covered scripts/tests/test_bids_validate.py
 
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        with:
+          flags: unittests
+          name: scilpy-unittests-${{ github.run_id }}
+          verbose: true
+          directory: .test_reports/
+          plugin: pycoverage
+          file: ./coverage.xml
+          fail_ci_if_error: true
+          root_dir: $GITHUB_WORKSPACE/scilpy
 
       - name: Upload test reports and coverage to artifacts
         uses: actions/upload-artifact@v4.3.1

From b1fe1f3cfa6fe7ca94e095655f3f84e188e5b07d Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Tue, 6 Feb 2024 22:51:17 -0500
Subject: [PATCH 50/53] downgrade action

---
 .github/workflows/test.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 2e5ce5665..f004345ca 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -53,7 +53,7 @@ jobs:
           pytest --cov-report term-missing:skip-covered scripts/tests/test_bids_validate.py
 
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v3
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
@@ -61,7 +61,6 @@ jobs:
           name: scilpy-unittests-${{ github.run_id }}
           verbose: true
           directory: .test_reports/
-          plugin: pycoverage
           file: ./coverage.xml
           fail_ci_if_error: true
           root_dir: $GITHUB_WORKSPACE/scilpy

From f4530c3a22b2e9062343f3f1ae3d4d5b352ab5b9 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Wed, 7 Feb 2024 00:54:33 -0500
Subject: [PATCH 51/53] fix

---
 .github/workflows/test.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index f004345ca..b919cf600 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -61,9 +61,8 @@ jobs:
           name: scilpy-unittests-${{ github.run_id }}
           verbose: true
           directory: .test_reports/
-          file: ./coverage.xml
           fail_ci_if_error: true
-          root_dir: $GITHUB_WORKSPACE/scilpy
+          root_dir: $GITHUB_WORKSPACE/scilpy/
 
       - name: Upload test reports and coverage to artifacts
         uses: actions/upload-artifact@v4.3.1

From 6507f4ff022998d0498625c0a95df255e00edb9c Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Wed, 7 Feb 2024 01:13:53 -0500
Subject: [PATCH 52/53] production ready

---
 .github/workflows/build.yml               |  28 -----
 .github/workflows/freeze_requirements.yml |   2 +-
 .github/workflows/hello_world.yml         |  10 --
 .github/workflows/test.yml                |   4 +-
 Jenkinsfile                               | 121 ----------------------
 5 files changed, 2 insertions(+), 163 deletions(-)
 delete mode 100644 .github/workflows/build.yml
 delete mode 100644 .github/workflows/hello_world.yml
 delete mode 100644 Jenkinsfile

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
deleted file mode 100644
index b2c3c96d9..000000000
--- a/.github/workflows/build.yml
+++ /dev/null
@@ -1,28 +0,0 @@
-name: Build Docker with selected version
-
-on:
-  workflow_dispatch:
-    inputs:
-      scilpy_commit:
-        description: Scilpy commit id
-        required: true
-
-jobs:
-  Build_Docker:
-
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v2
-        name: Check out repository
-      - name: Change scilpy version
-        run: sed -i '/ENV SCILPY_VERSION=/c\ENV SCILPY_VERSION=${{ github.event.inputs.scilpy_commit }}' containers/Dockerfile
-      - uses: mr-smithers-excellent/docker-build-push@v3.1
-        name: Docker Build & Push
-        with:
-          image: scilus/scilpy
-          tag: dev
-          dockerfile: containers/Dockerfile
-          registry: docker.io
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
diff --git a/.github/workflows/freeze_requirements.yml b/.github/workflows/freeze_requirements.yml
index de49439f5..d63a55f11 100644
--- a/.github/workflows/freeze_requirements.yml
+++ b/.github/workflows/freeze_requirements.yml
@@ -7,7 +7,7 @@ on:
 
 jobs:
   freeze_requirements:
-    runs-on: ubuntu-latest
+    runs-on: scilus-runners
     steps:
       - 
         name: Checkout scilpy
diff --git a/.github/workflows/hello_world.yml b/.github/workflows/hello_world.yml
deleted file mode 100644
index c540c0f5f..000000000
--- a/.github/workflows/hello_world.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-name: Actions Runner Controller Demo
-on:
-  workflow_dispatch:
-
-jobs:
-  Explore-GitHub-Actions:
-    # You need to use the INSTALLATION_NAME from the previous step
-    runs-on: scilus-runners
-    steps:
-    - run: echo "🎉 This job uses runner scale set runners!"
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index b919cf600..4bca3eb92 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -7,7 +7,6 @@ on:
   pull_request_target:
     branches:
       - master
-  workflow_dispatch:
 
 env:
   MPLBACKEND: agg
@@ -49,8 +48,7 @@ jobs:
       - name: Run tests
         run: |
           export C_INCLUDE_PATH=$pythonLocation/include/python${{ steps.python-selector.outputs.python-version }}:$C_INCLUDE_PATH
-          git config --global --add safe.directory "$GITHUB_WORKSPACE"
-          pytest --cov-report term-missing:skip-covered scripts/tests/test_bids_validate.py
+          pytest --cov-report term-missing:skip-covered
 
