format + more docs

docs/src/experiment_setup_guide.md

@@ -4,17 +4,32 @@ Please read this entire guide before setting up an experiment.
 
 ## Summary
 
+The overall pipeline is as follows:
+
+Observations are generated (or obtained) and then processed through the observation map. 
+For the example experiment, `sphere_held_suarez_rhoe_equilmoist`, this is done by running 
+`sbatch experiments/sphere_held_suarez_rhoe_equilmoist/generate_observations.sbatch`.
+
+Once the observations have been processed, the actual calibration pipeline can be run via
+`bash job_array.sh sphere_held_suarez_rhoe_equilmoist 8`.
+The command line interface will change, but for now, the first entry is the experiment id and the second is the number of tasks to use per ensemble member.
+
+This consists of three `sbatch` scripts:
+- `initialize.sbatch` initializes the Julia project and the ensemble
+- `model_run.sbatch` runs an individual forward model
+- `update.sbatch` performs the update step and sets up the next iteration
+
 To calibrate parameters, you need:
 - Atmos model configuration
+- Steady-state restart file
 - EKP configuration 
 - Prior parameter distributions
-- Steady-state restart file
 - Truth and noise data JLD2 files
 - Observation map script with a function `observation_map(iteration)`
 
-Examples of all of these can be found in `experiments/sphere_held_suarez_rhoe_equilmoist`
+These components are detailed in the guide below. Examples of all of these can also be found in `experiments/sphere_held_suarez_rhoe_equilmoist`
 
-First, create a folder for your experiment with a descriptive job id in the `experiments/` folder. All of the components described below will be stored in this folder. An existing example is found in `experiments/sphere_held_suarez_rhoe_equilmoist`. This experiment has examples for each component.
+First, create a folder for your experiment with a descriptive job id in the `experiments/` folder. All of the components described below will be stored in this folder.
 
 ## Atmos Configuration File
 This is the ClimaAtmos configuration which will be used to run all simulations in the calibration. The only changes between model runs are the parameters selected for calibration.

src/ekp_interface.jl

@@ -10,7 +10,7 @@ using EnsembleKalmanProcesses.TOMLInterface
     path_to_iteration(output_dir, iteration)
 Returns the path to the iteration folder within `output_dir` for the given iteration number.
 """
-path_to_iteration(output_dir, iteration) = 
+path_to_iteration(output_dir, iteration) =
     joinpath(output_dir, join(["iteration", lpad(iteration, 3, "0")], "_"))
 
 """