cmake updates and unit test fixes - 2.13.1

* Updating development version to 2.13-dev * Release guidelines update * Add Changes to Changelog (#604) * Remoev UWGeodynamics installation from dockerfiles * Petsc 3.17 compatibility and removing duplicate examples python scripts * Add petsc variants to conda recipe * Add python 3.10 conda builds to actions. * Change PETSC and MPICH versions * Fix MPICH complaining... * Getting Dockerfiles ready: Ubuntu 22.04LTS and python 3.10. Note that this will fail for now because of h5py not being compatible. PR is on its way. * Update README * Update README * Transfer UWGeo documentation to Underworld * Remove python3-numpy-dbg for now * Fix Documentation Links (UWGeodynamics) Fix visualisation imports * Fix imports (UWGeodynamics) * Change Depth documentation toctree * UWGeodynamics Merging * Run tests * Move tests * H5py 3.7 is released, Use it in docker. * Typo in Petsc Dockerfile * Getting UWGeo internals to use uw2 mpi4py interface (#612) * Getting UWGeo internals to use uw2 mpi4py interface * Update CHANGES.md * ask per 2.13 release (#615) 2.13 release Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au> * Update _version.py * Fix for analytic ID, which changed during cmake update. Ganalytics should now be right * Typo fix for 3.10 * Dockerfile improvement - should be a single layer command * safer #define when not using an official release of petsc * Update PetscOptionsBegin() to be dev compatible. see https://gitlab.com/petsc/petsc/-/blob/f3ed01cd9ab452072c1a44e935347389f67d72c6/doc/docs/changes/dev.rst * cmake updates for $PETSC_DIR and $PETSC_ARCH. Now it displays $PKG_CONFIG_PATH * Remove some output files that shouldn't be stored. * Fixing the pytest interfaces to pick up ipynb Cleaning the test dir also * Add a RuntimeError exception for fields without units * Update tests - they weren't RUNNING! Need to workout how to run collective_fail.py under pytest. Think it's hard because the returncodes are non 0 by choice... but pytest picks up on it. * Only check rank==1 for collective test * Update CI.yml * Update CI.yml add nbmake for testing ipynb * Update _version.py * Update CHANGES.md Co-authored-by: Romain Beucher <romain.beucher@anu.edu.au>
underworldcode · Aug 15, 2022 · 2941f8e · 2941f8e
1 parent 6e428f9
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -228,9 +228,10 @@ jobs:
 
       - name: Run Tests
         run: |
-          pip install pytest
-          pytest -vvv docs/pytests
-          cd docs/test
+          pip install pytest nbmake
+          cd docs
+          pytest -vvv pytests/*
+          cd test
           cp -rf ../UWGeodynamics/examples UWGeodynamics/.
           cp -rf ../UWGeodynamics/tutorials UWGeodynamics/.
           cp -rf ../UWGeodynamics/benchmarks UWGeodynamics/.

diff --git a/CHANGES.md b/CHANGES.md
@@ -1,7 +1,13 @@
 CHANGES: Underworld2
 =======================
 
-Release 2.13-0 [2022-05-25]
+Release 2.13.1 [2022-08-15]
+---------------------------
+Fixes:
+ * Improved CMAKE workflow.
+ * Fixes to failing unit tests.
+
+Release 2.13.0 [2022-05-25]
 -----------------------------
 
