From e8ee7af12fada360ec4a1704fc0c2a4a9c1e85c3 Mon Sep 17 00:00:00 2001
From: David Ketcheson <dketch@gmail.com>
Date: Mon, 30 Oct 2023 13:49:50 +0300
Subject: [PATCH 1/2] Update meson build to include fortran extensions for
 examples.

Also fix a bug in which the SharpClaw fortran extensions were
not properly compiled.
---
 examples/acoustics_2d_mapped/__init__.py    |   0
 examples/euler_1d/shocksine.py              |  26 +--
 examples/euler_1d/woodward_colella_blast.py |  38 +---
 examples/shallow_sphere/Rossby_wave.py      |  20 +-
 src/pyclaw/meson.build                      | 201 +++++++++++++++++++-
 5 files changed, 212 insertions(+), 73 deletions(-)
 create mode 100644 examples/acoustics_2d_mapped/__init__.py

diff --git a/examples/acoustics_2d_mapped/__init__.py b/examples/acoustics_2d_mapped/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/examples/euler_1d/shocksine.py b/examples/euler_1d/shocksine.py
index b4d69eb17..97e271c61 100755
--- a/examples/euler_1d/shocksine.py
+++ b/examples/euler_1d/shocksine.py
@@ -59,26 +59,12 @@ def setup(use_petsc=False,iplot=False,htmlplot=False,outdir='./_output',solver_t
         solver.cfl_desired = 0.6
         solver.cfl_max = 0.7
         if use_char_decomp:
-            try:
-                from . import sharpclaw1               # Import custom Fortran code
-                solver.fmod = sharpclaw1
-                solver.tfluct_solver = tfluct_solver     # Use total fluctuation solver for efficiency
-                if solver.tfluct_solver:
-                    try:
-                        from . import euler_tfluct
-                        solver.tfluct = euler_tfluct
-                    except ImportError:
-                        import logging
-                        logger = logging.getLogger()
-                        logger.error('Unable to load tfluct solver, did you run make?')
-                        print('Unable to load tfluct solver, did you run make?')
-                        raise
-            except ImportError:
-                import logging
-                logger = logging.getLogger()
-                logger.error('Unable to load sharpclaw1 solver, did you run make?')
-                print('Unable to load sharpclaw1 solver, did you run make?')
-                pass
+            from pyclaw.sharpclaw import euler_sharpclaw1               # Import custom Fortran code
+            solver.fmod = euler_sharpclaw1
+            solver.tfluct_solver = tfluct_solver     # Use total fluctuation solver for efficiency
+            if solver.tfluct_solver:
+                    from pyclaw.sharpclaw import euler_tfluct
+                    solver.tfluct = euler_tfluct
             solver.lim_type = 2             # WENO reconstruction
             solver.char_decomp = 2          # characteristic-wise reconstruction
     else:
diff --git a/examples/euler_1d/woodward_colella_blast.py b/examples/euler_1d/woodward_colella_blast.py
index 553ce3656..e6b8b238b 100755
--- a/examples/euler_1d/woodward_colella_blast.py
+++ b/examples/euler_1d/woodward_colella_blast.py
@@ -27,26 +27,6 @@
 from clawpack import riemann
 from clawpack.riemann.euler_with_efix_1D_constants import *
 
-# Compile Fortran code if not already compiled
-try:
-    from clawpack.pyclaw.examples.euler_1d import sharpclaw1
-except ImportError:
-    import os
-    from clawpack.pyclaw.util import inplace_build
-    this_dir = os.path.dirname(__file__)
-    if this_dir == '':
-        this_dir = os.path.abspath('.')
-    inplace_build(this_dir)
-    try:
-        # Now try to import again
-        from clawpack.pyclaw.examples.euler_1d import sharpclaw1
-    except ImportError:
-        import logging
-        logger = logging.getLogger()
-        logger.warn('unable to compile Fortran modules; some SharpClaw options will not be available for this example')
-        print('unable to compile Fortran modules; some SharpClaw options will not be available for this example')
-        raise
-
 gamma = 1.4 # Ratio of specific heats
 
