From 02baaee02e507d17bad172a8956fdb8a28180159 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Sat, 27 Nov 2021 22:13:24 -0600
Subject: [PATCH 01/14] [Python] Implement string output for
 Solution.write_yaml()

---
 interfaces/cython/cantera/base.pyx | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index 4ff9337ef38..1333705c1cc 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -283,14 +283,14 @@ cdef class _SolutionBase:
         """
         self.base.header().clear()
 
-    def write_yaml(self, filename, phases=None, units=None, precision=None,
+    def write_yaml(self, filename=None, phases=None, units=None, precision=None,
                    skip_user_defined=None, header=True):
         """
         Write the definition for this phase, any additional phases specified,
         and their species and reactions to the specified file.
 
         :param filename:
-            The name of the output file
+            The name of the output file; if ``None``, a YAML string is returned
         :param phases:
             Additional ThermoPhase / Solution objects to be included in the
             output file
@@ -328,6 +328,8 @@ cdef class _SolutionBase:
             Y.precision = precision
         if skip_user_defined is not None:
             Y.skip_user_defined = skip_user_defined
+        if filename is None:
+            return Y.to_string()
         Y.to_file(filename)
 
     def __getitem__(self, selection):

From 3052468ac93515d5d646951ad4c4fe9bf30030f9 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Tue, 13 Aug 2019 10:33:02 -0500
Subject: [PATCH 02/14] [Input] Implement pickle serialization for Solution
 objects

---
 interfaces/cython/cantera/base.pyx            | 26 +++++++++++++++++--
 interfaces/cython/cantera/test/test_thermo.py |  5 ----
 2 files changed, 24 insertions(+), 7 deletions(-)

diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index 1333705c1cc..21ff9f795d5 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -9,6 +9,18 @@ cdef class _SolutionBase:
                   source=None, yaml=None, thermo=None, species=(),
                   kinetics=None, reactions=(), **kwargs):
 
+        # run instantiation only if valid sources are specified
+        if origin or infile or source or yaml or (thermo and species):
+
+            self._cinit(infile=infile, name=name, adjacent=adjacent,
+                        origin=origin, source=source, yaml=yaml,
+                        thermo=thermo, species=species, kinetics=kinetics,
+                        reactions=reactions, **kwargs)
+
+    def _cinit(self, infile='', name='', adjacent=(), origin=None,
+                  source=None, yaml=None, thermo=None, species=(),
+                  kinetics=None, reactions=(), **kwargs):
+
         if 'phaseid' in kwargs:
             if name is not '':
                 raise AttributeError('duplicate specification of phase name')
@@ -351,8 +363,18 @@ cdef class _SolutionBase:
             for i,spec in enumerate(species):
                 self._selected_species[i] = self.species_index(spec)
 
-    def __reduce__(self):
-        raise NotImplementedError('Solution object is not picklable')
+    def __getstate__(self):
+        """Save complete information of the current phase for pickling."""
+        if self.kinetics.nTotalSpecies() > self.thermo.nSpecies():
+            raise NotImplementedError(
+                "Pickling of Interface objects is not implemented.")
+        return self.write_yaml(), self.state
+
+    def __setstate__(self, pkl):
+        """Restore Solution from pickled information."""
+        yml, state = pkl
+        self._cinit(yaml=yml)
+        self.state = state
 
     def __copy__(self):
         raise NotImplementedError('Solution object is not copyable')
diff --git a/interfaces/cython/cantera/test/test_thermo.py b/interfaces/cython/cantera/test/test_thermo.py
index 43f32bf55f8..a2189bf241c 100644
--- a/interfaces/cython/cantera/test/test_thermo.py
+++ b/interfaces/cython/cantera/test/test_thermo.py
@@ -740,11 +740,6 @@ def test_ref_info(self):
         self.assertNear(self.phase.min_temp, 300.0)
         self.assertNear(self.phase.max_temp, 3500.0)
 
-    def test_unpicklable(self):
-        import pickle
-        with self.assertRaises(NotImplementedError):
-            pickle.dumps(self.phase)
-
     def test_uncopyable(self):
         import copy
         with self.assertRaises(NotImplementedError):

