Merge remote-tracking branch 'clinssen/new_gsl' into block_diag

clinssen · Nov 21, 2024 · 55d29b4 · 55d29b4
2 parents f47a662 + 8a86b5e
commit 55d29b4
Show file tree

Hide file tree

Showing 2 changed files with 14 additions and 12 deletions.
diff --git a/.github/workflows/ode-toolbox-build.yml b/.github/workflows/ode-toolbox-build.yml
@@ -6,12 +6,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout ODE-toolbox code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Install apt dependencies
         run: |
@@ -47,31 +47,33 @@ jobs:
 
     steps:
       - name: Checkout ODE-toolbox code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Install apt dependencies
         run: |
           sudo apt update
           sudo apt install pkg-config python3-all-dev
 
       - name: Install GSL
+        if: ${{ matrix.with_gsl == '1' }}
         run: |
+          sudo apt remove libgsl27 libgsl-dev # remove system-wide GSL version that is installed by default
           cd ..
-          wget http://ftp.wrz.de/pub/gnu/gsl/gsl-2.5.tar.gz
-          tar -xzf gsl-2.5.tar.gz
-          cd gsl-2.5
+          wget https://mirror.ibcp.fr/pub/gnu/gsl/gsl-2.7.tar.gz # this should be "gsl-latest.tar.gz", but there is an issue with GSL 2.8 (see https://github.com/pygsl/pygsl/issues/62)
+          tar -xzf gsl-2.7.tar.gz
+          cd gsl-2.7
           ./configure && make && sudo make install
 
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade pip pytest pycodestyle codecov pytest-cov wheel
           python -m pip install numpy
-          if [ "${{ matrix.with_gsl }}" == "1" ]; then python -m pip install pygsl ; fi
+          if [ "${{ matrix.with_gsl }}" == "1" ]; then python3 -m pip install -v https://github.com/pygsl/pygsl/archive/refs/tags/v2.4.1.tar.gz ; fi # this should be "pip install pygsl", but see https://github.com/pygsl/pygsl/issues/59
           python -m pip install -r requirements.txt
           export PYTHON_VERSION=`python -c "import sys; print('.'.join(map(str, [sys.version_info.major, sys.version_info.minor])))"`
           echo "Python version detected:"

diff --git a/doc/index.rst b/doc/index.rst
@@ -41,9 +41,9 @@ ODE-toolbox is written in Python and leverages SymPy for the symbolic manipulati
 Installation
 ------------
 
-.. Attention:: SymPy releases after 1.4 introduce a fourfold regression in runtime performance on the ODE-toolbox unit tests, compared to SymPy 1.4. Unless this conflicts with other version requirements, we would recommend to use SymPy 1.4 for now (for example, by editing ``requirements.txt`` to read ``sympy==1.4``).
+.. Attention:: SymPy releases after 1.4 introduce a regression in runtime performance when computing matrix exponentials. Unless this conflicts with other version requirements, we recommend to use SymPy 1.4 for now (for example, by editing ``requirements.txt`` to read ``sympy==1.4``). This issue is being tracked at https://github.com/sympy/sympy/issues/23417.
 
-.. Attention:: The latest SymPy release at time of writing, 1.10.1, introduces an issue that prevents ODE-toolbox from being used with many common neuron models. Please see https://github.com/sympy/sympy/issues/23417 and use an older SymPy version until this issue has been resolved.
+.. Attention:: To perform solver benchmarking, ODE-toolbox relies on GSL and PyGSL. Currently, the latest PyGSL release is not compatible with GSL. We recommend to use GSL 2.7 for now. This issue is being tracked at https://github.com/pygsl/pygsl/issues/62.
 
 
 Prerequisites