Yaml2ck script #1286

bryanwweber · 2022-05-18T00:29:15Z

Changes proposed in this pull request

Add a yaml2ck script to convert YAML input files/Solution instances to Chemkin file(s)
~~TODO: Add a method to Solution to import and call yaml2ck.convert~~
~~TODO: Fix up the docstring~~

If applicable, fill in the issue number this pull request is fixing

Supersedes #1185
I tried to push an update to that branch and it closed the PR 🤷‍♂️

This also relies on the work in #1266 for some of the sorting, so it should be merged after that PR.

If applicable, provide an example illustrating new features this pull request is introducing

from cantera import yaml2ck
yaml2ck.convert("input_file.yaml")

Checklist

The pull request includes a clear description of this code change
Commit messages have short titles and reference relevant issues
Build passes (scons build & scons test) and unit tests address code coverage
Style & formatting of contributed code follows contributing guidelines
The pull request is ready for review

ischoegl

@bryanwweber ... thanks for picking this up! This overall looks really good, and I don't have any significant comments (other than formatting suggestions for yaml2ck --help).

Running this on my (windows) machine, I am, however, running into the following issue:

(cantera-dev) PS C:\Users\ischo\GitHub\cantera> python --version
Python 3.10.2
(cantera-dev) PS C:\Users\ischo\GitHub\cantera> yaml2ck .\h2o2.yaml
Traceback (most recent call last):
  File "C:\Users\ischo\miniconda3\envs\cantera-dev\lib\runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "C:\Users\ischo\miniconda3\envs\cantera-dev\lib\runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "C:\Users\ischo\miniconda3\envs\cantera-dev\Scripts\yaml2ck.exe\__main__.py", line 7, in <module>
  File "C:\Users\ischo\miniconda3\envs\cantera-dev\lib\site-packages\cantera\yaml2ck.py", line 685, in main
    output_paths = convert(
  File "C:\Users\ischo\miniconda3\envs\cantera-dev\lib\site-packages\cantera\yaml2ck.py", line 511, in convert
    solution = ct.Solution(solution, phase_name)
  File "build\python\cantera\base.pyx", line 71, in cantera._cantera._SolutionBase.__cinit__
    self._cinit(infile=infile, name=name, adjacent=adjacent, origin=origin,
  File "build\python\cantera\base.pyx", line 126, in cantera._cantera._SolutionBase._cinit
    self._init_yaml(infile, name, adjacent, yaml, transport_model)
  File "build\python\cantera\base.pyx", line 210, in cantera._cantera._SolutionBase._init_yaml
    stringify(infile), stringify(name), cxx_transport, adjacent_solns)
  File "build\python\cantera\utils.pyx", line 27, in cantera._cantera.stringify
    tmp = bytes(x.encode())
AttributeError: 'NoneType' object has no attribute 'encode'

despite scons test-python-convert passing.

interfaces/cython/cantera/yaml2ck.py

.github/workflows/main.yml

interfaces/cython/cantera/yaml2ck.py

bryanwweber · 2022-07-06T02:12:12Z

@ischoegl I think I fixed the problem you posted about NoneType, can you try now?

ischoegl · 2022-07-06T04:46:25Z

@bryanwweber ... better, but not quite:

(cantera-dev) PS C:\Users\ischo\GitHub\cantera> yaml2ck data/h2o2.yaml --mechanism=h2o2-test.ck --overwrite
Validating mechanism...PASSED.
Traceback (most recent call last):
  File "C:\Users\ischo\miniconda3\envs\cantera-dev\lib\runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "C:\Users\ischo\miniconda3\envs\cantera-dev\lib\runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "C:\Users\ischo\miniconda3\envs\cantera-dev\Scripts\yaml2ck.exe\__main__.py", line 7, in <module>
  File "C:\Users\ischo\miniconda3\envs\cantera-dev\lib\site-packages\cantera\yaml2ck.py", line 758, in main
    output = "\n".join(ck_paths)
TypeError: sequence item 0: expected str instance, WindowsPath found

ischoegl

@bryanwweber .... Thanks! Again, pretty minor things.

.github/workflows/main.yml

interfaces/cython/cantera/yaml2ck.py

ischoegl · 2022-07-06T10:17:34Z

Before I forget ... yaml2ck this should probably marked with .. versionadded:: 3.0

ischoegl

Everything else looks good

1

ischoegl · 2022-07-10T17:06:19Z

@bryanwweber … will approve this once the merge conflict is resolved

Removed redundant yaml reading Uses Cantera's new notes Refactored to classes Co-Authored-By: Kyle Niemeyer <kyleniemeyer@fastmail.com> Co-Authored-By: Phillip Mestas <phillip.mestas51@gmail.com> Co-Authored-By: Parker Clayton <17040941+parkerclayton@users.noreply.github.com> Update Chebyshev Fix Bryan Changes - Part Thermo Update yaml2ck.py

The error is just over 1e-7.

