Update README

Author: sbiquard

README.md

@@ -21,10 +21,7 @@ The software packages used are
 and [mappraiser](https://github.com/B3Dcmb/midapack/tree/gaps-maxL).
 They are provided as submodules in the `extern` folder so that the exact setup can be reproduced easily.
 
-The simulation worfklow, `so_mappraiser.py`, is a modified version of a script in sotodlib and can be obtained by running the following command:
-```bash
-patch extern/sotodlib/sotodlib/toast/scripts/so_sim.py -o so_mappraiser.py < so_sim.patch
-```
+The simulation worfklow, `so_mappraiser.py`, is a modified version of the `toast_so_sim.py` script in sotodlib.
 
 ## Files in this directory
 
@@ -34,6 +31,7 @@ Setup
 
 * `get_defaults.sh` : Use `so_mappraiser.py` to generate a default parameter file for reference
 * `sat.toml` : Master parameter file for the `so_mappraiser.py` workflow
+* `sat.par`, `atm.par` : Sets of command line parameters for the workflow
 * `ffp10_lensed_scl_100_nside0512.fits` : Input map to be observed during simulation
 
 Schedule files
@@ -48,6 +46,7 @@ Tests (laptop: truncated schedule, decimated focal plane)
   * `run.white.uniform.sh` : all detector _pairs_ have the same white noise level (but not detectors in a pair)
   * `run.white.variable.sh` : all detectors have different white noise levels
   * `run.one_over_f.sh` : all detectors have different 1/f noise parameters
+  * `run.atm.sh` : in addition to variable instrumental noise, simulate atmosphere
 * `tests/syst` : Evaluate the impact of systematic effects on the pair-differencing approach
   * `run.atm.cache.sh` : simulate and cache the atmosphere simulation
   * `run.baseline.sh` : run the baseline configuration (ideal case)
@@ -56,16 +55,16 @@ Tests (laptop: truncated schedule, decimated focal plane)
 Execution (Jean-Zay: full schedule)
 
 * `slurm/run.atm.cache.slurm` : Simulate and cache the atmosphere simulation
-* `slurm/run.baseline.slurm` : Run the baseline configuration (ideal case)
-* `slurm/run.gains.constant.slurm` : Run with gain errors which are the same for all detector pairs
-* `slurm/run.gains.random.slurm` : Run with Gaussian distributed gain errors
+* `slurm/get_sample_data.slurm` : Get sample observation data for testing
+* `slurm/opti/*`: Run the optimality tests
 
 Post-processing
 
-* `utils.py` : Some utility routines
-* `plot_maps.py` : Produce difference maps and histograms for a given run
-* `plot_maps_all.py` : Plot difference maps and histograms for all runs under a given directory
-* `spectrum.py` : Power spectrum routines
-* `get_mask_apo.py` : Create and save a mask (requires [NaMaster](https://namaster.readthedocs.io))
-* `compute_spectra.py` : Compute and save power spectra for all runs
+* `post/compute_spectra.py` : Compute and save power spectra for all runs
+* `post/get_input_spectra.py` : Compute and save power spectra of input map
+* `post/get_mask_apo.py` : Create and save a mask (requires [NaMaster](https://namaster.readthedocs.io))
+* `post/plot_maps_all.py` : Plot difference maps and histograms for all runs in a root directory
+* `post/plot_maps.py` : Produce difference maps and histograms for a given run
+* `post/plot_spectra.py` : Plot power spectra recursively for all runs in a root directory
+* `post/spectrum.py` : Power spectrum routines
 * `slurm/run.spectra.slurm` : Job script to compute power spectra