Merge pull request #52 from FormingWorlds/logging

Terminal logging

.github/workflows/tests.yaml

@@ -74,7 +74,7 @@ jobs:
       - name: Test with pytest
         run: |
           export FWL_DATA="/home/runner/work/fwl_data"
-          export SOCRATES="/home/runner/work/JANUS/JANUS/SOCRATES"
+          export RAD_DIR="/home/runner/work/JANUS/JANUS/SOCRATES"
           coverage run -m pytest
 
       - name: Report coverage

.gitignore

@@ -33,3 +33,5 @@ utils/*.ipynb*
 build/
 fwl_data*/
 dist/
+.pytest_cache
+

docs/getting_started.md

@@ -41,7 +41,7 @@ If you install and compile [SOCRATES](https://github.com/nichollsh/SOCRATES) you
 you can override the path using the `SOCRATES` environment variable, e.g.
 
 ```console
-SOCRATES=/home/user/path/to/SOCRATES pytest
+RAD_DIR=/home/user/path/to/SOCRATES pytest
 ```
 
 ### `FWL_DATA`

examples/SocRadConv.py

@@ -20,6 +20,9 @@
 import numpy as np
 from importlib.resources import files
 
+from janus.utils.logs import setup_logger
+log = setup_logger()
+
 from janus.modules import RadConvEqm, plot_fluxes, plot_emission
 from janus.utils import atmos, CleanOutputDir, DownloadSpectralFiles, DownloadStellarSpectra, plot_adiabats, ReadBandEdges, StellarSpectrum
 import mors
@@ -33,7 +36,7 @@
 ####################################
 if __name__ == "__main__":
 
-    print("Start JANUS")
+    log.info("Start JANUS")
 
     # Set up dirs
     if os.environ.get('RAD_DIR') == None:
@@ -83,7 +86,7 @@
     StellarSpectrum.PrepareStellarSpectrum(spec.wl, spec.fl, socstar)
 
     # Move/prepare spectral file
-    print("Inserting stellar spectrum")
+    log.info("Inserting stellar spectrum")
     StellarSpectrum.InsertStellarSpectrum(
         str(FWL_DATA_DIR / 'spectral_files'/'Oak'/'318'/'Oak.sf'),
         socstar,
@@ -99,10 +102,10 @@
     if cfg['star']['stellar_heating'] == False:
         atm.instellation = 0.
     else:
-        mors.DownloadEvolutionTracks("/Baraffe")
+        mors.DownloadEvolutionTracks("Baraffe")
         baraffe = mors.BaraffeTrack(star_mass)
-        atm.instellation = baraffe.BaraffeSolarConstant(time['star'], mean_distance)
-        print("Instellation:", round(atm.instellation), "W/m^2")
+        atm.instellation = baraffe.BaraffeSolarConstant(time['star'], mean_distance) 
+        log.info("Instellation: %.2e W/m^2" % atm.instellation)
 
     # Set up atmosphere with general adiabat
     atm_dry, atm = RadConvEqm(dirs,
@@ -132,4 +135,5 @@
     CleanOutputDir(dirs['output'])
 
     end = t.time()
-    print("Runtime:", round(end - start,2), "s")
+    log.info("Runtime: %.2f s" % float(end-start))
+

examples/demo_instellation.py

@@ -11,6 +11,9 @@
 import os, shutil, toml
 import numpy as np
 
+from janus.utils.logs import setup_logger
+log = setup_logger()
+
 from janus.modules import MCPA_CBL
 from janus.utils import atmos, CleanOutputDir, DownloadSpectralFiles, DownloadStellarSpectra, ReadBandEdges, StellarSpectrum
 
@@ -20,7 +23,7 @@
 
 if __name__=='__main__':
 
-    print("Start")
+    log.info("Start")
 
     # Set up dirs
     if os.environ.get('RAD_DIR') == None:
@@ -37,7 +40,7 @@
     os.mkdir(dirs["output"])
 
     #Download required spectral files
-    DownloadSpectralFiles("/Oak")
+    DownloadSpectralFiles("Oak")
     DownloadStellarSpectra()
 
