151 use pyccel 210 (#153)

**Solves the following issue(s):**

Closes #151

Things that did not work for me with pyccel 2.1:

- using `pyccel make ...` I get the [mysterious numpy
error](https://struphy-hub.github.io/struphy/sections/install.html#compilation-problems).
Using `pyccel compile ...` I don't get this error.
- `pyccel make -d kernel_file.txt` did not behave like a make file, i.e.
it recompiled everything on the second call.
- `pyccel clean` did not remove the .so files; `pyccel clean -s` removed
alos numpy and scipy stuff that I had to reinstall afterwards.

Author: spossann

.github/workflows/test-PR-unit-mpi.yml

@@ -0,0 +1,79 @@
+name: PR - unit tests with MPI in Container
+
+on:
+  pull_request:
+    branches:
+      - devel
+  push:
+    branches:
+      - devel
+  schedule:
+    # run at 1 a.m. on Sunday
+    - cron: "0 1 * * 0"
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash
+
+permissions:
+  contents: read
+
+jobs:
+  unit-tests-in-container-with-struphy:
+    runs-on: ubuntu-latest
+
+    container:
+      image: ghcr.io/struphy-hub/struphy/ubuntu-with-struphy:latest
+      credentials:
+        username: spossann
+        password: ${{ secrets.GHCR_TOKEN }}
+
+    steps:
+      - name: Check for dockerenv file
+        run: (ls /.dockerenv && echo Found dockerenv) || (echo No dockerenv)
+
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Check .testmondata 1
+        run: |
+          ls .testmon* || echo "No .testmondata"
+
+      - name: Setup cache for testmon
+        uses: actions/cache@v4
+        with:
+          path: |
+            .testmondata-unit-mpi
+          key: testmon-unit-mpi-${{ github.ref_name }}-${{ github.event.number }}-${{ github.run_number }}
+          restore-keys: |
+            testmon-unit-mpi-${{ github.ref_name }}-${{ github.event.number }}-
+            testmon-unit-mpi-${{ github.ref_name }}
+            testmon-unit-mpi-devel
+            testmon-unit-mpi-
+
+      - name: Check .testmondata 2
+        run: |
+          ls .testmon* || echo "No .testmondata"
+
+      - name: Install Struphy in Container
+        uses: ./.github/actions/install/struphy_in_container
+
+      - name: Compile Struphy
+        run: |
+          source /struphy_c_/env_c_/bin/activate
+          struphy compile
+
+      - name: Run unit tests with MPI
+        shell: bash
+        env:
+          TESTMON_DATAFILE: ${{ github.workspace }}/.testmondata-unit-mpi
+        # init .testmondata with non-MPI call
+        run: |
+          source /struphy_c_/env_c_/bin/activate
+          struphy test Maxwell
+          struphy test unit --mpi 2

.github/workflows/test-PR-unit.yml

@@ -1,4 +1,4 @@
-name: PR - unit tests in Container
+name: PR - unit tests serial in Container
 
 on:
   pull_request:
@@ -49,7 +49,6 @@ jobs:
         with:
           path: |
             .testmondata-unit
-            .testmondata-unit-mpi
           key: testmon-unit-${{ github.ref_name }}-${{ github.event.number }}-${{ github.run_number }}
           restore-keys: |
             testmon-unit-${{ github.ref_name }}-${{ github.event.number }}-
@@ -78,15 +77,4 @@ jobs:
           struphy compile --status
           pip show mpi4py
           pip uninstall -y mpi4py
-          struphy test unit
-
-      - name: Run unit tests with MPI
-        shell: bash
-        env:
-          TESTMON_DATAFILE: ${{ github.workspace }}/.testmondata-unit-mpi
-        # init .testmondata with non-MPI call
-        run: |
-          source /struphy_c_/env_c_/bin/activate
-          struphy test Maxwell
-          pip install -U mpi4py
-          struphy test unit --mpi 2
+          struphy test unit

pyproject.toml

@@ -25,7 +25,7 @@ classifiers = [
 dependencies = [
     'numpy',
     'cunumpy',
-    'pyccel>=2.0',
+    'pyccel>=2.1',
     'feectools',
     'scipy',
     'h5py',

…/bsplines/tests/test_bsplines_kernels.py …phy/bsplines/tests/test_bsplines_kers.pysrc/struphy/bsplines/tests/test_bsplines_kernels.py renamed to src/struphy/bsplines/tests/test_bsplines_kers.py src/struphy/bsplines/tests/test_bsplines_kernels.py renamed to src/struphy/bsplines/tests/test_bsplines_kers.py

@@ -35,7 +35,7 @@ all: $(OUTPUTS)
 	@for dep in $^ ; do \
 		echo $$dep ; \
     done
-	pyccel $(FLAGS) $(FLAGS_openmp_pic) $(FLAGS_openmp_mhd) $<
+	pyccel compile -v $(FLAGS) $(FLAGS_openmp_pic) $(FLAGS_openmp_mhd) $<
 	@echo ""
 
 #--------------------------------------

src/struphy/compile_struphy.mk

@@ -107,6 +107,11 @@ def struphy_compile(
     if delete:
         # (change dir not to be in source path)
         print("\nDeleting .f90/.c and .so files ...")
+        # TODO: for using pyccel clean in the future
+        # cmd = [
+        #     "pyccel",
+        #     "clean",
+        # ]
         cmd = [
             "make",
             "clean",
@@ -272,6 +277,15 @@ def struphy_compile(
 
         # compilation
         print("\nCompiling Struphy kernels ...")
+        kernel_file = os.path.join(libpath, "kernels.txt")
+        # TODO: for using pyccel make in the future
+        # cmd = [
+        #     "pyccel",
+        #     "make",
+        #     "-d",
+        #     kernel_file,
+        #     "-v",
+        # ]
         cmd = [
             "make",
             "-f",

src/struphy/console/compile.py

@@ -54,9 +54,12 @@ def update_state(state):
 
 
 def save_state(state, libpath=STRUPHY_LIBPATH):
-    """Save the state to the state.yml file."""
+    """Save the state to state.yml and write the kernels to kernels.txt."""
     state_file = os.path.join(libpath, "state.yml")
     dict_to_yaml(state, state_file)
+    if "kernels" in state:
+        kernel_file = os.path.join(libpath, "kernels.txt")
+        kernels_to_txt(state["kernels"], kernel_file)
 
 
 def print_all_attr(obj):
@@ -85,6 +88,15 @@ def dict_to_yaml(dictionary: dict, output: str):
             indent=4,
             line_break="\n",
         )
+    # print(f"dict written to {output}.")
+
+
+def kernels_to_txt(kernels: list, output: str):
+    """Write state[kernels] to .txt file for pyccel make."""
+    with open(output, "w") as file:
+        for ker in kernels:
+            file.write(f"{ker}\n")
+    # print(f"kernels written to {output}.")
 
 
 class MyDumper(yaml.SafeDumper):