Fix ruamel and pandas api by erwanp · Pull Request #1 · parks4/ctwrap

erwanp · 2025-08-11T08:25:21Z

Updating Ctwrap to latest standards, mirroring the PR microcombustion/ctwrap#93 that was cancelled because microcombution's ctwrap is now archived.

API updates

Fixing deprecation of yaml.load after 0.17.0
https://yaml.readthedocs.io/api/#transparent-usage-of-new-and-old-api

Fixes microcombustion/ctwrap#92

Also fixing deprecation of Deprecate Series / DataFrame.append pandas-dev/pandas#35407 beyond pandas>=1.4

# df = df.append(row, ignore_index=True)          # old syntax
 df = pd.concat([df, row.to_frame().T], ignore_index=True)

Also :

fixed pkg_resources
fixed pint

Result

List of Tests :

pytest .

================================================= test session starts =================================================
platform win32 -- Python 3.11.11, pytest-8.3.4, pluggy-1.5.0 -- C:\Users\erwan\anaconda3\envs\bloc\python.exe
cachedir: .pytest_cache
rootdir: C:\GitHub\ctwrap
configfile: pytest.ini
plugins: dash-2.18.2, cov-6.0.0
collected 147 items

tests/test_notebooks.py::TestNotebooks::test_commandline_example FAILED                                          [  0%]
tests/test_notebooks.py::TestNotebooks::test_equilibrium_example FAILED                                          [  1%]
tests/test_notebooks.py::TestNotebooks::test_freeflame_example FAILED                                            [  2%]
tests/test_notebooks.py::TestNotebooks::test_ignition_example FAILED                                             [  2%]
tests/test_notebooks.py::TestNotebooks::test_minimal_example FAILED                                              [  3%]
tests/test_output.py::TestOutput::test_dir PASSED                                                                [  4%]
tests/test_output.py::TestOutput::test_output PASSED                                                             [  4%]
tests/test_output.py::TestCSV::test_csv PASSED                                                                   [  5%]
tests/test_output.py::TestCSV::test_dir PASSED                                                                   [  6%]
tests/test_output.py::TestCSV::test_output PASSED                                                                [  6%]
tests/test_output.py::TestSolution::test_add PASSED                                                              [  7%]
tests/test_output.py::TestSolution::test_csv PASSED                                                              [  8%]
tests/test_output.py::TestSolution::test_dir PASSED                                                              [  8%]
tests/test_output.py::TestSolution::test_output PASSED                                                           [  9%]
tests/test_output.py::TestMixture::test_add PASSED                                                               [ 10%]
tests/test_output.py::TestMixture::test_csv PASSED                                                               [ 10%]
tests/test_output.py::TestMixture::test_dir PASSED                                                               [ 11%]
tests/test_output.py::TestMixture::test_output PASSED                                                            [ 12%]
tests/test_output.py::TestHDF::test_dir PASSED                                                                   [ 12%]
tests/test_output.py::TestHDF::test_hdf PASSED                                                                   [ 13%]
tests/test_output.py::TestHDF::test_output PASSED                                                                [ 14%]
tests/test_output.py::TestSolutionArray::test_dir FAILED                                                         [ 14%]
tests/test_output.py::TestSolutionArray::test_hdf FAILED                                                         [ 15%]
tests/test_output.py::TestSolutionArray::test_load_like FAILED                                                   [ 16%]
tests/test_output.py::TestSolutionArray::test_output FAILED                                                      [ 17%]
tests/test_output.py::TestFreeFlame::test_dir FAILED                                                             [ 17%]
tests/test_output.py::TestFreeFlame::test_load_like FAILED                                                       [ 18%]
tests/test_output.py::TestFreeFlame::test_output FAILED                                                          [ 19%]
tests/test_parser.py::TestUpdate::test_level1 PASSED                                                             [ 19%]
tests/test_parser.py::TestUpdate::test_level2 PASSED                                                             [ 20%]
tests/test_parser.py::TestUpdate::test_multi_level PASSED                                                        [ 21%]
tests/test_parser.py::TestParse::test_full PASSED                                                                [ 21%]
tests/test_parser.py::TestParse::test_no_unit1 PASSED                                                            [ 22%]
tests/test_parser.py::TestParse::test_no_unit2 PASSED                                                            [ 23%]
tests/test_parser.py::TestParse::test_string PASSED                                                              [ 23%]
tests/test_parser.py::TestWrite::test_full PASSED                                                                [ 24%]
tests/test_parser.py::TestWrite::test_no_unit1 PASSED                                                            [ 25%]
tests/test_parser.py::TestWrite::test_no_unit2 PASSED                                                            [ 25%]
tests/test_parser.py::TestWrite::test_string PASSED                                                              [ 26%]
tests/test_parser.py::TestPassing::test_parser PASSED                                                            [ 27%]
tests/test_parser.py::TestKeyStr::test_parser PASSED                                                             [ 27%]
tests/test_parser.py::TestNone::test_parser PASSED                                                               [ 28%]
tests/test_parser.py::TestParser::test_parser PASSED                                                             [ 29%]
tests/test_parser.py::TestMulti::test_parser PASSED                                                              [ 29%]
tests/test_parser.py::TestMulti::test_update_dict PASSED                                                         [ 30%]
tests/test_parser.py::TestMulti::test_update_parser PASSED                                                       [ 31%]
