Deprecate obsolete methods

.github/workflows/main.yml

@@ -282,13 +282,14 @@ jobs:
       - name: Install Apt dependencies
         run: |
           sudo apt update
-          sudo apt install libboost-dev gfortran graphviz liblapack-dev libblas-dev
+          sudo apt install libboost-dev gfortran graphviz liblapack-dev libblas-dev gcc-5 g++-5
       - name: Upgrade pip
         run: python3 -m pip install -U pip setuptools wheel
       - name: Install Python dependencies
         run: python3 -m pip install ruamel.yaml scons numpy cython h5py pandas matplotlib scipy
       - name: Build Cantera
-        run: python3 `which scons` build -j2 debug=n
+        # compile with GCC 5.5.0 on ubuntu-18.04
+        run: python3 `which scons` build -j2 debug=n CC=gcc-5 CXX=g++-5
       - name: Run the examples
         # See https://unix.stackexchange.com/a/392973 for an explanation of the -exec part
         run: |

include/cantera/kinetics/ChebyshevRate.h

@@ -124,11 +124,15 @@ class ChebyshevRate final : public ReactionRate
      *  @param units  Unit definitions specific to rate information
      */
     void setParameters(const AnyMap& node, const UnitStack& units);
+
+    void getParameters(AnyMap& rateNode) const;
+
+    //! @deprecated  To be removed after Cantera 3.0.
     void getParameters(AnyMap& rateNode, const Units& rate_units) const {
-        // @todo: deprecate, as second argument is no longer needed
+        warn_deprecated("ChebyshevRate:getParameters",
+            "To be removed after Cantera 3.0. Second argument is no longer needed.");
         return getParameters(rateNode);
     }
-    void getParameters(AnyMap& rateNode) const;
 
     virtual void validate(const std::string& equation, const Kinetics& kin);
 

include/cantera/kinetics/Falloff.h

@@ -98,7 +98,7 @@ class FalloffRate : public ReactionRate
      * @param c Vector of coefficients of the parameterization. The number and
      *     meaning of these coefficients is subclass-dependent.
      *
-     * @todo  deprecate; superseded by setFalloffCoeffs
+     * @deprecated  To be removed after Cantera 3.0; superseded by setFalloffCoeffs()
      */
     void init(const vector_fp& c);
 
@@ -161,9 +161,11 @@ class FalloffRate : public ReactionRate
 
     //! The size of the work array required.
     /**
-     * @todo  deprecate; only used by legacy framework
+     * @deprecated  To be removed after Cantera 3.0; unused.
      */
     virtual size_t workSize() const {
+        warn_deprecated("FalloffRate::workSize",
+            "To be removed after Cantera 3.0; unused.");
         return 0;
     }
 
@@ -182,9 +184,12 @@ class FalloffRate : public ReactionRate
     //! Get the values of the parameters for this object. *params* must be an
     //! array of at least nParameters() elements.
     /**
-     * @todo  deprecate; superseded by getFalloffCoeffs
+     * @deprecated  To be removed after Cantera 3.0; superseded by getFalloffCoeffs()
      */
-    virtual void getParameters(double* params) const {}
+    virtual void getParameters(double* params) const {
+        warn_deprecated("FalloffRate::getParameters",
+            "To be removed after Cantera 3.0; superseded by getFalloffCoeffs.");
+    }
 
     virtual void getParameters(AnyMap& node) const;
 
@@ -392,7 +397,7 @@ class TroeRate final : public FalloffRate
 
     //! Sets params to contain, in order, \f[ (A, T_3, T_1, T_2) \f]
     /**
-     * @todo  deprecate; superseded by getFalloffCoeffs
+     * @deprecated  To be removed after Cantera 3.0; superseded by getFalloffCoeffs()
      */
     virtual void getParameters(double* params) const;
 
@@ -495,7 +500,7 @@ class SriRate final : public FalloffRate
 
     //! Sets params to contain, in order, \f[ (a, b, c, d, e) \f]
     /**
-     * @todo  deprecate; superseded by getFalloffCoeffs
+     * @deprecated  To be removed after Cantera 3.0; superseded by getFalloffCoeffs()
      */
     virtual void getParameters(double* params) const;
 