 def setup(use_petsc=False,outdir='./_output',solver_type='sharpclaw',kernel_language='Fortran',tfluct_solver=True):
@@ -68,22 +48,12 @@ def setup(use_petsc=False,outdir='./_output',solver_type='sharpclaw',kernel_lang
         solver.cfl_desired = 0.6
         solver.tfluct_solver = tfluct_solver
         if solver.tfluct_solver:
-            try:
-                from clawpack.pyclaw.examples.euler_1d import euler_tfluct
-                solver.tfluct = euler_tfluct
-            except ImportError:
-                import logging
-                logger = logging.getLogger()
-                logger.error('Unable to load tfluct solver, did you run make?')
-                print('Unable to load tfluct solver, did you run make?')
-                raise
+            from clawpack.pyclaw.examples.euler_1d import euler_tfluct
+            solver.tfluct = euler_tfluct
         solver.lim_type = 1
         solver.char_decomp = 2
-        try:
-            from clawpack.pyclaw.examples.euler_1d import sharpclaw1
-            solver.fmod = sharpclaw1
-        except ImportError:
-            pass
+        from clawpack.pyclaw.sharpclaw import euler_sharpclaw1
+        solver.fmod = euler_sharpclaw1
     elif solver_type=='classic':
         solver = pyclaw.ClawSolver1D(rs)
         solver.limiters = 4
diff --git a/examples/shallow_sphere/Rossby_wave.py b/examples/shallow_sphere/Rossby_wave.py
index 7310d0019..1c86bf20f 100755
--- a/examples/shallow_sphere/Rossby_wave.py
+++ b/examples/shallow_sphere/Rossby_wave.py
@@ -27,24 +27,8 @@
 from clawpack.pyclaw.util import inplace_build
 from six.moves import range
 
-try:
-    from clawpack.pyclaw.examples.shallow_sphere import problem
-    from clawpack.pyclaw.examples.shallow_sphere import classic2
-
-except ImportError:
-    this_dir = os.path.dirname(__file__)
-    if this_dir == '':
-        this_dir = os.path.abspath('.')
-    inplace_build(this_dir)
-
-    try:
-        # Now try to import again
-        from clawpack.pyclaw.examples.shallow_sphere import problem
-        from clawpack.pyclaw.examples.shallow_sphere import classic2
-    except ImportError:
-        print("***\nUnable to import problem module or automatically build, try running (in the directory of this file):\n python setup.py build_ext -i\n***", file=sys.stderr)
-        raise
-
+from clawpack.pyclaw.examples.shallow_sphere import sw_sphere_problem
+from clawpack.pyclaw.classic import classic2_sw_sphere as classic2
 
 # Nondimensionalized radius of the earth
 Rsphere = 1.0
diff --git a/src/pyclaw/meson.build b/src/pyclaw/meson.build
index 6cc522b94..3203ed4bd 100644
--- a/src/pyclaw/meson.build
+++ b/src/pyclaw/meson.build
@@ -57,6 +57,169 @@ foreach subpkg, subsrcs: python_sources
   )
 endforeach
 