tests/test_parser.py::TestFailing::test_parser PASSED                                                            [ 31%]
tests/test_parser.py::TestInt::test_parser PASSED                                                                [ 32%]
tests/test_parser.py::TestFloat::test_parser PASSED                                                              [ 33%]
tests/test_parser.py::TestString::test_parser PASSED                                                             [ 34%]
tests/test_parser.py::TestYAML::test_freeflame PASSED                                                            [ 34%]
tests/test_parser.py::TestYAML::test_ignition FAILED                                                             [ 35%]
tests/test_parser.py::TestYAML::test_minimal FAILED                                                              [ 36%]
tests/test_strategy.py::TestReplace::test_entry PASSED                                                           [ 36%]
tests/test_strategy.py::TestReplace::test_missing1 PASSED                                                        [ 37%]
tests/test_strategy.py::TestReplace::test_missing2 PASSED                                                        [ 38%]
tests/test_strategy.py::TestReplace::test_nested PASSED                                                          [ 38%]
tests/test_strategy.py::TestParse::test_arange PASSED                                                            [ 39%]
tests/test_strategy.py::TestParse::test_linspace PASSED                                                          [ 40%]
tests/test_strategy.py::TestSweep::test_one PASSED                                                               [ 40%]
tests/test_strategy.py::TestSweep::test_three PASSED                                                             [ 41%]
tests/test_strategy.py::TestSweep::test_two PASSED                                                               [ 42%]
tests/test_strategy.py::TestStrategy::test_legacy PASSED                                                         [ 42%]
tests/test_strategy.py::TestStrategy::test_load PASSED                                                           [ 43%]
tests/test_strategy.py::TestStrategy::test_matrix PASSED                                                         [ 44%]
tests/test_strategy.py::TestStrategy::test_minimal PASSED                                                        [ 44%]
tests/test_strategy.py::TestStrategy::test_raises PASSED                                                         [ 45%]
tests/test_strategy.py::TestStrategy::test_sequence PASSED                                                       [ 46%]
tests/test_wrapper.py::TestLegacy::test_database PASSED                                                          [ 46%]
tests/test_wrapper.py::TestLegacy::test_handler PASSED                                                           [ 47%]
tests/test_wrapper.py::TestWrap::test_commandline PASSED                                                         [ 48%]
tests/test_wrapper.py::TestWrap::test_handler PASSED                                                             [ 48%]
tests/test_wrapper.py::TestWrap::test_main PASSED                                                                [ 49%]
tests/test_wrapper.py::TestWrap::test_parallel PASSED                                                            [ 50%]
tests/test_wrapper.py::TestWrap::test_restart PASSED                                                             [ 51%]
tests/test_wrapper.py::TestWrap::test_serial PASSED                                                              [ 51%]
tests/test_wrapper.py::TestWrap::test_simulation PASSED                                                          [ 52%]
tests/test_wrapper.py::TestMatrix::test_commandline PASSED                                                       [ 53%]
tests/test_wrapper.py::TestMatrix::test_handler PASSED                                                           [ 53%]
tests/test_wrapper.py::TestMatrix::test_main PASSED                                                              [ 54%]
tests/test_wrapper.py::TestMatrix::test_parallel PASSED                                                          [ 55%]
tests/test_wrapper.py::TestMatrix::test_restart PASSED                                                           [ 55%]
tests/test_wrapper.py::TestMatrix::test_serial PASSED                                                            [ 56%]
tests/test_wrapper.py::TestMatrix::test_simulation PASSED                                                        [ 57%]
tests/test_wrapper.py::TestLocal::test_commandline PASSED                                                        [ 57%]
tests/test_wrapper.py::TestLocal::test_handler PASSED                                                            [ 58%]
tests/test_wrapper.py::TestLocal::test_main PASSED                                                               [ 59%]
tests/test_wrapper.py::TestLocal::test_parallel PASSED                                                           [ 59%]
tests/test_wrapper.py::TestLocal::test_restart PASSED                                                            [ 60%]
tests/test_wrapper.py::TestLocal::test_serial PASSED                                                             [ 61%]
tests/test_wrapper.py::TestLocal::test_simulation PASSED                                                         [ 61%]
tests/test_wrapper.py::TestCustom::test_commandline PASSED                                                       [ 62%]
tests/test_wrapper.py::TestCustom::test_handler PASSED                                                           [ 63%]
tests/test_wrapper.py::TestCustom::test_main PASSED                                                              [ 63%]
tests/test_wrapper.py::TestCustom::test_parallel PASSED                                                          [ 64%]
tests/test_wrapper.py::TestCustom::test_restart PASSED                                                           [ 65%]
tests/test_wrapper.py::TestCustom::test_serial PASSED                                                            [ 65%]
tests/test_wrapper.py::TestCustom::test_simulation PASSED                                                        [ 66%]
tests/test_wrapper.py::TestIgnition::test_commandline PASSED                                                     [ 67%]
tests/test_wrapper.py::TestIgnition::test_handler PASSED                                                         [ 68%]
tests/test_wrapper.py::TestIgnition::test_main PASSED                                                            [ 68%]