From f50b6393ae8659101748152bbf412d75136001fa Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Fri, 16 Apr 2021 12:49:02 -0500
Subject: [PATCH 03/14] [Python] Mark SolutionArray as not picklable

---
 interfaces/cython/cantera/composite.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/interfaces/cython/cantera/composite.py b/interfaces/cython/cantera/composite.py
index 1d0caa0861c..fbb658fdb39 100644
--- a/interfaces/cython/cantera/composite.py
+++ b/interfaces/cython/cantera/composite.py
@@ -1375,6 +1375,12 @@ def strip_ext(source):
 
         return root_attrs
 
+    def __reduce__(self):
+        raise NotImplementedError('SolutionArray object is not picklable')
+
+    def __copy__(self):
+        raise NotImplementedError('SolutionArray object is not copyable')
+
 
 def _state2_prop(name, doc_source):
     # Factory for creating properties which consist of a tuple of two variables,

From 711d8b7ddd1a08ed75f8899d6740ca8d49189f39 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Sat, 27 Nov 2021 19:59:45 -0600
Subject: [PATCH 04/14] [Kinetics] Clarify base Kinetics::kineticsType as
 'None'

---
 include/cantera/kinetics/Kinetics.h | 2 +-
 src/kinetics/KineticsFactory.cpp    | 5 +++--
 test/kinetics/kineticsFromYaml.cpp  | 4 ++--
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/include/cantera/kinetics/Kinetics.h b/include/cantera/kinetics/Kinetics.h
index 8975dd1eb05..7647509e369 100644
--- a/include/cantera/kinetics/Kinetics.h
+++ b/include/cantera/kinetics/Kinetics.h
@@ -130,7 +130,7 @@ class Kinetics
     //! Each class derived from Kinetics should override this method to return
     //! a meaningful identifier.
     virtual std::string kineticsType() const {
-        return "Kinetics";
+        return "None";
     }
 
     //! Finalize Kinetics object and associated objects
diff --git a/src/kinetics/KineticsFactory.cpp b/src/kinetics/KineticsFactory.cpp
index 72e61b3fc43..c551b427820 100644
--- a/src/kinetics/KineticsFactory.cpp
+++ b/src/kinetics/KineticsFactory.cpp
@@ -42,6 +42,7 @@ Kinetics* KineticsFactory::newKinetics(XML_Node& phaseData,
 KineticsFactory::KineticsFactory() {
     reg("none", []() { return new Kinetics(); });
     addAlias("none", "Kinetics");
+    addAlias("none", "None");
     reg("gas", []() { return new GasKinetics(); });
     addAlias("gas", "gaskinetics");
     addAlias("gas", "Gas");
@@ -106,7 +107,7 @@ void addReactions(Kinetics& kin, const AnyMap& phaseNode, const AnyMap& rootNode
     vector<string> sections, rules;
 
     if (phaseNode.hasKey("reactions")) {
-        if (kin.kineticsType() == "Kinetics") {
+        if (kin.kineticsType() == "None") {
             throw InputFileError("addReactions", phaseNode["reactions"],
                 "Phase entry includes a 'reactions' field but does not "
                 "specify a kinetics model.");
@@ -137,7 +138,7 @@ void addReactions(Kinetics& kin, const AnyMap& phaseNode, const AnyMap& rootNode
                 rules.push_back(item.begin()->second.asString());
             }
         }
-    } else if (kin.kineticsType() != "Kinetics") {
+    } else if (kin.kineticsType() != "None") {
         if (rootNode.hasKey("reactions")) {
             // Default behavior is to add all reactions from the 'reactions'
             // section, if a 'kinetics' model has been specified
diff --git a/test/kinetics/kineticsFromYaml.cpp b/test/kinetics/kineticsFromYaml.cpp
index a3d0440a08a..97de849cf60 100644
--- a/test/kinetics/kineticsFromYaml.cpp
+++ b/test/kinetics/kineticsFromYaml.cpp
@@ -404,7 +404,7 @@ TEST(KineticsFromYaml, NoKineticsModelOrReactionsField1)
 {
     auto soln = newSolution("phase-reaction-spec1.yaml",
                             "nokinetics-noreactions");
-    EXPECT_EQ(soln->kinetics()->kineticsType(), "Kinetics");
+    EXPECT_EQ(soln->kinetics()->kineticsType(), "None");
     EXPECT_EQ(soln->kinetics()->nReactions(), (size_t) 0);
 }
 
