git: a1ae37b961a1 - main - science/cantera: update 3.0.1 → 3.1.0

Go to: [ bottom of page ] [ top of archives ] [ this month ]
From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Fri, 20 Dec 2024 11:53:21 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=a1ae37b961a1f1240a695ed0a4072db1b64081f3

commit a1ae37b961a1f1240a695ed0a4072db1b64081f3
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2024-12-20 11:14:25 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2024-12-20 11:53:17 +0000

    science/cantera: update 3.0.1 → 3.1.0
    
    Reported by:    portscout
---
 science/cantera/Makefile                          | 10 ++-
 science/cantera/distinfo                          |  8 +-
 science/cantera/files/patch-SConstruct            | 41 +++--------
 science/cantera/files/patch-src_matlab_SConscript | 11 ---
 science/cantera/pkg-plist                         | 89 +++++++++++++++--------
 5 files changed, 80 insertions(+), 79 deletions(-)

diff --git a/science/cantera/Makefile b/science/cantera/Makefile
index 914a8928850c..e1a761d88b94 100644
--- a/science/cantera/Makefile
+++ b/science/cantera/Makefile
@@ -1,11 +1,12 @@
 PORTNAME=	cantera
 DISTVERSIONPREFIX=	v
-DISTVERSION=	3.0.1
+DISTVERSION=	3.1.0
 CATEGORIES=	science # chemistry physics
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Chemical kinetics, thermodynamics, and transport tool suite
-WWW=		https://cantera.org/
+WWW=		https://cantera.org \
+		https://github.com/Cantera/cantera
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/License.txt
@@ -25,6 +26,9 @@ USE_LDCONFIG=	yes
 USE_GITHUB=	yes
 GH_ACCOUNT=	Cantera
 GH_TUPLE=	LLNL:sundials:887af43:sundials/ext/sundials # bundled sundials is only needed for the Octave option
+GH_TUPLE+=	cantera:cantera-example-data:1a5d27e:example_data/data/example_data
+
+NO_CCACHE=	yes # ccache breaks scons build for some reason
 
 MAKE_ARGS=	system_eigen='y' \
 		system_sundials='n' \
@@ -40,7 +44,7 @@ MAKE_ARGS=	system_eigen='y' \
 MAKE_ENV=	INSTALL_MANPAGES=y
 
 ALL_TARGET=	build
-TEST_TARGET=	test # some tests fail, see https://github.com/Cantera/cantera/issues/1095
+TEST_TARGET=	test # Multiple failures in the testsuite, see https://github.com/Cantera/cantera/issues/1829
 
 OPTIONS_DEFINE=		OCTAVE PYTHON
 OPTIONS_DEFAULT=	PYTHON # OCTAVE is off by default because Octave interface is not a frequently requested feature
diff --git a/science/cantera/distinfo b/science/cantera/distinfo
index 3cf6ea36ed62..23aeb4abaf41 100644
--- a/science/cantera/distinfo
+++ b/science/cantera/distinfo
@@ -1,5 +1,7 @@
-TIMESTAMP = 1726538499
-SHA256 (Cantera-cantera-v3.0.1_GH0.tar.gz) = 3c51803c2d776e4cb2fed14d5eb17b2fa78a274d0e54d87eb91f23afe3cc4a8c
-SIZE (Cantera-cantera-v3.0.1_GH0.tar.gz) = 2451841
+TIMESTAMP = 1734670500
+SHA256 (Cantera-cantera-v3.1.0_GH0.tar.gz) = 4d9004660d83ea5200216cbd465ae77277fde9191fd47d1eb30a68c1ad6ee09e
+SIZE (Cantera-cantera-v3.1.0_GH0.tar.gz) = 2605640
 SHA256 (LLNL-sundials-887af43_GH0.tar.gz) = 147919c4887c93157c9975f195e8d45903285b61303d42f9dfdee251468abdb7
 SIZE (LLNL-sundials-887af43_GH0.tar.gz) = 18888776
+SHA256 (cantera-cantera-example-data-1a5d27e_GH0.tar.gz) = 4c174c322c9c4bf4cbb878e4c7785dc12ced5541ecb129481e05b990cdd9b3d7
+SIZE (cantera-cantera-example-data-1a5d27e_GH0.tar.gz) = 244544
diff --git a/science/cantera/files/patch-SConstruct b/science/cantera/files/patch-SConstruct
index 1220b2aedf5c..9af97e09597e 100644
--- a/science/cantera/files/patch-SConstruct
+++ b/science/cantera/files/patch-SConstruct
@@ -1,8 +1,8 @@
 - the first part is fixing the configure failure, see https://github.com/Cantera/cantera/issues/1536
 