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
diff --git a/Jenkinsfile b/Jenkinsfile
deleted file mode 100644
index d13a0e7ef..000000000
--- a/Jenkinsfile
+++ /dev/null
@@ -1,121 +0,0 @@
-pipeline {
-    options {
-        disableConcurrentBuilds(abortPrevious: true)
-        throttleJobProperty(categories: ['ci_all_builds'],
-                            throttleEnabled: true,
-                            throttleOption: 'category')
-    }
-
-    agent any
-
-    stages {
-        stage('Build') {
-            stages {
-                stage('Python3.10') {
-                    steps {
-                        withPythonEnv('CPython-3.10') {
-                            sh '''
-                                pip3 install wheel==0.38.*
-                                pip3 install numpy==1.23.*
-                                pip3 install Cython==0.29.*
-                                pip3 install packaging==23.*
-                                pip3 install -e .
-                            '''
-                        }
-
-                    }
-                }
-            }
-        }
-
-        stage('Test') {
-            environment {
-                CODECOV_TOKEN = credentials('scilpy-codecov-token')
-                CODECOV_GIT_COMMIT = """${sh(
-                    returnStdout: true,
-                    script: 'git rev-parse $GIT_BRANCH'
-                ).trim()}"""
-                CODECOV_PARENT_COMMIT = """${sh(
-                    returnStdout: true,
-                    script: 'git merge-base origin/master $GIT_BRANCH'
-                ).trim()}"""
-            }
-            steps {
-                withPythonEnv('CPython-3.10') {
-                    sh '''
-                        pip3 install pytest-cov pytest-html
-                        pip3 install wheel==0.38.*
-                        pip3 install numpy==1.23.*
-                        pip3 install packaging==23.*
-                        pip3 install -e .
-                        export MPLBACKEND="agg"
-                        export OPENBLAS_NUM_THREADS=1
-                        pytest --cov-report term-missing:skip-covered
-                    '''
-                }
-                discoverGitReferenceBuild()
-                sh '''
-                    curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --no-default-keyring --import # One-time step
-                    curl -Os https://uploader.codecov.io/latest/linux/codecov
-                    curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM
-                    curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM.sig
-
-                    gpg --verify codecov.SHA256SUM.sig codecov.SHA256SUM
-                    shasum -a 256 -c codecov.SHA256SUM
-
-                    chmod +x codecov
-                    ./codecov -v -t ${CODECOV_TOKEN} \
-                        -f .test_reports/coverage.xml \
-                        -C ${CODECOV_GIT_COMMIT} \
-                        -N ${CODECOV_PARENT_COMMIT}
-                '''
-            }
-        }
-
-        stage('Deploy') {
-            when {
-                branch 'master'
-            }
-            steps {
-                echo 'Deploying.'
-            }
-        }
-    }
-    post {
-        always {
-            script {
-                if (env.CHANGE_ID) {
-                    if (pullRequest.createdBy != "arnaudbore"){
-                        pullRequest.createReviewRequests(['arnaudbore'])
-                    }
-                    else{
-                        pullRequest.createReviewRequests(['frheault'])
-                    }
-                }
-                xunit(
-                    checksName: '',
-                    tools: [JUnit(excludesPattern: '', failIfNotNew: false,
-                            pattern: '**/.test_reports/junit.xml',
-                            skipNoTestFiles: true,
-                            stopProcessingIfError: true)]
-                )
-            }
-        }
-        failure {
-            script {
-                // CHANGE_ID is set only for pull requests, so it is safe to access the pullRequest global variable
-                if (env.CHANGE_ID) {
-                    pullRequest.comment('Build Failed :boom: \n' + env.BUILD_URL)
-                }
-            }
-        }
-        success {
-            script {
-                // CHANGE_ID is set only for pull requests, so it is safe to access the pullRequest global variable
-                if (env.CHANGE_ID) {
-                    pullRequest.comment('Build passed ! Good Job :beers: !')
-                }
-            }
-        }
-    }
-}

From 697aa86cc3dc654caddd0a0c17193f1f1b3c3fd5 Mon Sep 17 00:00:00 2001
From: AlexVCaron <alex.valcourt.caron@usherbrooke.ca>
Date: Wed, 7 Feb 2024 14:24:52 -0500
Subject: [PATCH 53/53] cancel previous concurrent build

---
 .github/workflows/test.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4bca3eb92..ea2a4d5df 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -8,6 +8,10 @@ on:
     branches:
       - master
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+  
 env:
   MPLBACKEND: agg
   OPENBLAS_NUM_THREADS: 1