Merge branch 'master' into 257_verify_loop_fusion

.github/workflows/compilation.yml

@@ -51,14 +51,14 @@ on:
   push
 
 env:
-  CUDA_VERSION: 12.6.0
+  CUDA_VERSION: 12.6.2
   GFORTRAN_VERSION: 14.2.0
-  HDF5_VERSION: 1.14.4.3
+  HDF5_VERSION: 1.14.5
   NETCDF_C_VERSION: 4.9.2
   NETCDF_FORTRAN_VERSION: 4.6.1
-  NVFORTRAN_VERSION: 24.7
+  NVFORTRAN_VERSION: 24.9
   OPENMPI_VERSION: 5.0.5
-  PYTHON_VERSION: 3.12.5
+  PYTHON_VERSION: 3.13.0
 
 jobs:
   run_if_on_mirror:

.github/workflows/lfric_test.yml

@@ -47,7 +47,7 @@ jobs:
     runs-on: self-hosted
     env:
       LFRIC_APPS_REV: 3269
-      PYTHON_VERSION: 3.12.5
+      PYTHON_VERSION: 3.13.0
 
     steps:
     - uses: actions/checkout@v3

.github/workflows/nemo_tests.yml

@@ -46,13 +46,13 @@ jobs:
     if: ${{ github.repository == 'stfc/PSyclone-mirror' }}
     runs-on: self-hosted
     env:
-      HDF5_VERSION: 1.14.4.3
+      HDF5_VERSION: 1.14.5
       NETCDF_C_VERSION: 4.9.2
       NETCDF_FORTRAN_VERSION: 4.6.1
       NVFORTRAN_VERSION: 23.7
       ONEAPI_VERSION: 2024.2.1
       PERL_VERSION: 5.40.0
-      PYTHON_VERSION: 3.12.5
+      PYTHON_VERSION: 3.13.0
 
     steps:
     - uses: actions/checkout@v3

.github/workflows/python-package.yml

@@ -62,7 +62,7 @@ jobs:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.12'
+        python-version: '3.13'
     - run: sudo apt-get install -y graphviz doxygen
     - run: python -m pip install --upgrade pip
     - run: pip install .[doc]
@@ -83,7 +83,7 @@ jobs:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.12'
+        python-version: '3.13'
     - run: python -m pip install --upgrade pip
     - run: pip install .[doc]
     # Sphinx since version 7.2 (7.2.0/1/2) aborts with
@@ -99,7 +99,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.12]
+        python-version: [3.7, 3.8, 3.13]
     steps:
     - uses: actions/checkout@v4
       with:

changelog

@@ -243,6 +243,11 @@
 	83) PR #2743 for #2742. Ensure generated code for function spaces in
 	LFRic is always in a consistent order.
 
+	84) PR #2746. Update minor versions of CUDA, HDF5, nvfortran and
+	Python used in the CI.
+
+	85) PR #2748. Revert Python used on RTD to 3.12 as 3.13 unsupported.
+
 release 2.5.0 14th of February 2024
 
 	1) PR #2199 for #2189. Fix bugs with missing maps in enter data

doc/developer_guide/working_practises.rst

@@ -448,13 +448,13 @@ computational cost (so that we 'fail fast'):
  3. All links within the Sphinx documentation (rst files) are checked (see
     note below);
 
- 4. All of the examples are tested (for Python versions 3.7, 3.8 and 3.12)
+ 4. All of the examples are tested (for Python versions 3.7, 3.8 and 3.13)
     using the ``Makefile`` in the ``examples`` directory. No compilation is
     performed; only the ``transform`` (performs the PSyclone transformations)
     and ``notebook`` (runs the various Jupyter notebooks) targets are used.
     The ``transform`` target is run 2-way parallel (``-j 2``).
 
- 5. The full test suite is run for Python versions 3.7, 3.8 and 3.12 but
+ 5. The full test suite is run for Python versions 3.7, 3.8 and 3.13 but
     without the compilation checks. ``pytest`` is passed the ``-n auto`` flag
     so that it will run the tests in parallel on as many cores as are
     available (currently 2 on GHA instances).

doc/user_guide/getting_going.rst

@@ -212,7 +212,7 @@ Dependencies
 ------------
 
 PSyclone is written in Python so needs Python 3 to be installed on the
-target machine. PSyclone is regularly tested with Python 3.7, 3.8 and 3.12
+target machine. PSyclone is regularly tested with Python 3.7, 3.8 and 3.13
 but should work with any version >= 3.6. (The last PSyclone release to
 support Python 2.7 was version 2.1.0.)
 