@@ -412,7 +412,7 @@ TEST(KineticsFromYaml, NoKineticsModelOrReactionsField2)
 {
     auto soln = newSolution("phase-reaction-spec2.yaml",
                             "nokinetics-noreactions");
-    EXPECT_EQ(soln->kinetics()->kineticsType(), "Kinetics");
+    EXPECT_EQ(soln->kinetics()->kineticsType(), "None");
     EXPECT_EQ(soln->kinetics()->nReactions(), (size_t) 0);
 }
 

From c6c2aa2ea7443672b1bfa4bda6e08e1f2c6c4d83 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Sat, 27 Nov 2021 20:00:15 -0600
Subject: [PATCH 05/14] [Thermo] Clarify base ThermoPhase::type as 'None'

---
 include/cantera/thermo/ThermoPhase.h | 2 +-
 src/thermo/ThermoFactory.cpp         | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/include/cantera/thermo/ThermoPhase.h b/include/cantera/thermo/ThermoPhase.h
index 1c5762a9462..52d15a4dcb5 100644
--- a/include/cantera/thermo/ThermoPhase.h
+++ b/include/cantera/thermo/ThermoPhase.h
@@ -111,7 +111,7 @@ class ThermoPhase : public Phase
     //! @{
 
     virtual std::string type() const {
-        return "ThermoPhase";
+        return "None";
     }
 
     //! String indicating the mechanical phase of the matter in this Phase.
diff --git a/src/thermo/ThermoFactory.cpp b/src/thermo/ThermoFactory.cpp
index 6275397e923..b1828f3de74 100644
--- a/src/thermo/ThermoFactory.cpp
+++ b/src/thermo/ThermoFactory.cpp
@@ -48,6 +48,9 @@ std::mutex ThermoFactory::thermo_mutex;
 
 ThermoFactory::ThermoFactory()
 {
+    reg("none", []() { return new ThermoPhase(); });
+    addAlias("none", "ThermoPhase");
+    addAlias("none", "None");
     reg("ideal-gas", []() { return new IdealGasPhase(); });
     addAlias("ideal-gas", "IdealGas");
     reg("ideal-surface", []() { return new SurfPhase(); });

From 1dfa531eb3db0c260fbd6f2ee65d78652ad9e0e0 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Sat, 27 Nov 2021 21:23:53 -0600
Subject: [PATCH 06/14] [Transport] Register base model as 'none' in
 TransportFactory

---
 src/transport/TransportFactory.cpp | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/transport/TransportFactory.cpp b/src/transport/TransportFactory.cpp
index 6fe71260c48..f5a19bb9c91 100644
--- a/src/transport/TransportFactory.cpp
+++ b/src/transport/TransportFactory.cpp
@@ -29,10 +29,10 @@ std::mutex TransportFactory::transport_mutex;
 
 TransportFactory::TransportFactory()
 {
-    reg("", []() { return new Transport(); });
-    addAlias("", "Transport");
-    addAlias("", "None");
-    addAlias("", "none");
+    reg("none", []() { return new Transport(); });
+    addAlias("none", "Transport");
+    addAlias("none", "None");
+    addAlias("none", "");
     reg("unity-Lewis-number", []() { return new UnityLewisTransport(); });
     addAlias("unity-Lewis-number", "UnityLewis");
     reg("mixture-averaged", []() { return new MixTransport(); });
@@ -63,7 +63,7 @@ void TransportFactory::deleteFactory()
 Transport* TransportFactory::newTransport(const std::string& transportModel,
         ThermoPhase* phase, int log_level)
 {
-    if (transportModel != "DustyGas" && canonicalize(transportModel) == "") {
+    if (transportModel != "DustyGas" && canonicalize(transportModel) == "none") {
         return create(transportModel);
     }
     if (!phase) {

From 189d7260c53701ae369495fb6f2565e04a568ef3 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Sat, 27 Nov 2021 20:01:46 -0600
Subject: [PATCH 07/14] [Python] Enable safe handling of empty Solution objects

