From 358f697f584c21b2ee09b82e9ca5746e1f74d48f Mon Sep 17 00:00:00 2001
From: Pierre-antoine Comby <pierre-antoine.comby@crans.org>
Date: Mon, 3 Mar 2025 13:13:57 +0100
Subject: [PATCH 1/3] fix: use venv in all CI.

---
 .github/workflows/test-ci.yml | 60 +++++++++++++++++++++++------------
 1 file changed, 40 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/test-ci.yml b/.github/workflows/test-ci.yml
index 4720af6ae..d105f9884 100644
--- a/.github/workflows/test-ci.yml
+++ b/.github/workflows/test-ci.yml
@@ -16,6 +16,9 @@ env:
   PYTHON_VERSION: "3.10"
   BART_VERSION: "0.8.00"
   ref_backend: "finufft"
+  create_venv: "python -m venv $RUNNER_WORKSPACE/venv/"
+  activate_venv_venv: "source $RUNNER_WORKSPACE/venv/bin/activate"
+  setup_cuda: "export CUDA_BIN_PATH=/usr/local/cuda-12.1/;export PATH=/usr/local/cuda-12.1/bin/:${PATH};export LD_LIBRARY_PATH=/usr/local/cuda-12.1/lib64/:${LD_LIBRARY_PATH}"
 
 jobs:
   test-cpu:
@@ -44,6 +47,9 @@ jobs:
       - name: Install Python Deps
         shell: bash
         run: |
+          python --version
+          ${{env.create_venv}}
+          ${{env.activate_venv_venv}}
           python -m pip install --upgrade pip
           python -m pip install -e .[test]
 
@@ -51,21 +57,28 @@ jobs:
         if: ${{ matrix.backend == 'pynfft' || env.ref_backend == 'pynfft' }}
         shell: bash
         run: |
+          ${{env.activate_venv}}
           python -m pip install "pynfft2>=1.4.3"
 
       - name: Install pynufft
         if: ${{ matrix.backend == 'pynufft-cpu' || env.ref_backend == 'pynufft-cpu' }}
-        run: python -m pip install pynufft
+        run: |
+          ${{env.activate_venv}}
+          python -m pip install pynufft
 
       - name: Install finufft
         if: ${{ matrix.backend == 'finufft'  || env.ref_backend == 'finufft'}}
         shell: bash
-        run: python -m pip install finufft
+        run: |
+          ${{env.activate_venv}}
+          python -m pip install finufft
 
       - name: Install Sigpy
         if: ${{ matrix.backend == 'sigpy'  || env.ref_backend == 'sigpy'}}
         shell: bash
-        run: python -m pip install sigpy
+        run: |
+          ${{env.activate_venv}}
+          python -m pip install sigpy
 
       - name: Install BART
         if: ${{ matrix.backend == 'bart'  || env.ref_backend == 'bart'}}
@@ -81,12 +94,15 @@ jobs:
 
       - name: Install torchkbnufft-cpu
         if: ${{ matrix.backend == 'torchkbnufft-cpu'  || env.ref_backend == 'torchkbnufft-cpu'}}
-        run: python -m pip install torchkbnufft
+        run: |
+          ${{env.activate_venv}}
+          python -m pip install torchkbnufft
 
 
       - name: Run Tests
         shell: bash
         run: |
+          ${{env.activate_venv}}
           export COVERAGE_FILE=coverage_${{ matrix.backend }}
           pytest -k='operators' --backend ${{ matrix.backend }} --ref ${{ env.ref_backend }} --cov --disable-pytest-warnings --cov-branch --cov-report=term
       - name: Upload coverage
@@ -111,10 +127,8 @@ jobs:
       - name: Install mri-nufft and finufft
         shell: bash
         run: |
-          cd $RUNNER_WORKSPACE
-          python --version
-          python -m venv venv
-          source $RUNNER_WORKSPACE/venv/bin/activate
+          ${{ env.create_venv }}
+          ${{ env.activate_venv }}
           pip install --upgrade pip wheel
           pip install -e mri-nufft[test]
           pip install cupy-cuda12x finufft "numpy<2.0"
@@ -123,16 +137,14 @@ jobs:
         shell: bash
         if: ${{ matrix.backend != 'tensorflow'}}
         run: |
-          source $RUNNER_WORKSPACE/venv/bin/activate
+          source $RUNNER_WORKSPACE/venv/binactivate_venv
           pip install torch
 