---- SConstruct.orig	2023-08-22 21:34:46 UTC
+--- SConstruct.orig	2024-12-16 23:22:11 UTC
 +++ SConstruct
-@@ -846,6 +846,9 @@ if os.name == "nt":
+@@ -902,6 +902,9 @@ if os.name == "nt":
      for key,val in env["ENV"].items():
          env["ENV"][key] = str(val)
  
@@ -12,7 +12,7 @@
  else:
      env["INSTALL_MANPAGES"] = True
  
-@@ -880,6 +883,9 @@ elif "icx" in env.subst("$CC"):
+@@ -933,6 +936,9 @@ elif "clang" in env.subst("$CC"):
  elif "clang" in env.subst("$CC"):
      config.select("clang")
  
@@ -20,12 +20,12 @@
 +    config.select("clang")
 +
  else:
-     logger.error(f"Unrecognized C compiler {env['CC']!r}")
-     sys.exit(1)
-@@ -945,10 +951,10 @@ if "sdist" in COMMAND_LINE_TARGETS:
-     logger.info("'sdist' target was specified. Setting 'use_pch' to False.")
-     env["use_pch"] = False
- 
+     # Assume a GCC compatible compiler if nothing else
+     logger.warning(f"Unrecognized C compiler {env['CC']!r}")
+@@ -991,10 +997,10 @@ if 'sphinx' in COMMAND_LINE_TARGETS:
+     env['doxygen_docs'] = True
+ if 'sphinx' in COMMAND_LINE_TARGETS:
+     env['sphinx_docs'] = True
 -for arg in ARGUMENTS:
 -    if arg not in config:
 -        logger.error(f"Encountered unexpected command line option: {arg!r}")
@@ -35,24 +35,5 @@
 +#        logger.error(f"Encountered unexpected command line option: {arg!r}")
 +#        sys.exit(1)
  