tests/test_wrapper.py::TestIgnition::test_parallel FAILED                                                        [ 69%]
tests/test_wrapper.py::TestIgnition::test_restart PASSED                                                         [ 70%]
tests/test_wrapper.py::TestIgnition::test_serial PASSED                                                          [ 70%]
tests/test_wrapper.py::TestIgnition::test_simulation PASSED                                                      [ 71%]
tests/test_wrapper.py::TestSolution::test_commandline PASSED                                                                                [ 72%]
tests/test_wrapper.py::TestSolution::test_handler PASSED                                                                                    [ 72%]
tests/test_wrapper.py::TestSolution::test_main PASSED                                                                                       [ 73%]
tests/test_wrapper.py::TestSolution::test_parallel PASSED                                                                                   [ 74%]
tests/test_wrapper.py::TestSolution::test_restart PASSED                                                                                    [ 74%]
tests/test_wrapper.py::TestSolution::test_serial PASSED                                                                                     [ 75%]
tests/test_wrapper.py::TestSolution::test_simulation PASSED                                                                                 [ 76%]
tests/test_wrapper.py::TestEquilibrium::test_commandline PASSED                                                                             [ 76%]
tests/test_wrapper.py::TestEquilibrium::test_handler PASSED                                                                                 [ 77%]
tests/test_wrapper.py::TestEquilibrium::test_main PASSED                                                                                    [ 78%]
tests/test_wrapper.py::TestEquilibrium::test_parallel PASSED                                                                                [ 78%]
tests/test_wrapper.py::TestEquilibrium::test_restart PASSED                                                                                 [ 79%]
tests/test_wrapper.py::TestEquilibrium::test_serial PASSED                                                                                  [ 80%]
tests/test_wrapper.py::TestEquilibrium::test_simulation PASSED                                                                              [ 80%]
tests/test_wrapper.py::TestEquilibriumMulti::test_commandline PASSED                                                                        [ 81%]
tests/test_wrapper.py::TestEquilibriumMulti::test_handler PASSED                                                                            [ 82%]
tests/test_wrapper.py::TestEquilibriumMulti::test_main PASSED                                                                               [ 82%]
tests/test_wrapper.py::TestEquilibriumMulti::test_parallel PASSED                                                                           [ 83%]
tests/test_wrapper.py::TestEquilibriumMulti::test_restart PASSED                                                                            [ 84%]
tests/test_wrapper.py::TestEquilibriumMulti::test_serial PASSED                                                                             [ 85%]
tests/test_wrapper.py::TestEquilibriumMulti::test_simulation PASSED                                                                         [ 85%]
tests/test_wrapper.py::TestFreeFlame::test_commandline FAILED                                                                               [ 86%]
tests/test_wrapper.py::TestFreeFlame::test_handler PASSED                                                                                   [ 87%]
tests/test_wrapper.py::TestFreeFlame::test_main FAILED                                                                                      [ 87%]
tests/test_wrapper.py::TestFreeFlame::test_parallel FAILED                                                                                  [ 88%]
tests/test_wrapper.py::TestFreeFlame::test_restart PASSED                                                                                   [ 89%]
tests/test_wrapper.py::TestFreeFlame::test_serial FAILED                                                                                    [ 89%]
tests/test_wrapper.py::TestFreeFlame::test_simulation PASSED                                                                                [ 90%]
tests/test_wrapper.py::TestFreeFlameMatrix::test_commandline PASSED                                                                         [ 91%]
tests/test_wrapper.py::TestFreeFlameMatrix::test_handler PASSED                                                                             [ 91%]
tests/test_wrapper.py::TestFreeFlameMatrix::test_main FAILED                                                                                [ 92%]
tests/test_wrapper.py::TestFreeFlameMatrix::test_parallel FAILED                                                                            [ 93%]
tests/test_wrapper.py::TestFreeFlameMatrix::test_restart PASSED                                                                             [ 93%]
tests/test_wrapper.py::TestFreeFlameMatrix::test_serial PASSED                                                                              [ 94%]
tests/test_wrapper.py::TestFreeFlameMatrix::test_simulation PASSED                                                                          [ 95%]
tests/test_wrapper.py::TestInvalid::test_commandline PASSED                                                                                 [ 95%]
tests/test_wrapper.py::TestInvalid::test_handler PASSED                                                                                     [ 96%]
tests/test_wrapper.py::TestInvalid::test_main PASSED                                                                                        [ 97%]
tests/test_wrapper.py::TestInvalid::test_parallel PASSED                                                                                    [ 97%]
tests/test_wrapper.py::TestInvalid::test_restart PASSED                                                                                     [ 98%]
tests/test_wrapper.py::TestInvalid::test_serial PASSED                                                                                      [ 99%]
tests/test_wrapper.py::TestInvalid::test_simulation PASSED                                                                                  [100%]