       - name: Install backend
         shell: bash
         run: |
-          source $RUNNER_WORKSPACE/venv/bin/activate
-          export CUDA_BIN_PATH=/usr/local/cuda-12.1/
-          export PATH=/usr/local/cuda-12.1/bin/:${PATH}
-          export LD_LIBRARY_PATH=/usr/local/cuda-12.1/lib64/:${LD_LIBRARY_PATH}
+          ${{ env.activate_venv }}
+          ${{ env.setup_cuda }}
           if [[ ${{ matrix.backend }} == "torchkbnufft-gpu" ]]; then
             pip install torchkbnufft
           elif [[ ${{ matrix.backend }} == "tensorflow" ]]; then
@@ -146,8 +158,8 @@ jobs:
       - name: Run Tests
         shell: bash
         run: |
+          ${{ env.activate_venv }}
           cd $RUNNER_WORKSPACE/mri-nufft
-          source $RUNNER_WORKSPACE/venv/bin/activate
           export COVERAGE_FILE=coverage_${{ matrix.backend }}
           python -m pytest -k='operators' --ref ${{ env.ref_backend }} --backend ${{ matrix.backend }} --disable-pytest-warnings --cov --cov-branch --cov-report=term
 
@@ -205,21 +217,23 @@ jobs:
       - name: Install Python deps
         shell: bash
         run: |
+          ${{ env.create_venv }}
+          ${{ env.activate_venv }}
           python -m pip install --upgrade pip
           python -m pip install -e .[extra,test,dev]
           python -m pip install finufft pooch brainweb-dl torch fastmri
         
       - name: Install GPU related interfaces
         run: |
-          export CUDA_BIN_PATH=/usr/local/cuda-12.1/
-          export PATH=/usr/local/cuda-12.1/bin/:${PATH}
-          export LD_LIBRARY_PATH=/usr/local/cuda-12.1/lib64/:${LD_LIBRARY_PATH}
+          ${{ env.activate_venv }}
+          ${{ env.setup_cuda }}
           pip install cupy-cuda12x torch
           python -m pip install gpuNUFFT "cufinufft<2.3" sigpy scikit-image fastmri
 
       - name: Run examples
         shell: bash
         run: |
+          ${{ env.activate_venv }}
           export COVERAGE_FILE=coverage_plots
           pytest examples tests -k="not operators" --cov --cov-branch --cov-report=term
 
@@ -260,12 +274,15 @@ jobs:
       - name: add the coverage tool
         shell: bash
         run: |
+          ${{ env.create_venv }}
+          ${{ env.activate_venv }}
           python -m pip install --upgrade pip
           python -m pip install coverage[toml]
           python -m pip install -e .
 
       - name: Combine coverage
         run: |
+          ${{ env.activate_venv }}
           export COVERAGE_FILE=coverage_combined
           coverage combine -a coverage_data/*
 
@@ -277,6 +294,7 @@ jobs:
 
       - name: Reports
         run: |
+          ${{ env.activate_venv }}
           export COVERAGE_FILE=coverage_combined
           coverage xml
           coverage report
@@ -316,20 +334,22 @@ jobs:
       - name: Install dependencies
         shell: bash -l {0}
         run: |
+          ${{ env.create_venv }}
+          ${{ env.activate_venv }}
           python -m pip install --upgrade pip
           python -m pip install .[doc]
           python -m pip install finufft
       
       - name: Install GPU related interfaces
         run: |
-          export CUDA_BIN_PATH=/usr/local/cuda-12.1/
-          export PATH=/usr/local/cuda-12.1/bin/:${PATH}
-          export LD_LIBRARY_PATH=/usr/local/cuda-12.1/lib64/:${LD_LIBRARY_PATH}
+          ${{ env.activate_venv }}
+          ${{ env.setup_cuda }}
           pip install cupy-cuda12x torch
           python -m pip install gpuNUFFT "cufinufft<2.3"
       
       - name: Build API documentation
         run: |
+          ${{ env.activate_venv }}
           python -m sphinx docs docs_build
       
       - name: Display data

From 67ece186c5c1b5169f31f3d317d329e8535dcb5b Mon Sep 17 00:00:00 2001
From: Pierre-antoine Comby <pierre-antoine.comby@crans.org>
Date: Mon, 3 Mar 2025 13:20:12 +0100
Subject: [PATCH 2/3] more isolation.