- env["cantera_version"] = "3.0.0"
- # For use where pre-release tags are not permitted (MSI, sonames)
-@@ -2002,12 +2008,12 @@ if env["matlab_toolbox"] == "y":
-             "SUNDIALS libraries and skip building the Matlab toolbox.")
-         sys.exit(1)
- 
--    matlab_path = Path(matlab_path)
--    env["matlab_path"] = matlab_path.as_posix()
--    if not matlab_path.is_dir() and (matlab_path / "extern").is_dir():
--        logger.error(
--            f"Path set for 'matlab_path' is not correct. Path was {matlab_path!r}")
--        sys.exit(1)
-+    #matlab_path = Path(matlab_path)
-+    #env["matlab_path"] = matlab_path.as_posix()
-+    #if not matlab_path.is_dir() and (matlab_path / "extern").is_dir():
-+    #    logger.error(
-+    #        f"Path set for 'matlab_path' is not correct. Path was {matlab_path!r}")
-+    #    sys.exit(1)
- 
- 
- # **********************************************
+ # Store full config for doc build
+ if env['sphinx_docs']:
diff --git a/science/cantera/files/patch-src_matlab_SConscript b/science/cantera/files/patch-src_matlab_SConscript
deleted file mode 100644
index c192ea9fb1b7..000000000000
--- a/science/cantera/files/patch-src_matlab_SConscript
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/matlab/SConscript.orig	2023-08-22 21:34:46 UTC
-+++ src/matlab/SConscript
-@@ -48,7 +48,7 @@ elif localenv['OS'] == 'Darwin':
- 
- elif os.name == 'posix':
-     linklibs = list(env['cantera_libs'])
--    linklibs += ['mx', 'mex', 'mat'] + env['LIBM']
-+    linklibs += ['octave', 'octinterp'] + env['LIBM']
- 
-     if localenv['OS_BITS'] == 64:
-         matlab_libs = pjoin(localenv['matlab_path'], 'bin', 'glnxa64')
diff --git a/science/cantera/pkg-plist b/science/cantera/pkg-plist
index 05380d4dd123..43c08d4f98b4 100644
--- a/science/cantera/pkg-plist
+++ b/science/cantera/pkg-plist
@@ -1,6 +1,7 @@
 %%PYTHON%%bin/ck2yaml
 %%PYTHON%%bin/cti2yaml
 %%PYTHON%%bin/ctml2yaml
+%%PYTHON%%bin/lxcat2yaml
 %%PYTHON%%bin/yaml2ck
 include/cantera/base/AnyMap.h
 include/cantera/base/AnyMap.inl.h
@@ -127,14 +128,15 @@ include/cantera/kinetics/BulkKinetics.h
 include/cantera/kinetics/ChebyshevRate.h
 include/cantera/kinetics/Custom.h
 include/cantera/kinetics/EdgeKinetics.h
+include/cantera/kinetics/ElectronCollisionPlasmaRate.h
 include/cantera/kinetics/Falloff.h
-include/cantera/kinetics/GasKinetics.h
 include/cantera/kinetics/Group.h
 include/cantera/kinetics/ImplicitSurfChem.h
 include/cantera/kinetics/InterfaceKinetics.h
 include/cantera/kinetics/InterfaceRate.h
 include/cantera/kinetics/Kinetics.h
 include/cantera/kinetics/KineticsFactory.h
+include/cantera/kinetics/LinearBurkeRate.h
 include/cantera/kinetics/MultiRate.h
 include/cantera/kinetics/MultiRateBase.h
 include/cantera/kinetics/PlogRate.h
@@ -160,8 +162,6 @@ include/cantera/numerics/IdasIntegrator.h
 include/cantera/numerics/Integrator.h
 include/cantera/numerics/PreconditionerBase.h
 include/cantera/numerics/PreconditionerFactory.h
-include/cantera/numerics/ResidEval.h
-include/cantera/numerics/ResidJacEval.h
 include/cantera/numerics/SundialsContext.h
 include/cantera/numerics/ctlapack.h
 include/cantera/numerics/eigen_dense.h
@@ -172,6 +172,7 @@ include/cantera/numerics/sundials_headers.h
 include/cantera/oneD/Boundary1D.h
 include/cantera/oneD/Domain1D.h
 include/cantera/oneD/DomainFactory.h
+include/cantera/oneD/Flow1D.h
 include/cantera/oneD/IonFlow.h
 include/cantera/oneD/MultiJac.h
 include/cantera/oneD/MultiNewton.h
@@ -195,11 +196,9 @@ include/cantera/thermo/IdealGasPhase.h
 include/cantera/thermo/IdealMolalSoln.h
 include/cantera/thermo/IdealSolidSolnPhase.h
 include/cantera/thermo/IdealSolnGasVPSS.h
-include/cantera/thermo/IonsFromNeutralVPSSTP.h
 include/cantera/thermo/LatticePhase.h
 include/cantera/thermo/LatticeSolidPhase.h
 include/cantera/thermo/MargulesVPSSTP.h
-include/cantera/thermo/MaskellSolidSolnPhase.h
 include/cantera/thermo/MetalPhase.h
 include/cantera/thermo/MixtureFugacityTP.h
 include/cantera/thermo/MolalityVPSSTP.h
@@ -213,8 +212,6 @@ include/cantera/thermo/PDSS.h
 include/cantera/thermo/PDSSFactory.h
