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',

src/janus/utils/data.py

@@ -0,0 +1,78 @@
+import os
+from osfclient.api import OSF
+
+#project ID of the stellar evolution tracks folder in the OSF
+project_id = 'vehxg'
+
+basic_list =[
+        "/Dayspring/256",
+        "/Frostflow/256",
+        "/Legacy",
+        "/Mallard",
+        "/Oak",
+        "/Reach",
+        "/stellar_spectra"
+        ]
+
+def download_folder(storage, folder_name, local_path):
+    ''''
+    Download a specific folder in the OSF repository
+    
+    Inputs :
+        - storage     : OSF storage name 
+        - folder_name : folder name to be downloaded
+        - local_path  : local repository where data are saved
+    '''
+    for file in storage.files:
+        if file.path.startswith(folder_name):
+            local_file_path = local_path + file.path
+            #Create local directory if needed
+            os.makedirs(os.path.dirname(local_file_path), exist_ok=True)
+            #Download the file
+            with open(local_file_path, 'wb') as local_file:
+                file.write_to(local_file)
+    return
+
+def DownloadSpectralFiles(fname="",nband=256):
+    ''''
+    Download spectral files data
+    
+    Inputs :
+        - fname (optional) :    folder name, i.e. "/Dayspring"
+                                if not provided download all the basic list  
+        - nband (optional) :    number of band = 16, 48, 256, 4096 
+                                (only relevant for Dayspring, Frostflow and Honeyside)
+    '''
+
+    #Check if data environment variable is set up
+    fwl_data_dir = os.getenv('FWL_DATA')
+    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!")
+
+    #Create spectral file data repository if not existing
+    data_dir = fwl_data_dir + "/spectral_files"
+    if not os.path.exists(data_dir):
+        os.makedirs(data_dir)
+
+    #Link with OSF project repository
+    osf = OSF()
+    project = osf.project(project_id)
+    storage = project.storage('osfstorage')
+
+    #If no folder specified download all basic list
+    if not fname:
+        for folder in basic_list:
+            print(folder)
+            download_folder(storage,folder,data_dir)
+    elif fname in ["/Dayspring","/Frostflow","/Honeyside"]:
+        print("HERE ")
+        folder = fname + "/" + str(nband)
+        print(folder)
+        download_folder(storage,folder,data_dir)
+    elif fname in ["/Kynesgrove","/Legacy","/Mallard","/Oak","/Reach","/stellar_spectra"]:
+        folder = fname
+        download_folder(storage,folder,data_dir)
+    else:
+        print("Unrecognised folder name in DownloadSpectralFiles")
+
+    return

tests/test_instellation.py

@@ -11,12 +11,15 @@
 import janus.utils.StellarSpectrum as StellarSpectrum
 import janus.utils.phys as phys
 from janus.utils.ReadSpectralFile import ReadBandEdges
+from janus.utils.data import DownloadSpectralFiles
 
 def test_instellation():
 
     # 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/"
@@ -27,11 +30,15 @@ def test_instellation():
         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")

tests/test_runaway_greenhouse.py

@@ -12,12 +12,15 @@
 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
 
 def test_runaway_greenhouse():
 
     # 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/"
@@ -28,11 +31,15 @@ def test_runaway_greenhouse():
         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")