Collect build/test timing information and fix some bugs

.github/workflows/main.yml

@@ -38,11 +38,14 @@ jobs:
     - 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
+      run: python3 -m pip install ruamel.yaml scons numpy cython h5py pandas pytest
+        pytest-github-actions-annotate-failures
     - name: Build Cantera
-      run: python3 `which scons` build -j2 debug=n
+      run: python3 `which scons` build env_vars=all -j2 debug=n --debug=time
     - name: Test Cantera
-      run: python3 `which scons` test
+      run: python3 `which scons` test --debug=time
+      env:
+        GITHUB_ACTIONS: "true"
 
   macos-multiple-pythons:
     name: macOS with Python ${{ matrix.python-version }}
@@ -75,11 +78,14 @@ jobs:
     - name: Upgrade pip
       run: python3 -m pip install -U pip 'setuptools>=47.0.0,<48' wheel
     - name: Install Python dependencies
-      run: python3 -m pip install ruamel.yaml scons numpy cython h5py pandas
+      run: python3 -m pip install ruamel.yaml scons numpy cython h5py pandas pytest
+        pytest-github-actions-annotate-failures
     - name: Build Cantera
-      run: python3 `which scons` build -j2 debug=n
+      run: python3 `which scons` build env_vars=all -j3 debug=n --debug=time
     - name: Test Cantera
-      run: python3 `which scons` test
+      run: python3 `which scons` test --debug=time
+      env:
+        GITHUB_ACTIONS: "true"
 
   # Coverage is its own job because macOS builds of the samples
   # use Homebrew gfortran which is not compatible for coverage
@@ -88,7 +94,6 @@ jobs:
   coverage:
     name: Coverage
     runs-on: ubuntu-latest
-    needs: [ubuntu-multiple-pythons]
     steps:
     - uses: actions/checkout@v2
       name: Checkout the repository
@@ -105,13 +110,16 @@ jobs:
     - 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
+      run: python3 -m pip install ruamel.yaml scons numpy cython h5py pandas pytest
+        pytest-github-actions-annotate-failures
     - name: Build Cantera
       run: |
         python3 `which scons` build blas_lapack_libs=lapack,blas coverage=y \
-        optimize=n no_optimize_flags=-DNDEBUG -j2
+        optimize=n no_optimize_flags=-DNDEBUG env_vars=all -j2 --debug=time
     - name: Test Cantera
-      run: python3 `which scons` test
+      run: python3 `which scons` test --debug=time
+      env:
+        GITHUB_ACTIONS: "true"
     - name: Upload Coverage to Codecov
       run: bash <(curl -s https://codecov.io/bash)
       env:
@@ -180,7 +188,8 @@ jobs:
           python3-ruamel.yaml python-numpy cython3 libsundials-dev liblapack-dev \
           libblas-dev
       - name: Build Cantera
-        run: scons build python_cmd=/usr/bin/python3 blas_lapack_libs=lapack,blas -j2 debug=n
+        run: scons build python_cmd=/usr/bin/python3 blas_lapack_libs=lapack,blas -j2
+          debug=n --debug=time
       - name: Test Cantera
         run: scons test
 
@@ -326,7 +335,7 @@ jobs:
       - name: Install Python dependencies
         run: |
           python -m pip install -U pip 'setuptools>=47.0.0,<48'
-          python -m pip install scons pypiwin32 numpy ruamel.yaml cython h5py pandas
+          python -m pip install scons pypiwin32 numpy ruamel.yaml cython h5py pandas pytest pytest-github-actions-annotate-failures
       - name: Restore Boost cache
         uses: actions/cache@v2
         id: cache-boost
@@ -345,9 +354,11 @@ jobs:
           rm $BOOST_ROOT/download.7z
         shell: bash
       - name: Build Cantera
-        run: |
-          scons build -j2 boost_inc_dir=%BOOST_ROOT% debug=n VERBOSE=y python_package=full ^
-          msvc_version=${{ matrix.vs-toolset }} f90_interface=n
+        run: scons build -j2 boost_inc_dir=%BOOST_ROOT% debug=n VERBOSE=y
+          python_package=full env_vars=PYTHONPATH,GITHUB_ACTIONS
+          msvc_version=${{ matrix.vs-toolset }} f90_interface=n --debug=time
         shell: cmd
       - name: Test Cantera
-        run: scons test
+        run: scons test --debug=time
+        env:
+          GITHUB_ACTIONS: "true"

interfaces/cython/cantera/onedim.py

@@ -1613,6 +1613,8 @@ def set_initial_guess(self, data=None, group=None):
         `FlameBase.set_initial_guess`).
         """
         super().set_initial_guess(data=data, group=group)
+        if data:
+            return
 
