Performance optimization with MPASdiag

Author: mrixlam

README.md

@@ -24,7 +24,7 @@ conda create -n modvx python=3.10 -y
 conda activate modvx
 
 # Install dependencies
-conda install -y -c conda-forge numpy scipy xarray matplotlib pyyaml
+conda install -y -c conda-forge numpy scipy xarray matplotlib pyyaml pytest mpi4py netCDF4 ruff black pluggy coverage pytest-cov cartopy
 
 # Install modvx in development mode
 git clone https://github.com/mrixlam/modvx.git
@@ -198,7 +198,7 @@ pytest tests/
 Run tests with coverage report:
 
 ```bash
-pytest --cov=modvx tests/
+pytest --cov=modvx tests/ --cov-report=term-missing
 ```
 
 ## License

configs/test_liuz.yaml

@@ -4,48 +4,60 @@
 experiment_name: "liuz_3_3dhyb_asrama_asrmhs_atms2025"
 
 # MPAS mesh settings (update mpas_grid_file to point to your grid)
-mpas_grid_file: "fcst/liuz_3_3dhyb_asrama_asrmhs_atms2025/grid/x1.grid.nc"
+mpas_grid_file: "fcst/grids/x1.2621442.static.nc"
 mpas_remap_resolution: 0.1
 
 # Single cycle for testing
 initial_cycle_start: "20250613T00"
-final_cycle_start:   "20250613T00"
+final_cycle_start:   "20250709T00"
 
 forecast_step_hours:        12
 observation_interval_hours:  1
 cycle_interval_hours:       24
 forecast_length_hours:      240
 
-# Grid
+# Specify target resolution for regridding (obs grid in this case)
 target_resolution: "obs"
 
-# Single domain for quick test
+# List of verification domains 
 vxdomain:
   - "GLOBAL"
 
-# Minimal parameter sweep for testing
+# Percentile thresholds for categorical verification
 thresholds:
   - 90.0
+  - 95.0
+  - 97.5
+  - 99.0
+
+# Window sizes for neighborhood-based verification
 window_sizes:
   - 1
-
-# Variable names
+  - 3
+  - 5
+  - 7
+  - 9
+  - 11
+  - 13
+  - 15
+
+# Variable names for obs loading
 obs_var_name: "precip"
 
-# Directories (relative to base_dir) — update base_dir for your system
-base_dir: "/Users/mrislam/Documents/NCAR/precipvx"
+# Directories (relative to base_dir)
+base_dir: "/glade/work/mrislam/software/modvx"
 fcst_dir: "fcst"
 obs_dir:  "obs/FIMERG"
 mask_dir: "masks"
 output_dir: "output"
 debug_dir: "debug"
 
-# Obs vintage preference (LTE files for June/July 2025)
+# Obs vintage preference (LTE for Late Run, FNL for Final Run)
 obs_vintage_preference:
   - "FNL"
   - "LTE"
 
-# Runtime
+# Runtime settings
 verbose: true
-save_intermediate: false
+save_intermediate: true
 enable_logs: false

src/modvx/__init__.py

@@ -1,24 +1,20 @@
+#!/usr/bin/env python3
+
 """
-modvx — Model Verification Toolkit
-====================================
+Package entry points and convenience imports for modvx.
 
-A community Python package for computing spatial verification metrics
-(Fractions Skill Score, RMSE, and more) for gridded forecast experiments
-against satellite-based precipitation observations.
+This module exposes the primary public classes and helpers that make up the modvx verification toolkit. It provides a concise, importable surface for constructing configurations, building work-units, running parallel processing backends, performing I/O and data validation, computingperformance metrics, and producing plots. Importing from this module is the recommended way for downstream tools to access the canonical API.
 
-Classes
--------
-TaskManager        Orchestrates work-unit enumeration, logging, and execution.
-ParallelProcessor  MPI-based parallelism via mpi4py (graceful serial fallback).
-FileManager        All I/O: forecast/observation loading, caching, output writing.
-DataValidator      Grid preparation, regridding, mask application, QC checks.
-PerfMetrics        Verification scores (FSS, RMSE, …).
-Visualizer         Plotting: FSS-vs-lead-time, horizontal precip maps, diffs.
+Author: Rubaiat Islam
+Institution: Mesoscale & Microscale Meteorology Laboratory, NCAR
+Email: mrislam@ucar.edu
+Date: February 2026
+Version: 1.0.0
 """
 
 __version__ = "0.1.0"
 
-from modvx.config import ModvxConfig, load_config
+from modvx.config import ModvxConfig, load_config_from_yaml
 from modvx.task_manager import TaskManager
 from modvx.parallel import ParallelProcessor
 from modvx.file_manager import FileManager
@@ -28,7 +24,7 @@
 
 __all__ = [
     "ModvxConfig",
-    "load_config",
+    "load_config_from_yaml",
     "TaskManager",
     "ParallelProcessor",
     "FileManager",