fix: guard against empty peak array in get_ignition_delay

.travis.yml

@@ -11,16 +11,16 @@ language: generic
 matrix:
   include:
     - os: linux
-      env: PYTHON="3.5"
+      env: PYTHON="3.7"
 
     - os: linux
-      env: PYTHON="3.6"
+      env: PYTHON="3.9"
 
     - os: osx
-      env: PYTHON="3.5"
+      env: PYTHON="3.7"
 
     - os: osx
-      env: PYTHON="3.6"
+      env: PYTHON="3.9"
 
 # Install packages
 install:
@@ -43,7 +43,7 @@ install:
       conda env create -qf test-environment.yaml;
       conda activate py${PYTHON};
     else
-      if [[ "$PYTHON" == "3.6" && "$TRAVIS_OS_NAME" == "linux" ]]; then
+      if [[ "$PYTHON" == "3.9" && "$TRAVIS_OS_NAME" == "linux" ]]; then
         conda env update -qn base -f build-environment.yaml;
       fi
     fi
@@ -56,7 +56,7 @@ script:
   - set -e
   - if [[ -z "$TRAVIS_TAG" ]]; then
       pytest -vv --cov=./;
-      if [[ "$PYTHON" == "3.6" && "$TRAVIS_OS_NAME" == "linux" ]]; then
+      if [[ "$PYTHON" == "3.9" && "$TRAVIS_OS_NAME" == "linux" ]]; then
         git checkout -- test-environment.yaml;
         conda install -q sphinx doctr nbsphinx ipython;
         python setup.py install;
@@ -66,7 +66,7 @@ script:
         doctr deploy devel;
       fi
     else
-      if [[ "$PYTHON" == "3.6" && "$TRAVIS_OS_NAME" == "linux" ]]; then
+      if [[ "$PYTHON" == "3.9" && "$TRAVIS_OS_NAME" == "linux" ]]; then
         conda build conda.recipe;
         anaconda -t $ANACONDA_TOKEN upload $HOME/miniconda/conda-bld/*/pyteck*.tar.bz2;
         python setup.py install;
@@ -91,6 +91,6 @@ deploy:
     secure: "vaCCwVyZ8m+PDWub0kpPWYwwAUrtgnFQxU9qKc6VwIp3cCtYyEAZjTbAUzBfc/DsqmpCoLI62hYrQWqq0PwFfs4/1Ho+ppJuuiPvcIs0Syh8iv37YKnQG5Yjc9OjEGOY3ZScIUz57X67dst8HBiNHZnovwh5yxoGCTYrP0HdPlQbMkU6byzpXJ/+gzZaRiXXCPElEMf7HRuOZCkoDUIxypcBAvRHjyqI5TLecfkZBllkA3MFfEMT2mDurU4fmSsS7ndcKONaW9OKWSpSEItGle1Yq68qLN3xJIDSVfWg+vAUANuNAZJwo3CyfwPdxfWq4zth9+fY56ZJg3rz2QhC4kVJIOyNfyHyLdKXCQpCg2A0zcTMItnHafKm8eN2IPKNkO+HN1mpE6+G0UTnGfQtsA3FWQvedvA/WH5f226JJ1RNlJAsMDpf08WK7tTtc4rQ0Rm9TtKiblcZ+AxQMyZCdO3UxKCzqpusZmueIbr4koPFczaQYDsldWihboWp6ToAymI1XwcsSQTQTTcqGqt5ADuI9Ae0egWqpsAe72aiTYUR/FrIXD2ylSQl0E3UobjkYl+5kT4pJtF3TknJqN4VZDAbRP1IxPGcpNXLuZXekLpNaaDxJFepAnytWtIGd/W2vt+Afv5vt5VvGLFS56uuxOkLlIFebw0NfXnT1citLLM="
   on:
     tags: true
-    condition: $TRAVIS_OS_NAME == "linux" && $PYTHON == "3.6"
+    condition: $TRAVIS_OS_NAME == "linux" && $PYTHON == "3.9"
   distributions: "sdist bdist_wheel"
   skip_upload_docs: true

appveyor.yml

@@ -1,6 +1,6 @@
 version: 1.0.{build}
 environment:
-  PYTHON_LOC: "C:\\Miniconda36-x64"
+  PYTHON_LOC: "C:\\Miniconda3-x64"
 