---
 interfaces/cython/cantera/base.pyx | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index 21ff9f795d5..686adeb740a 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -16,6 +16,19 @@ cdef class _SolutionBase:
                         origin=origin, source=source, yaml=yaml,
                         thermo=thermo, species=species, kinetics=kinetics,
                         reactions=reactions, **kwargs)
+            return
+
+        self._base = CxxNewSolution()
+        self.base = self._base.get()
+        self.base.setSource(stringify("none"))
+
+        self.base.setThermo(newThermo(stringify("none")))
+        self.thermo = self.base.thermo().get()
+        self.base.setKinetics(newKinetics(stringify("none")))
+        self.kinetics = self.base.kinetics().get()
+        self.base.setTransport(newTransport(NULL, stringify("none")))
+        self.transport = self.base.transport().get()
+        self._selected_species = np.ndarray(0, dtype=np.uint64)
 
     def _cinit(self, infile='', name='', adjacent=(), origin=None,
                   source=None, yaml=None, thermo=None, species=(),

From 088d17f5a6d771e8190e255671f02431fa0c7e84 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Sat, 27 Nov 2021 20:14:02 -0600
Subject: [PATCH 08/14] [Thermo] Make error messages more meaningful

---
 include/cantera/thermo/Phase.h | 6 ++++--
 src/thermo/ThermoPhase.cpp     | 5 +++++
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/include/cantera/thermo/Phase.h b/include/cantera/thermo/Phase.h
index f80bbccc3db..7457fac1f6f 100644
--- a/include/cantera/thermo/Phase.h
+++ b/include/cantera/thermo/Phase.h
@@ -664,7 +664,8 @@ class Phase
      *  \rho, Y_1, \dots, Y_K) \f$. Alternatively, it returns a stored value.
      */
     virtual double pressure() const {
-        throw NotImplementedError("Phase::pressure");
+        throw NotImplementedError("Phase::pressure",
+            "Not implemented for thermo model '{}'", type());
     }
 
     //! Density (kg/m^3).
@@ -703,7 +704,8 @@ class Phase
      *  @param p input Pressure (Pa)
      */
     virtual void setPressure(double p) {
-        throw NotImplementedError("Phase::setPressure");
+        throw NotImplementedError("Phase::setPressure",
+            "Not implemented for thermo model '{}'", type());
     }
 
     //! Set the internally stored temperature of the phase (K).
diff --git a/src/thermo/ThermoPhase.cpp b/src/thermo/ThermoPhase.cpp
index 778f30ae66c..e46c47c934e 100644
--- a/src/thermo/ThermoPhase.cpp
+++ b/src/thermo/ThermoPhase.cpp
@@ -1403,6 +1403,11 @@ void ThermoPhase::getdlnActCoeffdlnN_numderiv(const size_t ld, doublereal* const
 
 std::string ThermoPhase::report(bool show_thermo, doublereal threshold) const
 {
+    if (type() == "None") {
+        throw NotImplementedError("ThermoPhase::report",
+            "Not implemented for thermo model 'None'");
+    }
+
     fmt::memory_buffer b;
     // This is the width of the first column of names in the report.
     int name_width = 18;

From 288111117d21c18b4a4c4c8e5fb3fd245f2b39b5 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Sat, 27 Nov 2021 20:45:58 -0600
Subject: [PATCH 09/14] [Python] Accommodate empty Kinetics objects

---
 interfaces/cython/cantera/kinetics.pyx | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/interfaces/cython/cantera/kinetics.pyx b/interfaces/cython/cantera/kinetics.pyx
index 94b24f01f38..acf5ed1d9de 100644
--- a/interfaces/cython/cantera/kinetics.pyx
+++ b/interfaces/cython/cantera/kinetics.pyx
@@ -8,6 +8,8 @@ from ctypes import c_int
 # e.g. class Solution. [Cython 0.16]
 cdef np.ndarray get_species_array(Kinetics kin, kineticsMethod1d method):
     cdef np.ndarray[np.double_t, ndim=1] data = np.empty(kin.n_total_species)
+    if kin.n_total_species == 0:
+        return data
     method(kin.kinetics, &data[0])
     # @todo: Fix _selected_species to work with interface kinetics
     if kin._selected_species.size:
@@ -17,6 +19,8 @@ cdef np.ndarray get_species_array(Kinetics kin, kineticsMethod1d method):
 
 cdef np.ndarray get_reaction_array(Kinetics kin, kineticsMethod1d method):
     cdef np.ndarray[np.double_t, ndim=1] data = np.empty(kin.n_reactions)
+    if kin.n_reactions == 0:
+        return data
     method(kin.kinetics, &data[0])
     return data
 