 include/cantera/thermo/PDSS_ConstVol.h
 include/cantera/thermo/PDSS_HKFT.h
-include/cantera/thermo/PDSS_IdealGas.h
-include/cantera/thermo/PDSS_IonsFromNeutral.h
 include/cantera/thermo/PDSS_SSVol.h
 include/cantera/thermo/PDSS_Water.h
 include/cantera/thermo/PengRobinson.h
@@ -249,7 +246,6 @@ include/cantera/transport/IonGasTransport.h
 include/cantera/transport/MixTransport.h
 include/cantera/transport/MultiTransport.h
 include/cantera/transport/Transport.h
-include/cantera/transport/TransportBase.h
 include/cantera/transport/TransportData.h
 include/cantera/transport/TransportFactory.h
 include/cantera/transport/UnityLewisTransport.h
@@ -618,16 +614,16 @@ lib/libcantera.a
 %%PYTHON%%lib/libcantera_python3_11.so
 lib/libcantera_shared.so
 lib/libcantera_shared.so.3
-lib/libcantera_shared.so.3.0.1
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.0.1.dist-info/INSTALLER
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.0.1.dist-info/LICENSE.txt
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.0.1.dist-info/METADATA
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.0.1.dist-info/RECORD
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.0.1.dist-info/REQUESTED
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.0.1.dist-info/WHEEL
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.0.1.dist-info/direct_url.json
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.0.1.dist-info/entry_points.txt
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.0.1.dist-info/top_level.txt
+lib/libcantera_shared.so.3.1.0
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.1.0.dist-info/INSTALLER
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.1.0.dist-info/LICENSE.txt
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.1.0.dist-info/METADATA
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.1.0.dist-info/RECORD
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.1.0.dist-info/REQUESTED
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.1.0.dist-info/WHEEL
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.1.0.dist-info/direct_url.json
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.1.0.dist-info/entry_points.txt
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/Cantera-3.1.0.dist-info/top_level.txt
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/__init__.pxd
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/_cantera%%PYTHON_EXT_SUFFIX%%.so
@@ -642,13 +638,19 @@ lib/libcantera_shared.so.3.0.1
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/KOH.yaml
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/SiF4_NH3_mec.yaml
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/YZA.yaml
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/air.yaml
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/airNASA9.yaml
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/covdepsurf.yaml
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/critical-properties.yaml
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/diamond.yaml
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/element-standard-entropies.yaml
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/example_data/YZA.yaml
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/example_data/ammonia-CO-H2-Alzueta-2023.yaml
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/example_data/ammonia-Ru-Ba-YSZ-CSM-2019.yaml
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/example_data/co2-thermo.yaml
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/example_data/covdepsurf.yaml
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/example_data/n-hexane-NUIG-2015.yaml
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/example_data/oxygen-plasma-itikawa.yaml
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/example_data/silicon_carbide.yaml
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/graphite.yaml
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/gri30.yaml
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/gri30_highT.yaml