@@ -604,7 +609,7 @@ class TsangRate final : public FalloffRate
 
     //! Sets params to contain, in order, \f[ (A, B) \f]
     /**
-     * @todo  deprecate; superseded by getFalloffCoeffs
+     * @deprecated  To be removed after Cantera 3.0; superseded by getFalloffCoeffs()
      */
     virtual void getParameters(double* params) const;
 

include/cantera/kinetics/InterfaceRate.h

@@ -110,7 +110,7 @@ class InterfaceRateBase
     //! Store parameters needed to reconstruct coverage dependencies
     //! @param dependencies  AnyMap receiving coverage information
     //! @param asVector  Optional boolean flag to override map output
-    //! @todo  Remove vector version (which currently only serves testing purposes)
+    //! @deprecated  After Cantera 3.0, the optional asVector argument will be removed.
     void getCoverageDependencies(AnyMap& dependencies, bool asVector=false) const;
 
     //! Add a coverage dependency for species *sp*, with exponential dependence

include/cantera/kinetics/PlogRate.h

@@ -171,10 +171,10 @@ class PlogRate final : public ReactionRate
     //! temperatures at each interpolation pressure. This is potentially an
     //! issue when one of the Arrhenius expressions at a particular pressure
     //! has a negative pre-exponential factor.
-    void validate(const std::string& equation, const Kinetics& kin) {
-        validate(equation);
-    }
+    void validate(const std::string& equation, const Kinetics& kin);
 
+    //! @deprecated  To be removed after Cantera 3.0;
+    //!              superseded by two-parameter version
     void validate(const std::string& equation);
 
     //! Return the pressures and Arrhenius expressions which comprise this

include/cantera/kinetics/Reaction.h

@@ -72,9 +72,18 @@ class Reaction
         return calculateRateCoeffUnits(kin);
     }
 
-    //! Ensure that the rate constant and other parameters for this reaction are
-    //! valid.
-    virtual void validate();
+    //! Ensure that the rate constant and other parameters for this reaction are valid.
+    //! @since  New in Cantera 3.0.
+    virtual void check();
+
+    //! Ensure that the rate constant and other parameters for this reaction are valid.
+    //! @deprecated  To be removed after Cantera 3.0. Replaceable by check.
+    virtual void validate() {
+        warn_deprecated("Reaction::validate",
+            "Deprecated in Cantera 3.0 and to be removed thereafter; replaceable "
+            "by Reaction::check.");
+        check();
+    }
 
     //! Perform validation checks that need access to a complete Kinetics objects, for
     // example to retrieve information about reactant / product species.

include/cantera/kinetics/ReactionRate.h

@@ -11,6 +11,7 @@
 #include "MultiRateBase.h"
 #include "cantera/base/AnyMap.h"
 #include "cantera/base/Units.h"
+#include "cantera/base/global.h"
 #include "cantera/base/ctexceptions.h"
 
 namespace Cantera
@@ -105,8 +106,12 @@ class ReactionRate
     virtual void validate(const std::string& equation, const Kinetics& kin) {}
 
     //! Validate the reaction rate expression (legacy call)
-    //! @todo deprecate in favor of two-parameter version
-    virtual void validate(const std::string& equation) {}
+    //! @deprecated  To be removed after Cantera 3.0.
+    //!              Superseded by two-parameter version
+    virtual void validate(const std::string& equation) {
+        warn_deprecated("ReactionRate::validate",
+            "To be removed after Cantera 3.0; superseded by two-parameter version.");
+    }
 
     //! Reaction rate index within kinetics evaluator
     size_t rateIndex() const {

interfaces/cython/cantera/_cantera.pxd

@@ -602,7 +602,6 @@ cdef extern from "cantera/kinetics/Reaction.h" namespace "Cantera":
         string equation()
         void setEquation(const string&) except +translate_exception
         string type()
-        void validate() except +translate_exception
         CxxAnyMap parameters(cbool) except +translate_exception
         CxxAnyMap input
         Composition reactants

platform/posix/SConscript

@@ -11,21 +11,6 @@ if env['INSTALL_MANPAGES']:
 
 ### Generate customized scripts ###
 
-# 'setup_cantera'
-if localenv['layout'] != 'debian' and env['OS'] != 'Windows':
-
-    def copy_var(target, source, env):
-        if env['python_prefix'] == 'USER':
-            env['python_module_loc_sc'] = ''
-        else:
-            env['python_module_loc_sc'] = env['python_module_loc']
-
-    for script in ['setup_cantera', 'setup_cantera.csh']:
-        target = env.SubstFile(script, script + '.in')
-        localenv.AddPreAction(target, copy_var)
-        localenv.Depends(target, env['install_python_action'])
-        install('$inst_bindir', target)
-
 # Cantera.mak include file for Makefile projects
 # cantera.pc for use with pkg-config
 

src/kinetics/Falloff.cpp

@@ -84,6 +84,8 @@ void FalloffData::restore()
 
 void FalloffRate::init(const vector_fp& c)
 {
+    warn_deprecated("FalloffRate::init",
+        "To be removed after Cantera 3.0; superseded by setFalloffCoeffs.");
     setFalloffCoeffs(c);
 }
 
