Various repo-wide fixes

[alongd]

No description provided.

[Copilot]

Pull request overview

Note

Copilot was unable to run its full agentic suite in this review.

Repo-wide reliability and housekeeping updates, focusing on hardening parsers/simulations, improving RMG execution robustness, and consolidating test/CI configuration.

Changes:

• Hardened multiple parsers/simulators with additional validation, safer parsing, and improved error handling/logging.
• Added walltime-based timeout handling for incore RMG runs and improved CI concurrency settings.
• Moved pytest warning filters into pyproject.toml, adjusted Makefile test targets, and cleaned up docs/editor configs.

Reviewed changes

Copilot reviewed 21 out of 21 changed files in this pull request and generated 11 comments.

Show a summary per file

File	Description
tests/test_main.py	Removes leftover debug prints from tests.
t3/utils/writer.py	Adds safer string/line parsing when generating RMG/PDep files.
t3/utils/rmg_shim.py	Improves cleanup reliability in atomic file writes with logging.
t3/utils/rmg_sa_parser.py	Makes SA CSV parsing more robust to unexpected kinetics parameter names.
t3/utils/libraries.py	Reduces lock acquisition/stale-lock timeouts.
t3/simulate/rmg_constant_tp.py	Fails fast on SA subprocess failure; warns on concentration sums.
t3/simulate/cantera_pfr_t_profile.py	Adds constant validation and runtime checks for density/velocity.
t3/simulate/cantera_pfr.py	Adds guards for invalid MW and mass flow rate.
t3/simulate/cantera_jsr.py	Adds guard for invalid residence time.
t3/simulate/cantera_base.py	Adds NaN/inf warning; makes IDT calculation more numerically robust.
t3/schema.py	Simplifies units validation condition.
t3/runners/rmg_runner.py	Adds walltime parsing + subprocess timeout for incore RMG execution.
t3/main.py	Plumbs max walltime into RMG runner; narrows exception handling.
pytest.ini	Removes pytest ini in favor of pyproject.toml.
pyproject.toml	Adds pytest warning filters under [tool.pytest.ini_options].
README.md	Reworks header placement (logo removed, title moved below badges).
Makefile	Adds --cov to targeted test commands.
CODE_OF_CONDUCT.md	Changes headings/title structure.
.vscode/settings.json	Removed editor-specific settings.
.vscode/launch.json	Removed editor-specific launch config.
.github/workflows/ci.yml	Adds push trigger and workflow concurrency cancellation.

Comments suppressed due to low confidence (1)

t3/runners/rmg_runner.py:1

• New walltime parsing and timeout behavior should be covered by unit tests (e.g., valid/invalid walltime strings, defaulting behavior, and a mocked subprocess.run timeout/returncode). Adding tests here would prevent regressions in RMG execution handling.

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[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 72.37%. Comparing base (069d4d2) to head (435b633).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #167      +/-   ##
==========================================
- Coverage   72.77%   72.37%   -0.41%     
==========================================
  Files          35       35              
  Lines        4668     4727      +59     
  Branches      985      998      +13     
==========================================
+ Hits         3397     3421      +24     
- Misses        944      968      +24     
- Partials      327      338      +11     

Flag	Coverage Δ
unittests	72.37% <ø> (-0.41%)	⬇️

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