fix codecov upload and refine coverage measurements, general improvements

[ilaflott]

Describe your changes

Testing

• All unit tests passing via CI
• Integration tests now run individually (guarded where unstable)
• Coverage successfully uploading to Codecov
• epmt check now runs verify_papiex_options in a guarded manner since it doesn't work, but otherwise epmt checks pass
• pylint failure threshold for epmt (without epmt-dash/ui) adjusted from 6.1 --> 6.5

CI/CD & Coverage Improvements

• .github/workflows/build_and_test_epmt.yml: syntax fixes, coverage now uses coveragerc, codecov upload now successful via use_pypi: true
• coveragerc: Added to omit specific directories from coverage (ui, test)
• Integration tests now broken out individually for better debugging and granular CI runs
• Added PAPI configuration options to Makefile (CONFIG_PAPIEX_PAPI, CONFIG_PAPIEX_DEBUG)

Bug Fixes

• src/epmt/epmt_cmd_dbcare.py: Fixed bug comparing list to int when counting post-processed jobs
• src/epmt/epmt_daemon.py: Fixed niters → maxiters bug in daemon loop iteration logic
• src/epmt/epmt_cmds.py: Re-enabled verify_papiex_options() call (guarded)

Code Quality (PEP 8 / Pylint)

• Whitespace cleanup, superfluous parentheses removal across multiple modules
• Import ordering improvements (per PEP 8 guidelines)
• Refactored complex boolean logic to use all() / any() for readability
• Converted inline comments to proper docstrings where appropriate
• Added sqlalchemy.orm.scoping.scoped_session to pylintrc ignored-classes (known pylint/SQLAlchemy clash)

Configuration Changes

• src/epmt/epmt_default_settings.py: Bumped retire_jobs_ndays from 13 → 14
• Makefile: Updated remote URLs to NOAA-GFDL GitHub, cleaned up commented-out code, syntax consistency

Deprecations/Removals

• Commented out risky epmt python subcommand (uses exec())
• Removed 012-python.bats integration test

Files Changed

• 25 files modified across source, tests, CI, and configuration

[codecov]

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[Copilot]

Pull request overview

This PR improves coverage tooling and CI integration, cleans up style/docstrings across several modules, and fixes a couple of functional bugs in job post-processing and daemon behavior. The main functional changes are in the database care workflow, daemon loop control, and coverage reporting pipeline.

Changes:

• Wire coverage runs to a shared coveragerc (excluding UI/tests) and enable reliable uploads to Codecov from CI.
• Clean up and refactor utility modules (epmtlib, epmt_job, epmt_concat, epmt_daemon, epmt_cmds) for clearer docstrings, simpler boolean logic, and minor bug fixes (e.g., dbcare post-processing count).
• Adjust default retention settings and Makefile URLs/scripts for the current hosting setup and build workflow.

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
.github/workflows/build_and_test_epmt.yml	Adds --cov-config=coveragerc to all pytest invocations, fixes a typo in COVERAGE_FILE, and configures Codecov v5 upload using the generated coverage.xml.
coveragerc	New coverage configuration omitting UI and test modules from coverage stats, aligning CI runs with intended measurement scope.
src/epmt/epmtlib.py	Converts many inline comments into docstrings and simplifies conditionals; introduces a notable issue where check_none still incorrectly checks membership against the characters of 'NONE' instead of the token 'NONE' itself.
src/epmt/epmt_job.py	Minor whitespace and readability tweaks (including use of all()/any() and simplified comparisons) in job ETL and post-processing code, with no apparent logic changes.
src/epmt/epmt_default_settings.py	Bumps retire_jobs_ndays from 13 to 14 days to adjust the default job retirement window.
src/epmt/epmt_daemon.py	Adds docstrings, cleans up logging and conditionals, and attempts to fix the niters behavior in daemon_loop, but the new termination condition (if 0 < iters <= niters) exits one iteration too early when niters > 1 and contradicts the documented semantics.
src/epmt/epmt_concat.py	Refactors conditionals for readability, improves docstrings, and slightly clarifies CLI argument parsing and CSV joining logic without changing behavior.
src/epmt/epmt_cmds.py	Whitespace and comment cleanup plus some boolean simplifications; functional behavior remains the same, including daemon-related tests that exercise daemon_loop(niters=1).
src/epmt/epmt_cmd_dbcare.py	Fixes the post-processing count bug by correctly taking len(post_process_jobs(jobs=job_list)) so the comparison against 0 uses an integer rather than a list.
Makefile	Cleans up commented-out variables, improves echo messaging, switches source URLs to NOAA-GFDL GitHub, and slightly refactors shell command sequencing while preserving overall build/release semantics.

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