     # Read spectrum
@@ -50,7 +53,7 @@
 
 
     # Setup spectral file
-    print("Inserting stellar spectrum")
+    log.info("Inserting stellar spectrum")
     StellarSpectrum.InsertStellarSpectrum(
         str(FWL_DATA_DIR / 'spectral_files'/'Oak'/'318'/'Oak.sf'),
         socstar,
@@ -66,7 +69,7 @@
     # Star luminosity
     time = { "planet": cfg['planet']['time'], "star": cfg['star']['time']}
     star_mass = cfg['star']['star_mass']
-    mors.DownloadEvolutionTracks("/Baraffe")
+    mors.DownloadEvolutionTracks("Baraffe")
     baraffe = mors.BaraffeTrack(star_mass)
 
     # Define volatiles by mole fractions
@@ -94,7 +97,7 @@
     ts_arr  = []    # surface temperature
     tr_arr  = []    # tropopause temperature
     for i in range(7):
-      print("Orbital separation = %.2f AU" % r_arr[i])
+      log.info("Orbital separation = %.2f AU" % r_arr[i])
 
       atm.instellation = baraffe.BaraffeSolarConstant(time['star'], r_arr[i])
       atmos.setTropopauseTemperature(atm)
@@ -121,14 +124,14 @@
       # Save netcdf
       atm.write_ncdf(dirs["output"]+"/profile%.2fAU.nc"%r_arr[i])
 
-      print(" ")
+      log.info(" ")
 
     save_arr = [r_arr, asf_arr, OLR_arr, net_arr, ts_arr, tr_arr]
     np.savetxt(dirs["output"]+"/data_%dK.csv"%T_magma,
                np.array(save_arr).T, fmt="%.5e", delimiter=",",
                header="r [AU],  S_0 [W m-2], OLR [W m-2], net [W m-2], ts [K], tr[K] ")
-
-    print("Making plots")
+    
+    log.info("Making plots")
 
     plt.ioff()
     fig,(ax1, ax2) = plt.subplots(2,1, figsize=(6,6.4))
@@ -188,4 +191,5 @@
     CleanOutputDir(dirs['output'])
 
     # Done
-    print("Done!")
+    log.info("Done!")
+

examples/demo_runaway_greenhouse.py

@@ -10,6 +10,9 @@
 from matplotlib.ticker import MultipleLocator
 from importlib.resources import files
 
+from janus.utils.logs import setup_logger
+log = setup_logger()
+
 from janus.modules import RadConvEqm
 from janus.utils import atmos, CleanOutputDir, DownloadSpectralFiles, DownloadStellarSpectra, ReadBandEdges, StellarSpectrum
 import mors
@@ -18,8 +21,8 @@
 
 if __name__=='__main__':
 
-    print("Start")
-    print(" ")
+    log.info("Start")
+    log.info(" ")
 
     # Set up dirs
     if os.environ.get('RAD_DIR') == None:
@@ -36,7 +39,7 @@
     os.mkdir(dirs["output"])
 
     #Download required spectral files
-    DownloadSpectralFiles("/Oak")
+    DownloadSpectralFiles("Oak")
     DownloadStellarSpectra()
 
     # Read spectrum
@@ -49,13 +52,13 @@
 
 
     # Setup spectral file
-    print("Inserting stellar spectrum")
+    log.info("Inserting stellar spectrum")
     StellarSpectrum.InsertStellarSpectrum(
         str(FWL_DATA_DIR / 'spectral_files'/'Oak'/'318'/'Oak.sf'),
         socstar,
         dirs["output"]
     )
-    print(" ")
+    log.info(" ")
     band_edges = ReadBandEdges(dirs["output"]+"star.sf")
 
     # Open config file
@@ -77,24 +80,24 @@
     atm = atmos.from_file(cfg_file, band_edges, vol_mixing=vol_mixing, vol_partial={})
 
     # Compute stellar heating
-    mors.DownloadEvolutionTracks("/Baraffe")
+    mors.DownloadEvolutionTracks("Baraffe")
     baraffe = mors.BaraffeTrack(star_mass)
     atm.instellation = baraffe.BaraffeSolarConstant(time['star'], mean_distance)
 