Summary of failures :

============================================================ short test summary info =============================================================
FAILED tests/test_notebooks.py::TestNotebooks::test_commandline_example - AssertionError: 1 is not false
FAILED tests/test_notebooks.py::TestNotebooks::test_equilibrium_example - AssertionError: 1 is not false
FAILED tests/test_notebooks.py::TestNotebooks::test_freeflame_example - AssertionError: 1 is not false
FAILED tests/test_notebooks.py::TestNotebooks::test_ignition_example - AssertionError: 1 is not false
FAILED tests/test_notebooks.py::TestNotebooks::test_minimal_example - AssertionError: 1 is not false
FAILED tests/test_output.py::TestSolutionArray::test_dir - AttributeError: 'SolutionArray' object has no attribute 'write_hdf'
FAILED tests/test_output.py::TestSolutionArray::test_hdf - AttributeError: 'SolutionArray' object has no attribute 'write_hdf'
FAILED tests/test_output.py::TestSolutionArray::test_load_like - AttributeError: 'SolutionArray' object has no attribute 'write_hdf'
FAILED tests/test_output.py::TestSolutionArray::test_output - AttributeError: 'SolutionArray' object has no attribute 'write_hdf'
FAILED tests/test_output.py::TestFreeFlame::test_dir - AttributeError: 'FreeFlame' object has no attribute 'write_hdf'
FAILED tests/test_output.py::TestFreeFlame::test_load_like - AttributeError: 'FreeFlame' object has no attribute 'write_hdf'
FAILED tests/test_output.py::TestFreeFlame::test_output - AttributeError: 'FreeFlame' object has no attribute 'write_hdf'
FAILED tests/test_parser.py::TestYAML::test_ignition - AttributeError: 'YAML' object has no attribute 'SafeLoader'
FAILED tests/test_parser.py::TestYAML::test_minimal - AttributeError: 'YAML' object has no attribute 'SafeLoader'
FAILED tests/test_wrapper.py::TestIgnition::test_parallel - AssertionError: False is not true
FAILED tests/test_wrapper.py::TestFreeFlame::test_commandline - AssertionError: 'C:\\Users\\erwan\\anaconda3\\envs\\bloc\\[11234 chars]\r\n' != ''
- C:\Users\erwan\anaconda3\envs\bloc\Lib\site-packages\cantera\onedim.py:194: DeprecationWarning: FactoryBase::canonicalize: Model name 'Mix' is deprecated. Use 'mixture-averaged' instead.
-   self.flame.transport_model = model
- C:\Users\erwan\anaconda3\envs\bloc\Lib\site-packages\cantera\onedim.py:194: DeprecationWarning: FactoryBase::canonicalize: Model name 'Mix' is deprecated. Use 'mixture-averaged' instead.
-   self.flame.transport_model = model
- C:\Users\erwan\anaconda3\envs\bloc\Lib\site-packages\cantera\onedim.py:194: DeprecationWarning: FactoryBase::canonicalize: Model name 'Mix' is deprecated. Use 'mixture-averaged' instead.
-   self.flame.transport_model = model
- C:\Users\erwan\anaconda3\envs\bloc\Lib\site-packages\cantera\onedim.py:194: DeprecationWarning: FactoryBase::canonicalize: Model name 'Mix' is deprecated. Use 'mixture-averaged' instead.
-   self.flame.transport_model = model
- C:\Users\erwan\anaconda3\envs\bloc\Lib\site-packages\cantera\onedim.py:194: DeprecationWarning: FactoryBase::canonicalize: Model name 'Mix' is deprecated. Use 'mixture-averaged' instead.
-   self.flame.transport_model = model
- C:\Users\erwan\anaconda3\envs\bloc\Lib\site-packages\cantera\onedim.py:194: DeprecationWarning: FactoryBase::canonicalize: Model name 'Mix' is deprecated. Use 'mixture-averaged' instead.
-   self.flame.transport_model = model
- C:\Users\erwan\anaconda3\envs\bloc\Lib\site-packages\cantera\onedim.py:194: DeprecationWarning: FactoryBase::canonicalize: Model name 'Mix' is deprecated. Use 'mixture-averaged' instead.
-   self.flame.transport_model = model
- C:\Users\erwan\anaconda3\envs\bloc\Lib\site-packages\cantera\onedim.py:194: DeprecationWarning: FactoryBase::canonicalize: Model name 'Mix' is deprecated. Use 'mixture-averaged' instead.
-   self.flame.transport_model = model
- C:\Users\erwan\anaconda3\envs\bloc\Lib\site-packages\cantera\onedim.py:194: DeprecationWarning: FactoryBase::canonicalize: Model name 'Mix' is deprecated. Use 'mixture-averaged' instead.
-   self.flame.transport_model = model
- C:\Users\erwan\anaconda3\envs\bloc\Lib\site-packages\cantera\onedim.py:194: DeprecationWarning: FactoryBase::canonicalize: Model name 'Mix' is deprecated. Use 'mixture-averaged' instead.
-   self.flame.transport_model = model
- Process Process-2:
- Traceback (most recent call last):
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 314, in _bootstrap
