Pull in main branch updates (#788)

* Remove duplicate ghostscript entry from base yaml

* Mjo date fix (#763)

* small fix

* Fix time range to work with YYYYMMDD or YYYYMMDDHH as well as original YYYY

* fix for dataset/time requested case

* Debug giss (#764)

* Add files via upload

* Debugging running on GISS files

* fix reconcile_names to use variable entry in dataset if name attribute is not defined
add option for user-defined frequency and adjust set_query routine to use this entry if it is set
fix preprocessor logging statement to use variable id attached to varlistentry

* update yaml templates for local directories

* initialize subprocessruntimewrapper.env_vars

* uncomment attribute restoration in xr_parser parse_dataset
add list of variables to drop from xr_parser parse_ds xr.decode_cf and a routine to restore attributes afterward to avoid attribute encoding errors

* added optional frequency entries to runtime templates

* remove files

* add frequency to ref_cli docs
clean up formatting in dev_git_intro and dev_cheatsheet

* add block to refine query with variable_id search if multiple assets are returned during the initial query
save deleted variable attributes in query to the associated parser object to restore before writing the processed files

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Co-authored-by: Fiaz Ahmed <15623379+ahmedfiaz@users.noreply.github.com>
Co-authored-by: Fiaz <fiaz.500@gmail.com>

* Bump intake esm version (#765)

* add -y flag to conda_env_setup env create call

* bump intake-esm, xarray, dask, and intake package versions in conda env files

* fix typos in env_python3_base_micromambe

* Update documentation with Globus links for obs_data and sample model data (#767)

* fix conditional when resolving cat_subset with multiple var_ids (#766)

* remove debugging print statement from preprocessor.py (#768)

* Update SST standard name to match common definition in fieldlist_CESM.jsonc

* Update python3 base (#775)

* add momgrid and doralite packages to python3 base env files

* fix typo in pip version

* Update copy_external_docs.py

Remove sites references from copy_external_docs
fix the pod_toc_header definition

* Add closing string to pod_toc_header def in copy_external_docs.py

* Update index.rst

Fix ref to pods_toc in index.rst

* Integrate MAR notebooks (#782)

* commit to update

* it works?

* update descriptions

* add run-MDTF [GFDL driver script] (#784)

* add run-MDTF [GFDL driver script]

* update pathing

* update readme

* remove unused os import

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Co-authored-by: Jess <20195932+wrongkindofdoctor@users.noreply.github.com>

* Update gen_index.py (#787)

---------

Co-authored-by: Dani Coleman <30841536+bitterbark@users.noreply.github.com>
Co-authored-by: Fiaz Ahmed <15623379+ahmedfiaz@users.noreply.github.com>
Co-authored-by: Fiaz <fiaz.500@gmail.com>
Co-authored-by: Jacob Mims <122570226+jtmims@users.noreply.github.com>

Author: 4 people