     #Run Janus
 
     # Run JANUS in a loop to generate runaway curve
-    print("Running JANUS...")
+    log.info("Running JANUS...")
     Ts_arr = np.linspace(200, 2800, 20)
     OLR_arr = []
     for i in range(20):
-      print("T_surf = %d K" % Ts_arr[i])
+      log.info("T_surf = %d K" % Ts_arr[i])
       atmos.setSurfaceTemperature(atm, Ts_arr[i])
 
       _, atm_moist = RadConvEqm(dirs, time, atm, standalone=True, cp_dry=False, trppD=False, rscatter=False)
 
       OLR_arr.append(atm_moist.LW_flux_up[0])
-      print(" ")
+      log.info(" ")
 
     OLR_arr = np.array(OLR_arr)
     Ts_arr  = np.array(Ts_arr)
@@ -110,7 +113,7 @@
                           dtype=float, skiprows=2, delimiter=',').T
 
     # Setup plot
-    print("Making plot")
+    log.info("Making plot")
     fig,ax = plt.subplots(1,1, figsize=(7,4))
 
     # Plot data
@@ -134,11 +137,12 @@
 
     fig.savefig(dirs["output"]+"runaway_demo.pdf", bbox_inches='tight')
     fig.savefig(dirs["output"]+"runaway_demo.png", bbox_inches='tight', dpi=190)
-    print(" ")
+    log.info(" ")
 
     # Tidy
     CleanOutputDir(os.getcwd())
     CleanOutputDir(dirs['output'])
 
     # Done
-    print("Done!")
+    log.info("Done!")
+

pyproject.toml

@@ -42,7 +42,6 @@ dependencies = [
   'tomlkit',
   'f90nml',
   'fwl-mors',
-  'datetime'
 ]
 
 [project.urls]

src/janus/modules/compute_moist_adiabat.py

@@ -15,6 +15,9 @@
 from janus.modules.water_cloud import simple_cloud
 from janus.modules.relative_humidity import compute_Rh
 
+import logging
+log = logging.getLogger("fwl."+__name__)
+
 import janus.utils.GeneralAdiabat as ga # Moist adiabat with multiple condensibles
 import janus.utils.socrates as socrates
 
@@ -50,7 +53,7 @@ def compute_moist_adiabat(atm, dirs, standalone, trppD, rscatter=False):
     atm_moist = socrates.radCompSoc(atm_moist, dirs, recalc=False, rscatter=rscatter)
 
     if standalone == True:
-        print("w/o stratosphere (net, OLR): " + str(round(atm_moist.net_flux[0], 3)) +" , "+str(round(atm_moist.LW_flux_up[0], 3)) + " W/m^2")
+        log.info("w/o stratosphere (net, OLR): %.3f, %.3f W/m^2" % ( atm_moist.net_flux[0] , atm_moist.LW_flux_up[0]))
 
     # Calculate tropopause
     if (trppD == True) or (atm_moist.trppT > atm_moist.minT):
@@ -67,6 +70,6 @@ def compute_moist_adiabat(atm, dirs, standalone, trppD, rscatter=False):
         atm_moist = socrates.radCompSoc(atm_moist, dirs, recalc=True, rscatter=rscatter)
 
         if standalone == True:
-            print("w/ stratosphere (net, OLR): " + str(round(atm_moist.net_flux[0], 3)) + " , " + str(round(atm_moist.LW_flux_up[0], 3)) + " W/m^2")
+            log.info("w/ stratosphere (net, OLR): %.3f, %.3f W/m^2" % (atm_moist.net_flux[0] , atm_moist.LW_flux_up[0] )) 
 
     return atm_moist

src/janus/modules/find_tropopause.py

@@ -11,6 +11,10 @@
 
 import numpy as np
 
+import logging 
+log = logging.getLogger("fwl."+__name__)
+
+
 def find_tropopause(atm_moist, dynamic: bool, verbose=True):
     """Computes tropopause location via two methods: dynamically based on heating rates, or by a set temperature value.
 