---
 .github/workflows/test-ci.yml | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/test-ci.yml b/.github/workflows/test-ci.yml
index d105f9884..d6ce3bd51 100644
--- a/.github/workflows/test-ci.yml
+++ b/.github/workflows/test-ci.yml
@@ -16,7 +16,7 @@ env:
   PYTHON_VERSION: "3.10"
   BART_VERSION: "0.8.00"
   ref_backend: "finufft"
-  create_venv: "python -m venv $RUNNER_WORKSPACE/venv/"
+  create_venv: "python -m venv $RUNNER_WORKSPACE/venv/ --clear"
   activate_venv_venv: "source $RUNNER_WORKSPACE/venv/bin/activate"
   setup_cuda: "export CUDA_BIN_PATH=/usr/local/cuda-12.1/;export PATH=/usr/local/cuda-12.1/bin/:${PATH};export LD_LIBRARY_PATH=/usr/local/cuda-12.1/lib64/:${LD_LIBRARY_PATH}"
 
@@ -104,7 +104,7 @@ jobs:
         run: |
           ${{env.activate_venv}}
           export COVERAGE_FILE=coverage_${{ matrix.backend }}
-          pytest -k='operators' --backend ${{ matrix.backend }} --ref ${{ env.ref_backend }} --cov --disable-pytest-warnings --cov-branch --cov-report=term
+          python -m pytest -k='operators' --backend ${{ matrix.backend }} --ref ${{ env.ref_backend }} --cov --disable-pytest-warnings --cov-branch --cov-report=term
       - name: Upload coverage
         uses: actions/upload-artifact@v4
         with:
@@ -129,16 +129,16 @@ jobs:
         run: |
           ${{ env.create_venv }}
           ${{ env.activate_venv }}
-          pip install --upgrade pip wheel
-          pip install -e mri-nufft[test]
-          pip install cupy-cuda12x finufft "numpy<2.0"
+          python -m pip install --upgrade pip wheel
+          python -m pip install -e mri-nufft[test]
+          python -m pip install cupy-cuda12x finufft "numpy<2.0"
 
       - name: Install torch with CUDA 12.1
         shell: bash
         if: ${{ matrix.backend != 'tensorflow'}}
         run: |
           source $RUNNER_WORKSPACE/venv/binactivate_venv
-          pip install torch
+          python -m pip install torch
 
       - name: Install backend
         shell: bash
@@ -146,13 +146,13 @@ jobs:
           ${{ env.activate_venv }}
           ${{ env.setup_cuda }}
           if [[ ${{ matrix.backend }} == "torchkbnufft-gpu" ]]; then
-            pip install torchkbnufft
+            python -m pip install torchkbnufft
           elif [[ ${{ matrix.backend }} == "tensorflow" ]]; then
-            pip install tensorflow-mri==0.21.0 tensorflow-probability==0.17.0 tensorflow-io==0.27.0 matplotlib==3.7
+            python -m pip install tensorflow-mri==0.21.0 tensorflow-probability==0.17.0 tensorflow-io==0.27.0 matplotlib==3.7
           elif [[ ${{ matrix.backend }} == "cufinufft" ]]; then
-            pip install "cufinufft<2.3" 
+            python -m pip install "cufinufft<2.3"
           else
-            pip install ${{ matrix.backend }}
+            python -m pip install ${{ matrix.backend }}
           fi
 
       - name: Run Tests

From d79e284c5319b6b86c8d1199405d9a8e7084136c Mon Sep 17 00:00:00 2001
From: Pierre-antoine Comby <pierre-antoine.comby@crans.org>
Date: Mon, 3 Mar 2025 13:26:13 +0100
Subject: [PATCH 3/3] update ci