Add more tests of the script.

Document all the parameters for functions. Remove unused options from the argument parser and change the default sorting to be in the source order, rather than sort by default.

Since ck2yaml.convert_mech takes a file name, not an open file, we use TemporaryDirectory and then create a file name relative to that folder. This change also consistently formats the output from TROE and SRI reaction types.

This method transparently passes arguments through to yaml2ck.convert.

The source keyword argument was removed when CTI/XML input was removed.

Python 3.7 requires the typing_extensions module. Scope it to 3.7 only for now, so it's more obvious when it can be removed.

Co-authored-by: Ingmar Schoegl <ischoegl@lsu.edu>

Add option parsing for Boolean options to add "--no-" prefix. Add version added directive and update docstrings.

ischoegl

LGTM 🎉

bryanwweber · 2022-07-11T08:49:09Z

Tagging @tsikes thanks for all your work here!

tsikes · 2022-07-11T22:11:38Z

@bryanwweber Thank you so much for carrying the torch the rest of the way! I'm happy to see this completed.

bryanwweber requested a review from ischoegl May 18, 2022 00:29

bryanwweber mentioned this pull request May 18, 2022

Yaml2ck script #1185

Closed

5 tasks

bryanwweber force-pushed the update-yaml2ck branch 2 times, most recently from f6b2b0b to 3140b20 Compare May 26, 2022 03:28

bryanwweber added Input Input parsing and conversion (for example, ck2yaml) enhancement labels May 26, 2022

bryanwweber force-pushed the update-yaml2ck branch 7 times, most recently from 0f29b61 to 06a18dd Compare May 27, 2022 17:01

bryanwweber force-pushed the update-yaml2ck branch from 06a18dd to 8f51c27 Compare June 24, 2022 19:39

bryanwweber requested a review from a team June 24, 2022 19:41

ischoegl reviewed Jul 3, 2022

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bryanwweber force-pushed the update-yaml2ck branch from 6d2e55d to 539d3b4 Compare July 10, 2022 16:22

bryanwweber force-pushed the update-yaml2ck branch from 6b9a395 to 5e18aaf Compare July 10, 2022 19:18

bryanwweber requested a review from ischoegl July 10, 2022 19:18

tsikes and others added 2 commits July 10, 2022 15:20

[yaml2ck] Fix tests comparison

6edc764

The error is just over 1e-7.

bryanwweber and others added 16 commits July 10, 2022 15:21

[yaml2ck] Refactor thermo string builder

b61ac0b

[yaml2ck] Refactor handling header text + metadata

9859520

[yaml2ck] Refactor other conversion methods

6973985

Add more tests of the script.

[yaml2ck] Add typing_extensions for py37 compat

0982a0d

[yaml2ck] Update docstrings

55a7cf2

Document all the parameters for functions. Remove unused options from the argument parser and change the default sorting to be in the source order, rather than sort by default.

[yaml2ck] Fix validation option for mechanism

eabf1fd

Since ck2yaml.convert_mech takes a file name, not an open file, we use TemporaryDirectory and then create a file name relative to that folder. This change also consistently formats the output from TROE and SRI reaction types.

[Cython] Add write_chemkin method to SolutionBase

a976a44

This method transparently passes arguments through to yaml2ck.convert.

[Doc] Delete source keyword for phases

4e51279

The source keyword argument was removed when CTI/XML input was removed.

[Doc] Add doc page for yaml2ck

20dbed8

[CI] Install typing_extensions on CI

a749678

Python 3.7 requires the typing_extensions module. Scope it to 3.7 only for now, so it's more obvious when it can be removed.

Update git-blame-ignore-revs after rebase merge

e47a532

Apply suggestions from code review

a65c552

Co-authored-by: Ingmar Schoegl <ischoegl@lsu.edu>

Address review comments about docs and testing

eda537a

[yaml2ck] Fix NoneType attribute error from CLI

c598aa4

[yaml2ck] Address review comments

22a4339

Add option parsing for Boolean options to add "--no-" prefix. Add version added directive and update docstrings.

[yaml2ck] Add note about global thermo temperature

e07fbfe

bryanwweber force-pushed the update-yaml2ck branch from 5e18aaf to e07fbfe Compare July 10, 2022 19:22

ischoegl approved these changes Jul 10, 2022

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ischoegl merged commit 51494f4 into Cantera:main Jul 11, 2022

bryanwweber deleted the update-yaml2ck branch July 11, 2022 08:48

This was referenced Aug 4, 2022

Export Solution to Chemkin Format Cantera/enhancements#52

Closed

Move Python test suite #1354

Merged

man page missing for yaml2ck #1361

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Yaml2ck script #1286

Yaml2ck script #1286

bryanwweber commented May 18, 2022 •

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tsikes commented Jul 11, 2022

Yaml2ck script #1286

Yaml2ck script #1286

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