 New:

diff --git a/docs/examples/03_BlankenbachBenchmark.ipynb b/docs/examples/03_BlankenbachBenchmark.ipynb
diff --git a/docs/examples/PressureSolution.png b/docs/examples/PressureSolution.png
diff --git a/docs/examples/output/Mesh.h5 b/docs/examples/output/Mesh.h5
diff --git a/docs/examples/output/pressureField.0.h5 b/docs/examples/output/pressureField.0.h5
diff --git a/docs/examples/output/pressureField.0.xdmf b/docs/examples/output/pressureField.0.xdmf
diff --git a/docs/examples/output/pressureField.20.h5 b/docs/examples/output/pressureField.20.h5
diff --git a/docs/examples/output/pressureField.20.xdmf b/docs/examples/output/pressureField.20.xdmf
diff --git a/docs/examples/output/pressureField.40.h5 b/docs/examples/output/pressureField.40.h5
diff --git a/docs/examples/output/pressureField.40.xdmf b/docs/examples/output/pressureField.40.xdmf
diff --git a/docs/examples/output/subduction.gldb b/docs/examples/output/subduction.gldb
diff --git a/docs/examples/output/summary.txt b/docs/examples/output/summary.txt
diff --git a/docs/examples/output/velocityField.0.h5 b/docs/examples/output/velocityField.0.h5
diff --git a/docs/examples/output/velocityField.0.xdmf b/docs/examples/output/velocityField.0.xdmf
diff --git a/docs/examples/output/velocityField.20.h5 b/docs/examples/output/velocityField.20.h5
diff --git a/docs/examples/output/velocityField.20.xdmf b/docs/examples/output/velocityField.20.xdmf
diff --git a/docs/examples/output/velocityField.40.h5 b/docs/examples/output/velocityField.40.h5
diff --git a/docs/examples/output/velocityField.40.xdmf b/docs/examples/output/velocityField.40.xdmf
diff --git a/docs/examples/output/vrms.txt b/docs/examples/output/vrms.txt
diff --git a/docs/pytests/test.py b/docs/pytests/test.py
@@ -1,14 +1,24 @@
-# test_user_guide.py
-
-import pathlib
 import subprocess
 import pytest
 import glob
 import ntpath
 import sys
+import underworld as uw
+from inspect import getsourcefile
+
+wdir = ntpath.dirname(getsourcefile(lambda:0))+"/../test/"
+
+pyscripts = [pytest.param(path, id=ntpath.basename(path)) for path in sorted(glob.glob(wdir+"/*.py"))]
+
+@pytest.mark.parametrize('pyscript', pyscripts)
+def test_python_execution(pyscript):
+    cp = subprocess.run([sys.executable, pyscript])
+    assert cp.returncode == 0
+
+ipynbscripts = [pytest.param(path, id=ntpath.basename(path)) for path in sorted(glob.glob(wdir+"/*.ipynb"))]
 
-scripts = [pytest.param(path, id=ntpath.basename(path)) for path in sorted(glob.glob("docs/test/*.py"))]
 
-@pytest.mark.parametrize('script', scripts)
-def test_script_execution(script):
-    subprocess.run([sys.executable, script])
+@pytest.mark.parametrize('ipynbscript', ipynbscripts)
+def test_ipynb_execution(ipynbscript):
+    cp = subprocess.run(["pytest", "--nbmake", ipynbscript])
+    assert cp.returncode == 0
diff --git a/docs/pytests/test_examples.py b/docs/pytests/test_examples.py
@@ -1,14 +1,17 @@
-# test_examples.py
-
-import pathlib
 import subprocess
 import pytest
 import glob
 import ntpath
 import sys
+import underworld as uw
+from inspect import getsourcefile
+
+wdir = ntpath.dirname(getsourcefile(lambda:0))+"/../examples/"
 
-scripts = [pytest.param(path, id=ntpath.basename(path)) for path in sorted(glob.glob("docs/examples/*.py"))]
+scripts = [pytest.param(path, id=ntpath.basename(path)) for path in sorted(glob.glob(wdir+"/*.ipynb"))]
 
 @pytest.mark.parametrize('script', scripts)
 def test_script_execution(script):
-    subprocess.run([sys.executable, script])
+    subprocess.run(["pytest", "--nbmake", script])
+    #subprocess.run([sys.executable, "-m", "pytest", "--nbmake", script])
+    #subprocess.run([sys.executable, script])