Merge pull request #27 from FormingWorlds/osf

Osf

.github/workflows/tests.yaml

@@ -48,5 +48,6 @@ jobs:
       - name: Test with pytest
         run: |
           pip install pytest
+          export FWL_DATA="./fwl_data"
           source SOCRATES/set_rad_env
           pytest

README.md

@@ -36,6 +36,14 @@ https://proteus-code.readthedocs.io
     * `git clone [email protected]:FormingWorlds/JANUS.git`
     * `cd JANUS`
     * `pip install -e .`
+3. Download spectral files from the [OSF repository](https://osf.io/vehxg/)
+    * Set the environment variable FWL_DATA to define where the spectral data files will be stored
+        * `export FWL_DATA=...`
+    * Run the following commands within a python environment (or script) to download all basic spectral files
+        * `from janus.utils.data import DownloadSpectralFiles`
+        * `DownloadSpectralFiles()`
+    * Alternatively, you can specify which spectral data you want to download, and optionally the number of bands
+    * `DownloadSpectralFiles("/Frostflow", 4096)`
 
 ### Run instructions
 In the examples folder you can find python scripts showing typical usecases/workflows of atmosphere modelling with Janus.

examples/SocRadConv.py

@@ -31,6 +31,7 @@
 from janus.utils.atmosphere_column import atmos
 import janus.utils.StellarSpectrum as StellarSpectrum
 from janus.utils.ReadSpectralFile import ReadBandEdges
+from janus.utils.data import DownloadSpectralFiles
 
 ####################################
 ##### Stand-alone initial conditions
@@ -42,6 +43,8 @@
     # Set up dirs
     if os.environ.get('RAD_DIR') == None:
         raise Exception("Socrates environment variables not set! Have you installed Socrates and sourced set_rad_env?")
+    if os.environ.get('FWL_DATA') == None:
+        raise Exception("The FWL_DATA environment variable where spectral data will be downloaded needs to be set up!")
     dirs = {
             "janus": str(files("janus"))+"/",
             "output": os.path.abspath(os.getcwd())+"/output/"
@@ -74,11 +77,15 @@
         shutil.rmtree(dirs["output"])
     os.mkdir(dirs["output"])
 
+    #Download required spectral files
+    DownloadSpectralFiles("/Dayspring")
+    DownloadSpectralFiles("/stellar_spectra")
+
     # Move/prepare spectral file
     print("Inserting stellar spectrum")
     StellarSpectrum.InsertStellarSpectrum(
-        dirs["janus"]+"data/spectral_files/Dayspring/256/Dayspring.sf",
-        dirs["janus"]+"data/spectral_files/stellar_spectra/Sun_t4_4Ga_claire_12.txt",
+        os.environ.get('FWL_DATA')+"/spectral_files/Dayspring/256/Dayspring.sf",
+        os.environ.get('FWL_DATA')+"/spectral_files/stellar_spectra/Sun_t4_4Ga_claire_12.txt",
         dirs["output"]
     )
 

examples/demo_instellation.py

@@ -18,6 +18,7 @@
 import janus.utils.StellarSpectrum as StellarSpectrum
 import janus.utils.phys as phys
 from janus.utils.ReadSpectralFile import ReadBandEdges
+from janus.utils.data import DownloadSpectralFiles
 
 if __name__=='__main__':
 
@@ -26,6 +27,8 @@
     # Set up dirs
     if os.environ.get('RAD_DIR') == None:
         raise Exception("Socrates environment variables not set! Have you installed Socrates and sourced set_rad_env?")
+    if os.environ.get('FWL_DATA') == None:
+        raise Exception("The FWL_DATA environment variable where spectral data will be downloaded needs to be set up!")
     dirs = {
             "janus": str(files("janus"))+"/",
             "output": os.path.abspath(os.getcwd())+"/output/"
@@ -36,11 +39,15 @@
         shutil.rmtree(dirs["output"])
     os.mkdir(dirs["output"])
 
+    #Download required spectral files
+    DownloadSpectralFiles("/Oak")
+    DownloadSpectralFiles("/stellar_spectra")
+
     # Setup spectral file
     print("Inserting stellar spectrum")
     StellarSpectrum.InsertStellarSpectrum(
-        dirs["janus"]+"data/spectral_files/Oak/Oak.sf",
-        dirs["janus"]+"data/spectral_files/stellar_spectra/Sun_t4_4Ga_claire_12.txt",
+        os.environ.get('FWL_DATA')+"/spectral_files/Oak/318/Oak.sf",
+        os.environ.get('FWL_DATA')+"/spectral_files/stellar_spectra/Sun_t4_4Ga_claire_12.txt",
         dirs["output"]
     )
     band_edges = ReadBandEdges(dirs["output"]+"star.sf")

examples/demo_runaway_greenhouse.py

@@ -17,6 +17,7 @@
 from janus.utils.atmosphere_column import atmos
 import janus.utils.StellarSpectrum as StellarSpectrum
 from janus.utils.ReadSpectralFile import ReadBandEdges
+from janus.utils.data import DownloadSpectralFiles
 
 if __name__=='__main__':
 
@@ -26,6 +27,8 @@
     # Set up dirs
     if os.environ.get('RAD_DIR') == None:
         raise Exception("Socrates environment variables not set! Have you installed Socrates and sourced set_rad_env?")
+    if os.environ.get('FWL_DATA') == None:
+        raise Exception("The FWL_DATA environment variable where spectral data will be downloaded needs to be set up!")
     dirs = {
             "janus": str(files("janus"))+"/",
             "output": os.path.abspath(os.getcwd())+"/output/"
@@ -36,11 +39,15 @@
         shutil.rmtree(dirs["output"])
     os.mkdir(dirs["output"])
 
+    #Download required spectral files
+    DownloadSpectralFiles("/Oak")
+    DownloadSpectralFiles("/stellar_spectra")
+
     # Setup spectral file
     print("Inserting stellar spectrum")
     StellarSpectrum.InsertStellarSpectrum(
-        dirs["janus"]+"data/spectral_files/Oak/Oak.sf",
-        dirs["janus"]+"data/spectral_files/stellar_spectra/Sun_t4_4Ga_claire_12.txt",
+        os.environ.get('FWL_DATA')+"/spectral_files/Oak/318/Oak.sf",
+        os.environ.get('FWL_DATA')+"/spectral_files/stellar_spectra/Sun_t4_4Ga_claire_12.txt",
         dirs["output"]
     )
     print(" ")

pyproject.toml

@@ -31,6 +31,7 @@ dependencies = [
   'natsort',
   'netcdf4',
   'numpy',
+  'osfclient',
   'pandas',
   'scipy',
   'seaborn',