examples/gocean/eg5/extract/Makefile

@@ -122,13 +122,13 @@ $(NAME): $(INF_LIB) $(EXTRACT_DIR)/$(LIB_NAME) $(KERNELS) alg.o psy.o
 #TODO #1757: $(INF_LIB) is required because of the meta-data in the
 #            kernel - once this is fixed, $(INF_LIB) can be removed.
 $(DRIVER_INIT).$(TYPE):	$(KERNELS) $(DRIVER_INIT).o
-	$(F90) $(KERNELS) $(DRIVER_INIT).o -o $(DRIVER_INIT).$(TYPE) \
+	$(F90) $(F90FLAGS) $(KERNELS) $(DRIVER_INIT).o -o $(DRIVER_INIT).$(TYPE) \
 		$(INF_LIB) $(EXTRACT_DIR)/$(LIB_NAME) $(LDFLAGS)
 
 #TODO #1757: $(INF_LIB) is required because of the meta-data in the
 #            kernel - once this is fixed, $(INF_LIB) can be removed.
 $(DRIVER_UPDATE).$(TYPE): $(KERNELS) $(DRIVER_UPDATE).o
-	$(F90) $(KERNELS) $(DRIVER_UPDATE).o -o $(DRIVER_UPDATE).$(TYPE) \
+	$(F90) $(F90FLAGS) $(KERNELS) $(DRIVER_UPDATE).o -o $(DRIVER_UPDATE).$(TYPE) \
 		$(INF_LIB) $(EXTRACT_DIR)/$(LIB_NAME) $(LDFLAGS)
 
 # The dl_esm_inf library

examples/nemo/eg5/Makefile

@@ -85,7 +85,7 @@ run: compile
 	IT=2 JPI=10 JPJ=10 JPK=5  ./traadv-$(TYPE).exe
 
 traadv-$(TYPE).exe: psy.o $(EXTRACT_DIR)/$(LIB_NAME)
-	$(F90) psy.o -o traadv-$(TYPE).exe $(EXTRACT_DIR)/$(LIB_NAME) $(LDFLAGS)
+	$(F90) $(F90FLAGS) psy.o -o traadv-$(TYPE).exe $(EXTRACT_DIR)/$(LIB_NAME) $(LDFLAGS)
 
 transform: kernels
 

src/psyclone/tests/psyad/main_test.py

@@ -121,8 +121,9 @@ def test_main_h_option(capsys):
     assert str(info.value) == "0"
     output, error = capsys.readouterr()
     assert error == ""
-    # The name of the executable is replaced with either pytest or -c
-    # when using pytest, therefore we split this test into sections.
+    # Python usage messages have seen slight tweaks over the years, e.g.,
+    # Python >= 3.13 tweaks the usage message to avoid repeating the args
+    # to an option between aliases, therefore we split this test into sections.
     assert "usage: " in output
     expected2 = (
         "[-h] [-oad OAD] [-v] [-t] [-api API] [-coord-arg COORD_ARG] "
@@ -133,9 +134,12 @@ def test_main_h_option(capsys):
         "positional arguments:\n"
         "  filename              tangent-linear kernel source\n\n")
     assert expected2 in output
+    assert ("  -h, --help            show this help message and exit\n"
+            in output)
+    assert ("  -a ACTIVE [ACTIVE ...], --active ACTIVE [ACTIVE ...]\n"
+            in output or
+            "  -a, --active ACTIVE [ACTIVE ...]\n" in output)
     expected3 = (
-        "  -h, --help            show this help message and exit\n"
-        "  -a ACTIVE [ACTIVE ...], --active ACTIVE [ACTIVE ...]\n"
         "                        names of active variables\n"
         "  -v, --verbose         increase the verbosity of the output\n"
         "  -t, --gen-test        generate a standalone unit test for the "
@@ -156,9 +160,6 @@ def test_main_h_option(capsys):
         "  -otest TEST_FILENAME  filename for the unit test (implies -t)\n"
         "  -oad OAD              filename for the transformed code\n")
     assert expected3 in output
-    assert ("-otest TEST_FILENAME  filename for the unit test (implies -t)"
-            in output)
-    assert "-oad OAD              filename for the transformed code" in output
 
 
 # no args

tutorial/practicals/nemo/2_nemo_profiling/Makefile

@@ -108,7 +108,7 @@ transform:
                      -o output_3.f90 -l output tra_adv_mod.F90
 
 compile: transform $(KERNELS) output.o solutions/runner.o
-	$(F90) $(KERNELS) output.o solutions/runner.o -o $(NAME) \
+	$(F90) $(F90FLAGS) $(KERNELS) output.o solutions/runner.o -o $(NAME) \
 	       $(PROFILE_WRAPPER_LINK) $(PROFILE_LINK)
 
 # Only used for the compile CI target to compile the solution file