@@ -663,15 +665,16 @@ lib/libcantera_shared.so.3.0.1
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/ohn.yaml
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/ptcombust.yaml
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/silicon.yaml
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/silicon_carbide.yaml
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/sofc.yaml
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/data/water.yaml
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/delegator.pxd
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/drawnetwork.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/examples/README.txt
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/func1.pxd
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/interrupts.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/kinetics.pxd
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/liquidvapor.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/lxcat2yaml.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/mixture.pxd
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/onedim.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/cantera/preconditioners.pxd
@@ -692,13 +695,19 @@ lib/libcantera_shared.so.3.0.1
 libdata/pkgconfig/cantera.pc
 %%DATADIR%%/data/KOH.yaml
 %%DATADIR%%/data/SiF4_NH3_mec.yaml
-%%DATADIR%%/data/YZA.yaml
 %%DATADIR%%/data/air.yaml
 %%DATADIR%%/data/airNASA9.yaml
-%%DATADIR%%/data/covdepsurf.yaml
 %%DATADIR%%/data/critical-properties.yaml
 %%DATADIR%%/data/diamond.yaml
 %%DATADIR%%/data/element-standard-entropies.yaml
+%%DATADIR%%/data/example_data/YZA.yaml
+%%DATADIR%%/data/example_data/ammonia-CO-H2-Alzueta-2023.yaml
+%%DATADIR%%/data/example_data/ammonia-Ru-Ba-YSZ-CSM-2019.yaml
+%%DATADIR%%/data/example_data/co2-thermo.yaml
+%%DATADIR%%/data/example_data/covdepsurf.yaml
+%%DATADIR%%/data/example_data/n-hexane-NUIG-2015.yaml
+%%DATADIR%%/data/example_data/oxygen-plasma-itikawa.yaml
+%%DATADIR%%/data/example_data/silicon_carbide.yaml
 %%DATADIR%%/data/graphite.yaml
 %%DATADIR%%/data/gri30.yaml
 %%DATADIR%%/data/gri30_highT.yaml
@@ -713,16 +722,17 @@ libdata/pkgconfig/cantera.pc
 %%DATADIR%%/data/ohn.yaml
 %%DATADIR%%/data/ptcombust.yaml
 %%DATADIR%%/data/silicon.yaml
-%%DATADIR%%/data/silicon_carbide.yaml
 %%DATADIR%%/data/sofc.yaml
 %%DATADIR%%/data/water.yaml
 %%DATADIR%%/doc/LICENSE.txt
 %%DATADIR%%/samples/clib/CMakeLists.txt
+%%DATADIR%%/samples/clib/README.rst
 %%DATADIR%%/samples/clib/SConstruct
 %%DATADIR%%/samples/clib/demo.c
 %%DATADIR%%/samples/cxx/LiC6_electrode/CMakeLists.txt
 %%DATADIR%%/samples/cxx/LiC6_electrode/LiC6_electrode.cpp
 %%DATADIR%%/samples/cxx/LiC6_electrode/SConstruct
+%%DATADIR%%/samples/cxx/README.rst
 %%DATADIR%%/samples/cxx/bvp/BoundaryValueProblem.h
 %%DATADIR%%/samples/cxx/bvp/CMakeLists.txt
 %%DATADIR%%/samples/cxx/bvp/SConstruct
@@ -755,30 +765,44 @@ libdata/pkgconfig/cantera.pc
 %%DATADIR%%/samples/cxx/rankine/CMakeLists.txt
 %%DATADIR%%/samples/cxx/rankine/SConstruct
 %%DATADIR%%/samples/cxx/rankine/rankine.cpp
+%%PYTHON%%%%DATADIR%%/samples/python/README.rst
+%%PYTHON%%%%DATADIR%%/samples/python/kinetics/README.rst
 %%PYTHON%%%%DATADIR%%/samples/python/kinetics/blowers_masel.py
 %%PYTHON%%%%DATADIR%%/samples/python/kinetics/custom_reactions.py
+%%PYTHON%%%%DATADIR%%/samples/python/kinetics/diamond_cvd.py
 %%PYTHON%%%%DATADIR%%/samples/python/kinetics/extract_submechanism.py
+%%PYTHON%%%%DATADIR%%/samples/python/kinetics/interactive_path_diagram.py
+%%PYTHON%%%%PYTHON%%%%DATADIR%%/samples/python/kinetics/jet_stirred_reactor.py
+%%PYTHON%%%%DATADIR%%/samples/python/kinetics/lithium_ion_battery.py
 %%PYTHON%%%%DATADIR%%/samples/python/kinetics/mechanism_reduction.py
 %%PYTHON%%%%DATADIR%%/samples/python/kinetics/reaction_path.py
-%%PYTHON%%%%DATADIR%%/samples/python/multiphase/adiabatic.py
-%%PYTHON%%%%DATADIR%%/samples/python/multiphase/plasma_equilibrium.py
+%%PYTHON%%%%DATADIR%%/samples/python/kinetics/shock_tube.py
+%%PYTHON%%%%DATADIR%%/samples/python/kinetics/sofc.py
+%%PYTHON%%%%DATADIR%%/samples/python/onedim/README.rst