+examples = {
+  '' : [
+    '__init__.py'
+  ],
+  'acoustics_1d_homogeneous' : [
+    '__init__.py',
+    'acoustics_1d.py',
+    'test_acoustics.py',
+  ],
+  'acoustics_2d_homogeneous' : [
+    '__init__.py',
+    'acoustics_2d.py',
+    'test_2d_acoustics.py',
+  ],
+  'acoustics_2d_mapped' : [
+    '__init__.py',
+    'acoustics_2d_inclusions.py',
+    'test_acoustics_2d_mapped.py',
+  ],
+  'acoustics_2d_variable' : [
+    '__init__.py',
+    'acoustics_2d_interface.py',
+    'test_acoustics_2d_variable.py',
+    'test_acoustics_2d_variable_io.py',
+  ],
+  'acoustics_3d_variable' : [
+    '__init__.py',
+    'acoustics_3d_interface.py',
+    'test_3d_acoustics.py',
+  ],
+  'advection_1d' : [
+    '__init__.py',
+    'advection_1d.py',
+    'advection_1d_nonunif.py',
+    'test_advection.py',
+    'test_advection_nonunif.py',
+  ],
+  'advection_1d_variable' : [
+    '__init__.py',
+    'variable_coefficient_advection.py',
+  ],
+  'advection_2d' : [
+    '__init__.py',
+    'advection_2d.py',
+  ],
+  'advection_2d_annulus' : [
+    '__init__.py',
+    'advection_annulus.py',
+    'mapc2p.py',
+  ],
+  'advection_reaction_2d' : [
+    '__init__.py',
+    'advection_reaction.py',
+    'test_advection_reaction.py',
+  ],
+  'burgers_1d' : [
+    '__init__.py',
+    'burgers_1d.py',
+  ],
+  'cubic_1d' : [
+    '__init__.py',
+    'cubic.py',
+    'test_cubic.py',
+  ],
+  'euler_1d' : [
+    '__init__.py',
+    'shocksine.py',
+    'shocktube.py',
+    'test_shocksine.py',
+    'test_shocktube.py',
+    'test_woodward_colella_blast.py',
+    'woodward_colella_blast.py',
+  ],
+  'euler_2d' : [
+    '__init__.py',
+    'euler_2d.py',
+    'quadrants.py',
+    'shock_bubble_interaction.py',
+    'shock_forward_step.py',
+    'test_euler2d_shockbubble.py',
+    'test_quadrants.py',
+  ],
+  'euler_3d' : [
+    'Sedov.py',
+    '__init__.py',
+    'shock_bubble.py',
+    'shocktube.py',
+    'test_sedov_and_hdf.py',
+  ],
+  'euler_gravity_3d' : [
+    'plotCreateVisitXDMF.py',
+    'rising_hot_sphere.py',
+    'rising_hot_sphere_spherical.py',
+    'test_rising_hot_sphere.py',
+    'visitHDF5XDMF.py',
+  ],
+  'iso_c_advection' : [
+    '__init__.py',
+    'iso_c_advection.py',
+    'iso_c_solver.py',
+  ],
+  'kpp' : [
+    '__init__.py',
+    'kpp.py',
+  ],
+  'mhd_1d' : [
+    '__init__.py',
+    'shocktube.py',
+    'test_shocktube.py',
+  ],
+  'peano_shallow_2d' : [
+    'setplot.py',
+    'shallow2D.py',
+    'test_identical_grids.py',
+    'test_peano_solver.py',
+  ],
+  'psystem_2d' : [
+    '__init__.py',
+    'psystem_2d.py',
+    'test_2d_psystem.py',
+  ],
+  'shallow_1d' : [
+    '__init__.py',
+    'dam_break.py',
+    'sill.py',
+    'test_dambreak.py',
+    'test_sill.py',
+  ],
+  'shallow_2d' : [
+    '__init__.py',
+    'radial_dam_break.py',
+    'sill.py',
+    'test_dambreak.py',
+    'test_sill.py',
+  ],
+  'shallow_sphere' : [
+    '__init__.py',
+    'setplot.py',
+    'test_shallow_sphere.py',
+    'Rossby_wave.py',
+  ],
+  'stegoton_1d' : [
+    '__init__.py',
+    'stegoton.py',
+    'test_stego.py',
+  ],
+  'traffic' : [
+    '__init__.py',
+    'traffic.py',
+  ],
+}
+
+foreach ex, exsrcs: examples
+  sources = []
+  foreach src: exsrcs
+    sources += '../../examples' / ex / src
+  endforeach
+  py.install_sources(
+    sources,
+    subdir: pkg_dir / 'examples' / ex
+  )
+endforeach
+
 py.install_sources(
     'log.config',
     subdir: pkg_dir
@@ -67,14 +230,20 @@ fortran_extensions = {
     'classic1': ['limiter.f90','philim.f90','step1.f90'],
     'classic2': ['limiter.f90','philim.f90','flux2.f90','step2ds.f90','step2.f90'],
     'classic3': ['limiter.f90','philim.f90','flux3.f90','step3ds.f90','step3.f90'],
+    'classic2_sw_sphere': ['limiter.f90','philim.f90','flux2.f90','step2ds.f90','../../../examples/shallow_sphere/step2qcor.f90','../../../examples/shallow_sphere/qcor.f90'],
   },
   'sharpclaw': {
     'sharpclaw1': ['ClawParams.f90','weno.f90','reconstruct.f90','evec.f90','workspace.f90','flux1.f90'],
     'sharpclaw2': ['ClawParams.f90','weno.f90','reconstruct.f90','evec.f90','workspace.f90','flux2.f90','flux1.f90'],
     'sharpclaw3': ['ClawParams.f90','weno.f90','reconstruct.f90','evec.f90','workspace.f90','flux3.f90','flux1.f90'],
+    # 1D Euler with characteristic decomposition for SharpClaw limiting
+    'euler_sharpclaw1': ['ClawParams.f90','weno.f90','reconstruct.f90','../../../examples/euler_1d/evec.f90','workspace.f90','flux1.f90'],
+    'euler_tfluct1': ['../../../examples/euler_1d/euler_tfluct.f90'],
   },
 }
 
