#20 Add conda variants for cells example

Chaste · Nov 6, 2024 · 659fca1 · 659fca1
1 parent 1e82dc2
commit 659fca1
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Showing 13 changed files with 53 additions and 33 deletions.
diff --git a/.github/workflows/test-cells-conda.yml b/.github/workflows/test-cells-conda.yml
@@ -1,4 +1,4 @@
-name: test-cells
+name: test-cells-conda
 
 on:
   workflow_dispatch:
@@ -7,7 +7,7 @@ on:
       - "**"
 
 jobs:
-  test-cells:
+  test-cells-conda:
     runs-on: ubuntu-latest
 
     strategy:
@@ -16,7 +16,7 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
 
     concurrency:
-      group: test-cells-${{ github.ref }}-${{ matrix.python-version }}
+      group: test-cells-conda-${{ github.ref }}-${{ matrix.python-version }}
       cancel-in-progress: true
 
     defaults:
@@ -39,7 +39,6 @@ jobs:
           use-mamba: true
           miniforge-version: latest
           python-version: ${{ matrix.python-version }}
-          activate-environment: test_cells
           channels: conda-forge
 
       - name: Install cppwg
@@ -48,8 +47,7 @@ jobs:
           python -m pip install .
 
       - name: Install requirements
-        run: |
-          mamba install --yes --file requirements.txt
+        run: mamba install --yes --file requirements.txt
         working-directory: examples/cells
 
       - name: Set config paths
@@ -78,14 +76,16 @@ jobs:
           grep "Unknown class" build/cppwg.log
         working-directory: examples/cells
 
+      - name: Install conda-build tools
+        run: mamba install boa conda-build conda-verify
+
       - name: Build
-        run: conda build conda-recipe
-        working-directory: examples/cells
+        run: conda mambabuild recipe -m variants/python${{ matrix.python-version }}.yaml
+        working-directory: examples/cells/conda
 
       - name: Install
-        run: conda install --use-local pycells
-        working-directory: examples/cells
+        run: mamba install --use-local pycells
 
       - name: Test
-        run: python -m unittest discover -s tests
+        run: python -m unittest discover tests
         working-directory: examples/cells
diff --git a/.github/workflows/test-cells-ubuntu.yml b/.github/workflows/test-cells-ubuntu.yml
@@ -64,5 +64,5 @@ jobs:
         working-directory: examples/cells
 
       - name: Test
-        run: python -m unittest discover -s tests
+        run: python -m unittest discover tests
         working-directory: examples/cells
diff --git a/examples/cells/conda-recipe/build.sh b/examples/cells/conda-recipe/build.sh
diff --git a/examples/cells/conda/recipe/build.sh b/examples/cells/conda/recipe/build.sh
@@ -0,0 +1,8 @@
+#!/bin/bash -ex
+
+export CMAKE_PREFIX_PATH="$PREFIX;$CMAKE_PREFIX_PATH"
+export PETSC_DIR="$PREFIX"
+export PETSC_ARCH=
+export VTK_DIR="$PREFIX"
+
+$PYTHON -m pip install -v --no-build-isolation .
diff --git a/examples/cells/conda-recipe/meta.yaml → examples/cells/conda/recipe/meta.yaml b/examples/cells/conda-recipe/meta.yaml → examples/cells/conda/recipe/meta.yaml
@@ -6,26 +6,20 @@ package:
   version: {{ version }}
 
 source:
-  path: ..
+  path: ../..
 
 build:
   number: {{ build }}
 
 requirements:
-  build:
-    - cmake
-    - ninja
-    - pip
-    - python
-    - scikit-build
-    - setuptools
-
   host:
     - mpi4py
-    - mpich
+    - openmpi
     - petsc
     - petsc4py
+    - pip
     - python
+    - scikit-build-core
     - vtk
 
 test:

diff --git a/examples/cells/conda/variants/python3.10.yaml b/examples/cells/conda/variants/python3.10.yaml
@@ -0,0 +1,2 @@
+python:
+  - 3.10.*
diff --git a/examples/cells/conda/variants/python3.11.yaml b/examples/cells/conda/variants/python3.11.yaml
@@ -0,0 +1,2 @@
+python:
+  - 3.11.*
diff --git a/examples/cells/conda/variants/python3.12.yaml b/examples/cells/conda/variants/python3.12.yaml
@@ -0,0 +1,2 @@
+python:
+  - 3.12.*
diff --git a/examples/cells/conda/variants/python3.13.yaml b/examples/cells/conda/variants/python3.13.yaml
@@ -0,0 +1,2 @@
+python:
+  - 3.13.*
diff --git a/examples/cells/conda/variants/python3.8.yaml b/examples/cells/conda/variants/python3.8.yaml
@@ -0,0 +1,2 @@
+python:
+  - 3.8.*
diff --git a/examples/cells/conda/variants/python3.9.yaml b/examples/cells/conda/variants/python3.9.yaml
@@ -0,0 +1,2 @@
+python:
+  - 3.9.*
diff --git a/examples/cells/requirements.txt b/examples/cells/requirements.txt
@@ -1,4 +1,4 @@
-mpich
+openmpi
 mpi4py
 petsc
 petsc4py

diff --git a/examples/cells/src/cpp/utils/PetscUtils.cpp b/examples/cells/src/cpp/utils/PetscUtils.cpp
@@ -12,7 +12,11 @@ void PetscUtils::Initialise()
 {
     if (!PetscUtils::IsInitialised())
     {
+#if PETSC_VERSION_GE(3, 19, 0)
+        PetscInitialize(PETSC_NULLPTR, PETSC_NULLPTR, PETSC_NULLPTR, PETSC_NULLPTR);
+#else
         PetscInitialize(PETSC_NULL, PETSC_NULL, PETSC_NULL, PETSC_NULL);
+#endif
     }
 }
 
@@ -27,7 +31,7 @@ int PetscUtils::GetSize()
 {
     if (!PetscUtils::IsInitialised())
     {
-        return -1;
+        PetscUtils::Initialise();
     }
 
     PetscInt size;
@@ -39,7 +43,7 @@ int PetscUtils::GetRank()
 {
     if (!PetscUtils::IsInitialised())
     {
-        return -1;
+        PetscUtils::Initialise();
     }
 
     PetscInt rank;
@@ -49,9 +53,14 @@ int PetscUtils::GetRank()
 
 Vec PetscUtils::CreateVec(int size)
 {
-    Vec vec;
-    VecCreate(PETSC_COMM_WORLD, &vec);
-    VecSetSizes(vec, PETSC_DECIDE, size);
-    VecSetType(vec, VECMPI);
-    return vec;
+    if (!PetscUtils::IsInitialised())
+    {
+        PetscUtils::Initialise();
+    }
+
+    Vec v;
+    VecCreate(PETSC_COMM_WORLD, &v);
+    VecSetSizes(v, PETSC_DECIDE, size);
+    VecSetFromOptions(v);
+    return v;
 }
-Original file line number
+Diff line change
@@ -1,4 +1,4 @@
-    mpich
+    openmpi
     mpi4py
     petsc
     petsc4py
@@ Expand Down @@