-     self.run()
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 108, in run
-     self._target(*self._args, **self._kwargs)
-   File "c:\github\ctwrap\ctwrap\handler.py", line 528, in _worker
-     out.save(data, entry=task, variation=variations[task], errored=errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 274, in save
-     _save_hdf(data, self.settings, entry, variation, errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 402, in _save_hdf
-     data.write_hdf(filename=filename, group=entry,
-     ^^^^^^^^^^^^^^
- AttributeError: 'FreeFlame' object has no attribute 'write_hdf'
- Process Process-10:
- Traceback (most recent call last):
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 314, in _bootstrap
-     self.run()
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 108, in run
-     self._target(*self._args, **self._kwargs)
-   File "c:\github\ctwrap\ctwrap\handler.py", line 528, in _worker
-     out.save(data, entry=task, variation=variations[task], errored=errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 274, in save
-     _save_hdf(data, self.settings, entry, variation, errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 402, in _save_hdf
-     data.write_hdf(filename=filename, group=entry,
-     ^^^^^^^^^^^^^^
- AttributeError: 'FreeFlame' object has no attribute 'write_hdf'
- Process Process-5:
- Traceback (most recent call last):
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 314, in _bootstrap
-     self.run()
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 108, in run
-     self._target(*self._args, **self._kwargs)
-   File "c:\github\ctwrap\ctwrap\handler.py", line 528, in _worker
-     out.save(data, entry=task, variation=variations[task], errored=errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 274, in save
-     _save_hdf(data, self.settings, entry, variation, errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 402, in _save_hdf
-     data.write_hdf(filename=filename, group=entry,
-     ^^^^^^^^^^^^^^
- AttributeError: 'FreeFlame' object has no attribute 'write_hdf'
- Process Process-1:
- Traceback (most recent call last):
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 314, in _bootstrap
-     self.run()
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 108, in run
-     self._target(*self._args, **self._kwargs)
-   File "c:\github\ctwrap\ctwrap\handler.py", line 528, in _worker
-     out.save(data, entry=task, variation=variations[task], errored=errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 274, in save
-     _save_hdf(data, self.settings, entry, variation, errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 402, in _save_hdf
-     data.write_hdf(filename=filename, group=entry,
-     ^^^^^^^^^^^^^^
- AttributeError: 'FreeFlame' object has no attribute 'write_hdf'
- Process Process-9:
- Traceback (most recent call last):
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 314, in _bootstrap
-     self.run()
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 108, in run
-     self._target(*self._args, **self._kwargs)
-   File "c:\github\ctwrap\ctwrap\handler.py", line 528, in _worker
-     out.save(data, entry=task, variation=variations[task], errored=errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 274, in save
-     _save_hdf(data, self.settings, entry, variation, errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 402, in _save_hdf
-     data.write_hdf(filename=filename, group=entry,
-     ^^^^^^^^^^^^^^
- AttributeError: 'FreeFlame' object has no attribute 'write_hdf'
- Process Process-8:
- Traceback (most recent call last):
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 314, in _bootstrap
-     self.run()
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 108, in run
-     self._target(*self._args, **self._kwargs)
-   File "c:\github\ctwrap\ctwrap\handler.py", line 528, in _worker
-     out.save(data, entry=task, variation=variations[task], errored=errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 274, in save
-     _save_hdf(data, self.settings, entry, variation, errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 402, in _save_hdf
-     data.write_hdf(filename=filename, group=entry,
-     ^^^^^^^^^^^^^^
- AttributeError: 'FreeFlame' object has no attribute 'write_hdf'
- Process Process-6:
- Traceback (most recent call last):
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 314, in _bootstrap