 skip_tags: true
 
@@ -10,20 +10,20 @@ install:
   - cmd: conda config --append channels conda-forge
   - cmd: conda update conda
   - cmd: conda update -q --all
-  - ps: (get-content test-environment.yaml) | %{$_ -replace "\$\{PYTHON\}","3.5"} | set-content test-environment.yaml
+  - ps: (get-content test-environment.yaml) | %{$_ -replace "\$\{PYTHON\}","3.7"} | set-content test-environment.yaml
   - cmd: conda env create -qf test-environment.yaml
   - cmd: git checkout -- test-environment.yaml
-  - ps: (get-content test-environment.yaml) | %{$_ -replace "\$\{PYTHON\}","3.6"} | set-content test-environment.yaml
+  - ps: (get-content test-environment.yaml) | %{$_ -replace "\$\{PYTHON\}","3.9"} | set-content test-environment.yaml
   - cmd: conda env create -qf test-environment.yaml
   - cmd: conda info -a
-  - ps: Write-Host "Packages in py3.5 Environment:"
-  - cmd: conda list -n py3.5
-  - ps: Write-Host "Packages in py3.6 Environment:"
-  - cmd: conda list -n py3.6
+  - ps: Write-Host "Packages in py3.7 Environment:"
+  - cmd: conda list -n py3.7
+  - ps: Write-Host "Packages in py3.9 Environment:"
+  - cmd: conda list -n py3.9
 
 build_script:
-  - cmd: call %PYTHON_LOC%\Scripts\activate.bat py3.5
+  - cmd: call %PYTHON_LOC%\Scripts\activate.bat py3.7
   - cmd: pytest -vv --cov=./ --cov-append
-  - cmd: call %PYTHON_LOC%\Scripts\activate.bat py3.6
+  - cmd: call %PYTHON_LOC%\Scripts\activate.bat py3.9
   - cmd: pytest -vv --cov=./ --cov-append
   - cmd: codecov -X gcov

conda.recipe/meta.yaml

@@ -14,12 +14,12 @@ build:
 
 requirements:
   build:
-    - python >=3.5
+    - python >=3.7,<3.10
     - setuptools
     - pip
 
   run:
-    - python
+    - python >=3.7,<3.10
     - pyyaml >=3.12,<4.0
     - numpy >=1.13.1
     - scipy >=1.0.0

docs/conf.py

@@ -51,7 +51,7 @@
 napoleon_numpy_docstring = True
 napoleon_google_docstring = False
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/3.6', None),
+    'python': ('https://docs.python.org/3', None),
     'numpy': ('http://docs.scipy.org/doc/numpy/', None),
 }
 

pyteck/simulation.py

@@ -96,51 +96,67 @@ def create_volume_history(mech, temp, pres, reactants, pres_rise, time_end):
 def get_ignition_delay(time, target, target_name, ignition_type):
     """Identify ignition delay based on time, target, and type of detection.
     """
+    no_ignition_delay = np.array([0.0])
+
     if ignition_type == 'max':
         # Get indices of peaks
         peak_inds = detect_peaks(target, edge=None, mph=1.e-9*np.max(target))
 
-        # Get index of largest peak (overall ignition delay)
-        max_ind = peak_inds[np.argmax(target[peak_inds])]
-
-        #ign_delays = time[peak_inds[np.where((time[peak_inds[peak_inds <= max_ind]]) > 0.0)]]
-
-        ign_delays = time[peak_inds[peak_inds <= max_ind]]
+        if peak_inds.size == 0:
+            return no_ignition_delay
+        else:
+            # Get index of largest peak (overall ignition delay)
+            max_ind = peak_inds[np.argmax(target[peak_inds])]
+            ign_delays = time[peak_inds[peak_inds <= max_ind]]
 
     elif ignition_type == 'd/dt max':
         target = first_derivative(time, target)
         # Get indices of peaks. Set a minimum peak height of 1e-7% of the
         # maximum value to avoid noise peaks.
         peak_inds = detect_peaks(target, edge=None, mph=1.e-9*np.max(target))
 
-        # Get index of largest peak (overall ignition delay)
-        max_ind = peak_inds[np.argmax(target[peak_inds])]
-
-        ign_delays = time[peak_inds[np.where((time[peak_inds[peak_inds <= max_ind]]) > 0.0)]]
+        if peak_inds.size == 0:
+            return no_ignition_delay
+        else:
+            # Get index of largest peak (overall ignition delay)
+            max_ind = peak_inds[np.argmax(target[peak_inds])]
+            ign_delays = time[peak_inds[np.where((time[peak_inds[peak_inds <= max_ind]]) > 0.0)]]
 
     elif ignition_type == '1/2 max':
         # maximum value, and associated index
         max_val = np.max(target)
         peak_inds = detect_peaks(target, edge=None, mph=1.e-9*np.max(target))
-        max_ind = peak_inds[np.argmax(target[peak_inds])]
 