---
 .github/workflows/test-ci.yml | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/test-ci.yml b/.github/workflows/test-ci.yml
index d6ce3bd51..c4d7f04cd 100644
--- a/.github/workflows/test-ci.yml
+++ b/.github/workflows/test-ci.yml
@@ -16,8 +16,8 @@ env:
   PYTHON_VERSION: "3.10"
   BART_VERSION: "0.8.00"
   ref_backend: "finufft"
-  create_venv: "python -m venv $RUNNER_WORKSPACE/venv/ --clear"
-  activate_venv_venv: "source $RUNNER_WORKSPACE/venv/bin/activate"
+  create_venv: "python -m venv $RUNNER_WORKSPACE/venv"
+  activate_venv: "source $RUNNER_WORKSPACE/venv/bin/activate"
   setup_cuda: "export CUDA_BIN_PATH=/usr/local/cuda-12.1/;export PATH=/usr/local/cuda-12.1/bin/:${PATH};export LD_LIBRARY_PATH=/usr/local/cuda-12.1/lib64/:${LD_LIBRARY_PATH}"
 
 jobs:
@@ -48,8 +48,8 @@ jobs:
         shell: bash
         run: |
           python --version
-          ${{env.create_venv}}
-          ${{env.activate_venv_venv}}
+          ${{ env.create_venv }}
+          ${{ env.activate_venv }}
           python -m pip install --upgrade pip
           python -m pip install -e .[test]
 
@@ -57,27 +57,27 @@ jobs:
         if: ${{ matrix.backend == 'pynfft' || env.ref_backend == 'pynfft' }}
         shell: bash
         run: |
-          ${{env.activate_venv}}
+          ${{ env.activate_venv }}
           python -m pip install "pynfft2>=1.4.3"
 
       - name: Install pynufft
         if: ${{ matrix.backend == 'pynufft-cpu' || env.ref_backend == 'pynufft-cpu' }}
         run: |
-          ${{env.activate_venv}}
+          ${{ env.activate_venv }}
           python -m pip install pynufft
 
       - name: Install finufft
         if: ${{ matrix.backend == 'finufft'  || env.ref_backend == 'finufft'}}
         shell: bash
         run: |
-          ${{env.activate_venv}}
+          ${{ env.activate_venv }}
           python -m pip install finufft
 
       - name: Install Sigpy
         if: ${{ matrix.backend == 'sigpy'  || env.ref_backend == 'sigpy'}}
         shell: bash
         run: |
-          ${{env.activate_venv}}
+          ${{ env.activate_venv }}
           python -m pip install sigpy
 
       - name: Install BART
@@ -95,14 +95,14 @@ jobs:
       - name: Install torchkbnufft-cpu
         if: ${{ matrix.backend == 'torchkbnufft-cpu'  || env.ref_backend == 'torchkbnufft-cpu'}}
         run: |
-          ${{env.activate_venv}}
+          ${{ env.activate_venv }}
           python -m pip install torchkbnufft
 
 
       - name: Run Tests
         shell: bash
         run: |
-          ${{env.activate_venv}}
+          ${{ env.activate_venv }}
           export COVERAGE_FILE=coverage_${{ matrix.backend }}
           python -m pytest -k='operators' --backend ${{ matrix.backend }} --ref ${{ env.ref_backend }} --cov --disable-pytest-warnings --cov-branch --cov-report=term
       - name: Upload coverage
@@ -130,14 +130,14 @@ jobs:
           ${{ env.create_venv }}
           ${{ env.activate_venv }}
           python -m pip install --upgrade pip wheel
-          python -m pip install -e mri-nufft[test]
+          python -m pip install -e .[test]
           python -m pip install cupy-cuda12x finufft "numpy<2.0"
 
       - name: Install torch with CUDA 12.1
         shell: bash
         if: ${{ matrix.backend != 'tensorflow'}}
         run: |
-          source $RUNNER_WORKSPACE/venv/binactivate_venv
+          ${{ env.activate_venv }}
           python -m pip install torch
 
       - name: Install backend