 %%PYTHON%%%%DATADIR%%/samples/python/onedim/adiabatic_flame.py
 %%PYTHON%%%%DATADIR%%/samples/python/onedim/burner_flame.py
+%%PYTHON%%%%DATADIR%%/samples/python/onedim/catalytic_combustion.py
 %%PYTHON%%%%DATADIR%%/samples/python/onedim/diffusion_flame.py
 %%PYTHON%%%%DATADIR%%/samples/python/onedim/diffusion_flame_batch.py
+%%PYTHON%%%%DATADIR%%/samples/python/onedim/diffusion_flame_continuation.py
 %%PYTHON%%%%DATADIR%%/samples/python/onedim/diffusion_flame_extinction.py
 %%PYTHON%%%%DATADIR%%/samples/python/onedim/flame_fixed_T.py
 %%PYTHON%%%%DATADIR%%/samples/python/onedim/flame_initial_guess.py
+%%PYTHON%%%%DATADIR%%/samples/python/onedim/flame_speed.py
+%%PYTHON%%%%DATADIR%%/samples/python/onedim/flame_speed_convergence_analysis.py
 %%PYTHON%%%%DATADIR%%/samples/python/onedim/flamespeed_sensitivity.py
 %%PYTHON%%%%DATADIR%%/samples/python/onedim/ion_burner_flame.py
 %%PYTHON%%%%DATADIR%%/samples/python/onedim/ion_free_flame.py
 %%PYTHON%%%%DATADIR%%/samples/python/onedim/premixed_counterflow_flame.py
 %%PYTHON%%%%DATADIR%%/samples/python/onedim/premixed_counterflow_twin_flame.py
 %%PYTHON%%%%DATADIR%%/samples/python/onedim/stagnation_flame.py
-%%PYTHON%%%%DATADIR%%/samples/python/onedim/tdata.dat
+%%PYTHON%%%%DATADIR%%/samples/python/reactors/1D_packed_bed.py
+%%PYTHON%%%%DATADIR%%/samples/python/reactors/1D_pfr_surfchem.py
 %%PYTHON%%%%DATADIR%%/samples/python/reactors/NonIdealShockTube.py
 %%PYTHON%%%%DATADIR%%/samples/python/reactors/PorousMediaBurner.py
+%%PYTHON%%%%DATADIR%%/samples/python/reactors/README.rst
 %%PYTHON%%%%DATADIR%%/samples/python/reactors/combustor.py
+%%PYTHON%%%%DATADIR%%/samples/python/reactors/continuous_reactor.py
 %%PYTHON%%%%DATADIR%%/samples/python/reactors/custom.py
 %%PYTHON%%%%DATADIR%%/samples/python/reactors/custom2.py
 %%PYTHON%%%%DATADIR%%/samples/python/reactors/fuel_injection.py
@@ -787,28 +811,29 @@ libdata/pkgconfig/cantera.pc
 %%PYTHON%%%%DATADIR%%/samples/python/reactors/periodic_cstr.py
 %%PYTHON%%%%DATADIR%%/samples/python/reactors/pfr.py
 %%PYTHON%%%%DATADIR%%/samples/python/reactors/piston.py
+%%PYTHON%%%%DATADIR%%/samples/python/reactors/plasma.py
 %%PYTHON%%%%DATADIR%%/samples/python/reactors/preconditioned_integration.py
 %%PYTHON%%%%DATADIR%%/samples/python/reactors/reactor1.py
 %%PYTHON%%%%DATADIR%%/samples/python/reactors/reactor2.py
 %%PYTHON%%%%DATADIR%%/samples/python/reactors/sensitivity1.py
 %%PYTHON%%%%DATADIR%%/samples/python/reactors/surf_pfr.py
 %%PYTHON%%%%DATADIR%%/samples/python/reactors/surf_pfr_chain.py
-%%PYTHON%%%%DATADIR%%/samples/python/surface_chemistry/1D_pfr_surfchem.py
-%%PYTHON%%%%DATADIR%%/samples/python/surface_chemistry/catalytic_combustion.py
-%%PYTHON%%%%DATADIR%%/samples/python/surface_chemistry/diamond_cvd.py
-%%PYTHON%%%%DATADIR%%/samples/python/surface_chemistry/lithium_ion_battery.py
-%%PYTHON%%%%DATADIR%%/samples/python/surface_chemistry/sofc.py
+%%PYTHON%%%%DATADIR%%/samples/python/thermo/README.rst
+%%PYTHON%%%%DATADIR%%/samples/python/thermo/adiabatic.py
 %%PYTHON%%%%DATADIR%%/samples/python/thermo/coverage_dependent_surf.py
 %%PYTHON%%%%DATADIR%%/samples/python/thermo/critical_properties.py
+%%PYTHON%%%%DATADIR%%/samples/python/thermo/equations_of_state.py
 %%PYTHON%%%%DATADIR%%/samples/python/thermo/equivalenceRatio.py
 %%PYTHON%%%%DATADIR%%/samples/python/thermo/isentropic.py
 %%PYTHON%%%%DATADIR%%/samples/python/thermo/isentropic_units.py
 %%PYTHON%%%%DATADIR%%/samples/python/thermo/mixing.py
+%%PYTHON%%%%DATADIR%%/samples/python/thermo/plasma_equilibrium.py
 %%PYTHON%%%%DATADIR%%/samples/python/thermo/rankine.py
 %%PYTHON%%%%DATADIR%%/samples/python/thermo/rankine_units.py
 %%PYTHON%%%%DATADIR%%/samples/python/thermo/sound_speed.py
 %%PYTHON%%%%DATADIR%%/samples/python/thermo/sound_speed_units.py
 %%PYTHON%%%%DATADIR%%/samples/python/thermo/vapordome.py
+%%PYTHON%%%%DATADIR%%/samples/python/transport/README.rst
 %%PYTHON%%%%DATADIR%%/samples/python/transport/dusty_gas.py
 %%PYTHON%%%%DATADIR%%/samples/python/transport/multiprocessing_viscosity.py
 %%OCTAVE%%%%DATADIR%%/samples/matlab/PFR_solver.m