-        # TODO: interpolate for actual half-max value
-        # Find index associated with the 1/2 max value, but only consider
-        # points before the peak
-        half_idx = (np.abs(target[0:max_ind] - 0.5 * max_val)).argmin()
-        ign_delays = np.array([time[half_idx]])
+        if peak_inds.size == 0:
+            return no_ignition_delay
+        else:
+            max_ind = peak_inds[np.argmax(target[peak_inds])]
+            # TODO: interpolate for actual half-max value
+            # Find index associated with the 1/2 max value, but only consider
+            # points before the peak
+            half_idx = (np.abs(target[0:max_ind] - 0.5 * max_val)).argmin()
+            ign_delays = np.array([time[half_idx]])
 
     elif ignition_type == 'd/dt max extrapolated':
         # First need to evaluate derivative of the target
         target_derivative = first_derivative(time, target)
+        max_derivative = np.max(target_derivative)
+
+        if not np.isfinite(max_derivative) or max_derivative <= 0.0:
+            return no_ignition_delay
 
         # Get indices of peaks, and index of largest peak, which corresponds to
-        # the point of maximum deriative
-        peak_inds = detect_peaks(target_derivative, edge=None, mph=1.e-9*np.max(target))
-        max_ind = peak_inds[np.argmax(target_derivative[peak_inds])]
+        # the point of maximum derivative
+        peak_inds = detect_peaks(target_derivative, edge=None, mph=1.e-9*max_derivative)
 
-        # use slope to extrapolate to intercept with baseline value (0 by default)
-        ign_delays = np.array([time[max_ind] - (target[max_ind] / target_derivative[max_ind])])
+        if peak_inds.size == 0:
+            return no_ignition_delay
+        else:
+            max_ind = peak_inds[np.argmax(target_derivative[peak_inds])]
+            if target_derivative[max_ind] <= 0.0:
+                return no_ignition_delay
+            # use slope to extrapolate to intercept with baseline value (0 by default)
+            ign_delays = np.array([time[max_ind] - (target[max_ind] / target_derivative[max_ind])])
 
         # TODO: handle target with nonzero baseline?
     else:

pyteck/tests/test_simulation.py

@@ -301,6 +301,53 @@ def test_derivative_max_extrapolated(self):
                            rtol=1e-4
                            )
 
+    def test_derivative_max_extrapolated_nonpositive_derivative_returns_zero(self, monkeypatch):
+        """Do not extrapolate when the derivative maximum is not positive.
+        """
+        times = np.linspace(0, 1, 3)
+        target = np.ones_like(times)
+        derivative = np.array([-1.0, 0.0, -1.0])
+
+        monkeypatch.setattr(
+            simulation, 'first_derivative',
+            lambda time, target: derivative
+            )
+
+        ignition_delays = simulation.get_ignition_delay(
+            times, target, 'species', 'd/dt max extrapolated'
+            )
+
+        assert ignition_delays[0] == 0.0
+
+    @pytest.mark.parametrize('ignition_type', [
+        'max',
+        'd/dt max',
+        '1/2 max',
+        'd/dt max extrapolated',
+    ])
+    def test_flat_signal_returns_zero_without_dumping_target_data(self, ignition_type):
+        """Flat signals are expected non-ignitions, not debug-dump cases.
+        """
+        times = np.linspace(0, 1, 100)
+        target = np.zeros_like(times)
+
+        cwd = os.getcwd()
+        with TemporaryDirectory() as temp_dir:
+            os.chdir(temp_dir)
+            try:
+                ignition_delays = simulation.get_ignition_delay(
+                    times, target, 'species', ignition_type
+                    )
+                dumped_files = [
+                    filename for filename in os.listdir(temp_dir)
+                    if filename.startswith('target-data-') and filename.endswith('.out')
+                    ]
+            finally:
+                os.chdir(cwd)
+
+        assert ignition_delays[0] == 0.0
+        assert dumped_files == []
+
     def test_not_supported_type(self):
         """Test that a non-supported type raises a warning and returns zero.
         """

setup.py

@@ -26,9 +26,9 @@
 long_description = readme + '\n\n' + changelog + '\n\n' + citation
 
 install_requires = [
-    'pyyaml>=3.12,<4.0',
-    'pint>=0.7.2,<0.9',
-    'numpy>=1.13.0,<2.0',
+    'pyyaml>=3.12',
+    'pint>=0.7.2',
+    'numpy>=1.13.0',
     'tables',
     'pyked>=0.4.1',
     'scipy>=1.0.0',
@@ -60,6 +60,7 @@
     package_data={'pyteck': ['tests/*.xml', 'tests/*.yaml', 'tests/dataset_file.txt', 'tests/*.cti']},
     install_requires=install_requires,
     zip_safe=False,
+    python_requires='>=3.7,<3.10',
 
     license='MIT License',
 
@@ -76,8 +77,9 @@
         'License :: OSI Approved :: MIT License',
         'Natural Language :: English',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.5',
-        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
         'Topic :: Scientific/Engineering :: Chemistry',
     ],
     keywords='chemical_kinetics',