[1pt] PR: Replace fiona with pyogrio

[mluck]

Replace fiona with pyogrio to improve I/O speed. geopandas will use pyogrio by default starting with version 1.0. pyarrow was also added as an environment variable to further speedup I/O. As a result of the changes in this PR, fim_pipeline.sh runs approximately 10% faster. Closes #1072.

Changes

• Pipfile: Upgraded geopandas from v0.12.2 to v0.14.3, added pyogrio, and fixed version of pyflwdir.
• src/bash_variables.env: Added environment variable for pyogrio to use pyarrow

The remaining files were modified to add pyogrio:

• data/
  • bathymetry/preprocess_bathymetry.py, ble/ble_benchmark/create_flow_forecast_file.py, esri.py, nld/levee_download.py, usgs/acquire_and_preprocess_3dep_dems.py, wbd/clip_vectors_to_wbd.py, wbd/preprocess_wbd.py, write_parquet_from_calib_pts.py: Added pyogrio and pyarrow
• src/
  • add_crosswalk.py, associate_levelpaths_with_levees.py, bathy_rc_adjust.py, bathymetric_adjustment.py, buffer_stream_branches.py, build_stream_traversal.py, crosswalk_nwm_demDerived.py, derive_headwaters.py, derive_level_paths.py, edit_points.py, filter_catchments_and_add_attributes.py, finalize_srcs.py, make_stages_and_catchlist.py, mask_dem.py, reachID_grid_to_vector_points.py, split_flows.py, src_adjust_spatial_obs.py, stream_branches.py, subset_catch_list_by_branch_id.py, usgs_gage_crosswalk.py, usgs_gage_unit_setup.py, utils/shared_functions.py
• tools/
  • adjust_rc_with_feedback.py, check_deep_flooding.py, create_flow_forecast_file.py, eval_plots.py, evaluate_continuity.py, evaluate_crosswalk.py, fimr_to_benchmark.py, find_max_catchment_breadth.py, generate_categorical_fim.py, generate_categorical_fim_flows.py, generate_categorical_fim_mapping.py, generate_nws_lid.py, hash_compare.py, inundate_events.py, inundation.py, make_boxes_from_bounds.py, mosaic_inundation.py, overlapping_inundation.py, rating_curve_comparison.py, rating_curve_get_usgs_curves.py, test_case_by_hydro_id.py, tools_shared_functions.py

Removals

Testing

fim_pipeline.sh ran approximately 10% faster on two HUCs (12040101 and 12090301). Inundation metrics (CSI and MCC were identical to dev (4.4.10.0).

HUC8	4.4.10.0	pyogrio	pygrio + pyarrow
12040101	34:02	31:05	30:36
12090301	54:05	48:20	47:26

Issuer Checklist (For developer use)

You may update this checklist before and/or after creating the PR. If you're unsure about any of them, please ask, we're here to help! These items are what we are going to look for before merging your code.

• Informative and human-readable title, using the format: [_pt] PR: <description>
• Links are provided if this PR resolves an issue, or depends on another other PR
• If submitting a PR to the dev branch (the default branch), you have a descriptive Feature Branch name using the format: dev-<description-of-change> (e.g. dev-revise-levee-masking)
• Changes are limited to a single goal (no scope creep)
• The feature branch you're submitting as a PR is up to date (merged) with the latest dev branch
• pre-commit hooks were run locally
• Any change in functionality is tested
• Passes all unit tests locally (inside interactive Docker container, at /foss_fim/, run: pytest unit_tests/)
• New functions are documented (with a description, list of inputs, and expected output)
• Placeholder code is flagged / future todos are captured in comments
• CHANGELOG updated with template version number, e.g. 4.x.x.x
• Reviewers requested
• Add yourself as an assignee in the PR as well as the FIM Technical Lead

Merge Checklist (For Technical Lead use only)

• Update CHANGELOG with latest version number and merge date
• Update the Citation.cff file to reflect the latest version number in the CHANGELOG
• If applicable, update README with major alterations

[RobHanna-NOAA]

ran against the full unit test set of HUCs with the new docker container from here. It all ran perfectly well and all of the eval plots were identical to recent previous runs.