Add climo wrapper

[ceblanton]

Ian: @ceblanton and @ilaflott collab, i'll be summarizing what's up here soon

the main mission- climatology calculations

• new CLI routine and submodule, fre app gen-time-averages-wrapper / generate_time_averages.generate_wrapper, which generates an output climatology
• new CLI command and submodule, fre app combine-time-averages / generate_time_averages.combine, combines files holding individual monthly averages into one for the climatology generation
• tests for each: generate_time_averages/tests/test_wrapper.py, generate_time_averages/tests/test_combine.py
• 61117 lines of cdl over 34 cdl files containing test data

small side quests, tweaks

• gfdl_msd_schemas update (removes do_timeavgs as option, superceded by climatology), tweaks to testing yaml configs in this repo removing the do_timeavgs key
• moved fre/app/tests/test_mask_atmost_plevel.py to fre/app/mask_atmos_plevel/tests, and gave it an __init__.py for coverage/linting

bigger side quests, efforts

general fre/app/generate_time_averages improvements

• typing additions
• pylint oriented edits for all files based on current repo standard
• improved exception handling and tests for it
• rewritten tests/test_generate_time_averages from the ground-up, heavily leveraging pytest.parameterize, increased clarity into testing approach, etc.
• small tests covering previous uncovered lines, and small tweaks to certain logic structures to enhance testability
• some print statements in non-testing code still remained, this was fully removed and replaced entirely with fre_logger usage

.github/workflows revamped:

• channel configuration now explicit + equivalent in create_test_conda_env, build_conda, publish_conda workflows, set_channel_priority is now strict
• workflows also factorized into more numerous, smaller steps for easier nav
• conda-forge::conda-verify and conda-forge::anaconda-client don't really do anything since they're really for uploading to conda channels r and main, and so are removed from publish_conda
• fixed a bug causing the spell_check workflow to redundantly run twice each push
• create_test_conda_env now explicitly activates the fre-cli environment after conda init, which is enabled by sourcing conda/etc/profile.d/conda.sh
• all CI/CD containers in this repo no longer use ghcr.io/noaa-gfdl/fre-cli:miniconda24.7.1_gcc14.2.0, and instead now use ghcr.io/noaa-gfdl/fre-cli:miniconda24_gcc14_v2

packaging changes:

• pyproject.toml list of deps changed to include analysis_scripts, cftime, netCDF4, numpy and pyyaml, all of which are explicitly called in the body of the code and are pip/python packages. also removes pylint and pytest under this section and puts them under the test-specific reqs
• meta.yaml now defaults to conda-package version develop when there's no git tag, certain version reqs added to help with environment resolution, noaa-gfdl packages are all pinned to specific versions. we now explicitly ask for netCDF4=1.7.* and xarray>=2024.* to avoid certain behaviors assoc. with earlier versions calling test failures. Jinja2 no longer needs to be specifically version 3.0.*, just greater than 3. numpy set to 1.26.*, pylint, pytest and pytest-cov are added to the test: requires: section instead
• environment.yaml tweaked similarly to above dependency lists, but still contains the testing requirements.
• pylintrc now included in repo and is used for configuring the pylint standards, fail-under set to 7.5, max-positional-arguments increased to 6 from 5, workflow calls to pylint now use the config file instead

Checklist before requesting a review

• I ran my code
• I tried to make my code readable
• I tried to comment my code
• I wrote a new test, if applicable
• I wrote new instructions/documentation, if applicable
• I ran pytest and inspected it's output
• I ran pylint and attempted to implement some of it's feedback
• No print statements; all user-facing info uses logging module

[ilaflott]

solid effort again! i still think calling this a wrapper is implying the wrong thing about the code's structure, but aside from the name this is looking great

[ilaflott]

@singhd789 @mlee03 i didn't quite get to all the feedback, but i got to a bunch of it and some of it i don't want to resolve without yee eyez

[mlee03]

@ilaflott I can't find the resolve conversation button lol. But all's good with me~
My comments were just annoying style change suggestions~

[singhd789]

My comments were addressed. Great work Ian