-     self.run()
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 108, in run
-     self._target(*self._args, **self._kwargs)
-   File "c:\github\ctwrap\ctwrap\handler.py", line 528, in _worker
-     out.save(data, entry=task, variation=variations[task], errored=errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 274, in save
-     _save_hdf(data, self.settings, entry, variation, errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 402, in _save_hdf
-     data.write_hdf(filename=filename, group=entry,
-     ^^^^^^^^^^^^^^
- AttributeError: 'FreeFlame' object has no attribute 'write_hdf'
- Process Process-3:
- Traceback (most recent call last):
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 314, in _bootstrap
-     self.run()
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 108, in run
-     self._target(*self._args, **self._kwargs)
-   File "c:\github\ctwrap\ctwrap\handler.py", line 528, in _worker
-     out.save(data, entry=task, variation=variations[task], errored=errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 274, in save
-     _save_hdf(data, self.settings, entry, variation, errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 402, in _save_hdf
-     data.write_hdf(filename=filename, group=entry,
-     ^^^^^^^^^^^^^^
- AttributeError: 'FreeFlame' object has no attribute 'write_hdf'
- Process Process-4:
- Traceback (most recent call last):
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 314, in _bootstrap
-     self.run()
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 108, in run
-     self._target(*self._args, **self._kwargs)
-   File "c:\github\ctwrap\ctwrap\handler.py", line 528, in _worker
-     out.save(data, entry=task, variation=variations[task], errored=errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 274, in save
-     _save_hdf(data, self.settings, entry, variation, errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 402, in _save_hdf
-     data.write_hdf(filename=filename, group=entry,
-     ^^^^^^^^^^^^^^
- AttributeError: 'FreeFlame' object has no attribute 'write_hdf'
- Process Process-7:
- Traceback (most recent call last):
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 314, in _bootstrap
-     self.run()
-   File "C:\Users\erwan\anaconda3\envs\bloc\Lib\multiprocessing\process.py", line 108, in run
-     self._target(*self._args, **self._kwargs)
-   File "c:\github\ctwrap\ctwrap\handler.py", line 528, in _worker
-     out.save(data, entry=task, variation=variations[task], errored=errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 274, in save
-     _save_hdf(data, self.settings, entry, variation, errored)
-   File "c:\github\ctwrap\ctwrap\output.py", line 402, in _save_hdf
-     data.write_hdf(filename=filename, group=entry,
-     ^^^^^^^^^^^^^^
- AttributeError: 'FreeFlame' object has no attribute 'write_hdf'
- c:\github\ctwrap\ctwrap\output.py:349: RuntimeWarning: Output of metadata failed with error message:
- [Errno 2] Unable to synchronously open file (unable to open file: name = 'C:\GitHub\ctwrap\ctwrap\yaml\freeflame.h5', errno = 2, error message = 'No such file or directory', flags = 1, o_flags = 2)
-   warnings.warn(msg, RuntimeWarning)
FAILED tests/test_wrapper.py::TestFreeFlame::test_main - AssertionError: "C:\\Users\\erwan\\anaconda3\\envs\\bloc\[195 chars]\r\n" != ''
- C:\Users\erwan\anaconda3\envs\bloc\Lib\site-packages\cantera\onedim.py:194: DeprecationWarning: FactoryBase::canonicalize: Model name 'Mix' is deprecated. Use 'mixture-averaged' instead.
-   self.flame.transport_model = model
FAILED tests/test_wrapper.py::TestFreeFlame::test_parallel - AssertionError: False is not true
FAILED tests/test_wrapper.py::TestFreeFlame::test_serial - AttributeError: 'FreeFlame' object has no attribute 'write_hdf'
FAILED tests/test_wrapper.py::TestFreeFlameMatrix::test_main - AssertionError: "C:\\Users\\erwan\\anaconda3\\envs\\bloc\[195 chars]\r\n" != ''
- C:\Users\erwan\anaconda3\envs\bloc\Lib\site-packages\cantera\onedim.py:194: DeprecationWarning: FactoryBase::canonicalize: Model name 'Mix' is deprecated. Use 'mixture-averaged' instead.
-   self.flame.transport_model = model
FAILED tests/test_wrapper.py::TestFreeFlameMatrix::test_parallel - AssertionError: False is not true
============================================= 21 failed, 126 passed, 4 warnings in 362.96s (0:06:02) =============================================