From 0cdee6f3582c139a456f252c1e6ca57cf710d9db Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Wed, 8 Dec 2021 19:03:15 -0600
Subject: [PATCH 10/14] [Python] Ensure transport handler is always properly
 set

---
 interfaces/cython/cantera/base.pyx      | 11 ++++++++---
 interfaces/cython/cantera/transport.pyx |  1 +
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index 686adeb740a..346cf639965 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -177,6 +177,9 @@ cdef class _SolutionBase:
             self.base.setKinetics(newKinetics(stringify("none")))
         self.kinetics = self.base.kinetics().get()
 
+        # Transport
+        self.transport = self.base.transport().get()
+
     def _init_cti_xml(self, infile, name, adjacent, source):
         """
         Instantiate a set of new Cantera C++ objects from a CTI or XML
@@ -381,12 +384,14 @@ cdef class _SolutionBase:
         if self.kinetics.nTotalSpecies() > self.thermo.nSpecies():
             raise NotImplementedError(
                 "Pickling of Interface objects is not implemented.")
-        return self.write_yaml(), self.state
+        transport_model = pystr(self.transport.transportType())
+        return self.write_yaml(), self.state, transport_model
 
     def __setstate__(self, pkl):
         """Restore Solution from pickled information."""
-        yml, state = pkl
-        self._cinit(yaml=yml)
+        yml, state, transport_model = pkl
+        self._cinit(yaml=yml, transport_model=transport_model)
+
         self.state = state
 
     def __copy__(self):
diff --git a/interfaces/cython/cantera/transport.pyx b/interfaces/cython/cantera/transport.pyx
index d87a452803e..751e73c9ca1 100644
--- a/interfaces/cython/cantera/transport.pyx
+++ b/interfaces/cython/cantera/transport.pyx
@@ -168,6 +168,7 @@ cdef class Transport(_SolutionBase):
     # The signature of this function causes warnings for Sphinx documentation
     def __init__(self, *args, **kwargs):
         if self.transport == NULL:
+            # @todo ... after removal of CTI/XML, this should be handled by base.pyx
             if 'transport_model' not in kwargs:
                 self.base.setTransport(newTransport(self.thermo, stringify("default")))
             else:

From aef96df09d8d4be5c428cade37d4fb8c610bc852 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Tue, 14 Dec 2021 08:53:25 -0600
Subject: [PATCH 11/14] [Python] Simplify pickle and update instantiation logic

---
 interfaces/cython/cantera/base.pyx | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index 346cf639965..7c70fb14128 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -384,15 +384,12 @@ cdef class _SolutionBase:
         if self.kinetics.nTotalSpecies() > self.thermo.nSpecies():
             raise NotImplementedError(
                 "Pickling of Interface objects is not implemented.")
-        transport_model = pystr(self.transport.transportType())
-        return self.write_yaml(), self.state, transport_model
+        return self.write_yaml()
 
     def __setstate__(self, pkl):
         """Restore Solution from pickled information."""
-        yml, state, transport_model = pkl
-        self._cinit(yaml=yml, transport_model=transport_model)
-
-        self.state = state
+        yml = pkl
+        self._cinit(yaml=yml)
 
     def __copy__(self):
         raise NotImplementedError('Solution object is not copyable')

From 24a7d3c0f4e4421a34daf12bcaa1af0fb4ff57c7 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Tue, 14 Dec 2021 09:45:47 -0600
Subject: [PATCH 12/14] [Python] Ensure that ThermoPhase constructor is always
 called first