@@ -244,11 +246,15 @@ void TroeRate::setFalloffCoeffs(const vector_fp& c)
 
 void TroeRate::getFalloffCoeffs(vector_fp& c) const
 {
-    c.resize(4, 0.);
-    getParameters(c.data());
-    if (std::abs(c[3]) < SmallNumber) {
+    if (std::abs(m_t2) < SmallNumber) {
         c.resize(3);
+    } else {
+        c.resize(4, 0.);
+        c[3] = m_t2;
     }
+    c[0] = m_a;
+    c[1] = 1.0 / m_rt3;
+    c[2] = 1.0 / m_rt1;
 }
 
 void TroeRate::updateTemp(double T, double* work) const
@@ -293,6 +299,8 @@ void TroeRate::setParameters(const AnyMap& node, const UnitStack& rate_units)
 }
 
 void TroeRate::getParameters(double* params) const {
+    warn_deprecated("TroeRate::getParameters",
+        "To be removed after Cantera 3.0; superseded by getFalloffCoeffs.");
     params[0] = m_a;
     params[1] = 1.0/m_rt3;
     params[2] = 1.0/m_rt1;
@@ -356,11 +364,16 @@ void SriRate::setFalloffCoeffs(const vector_fp& c)
 
 void SriRate::getFalloffCoeffs(vector_fp& c) const
 {
-    c.resize(5, 0.);
-    getParameters(c.data());
     if (m_e < SmallNumber && std::abs(m_e - 1.) < SmallNumber) {
         c.resize(3);
+    } else {
+        c.resize(5, 0.);
+        c[3] = m_d;
+        c[4] = m_e;
     }
+    c[0] = m_a;
+    c[1] = m_b;
+    c[2] = m_c;
 }
 
 void SriRate::updateTemp(double T, double* work) const
@@ -406,6 +419,8 @@ void SriRate::setParameters(const AnyMap& node, const UnitStack& rate_units)
 
 void SriRate::getParameters(double* params) const
 {
+    warn_deprecated("SriRate::getParameters",
+        "To be removed after Cantera 3.0; superseded by getFalloffCoeffs.");
     params[0] = m_a;
     params[1] = m_b;
     params[2] = m_c;
@@ -460,11 +475,13 @@ void TsangRate::setFalloffCoeffs(const vector_fp& c)
 
 void TsangRate::getFalloffCoeffs(vector_fp& c) const
 {
-    c.resize(2, 0.);
-    getParameters(c.data());
-    if (m_b < SmallNumber) {
+    if (std::abs(m_b) < SmallNumber) {
         c.resize(1);
+    } else {
+        c.resize(2, 0.);
+        c[1] = m_b;
     }
+    c[0] = m_a;
 }
 
 void TsangRate::updateTemp(double T, double* work) const
@@ -502,6 +519,8 @@ void TsangRate::setParameters(const AnyMap& node, const UnitStack& rate_units)
 }
 
 void TsangRate::getParameters(double* params) const {
+    warn_deprecated("TsangRate::getParameters",
+        "To be removed after Cantera 3.0; superseded by getFalloffCoeffs.");
     params[0] = m_a;
     params[1] = m_b;
 }

src/kinetics/InterfaceRate.cpp

@@ -168,6 +168,8 @@ void InterfaceRateBase::getCoverageDependencies(AnyMap& dependencies,
     for (size_t k = 0; k < m_cov.size(); k++) {
         if (asVector) {
             // this preserves the previous 'coverage_deps' units
+            warn_deprecated("InterfaceRateBase::getCoverageDependencies",
+                "To be changed after Cantera 3.0: second argument will be removed.");
             vector_fp dep(3);
             dep[0] = m_ac[k];
             dep[1] = m_mc[k];

src/kinetics/Kinetics.cpp

@@ -616,7 +616,7 @@ void Kinetics::resizeSpecies()
 
 bool Kinetics::addReaction(shared_ptr<Reaction> r, bool resize)
 {
-    r->validate();
+    r->check();
     r->validate(*this);
 
     if (m_kk == 0) {