Fix compilation warnings

SConstruct

@@ -1604,6 +1604,10 @@ if env['python_package'] != 'none':
                 f"Cython is an incompatible version: Found {cython_version} but "
                 f"{cython_min_version} or newer is required.")
             warn_no_full_package = True
+        elif cython_version < parse_version("3.0.0"):
+            logger.info(
+                f"Using Cython version {cython_version} (uses legacy NumPy API)")
+            env["numpy_1_7_API"] = True
         else:
             logger.info(f"Using Cython version {cython_version}")
 

include/cantera/numerics/PreconditionerBase.h

@@ -32,6 +32,8 @@ class PreconditionerBase
 public:
     PreconditionerBase() {}
 
+    virtual ~PreconditionerBase() {}
+
     //! Set a value at the specified row and column of the jacobian triplet vector
     //! @param row row in the jacobian matrix
     //! @param col column in the jacobian matrix

include/cantera/zeroD/IdealGasConstPressureMoleReactor.h

@@ -43,7 +43,7 @@ class IdealGasConstPressureMoleReactor : public MoleReactor
 protected:
     vector_fp m_hk; //!< Species molar enthalpies
 
-    const int m_sidx = 1;
+    const size_t m_sidx = 1;
 };
 
 }

include/cantera/zeroD/MoleReactor.h

@@ -47,7 +47,7 @@ class MoleReactor : public Reactor
     virtual void getSurfaceInitialConditions(double* y);
 
     //! const value for the species start index
-    const int m_sidx = 2;
+    const size_t m_sidx = 2;
 };
 
 }

interfaces/cython/SConscript

@@ -78,6 +78,9 @@ elif localenv['OS'] == 'Cygwin':
     # extract 'pythonX.Y' from 'libpythonX.Y.dll.a'
     localenv.Append(LIBS=pylib[3:-6])
 
+if "numpy_1_7_API" in localenv:
+    localenv.Append(CPPDEFINES="NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION")
+
 localenv["module_ext"] = module_ext
 setup_cfg = localenv.SubstFile("setup.cfg", "setup.cfg.in")
 readme = localenv.Command("README.rst", "#README.rst", Copy("$TARGET", "$SOURCE"))

src/thermo/Elements.cpp

@@ -207,7 +207,7 @@ static vector<isotopeWeightData> isotopeWeightTable {
 // This is implemented as a separate function from elementSymbols() because this pattern
 // allows elementSymbols() to return a const reference to the data.
 vector<string> elementVectorsFromSymbols() {
-	vector<string> values;
+    vector<string> values;
     for (const auto& atom : atomicWeightTable) {
         values.push_back(atom.symbol);
     }
@@ -279,7 +279,7 @@ double getElementWeight(const std::string& ename)
 
 double getElementWeight(int atomicNumber)
 {
-    size_t num = numElementsDefined();
+    int num = numElementsDefined();
     if (atomicNumber > num || atomicNumber < 1) {
         throw IndexError("getElementWeight", "atomicWeightTable", atomicNumber, num);
     }
@@ -309,10 +309,9 @@ string getElementSymbol(const std::string& ename)
 
 string getElementSymbol(int atomicNumber)
 {
-    size_t num = numElementsDefined();
+    int num = numElementsDefined();
     if (atomicNumber > num || atomicNumber < 1) {
-        throw IndexError("getElementSymbol", "atomicWeightTable", atomicNumber,
-                         num);
+        throw IndexError("getElementSymbol", "atomicWeightTable", atomicNumber, num);
     }
     return atomicWeightTable[atomicNumber - 1].symbol;
 }
@@ -335,10 +334,9 @@ string getElementName(const std::string& ename)
 
 string getElementName(int atomicNumber)
 {
-    size_t num = numElementsDefined();
+    int num = numElementsDefined();
     if (atomicNumber > num || atomicNumber < 1) {
-        throw IndexError("getElementName", "atomicWeightTable", atomicNumber,
-                         num);
+        throw IndexError("getElementName", "atomicWeightTable", atomicNumber, num);
     }
     return atomicWeightTable[atomicNumber - 1].fullName;
 }
@@ -349,14 +347,14 @@ int getAtomicNumber(const std::string& ename)
     size_t numIsotopes = numIsotopesDefined();
     string symbol = trimCopy(ename);
     string name = toLowerCopy(symbol);
-    for (int i = 0; i < numElements; i++) {
+    for (size_t i = 0; i < numElements; i++) {
         if (symbol == atomicWeightTable[i].symbol) {
-            return i+1;
+            return i + 1;
         } else if (name == atomicWeightTable[i].fullName) {
-            return i+1;
+            return i + 1;
         }
     }
-    for (int i = 0; i < numIsotopes; i++) {
+    for (size_t i = 0; i < numIsotopes; i++) {
         if (symbol == isotopeWeightTable[i].symbol) {
             return isotopeWeightTable[i].atomicNumber;
         } else if (name == isotopeWeightTable[i].fullName) {