---
 interfaces/cython/cantera/_cantera.pxd   | 2 +-
 interfaces/cython/cantera/base.pyx       | 1 +
 interfaces/cython/cantera/composite.py   | 6 +++---
 interfaces/cython/cantera/liquidvapor.py | 2 +-
 interfaces/cython/cantera/thermo.pyx     | 3 +++
 5 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/interfaces/cython/cantera/_cantera.pxd b/interfaces/cython/cantera/_cantera.pxd
index 30223c9798d..1e624510666 100644
--- a/interfaces/cython/cantera/_cantera.pxd
+++ b/interfaces/cython/cantera/_cantera.pxd
@@ -1246,6 +1246,7 @@ cdef class _SolutionBase:
     cdef int thermo_basis
     cdef np.ndarray _selected_species
     cdef object parent
+    cdef public object _references
 
 cdef class Species:
     cdef shared_ptr[CxxSpecies] _species
@@ -1261,7 +1262,6 @@ cdef class ThermoPhase(_SolutionBase):
     cpdef int species_index(self, species) except *
     cdef np.ndarray _getArray1(self, thermoMethod1d method)
     cdef void _setArray1(self, thermoMethod1d method, values) except *
-    cdef public object _references
 
 cdef class InterfacePhase(ThermoPhase):
     cdef CxxSurfPhase* surf
diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index 7c70fb14128..d8a5cfacafa 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -10,6 +10,7 @@ cdef class _SolutionBase:
                   kinetics=None, reactions=(), **kwargs):
 
         # run instantiation only if valid sources are specified
+        self._references = None
         if origin or infile or source or yaml or (thermo and species):
 
             self._cinit(infile=infile, name=name, adjacent=adjacent,
diff --git a/interfaces/cython/cantera/composite.py b/interfaces/cython/cantera/composite.py
index fbb658fdb39..4fa8ff51592 100644
--- a/interfaces/cython/cantera/composite.py
+++ b/interfaces/cython/cantera/composite.py
@@ -25,7 +25,7 @@
     import pandas as _pandas
 
 
-class Solution(ThermoPhase, Kinetics, Transport):
+class Solution(Transport, Kinetics, ThermoPhase):
     """
     A class for chemically-reacting solutions. Instances can be created to
     represent any type of solution -- a mixture of gases, a liquid solution, or
@@ -101,7 +101,7 @@ class Solution(ThermoPhase, Kinetics, Transport):
     __slots__ = ()
 
 
-class Interface(InterfacePhase, InterfaceKinetics):
+class Interface(InterfaceKinetics, InterfacePhase):
     """
     Two-dimensional interfaces.
 
@@ -121,7 +121,7 @@ class Interface(InterfacePhase, InterfaceKinetics):
     __slots__ = ('_phase_indices',)
 
 
-class DustyGas(ThermoPhase, Kinetics, DustyGasTransport):
+class DustyGas(DustyGasTransport, Kinetics, ThermoPhase):
     """
     A composite class which models a gas in a stationary, solid, porous medium.
 
diff --git a/interfaces/cython/cantera/liquidvapor.py b/interfaces/cython/cantera/liquidvapor.py
index 8bf6a17d834..48a5837263c 100644
--- a/interfaces/cython/cantera/liquidvapor.py
+++ b/interfaces/cython/cantera/liquidvapor.py
@@ -41,7 +41,7 @@ def Water(backend='Reynolds'):
     :ct:WaterSSTP and :ct:WaterTransport in the Cantera C++ source
     code documentation.
     """
-    class WaterWithTransport(PureFluid, _cantera.Transport):
+    class WaterWithTransport(_cantera.Transport, PureFluid):
         __slots__ = ()
 
     if backend == 'Reynolds':
diff --git a/interfaces/cython/cantera/thermo.pyx b/interfaces/cython/cantera/thermo.pyx
index 9499bbd7ee0..9a4e5de2f55 100644
--- a/interfaces/cython/cantera/thermo.pyx
+++ b/interfaces/cython/cantera/thermo.pyx
@@ -330,6 +330,9 @@ cdef class ThermoPhase(_SolutionBase):
         super().__init__(*args, **kwargs)
         if 'source' not in kwargs:
             self.thermo_basis = mass_basis
+        # In composite objects, the ThermoPhase constructor needs to be called first
+        # to prevent instantiation of stand-alone 'Kinetics' or 'Transport' objects.
+        # The following is used as a sentinel.
         self._references = weakref.WeakKeyDictionary()
 
     property thermo_model:

From c31e757e7e1683ffb860f1c98f8bf6218d84385e Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Tue, 14 Dec 2021 09:47:55 -0600
Subject: [PATCH 13/14] [Python] Prevent stand-alone Kinetics and Transport
 objects

Also, catch edge cases that provide insufficient information for
phase instantiation.
---
 interfaces/cython/cantera/base.pyx      | 7 ++++---
 interfaces/cython/cantera/kinetics.pyx  | 7 +++++++
 interfaces/cython/cantera/transport.pyx | 5 +++++
 3 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/interfaces/cython/cantera/base.pyx b/interfaces/cython/cantera/base.pyx
index d8a5cfacafa..563f546dfee 100644
--- a/interfaces/cython/cantera/base.pyx
+++ b/interfaces/cython/cantera/base.pyx
@@ -18,6 +18,9 @@ cdef class _SolutionBase:
                         thermo=thermo, species=species, kinetics=kinetics,
                         reactions=reactions, **kwargs)
             return
+        elif any([infile, source, adjacent, origin, source, yaml,
+                  thermo, species, kinetics, reactions, kwargs]):
+            raise ValueError("Arguments are insufficient to define a phase")
 
         self._base = CxxNewSolution()
         self.base = self._base.get()
@@ -89,10 +92,8 @@ cdef class _SolutionBase:
         # Parse inputs
         if infile or source:
             self._init_cti_xml(infile, name, adjacent, source)
-        elif thermo and species:
-            self._init_parts(thermo, species, kinetics, adjacent, reactions)
         else:
-            raise ValueError("Arguments are insufficient to define a phase")
+            self._init_parts(thermo, species, kinetics, adjacent, reactions)
 
         self._selected_species = np.ndarray(0, dtype=np.uint64)
 
diff --git a/interfaces/cython/cantera/kinetics.pyx b/interfaces/cython/cantera/kinetics.pyx
index acf5ed1d9de..d213f56e32f 100644
--- a/interfaces/cython/cantera/kinetics.pyx
+++ b/interfaces/cython/cantera/kinetics.pyx
@@ -64,6 +64,13 @@ cdef class Kinetics(_SolutionBase):
     of progress, species production rates, and other quantities pertaining to
     a reaction mechanism.
     """
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        if self._references is None:
+            raise ValueError(
+                "Cannot instantiate stand-alone 'Kinetics' object as it requires an "
+                "associated thermo phase.\nAll 'Kinetics' methods should be accessed "
+                "from a 'Solution' object.")
 
     property kinetics_model:
         """
diff --git a/interfaces/cython/cantera/transport.pyx b/interfaces/cython/cantera/transport.pyx
index 751e73c9ca1..3f1874b1a98 100644
--- a/interfaces/cython/cantera/transport.pyx
+++ b/interfaces/cython/cantera/transport.pyx
@@ -179,6 +179,11 @@ cdef class Transport(_SolutionBase):
             self.transport = self.base.transport().get()
 
         super().__init__(*args, **kwargs)
+        if self._references is None:
+            raise ValueError(
+                "Cannot instantiate stand-alone 'Transport' object as it requires an "
+                "associated thermo phase.\nAll 'Transport' methods should be accessed "
+                "from a 'Solution' object.")
 
     property transport_model:
         """

From e3a7e289afb53271b788801be1de47f361215157 Mon Sep 17 00:00:00 2001
From: Ingmar Schoegl <ischoegl@lsu.edu>
Date: Sat, 27 Nov 2021 20:46:38 -0600
Subject: [PATCH 14/14] [UnitTests] Add tests for pickling and empty objects