@@ -26,8 +30,7 @@ def find_tropopause(atm_moist, dynamic: bool, verbose=True):
     # Heating criterion
     if dynamic:
 
-        if verbose:
-            print("TROPOPAUSE SET BY HEATING")
+        log.debug("TROPOPAUSE SET BY HEATING")
 
         # Find tropopause index
         trpp_idx   = 0 
@@ -44,7 +47,6 @@ def find_tropopause(atm_moist, dynamic: bool, verbose=True):
         if np.size(signchange_indices) > 0 and np.max(atm_moist.net_heating) > DeltaT_max_sign:
 
             # First guess: maximum heating index
-            # print(np.argmax(atm_moist.net_heating))
             max_heat_idx = np.argmax(atm_moist.net_heating)
 
             # Lower height while heating still significant
@@ -84,18 +86,14 @@ def find_tropopause(atm_moist, dynamic: bool, verbose=True):
         # If significant tropopause found or isothermal atmosphere from stellar heating
         if trpp_idx != 0:
 
-            # # Print tropopause index for debugging
-            # print("Tropopause @ (index, P/Pa, T/K):", trpp_idx, round(atm_moist.pl[trpp_idx],3), round(atm_moist.tmpl[trpp_idx],3))
-
             atm_moist.trppidx   = trpp_idx                  # index
             atm_moist.trppP     = atm_moist.pl[trpp_idx]    # pressure 
             atm_moist.trppT     = atm_moist.tmpl[trpp_idx]  # temperature
 
     # Temperature criterion
     else:
 
-        if verbose:
-            print("TROPOPAUSE SET BY CONTANT VALUE OF", atm_moist.trppT, "K")
+        log.debug("TROPOPAUSE SET BY CONTANT VALUE OF %.2f K"%atm_moist.trppT)
 
         # Tropopause is triggered
         if np.any(atm_moist.tmpl <= atm_moist.trppT) or np.any(atm_moist.tmp <= atm_moist.trppT):

src/janus/modules/relative_humidity.py

@@ -41,23 +41,11 @@ def update_for_constant_RH(atm, R_h):
     """
 
     p_sat = [ga.p_sat('H2O', atm.tmp[i]) for i in range(len(atm.p))]
-    #print("update_for_constant_RH: p_sat = ", p_sat)
 
     i_lcl, lcl = find_intersection(p_sat, atm.p_vol['H2O'], tolerance=1e0)
-    #print("update_for_constant_RH: atm.p[i_lcl:] = ", atm.p[i_lcl:])
-    #print("update_for_constant_RH: atm.p_vol['H2O'][i_lcl:] = ", atm.p_vol['H2O'][i_lcl:])
-    #print("update_for_constant_RH: R_h[i_lcl:] = ", R_h[i_lcl:])
-    #print("update_for_constant_RH: atm.ps = ", atm.ps)
-    #print("update_for_constant_RH: atm.x_gas['H2O'][i_lcl:] = ", atm.x_gas['H2O'][i_lcl:])
 
-    #atm.p_vol['H2O'][i_lcl:] = R_h[i_lcl:] * p_sat[i_lcl:]  # Updating the partial pressure of H2O from the LCL down
     atm.p_vol['H2O'] = R_h * p_sat
-    #print("update_for_constant_RH: updated atm.p_vol['H2O'][i_lcl:] = ", atm.p_vol['H2O'][i_lcl:])
     atm.p = sum(atm.p_vol[molecule] for molecule in atm.vol_list.keys()) # Updating the total pressure
-    #print("update_for_constant_RH: updated atm.p[i_lcl:] = ", atm.p[i_lcl:])
     atm.ps = float(sum(atm.p_vol[molecule][-1] for molecule in atm.vol_list.keys())) # Not forgetting the surface pressure
-    #print("update_for_constant_RH: updated atm.ps = ", atm.ps)
-    #atm.x_gas['H2O'][i_lcl:] = R_h[i_lcl:] * p_sat[i_lcl:] / atm.p[i_lcl:] # Updating the mixing ratio of H2O
-    #print("atm.p_vol['H2O'][-1], atm.x_gas['H2O'], p_sat[-1] = ", atm.p_vol['H2O'][-1], atm.x_gas['H2O'][-1], p_sat[-1])
 
     return atm