Final To-Do

write_hdf does not seem to be a public method of FreeFlame according to Cantera main code; to_hdf() was created for SolutionArray but not for FreeFlame ==> won't fix it in ctwarp for the moment
Model name 'Mix' is deprecated. Use 'mixture-averaged' instead. : I haven't looked into this
Investigate AssertionError: 1 is not false of failing TestNotebooks
Investigate failing TestIgnition::test_parallel

"(if X and pd.Series) was creating ambiguity errors in the evaluation of True/False of the Series"

erwanp · 2025-08-11T08:27:06Z

Merging as is; this is the version used in Bloc. A new PR will follow with updates to fix the rest of the API.

Final To-Do

write_hdf does not seem to be a public method of FreeFlame according to Cantera main code; to_hdf() was created for SolutionArray but not for FreeFlame ==> won't fix it in ctwarp for the moment
Model name 'Mix' is deprecated. Use 'mixture-averaged' instead. : I haven't looked into this
Investigate AssertionError: 1 is not false of failing TestNotebooks
Investigate failing TestIgnition::test_parallel

erwanp added 10 commits December 31, 2024 22:51

fix ruamel api

6180627

safe loader to mirror yaml.SafeLoader

5e1ce74

fixing handler

e4c372c

fixing dump

b0585b2

fixed deprecation of pandas.Dataframe.append

935753a

fix pkg_resources dependency, pint, and all tests

35359a9

fix pandas & output

3df62e7

typo

68fcc2d

fix SafeLoader failures

9b2457f

fix problems when reading pd.Series

210de75

"(if X and pd.Series) was creating ambiguity errors in the evaluation of True/False of the Series"

erwanp changed the title ~~Fix new ruamel api~~ Fix ruamel and pandas api Aug 11, 2025

erwanp merged commit 9ce6eb9 into main Aug 11, 2025
0 of 2 checks passed

erwanp mentioned this pull request Aug 11, 2025

Finish Fixing API with modern Cantera #2

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Fix ruamel and pandas api#1

Fix ruamel and pandas api#1
erwanp merged 10 commits intomainfrom
fix/new_ruamel_api

erwanp commented Aug 11, 2025

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erwanp commented Aug 11, 2025 •

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erwanp commented Aug 11, 2025

API updates

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Final To-Do

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erwanp commented Aug 11, 2025 •

edited

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