         Yu = self.reactants.Y
         Tu = self.reactants.T

interfaces/cython/cantera/test/test_onedim.py

@@ -823,7 +823,7 @@ def time_step_func(dt):
 
     def run_extinction(self, mdot_fuel, mdot_ox, T_ox, width, P):
         self.create_sim(fuel='H2:1.0', oxidizer='O2:1.0', p=ct.one_atm*P,
-                        mdot_fuel=mdot_fuel, mdot_ox=mdot_ox, width=width)
+                        mdot_fuel=mdot_fuel, mdot_ox=mdot_ox, T_ox=T_ox, width=width)
         self.sim.solve(loglevel=0, auto=True)
         self.assertFalse(self.sim.extinct())
 

interfaces/cython/cantera/test/test_reactor.py

@@ -1442,6 +1442,8 @@ def calc_dtdh(self, species):
         dtdp = ((t[-1] - tig)*S[-1,:]*Tf - np.trapz(S*T[:,None], t, axis=0))/(Tf-To)
         return dtdp
 
+    # See https://github.com/Cantera/enhancements/issues/55
+    @unittest.skip("Integration of sensitivity ODEs is unreliable")
     def test_ignition_delay_sensitivity(self):
         species = ('H2', 'H', 'O2', 'H2O2', 'H2O', 'OH', 'HO2')
         dtigdh_cvodes = self.calc_dtdh(species)

interfaces/cython/cantera/test/utilities.py

@@ -20,6 +20,7 @@ def setUpClass(cls):
                                                 '..', '..', '..', '..'))
         if os.path.exists(os.path.join(root_dir, 'SConstruct')):
             cls.test_work_dir = os.path.join(root_dir, 'test', 'work', 'python')
+            cls.using_tempfile = False
             try:
                 os.makedirs(cls.test_work_dir)
             except OSError as e:
@@ -31,6 +32,7 @@ def setUpClass(cls):
                     raise
         else:
             cls.test_work_dir = tempfile.mkdtemp()
+            cls.using_tempfile = True
 
         cantera.make_deprecation_warnings_fatal()
         cantera.add_directory(cls.test_work_dir)
@@ -41,7 +43,7 @@ def setUpClass(cls):
     @classmethod
     def tearDownClass(cls):
         # Remove the working directory after testing, but only if its a temp directory
-        if tempfile.tempdir is not None:
+        if getattr(cls, "using_tempfile", False):
             try:
                 shutil.rmtree(cls.test_work_dir)
             except OSError:

src/base/AnyMap.cpp

@@ -39,6 +39,7 @@ bool isFloat(const std::string& val)
     int numDot = 0;
     int numExp = 0;
     int istart = 0;
+    int numDigit = 0;
     char ch = str[0];
     if (ch == '+' || ch == '-') {
         istart = 1;
@@ -49,6 +50,7 @@ bool isFloat(const std::string& val)
     for (size_t i = istart; i < str.size(); i++) {
         ch = str[i];
         if (isdigit(ch)) {
+            numDigit++;
         } else if (ch == '.') {
             numDot++;
             if (numDot > 1) {
@@ -59,7 +61,7 @@ bool isFloat(const std::string& val)
             }
         } else if (ch == 'e' || ch == 'E') {
             numExp++;
-            if (numExp > 1 || i == str.size() - 1) {
+            if (numExp > 1 || numDigit == 0 || i == str.size() - 1) {
                 return false;
             }
             ch = str[i+1];

src/base/units.h

@@ -3,15 +3,13 @@
  * Header for units conversion utilities, which are used to translate
  * user input from input files (See \ref inputfiles and
  * class \link Cantera::Unit Unit\endlink).
- *
- * This header is included only by file misc.cpp.
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or
 // at https://cantera.org/license.txt for license and copyright information.
 
-#ifndef CT_UNITS_H
-#define CT_UNITS_H
+#ifndef CT_LEGACY_UNITS_H
+#define CT_LEGACY_UNITS_H
 
 #include "cantera/base/ct_defs.h"
 #include "cantera/base/ctexceptions.h"

src/pch/system.h

@@ -15,5 +15,6 @@
 
 #include <boost/algorithm/string.hpp>
 #include "cantera/base/fmt.h"
+#include "cantera/base/AnyMap.h"
 