---
 .../cython/cantera/test/test_composite.py     | 89 +++++++++++++++++++
 1 file changed, 89 insertions(+)

diff --git a/interfaces/cython/cantera/test/test_composite.py b/interfaces/cython/cantera/test/test_composite.py
index 49de22a99ef..04a52782b56 100644
--- a/interfaces/cython/cantera/test/test_composite.py
+++ b/interfaces/cython/cantera/test/test_composite.py
@@ -2,6 +2,7 @@
 
 import numpy as np
 from collections import OrderedDict
+import pickle
 
 import cantera as ct
 from cantera.composite import _h5py, _pandas
@@ -116,6 +117,94 @@ def check(a, b):
                     raise TypeError(msg) from inst
 
 
+class TestPickle(utilities.CanteraTest):
+
+    def test_pickle_gas(self):
+        gas = ct.Solution("h2o2.yaml", transport_model=None)
+        gas.TPX = 500, 500000, "H2:.75,O2:.25"
+        with open("gas.pkl", "wb") as pkl:
+            pickle.dump(gas, pkl)
+
+        with open("gas.pkl", "rb") as pkl:
+            gas2 = pickle.load(pkl)
+        self.assertNear(gas.T, gas2.T)
+        self.assertNear(gas.P, gas2.P)
+        self.assertArrayNear(gas.X, gas2.X)
+
+        self.assertEqual(gas2.transport_model, "None")
+
+    def test_pickle_gas_with_transport(self):
+        gas = ct.Solution("h2o2.yaml")
+        gas.TPX = 500, 500000, "H2:.75,O2:.25"
+        gas.transport_model = "Multi"
+        with open("gas.pkl", "wb") as pkl:
+            pickle.dump(gas, pkl)
+
+        with open("gas.pkl", "rb") as pkl:
+            gas2 = pickle.load(pkl)
+        self.assertNear(gas.T, gas2.T)
+        self.assertNear(gas.P, gas2.P)
+        self.assertArrayNear(gas.X, gas2.X)
+
+        self.assertEqual(gas2.transport_model, "Multi")
+
+    def test_pickle_interface(self):
+        gas = ct.Solution("diamond.yaml", "gas")
+        solid = ct.Solution("diamond.yaml", "diamond")
+        interface = ct.Interface("diamond.yaml", "diamond_100", (gas, solid))
+
+        with self.assertRaises(NotImplementedError):
+            with open("interface.pkl", "wb") as pkl:
+                pickle.dump(interface, pkl)
+
+
+class TestEmptyThermoPhase(utilities.CanteraTest):
+    """ Test empty Solution object """
+    @classmethod
+    def setUpClass(cls):
+        utilities.CanteraTest.setUpClass()
+        cls.gas = ct.ThermoPhase()
+
+    def test_empty_report(self):
+        with self.assertRaisesRegex(ct.CanteraError, "NotImplementedError"):
+            self.gas()
+
+    def test_empty_TP(self):
+        with self.assertRaisesRegex(ct.CanteraError, "NotImplementedError"):
+            self.gas.TP = 300, ct.one_atm
+
+    def test_empty_equilibrate(self):
+        with self.assertRaisesRegex(ct.CanteraError, "NotImplementedError"):
+            self.gas.equilibrate("TP")
+
+
+class TestEmptySolution(TestEmptyThermoPhase):
+    """ Test empty Solution object """
+    @classmethod
+    def setUpClass(cls):
+        utilities.CanteraTest.setUpClass()
+        cls.gas = ct.Solution()
+
+    def test_empty_composite(self):
+        self.assertEqual(self.gas.thermo_model, "None")
+        self.assertEqual(self.gas.composite, ("None", "None", "None"))
+
+
+class TestEmptyEdgeCases(utilities.CanteraTest):
+    """ Test for edge cases where constructors are not allowed """
+    def test_empty_phase(self):
+        with self.assertRaisesRegex(ValueError, "Arguments are insufficient to define a phase"):
+            ct.ThermoPhase(thermo="ideal-gas")
+
+    def test_empty_kinetics(self):
+        with self.assertRaisesRegex(ValueError, "Cannot instantiate"):
+            ct.Kinetics()
+
+    def test_empty_transport(self):
+        with self.assertRaisesRegex(ValueError, "Cannot instantiate"):
+            ct.Transport()
+
+
 class TestSolutionArrayIO(utilities.CanteraTest):
     """ Test SolutionArray file IO """
     @classmethod