Update read module coordinate dimension manipulations to use new xarray index #473
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* Adding argo search and download script * Create get_argo.py Download the 'classic' argo data with physical variables only * begin implementing argo dataset * 1st draft implementing argo dataset * implement search_data for physical argo * doctests and general cleanup for physical argo query * beginning of BGC Argo download * parse BGC profiles into DF * plan to query BGC profiles * validate BGC param input function * order BGC params in order in which they should be queried * fix bug in parse_into_df() - init blank df to take in union of params from all profiles * identify profiles from initial API request containing all required params * creates df with only profiles that contain all user specified params Need to dload additional params * modified to populate prof df by querying individual profiles * finished up BGC argo download! * assert bounding box type in Argo init, begin framework for unit tests * Adding argo search and download script * Create get_argo.py Download the 'classic' argo data with physical variables only * begin implementing argo dataset * 1st draft implementing argo dataset * implement search_data for physical argo * doctests and general cleanup for physical argo query * beginning of BGC Argo download * parse BGC profiles into DF * plan to query BGC profiles * validate BGC param input function * order BGC params in order in which they should be queried * fix bug in parse_into_df() - init blank df to take in union of params from all profiles * identify profiles from initial API request containing all required params * creates df with only profiles that contain all user specified params Need to dload additional params * modified to populate prof df by querying individual profiles * finished up BGC argo download! * assert bounding box type in Argo init, begin framework for unit tests * need to confirm spatial extent is bbox * begin test case for available profiles * add tests for argo.py * add typing, add example json, and use it to test parsing * update argo to submit successful api request (update keys and values submitted) * first pass at porting argo over to metadata+per profile download (WIP) * basic working argo script * simplify parameter validation (ordered list no longer needed) * add option to delete existing data before new download * continue cleaning up argo.py * fix download_by_profile to properly store all downloaded data * remove old get_argo.py script * remove _filter_profiles function in favor of submitting data kwarg in request * start filling in docstrings * clean up nearly duplicate functions * add more docstrings * get a few minimal argo tests working * add bgc argo params. begin adding merge for second download runs * some changes * WIP test commit to see if can push to GH * WIP handling argo merge issue * update profile to df to return df and move merging to get_dataframe * merge profiles with existing df * clean up docstrings and code * add test_argo.py * add prelim test case for adding to Argo df * remove sandbox files * remove bgc argo test file * update variables notebook from development * simplify import statements * quickfix for granules error * draft subpage on available QUEST datasets * small reference fix in text * add reference to top of .rst file * test argo df merge * add functionality to Quest class to pass search criteria to all datasets * add functionality to Quest class to pass search criteria to all datasets * update dataset docstrings; reorder argo.py to match * implement quest search+download for IS2 * move spatial and temporal properties from query to genquery * add query docstring test for cycles,tracks to test file * add quest test module * standardize print outputs for quest search and download; is2 download needs auth updates * remove extra files from this branch * comment out argo portions of quest for PR * remove argo-branch-only init file * remove argo script from branch * remove argo test file from branch * comment out another line of argo stuff * Update quest.py Added Docstrings to functions within quest.py and edited the primary docstring for the QUEST class here. Note I did not add Docstrings to the implicit __self__ function. * Update test_quest.py Added comments (not Docstrings) to test functions * Update dataset.py Minor edits to the doc strings * Update quest.py Edited docstrings * catch error with downloading datasets in Quest; template test case for multi dataset query --------- Co-authored-by: Kelsey Bisson <48059682+kelseybisson@users.noreply.github.com> Co-authored-by: Romina <romina.piunno@gmail.com> Co-authored-by: zachghiaccio <zhfair@umich.edu> Co-authored-by: Zach Fair <48361714+zachghiaccio@users.noreply.github.com>
* add OA API warning * comment out tests that use OA API --------- Co-authored-by: GitHub Action <rwegener2@users.noreply.github.com>
--------- Co-authored-by: GitHub Action <jpswinski@users.noreply.github.com>
* add filelist and product properties to Read object * deprecate filename_pattern and product class Read inputs * transition to data_source input as a string (including glob string) or list * update tutorial with changes and user guidance for using glob --------- Co-authored-by: Jessica Scheick <JessicaS11@users.noreply.github.com>
* add kwarg acceptance for data queries and download_all in quest * Add QUEST dataset page to RTD --------- Co-authored-by: zachghiaccio <zhfair@umich.edu>
Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Jessica Scheick <JessicaS11@users.noreply.github.com>
Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Jessica Scheick <JessicaS11@users.noreply.github.com>
Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Jessica Scheick <JessicaS11@users.noreply.github.com>
Refactor Variables class to be user facing functionality
…d remove xarray warning
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I will automatically update this comment whenever this PR is modified |
JessicaS11
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Since the data read-in module was built, xarray has added explicit indexing, which was causing a warning (
read.py:599: UserWarning: rename 'delta_time' to 'photon_idx' does not create an index anymore. Try using swap_dims instead or use set_index after rename to create an indexed coordinate.) to appear during thereader.load()step when coordinate dimensions were manipulated internally. This PR updates that portion of the code to use.swap_dims, greatly simplifying it and removing the warning.