 #endif

test/SConscript

@@ -115,14 +115,18 @@ def addPythonTest(testname, subdir, script, interpreter, outfile,
     Create targets for running and resetting a test script.
     """
     def scriptRunner(target, source, env):
+        unittest_outfile = File("#test/work/python-results.txt").abspath
+        pytest_outfile = File("#test/work/pytest.xml").abspath
         """Scons Action to run a test script using the specified interpreter"""
         workDir = Dir('#test/work').abspath
         passedFile = target[0]
         testResults.tests.pop(passedFile.name, None)
         if not os.path.isdir(workDir):
             os.mkdir(workDir)
-        if os.path.exists(outfile):
-            os.remove(outfile)
+        if os.path.exists(unittest_outfile):
+            os.remove(unittest_outfile)
+        if os.path.exists(pytest_outfile):
+            os.remove(pytest_outfile)
 
         environ = dict(env['ENV'])
         for k,v in env_vars.items():
@@ -145,7 +149,7 @@ def addPythonTest(testname, subdir, script, interpreter, outfile,
             sys.exit(1)
 
         failures = 0
-        if os.path.exists(outfile):
+        if os.path.exists(unittest_outfile):
             # Determine individual test status
             for line in open(outfile):
                 status, name = line.strip().split(': ', 1)
@@ -154,6 +158,18 @@ def addPythonTest(testname, subdir, script, interpreter, outfile,
                 elif status in ('FAIL', 'ERROR'):
                     testResults.failed[':'.join((testname,name))] = 1
                     failures += 1
+        elif os.path.exists(pytest_outfile):
+            results = ElementTree.parse(pytest_outfile)
+            for test in results.findall('.//testcase'):
+                class_name = test.get('classname')
+                if class_name.startswith("build.python.cantera.test."):
+                    class_name = class_name[26:]
+                test_name = "python: {}.{}".format(class_name, test.get('name'))
+                if test.findall('failure'):
+                    testResults.failed[test_name] = 1
+                    failures += 1
+                else:
+                    testResults.passed[test_name] = 1
 
         if code and failures == 0:
             # Failure, but unable to determine status of individual tests. This

test/python/runCythonTests.py

@@ -20,19 +20,16 @@
 
 import sys
 import os
+from pathlib import Path
 
 cantera_root = os.path.relpath(__file__).split(os.sep)[:-1] + ['..', '..']
-module_path = os.path.abspath(os.sep.join(cantera_root + ['build']))
-
-if 'PYTHONPATH' in os.environ:
-    os.environ['PYTHONPATH'] = module_path + os.path.pathsep + os.environ['PYTHONPATH']
-else:
-    os.environ['PYTHONPATH'] = module_path
-
-sys.path.insert(0, module_path)
 os.chdir(os.sep.join(cantera_root + ['test', 'work']))
 
-from cantera.test.utilities import unittest
+import unittest
+try:
+    import pytest
+except ImportError:
+    pytest = None
 import cantera
 import cantera.test
 
@@ -77,19 +74,36 @@ def addError(self, test, err):
     else:
         fast_fail = False
         subset_start = 1
-    loader = unittest.TestLoader()
-    runner = unittest.TextTestRunner(
-        verbosity=2, resultclass=TestResult, failfast=fast_fail
-    )
-    suite = unittest.TestSuite()
-    subsets = []
-    for name in sys.argv[subset_start:]:
-        subsets.append('cantera.test.test_' + name)
-
-    if not subsets:
-        subsets.append('cantera.test')
-
-    suite = loader.loadTestsFromNames(subsets)
-
-    results = runner.run(suite)
-    sys.exit(len(results.errors) + len(results.failures))
+
+    if pytest is not None:
+        base = Path(cantera.__file__).parent.joinpath('test')
+        subsets = []
+        for name in sys.argv[subset_start:]:
+            subsets.append(str(base.joinpath(f"test_{name}.py")))
+
+        if not subsets:
+            subsets.append(str(base))
+
+        pytest_args = ["-raP", "--durations=50", "--junitxml=pytest.xml"]
+        if fast_fail:
+            pytest_args.insert(0, "-x")
+
+        ret_code = pytest.main(pytest_args + subsets)
+        sys.exit(ret_code)
+    else:
+        loader = unittest.TestLoader()
+        runner = unittest.TextTestRunner(
+            verbosity=2, resultclass=TestResult, failfast=fast_fail
+        )
+        suite = unittest.TestSuite()
+        subsets = []
+        for name in sys.argv[subset_start:]:
+            subsets.append('cantera.test.test_' + name)
+
+        if not subsets:
+            subsets.append('cantera.test')
+
+        suite = loader.loadTestsFromNames(subsets)
+
+        results = runner.run(suite)
+        sys.exit(len(results.errors) + len(results.failures))