+numpy_nodepr_api = '-DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION'
+
 foreach subpkg, module: fortran_extensions
   srcdir = join_paths(subpkg.split('.'))
   foreach ext_name, sources : module
@@ -82,14 +251,20 @@ foreach subpkg, module: fortran_extensions
     foreach src: sources
       ext_srcs += srcdir / src
     endforeach
+    f2py_extra = []
+    #if subpkg == 'sharpclaw'
+    if 'ClawParams.f90' in sources
+        f2py_extra += ext_name + '-f2pywrappers2.f90'
+    endif
     f2py_srcs = custom_target(
       command: [f2py, ext_name],
       input: ext_srcs,
-      output: [ext_name + 'module.c', ext_name + '-f2pywrappers.f'],
+      output: [ext_name + 'module.c', ext_name + '-f2pywrappers.f', f2py_extra],
     )
     py.extension_module(
       ext_name, [ext_srcs, f2py_srcs],
       incdir_f2py / 'fortranobject.c',
+      c_args: [numpy_nodepr_api],
       include_directories: inc_np,
       dependencies : py_dep,
       subdir: 'clawpack/pyclaw/' + srcdir,
@@ -106,3 +281,27 @@ py.extension_module(
     subdir: 'clawpack/pyclaw/limiters/weno',
     install : true
 )
+
+# Special extensions for examples
+
+ext_name = 'sw_sphere_problem'
+ext_srcs = [
+  '../../examples/shallow_sphere/mapc2p.f90',
+  '../../examples/shallow_sphere/setaux.f90',
+  '../../examples/shallow_sphere/qinit.f90',
+  '../../examples/shallow_sphere/src2.f90',
+]
+f2py_srcs = custom_target(
+  command: [f2py, ext_name],
+  input: ext_srcs,
+  output: [ext_name + 'module.c', ext_name + '-f2pywrappers.f'],
+)
+
+py.extension_module(
+  ext_name, [ext_srcs, f2py_srcs],
+  incdir_f2py / 'fortranobject.c',
+  include_directories: inc_np,
+  dependencies : py_dep,
+  subdir: 'clawpack/pyclaw/examples/shallow_sphere',
+  install : true
+)

From d7094efff53c926740a0503b45a83206de2d6c34 Mon Sep 17 00:00:00 2001
From: David Ketcheson <dketch@gmail.com>
Date: Tue, 31 Oct 2023 11:46:44 +0300
Subject: [PATCH 2/2] Use CLAW env variable to set path for editable installs.

The old approach doesn't work with meson, but this does.
---
 src/pyclaw/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/pyclaw/__init__.py b/src/pyclaw/__init__.py
index 448cf36a4..6c9a62ea9 100644
--- a/src/pyclaw/__init__.py
+++ b/src/pyclaw/__init__.py
@@ -5,8 +5,11 @@
 import logging, logging.config
 
 
+CLAW_dir = os.environ.get('CLAW')
+if CLAW_dir == None:
+    raise Exception('You must set the CLAW environment to use an editable install.')
 # To get pyclaw.examples
-_path = os.path.dirname(os.path.dirname(__path__[0]))
+_path = os.path.dirname(os.path.join(CLAW_dir, 'clawpack'))
 if os.path.isdir(_path):
     __path__.append(_path)
 del _path