Replaced wget with urllib.request, updated tutorials, errors and warn…

…ings in get_model, bug fix get_data with petitCODE, smooth parameter in get_model
tomasstolker · Jan 30, 2020 · 23947fc · 23947fc
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diff --git a/docs/tutorials/atmospheric_models.ipynb b/docs/tutorials/atmospheric_models.ipynb
@@ -97,9 +97,9 @@
    ],
    "source": [
     "database.add_model(model='drift-phoenix',\n",
-    "                   wavel_range=(0.5, 10.),\n",
-    "                   teff_range=None,\n",
-    "                   spec_res=None)"
+    "                   wavel_range=None,\n",
+    "                   spec_res=None,\n",
+    "                   teff_range=None)"
    ]
   },
   {

diff --git a/docs/tutorials/color_magnitude_broadband.ipynb b/docs/tutorials/color_magnitude_broadband.ipynb
@@ -27,9 +27,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import species\n",
-    "import wget\n",
-    "import numpy as np"
+    "import urllib.request\n",
+    "import numpy as np\n",
+    "import species"
    ]
   },
   {
@@ -201,7 +201,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The isochrones from the AMES-Cond and AMES-Dusty evolutionary models are downloaded with `wget`."
+    "The isochrones from the AMES-Cond and AMES-Dusty evolutionary models are downloaded with `urllib.request`."
    ]
   },
   {
@@ -221,11 +221,18 @@
     }
    ],
    "source": [
-    "wget.download('https://phoenix.ens-lyon.fr/Grids/AMES-Cond/ISOCHRONES/model.AMES-Cond-2000.M-0.0.NaCo.Vega',\n",
-    "              out='data/model.AMES-Cond-2000.M-0.0.NaCo.Vega')\n",
-    "\n",
-    "wget.download('https://phoenix.ens-lyon.fr/Grids/AMES-Dusty/ISOCHRONES/model.AMES-dusty.M-0.0.NaCo.Vega',\n",
-    "              out='data/model.AMES-dusty.M-0.0.NaCo.Vega')"
+    "urllib.request.urlretrieve('https://phoenix.ens-lyon.fr/Grids/AMES-Cond/ISOCHRONES/model.AMES-Cond-2000.M-0.0.NaCo.Vega',\n",
+    "                           'data/model.AMES-Cond-2000.M-0.0.NaCo.Vega')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "urllib.request.urlretrieve('https://phoenix.ens-lyon.fr/Grids/AMES-Dusty/ISOCHRONES/model.AMES-dusty.M-0.0.NaCo.Vega',\n",
+    "                           'data/model.AMES-dusty.M-0.0.NaCo.Vega')"
    ]
   },
   {
@@ -295,13 +302,13 @@
    "source": [
     "database.add_model(model='ames-cond',\n",
     "                   wavel_range=(0.5, 10.),\n",
-    "                   teff_range=(100., 4000.),\n",
-    "                   spec_res=1000.)\n",
+    "                   spec_res=1000.,\n",
+    "                   teff_range=(100., 4000.))\n",
     "\n",
     "database.add_model(model='ames-dusty',\n",
     "                   wavel_range=(0.5, 10.),\n",
-    "                   teff_range=(100., 4000.),\n",
-    "                   spec_res=1000.)"
+    "                   spec_res=1000.,\n",
+    "                   teff_range=(100., 4000.))"
    ]
   },
   {

diff --git a/docs/tutorials/color_magnitude_narrowband.ipynb b/docs/tutorials/color_magnitude_narrowband.ipynb
@@ -27,9 +27,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import species\n",
-    "import wget\n",
-    "import numpy as np"
+    "import urllib.request\n",
+    "import numpy as np\n",
+    "import species"
    ]
   },
   {
@@ -1060,8 +1060,8 @@
    "source": [
     "database.add_model(model='ames-cond',\n",
     "                   wavel_range=(0.5, 10.),\n",
-    "                   teff_range=(100., 4000.),\n",
-    "                   spec_res=1000.)"
+    "                   spec_res=1000.\n",
+    "                   teff_range=(100., 4000.))"
    ]
   },
   {
@@ -1090,8 +1090,8 @@
    "source": [
     "database.add_model(model='ames-dusty',\n",
     "                   wavel_range=(0.5, 10.),\n",
-    "                   teff_range=(100., 4000.),\n",
-    "                   spec_res=1000.)"
+    "                   spec_res=1000.\n",
+    "                   teff_range=(100., 4000.))"
    ]
   },
   {
@@ -1118,10 +1118,18 @@
     }
    ],
    "source": [
-    "wget.download('https://phoenix.ens-lyon.fr/Grids/AMES-Cond/ISOCHRONES/model.AMES-Cond-2000.M-0.0.NaCo.Vega',\n",
-    "              out='data/model.AMES-Cond-2000.M-0.0.NaCo.Vega')\n",
-    "wget.download('https://phoenix.ens-lyon.fr/Grids/AMES-Dusty/ISOCHRONES/model.AMES-dusty.M-0.0.NaCo.Vega',\n",
-    "              out='data/model.AMES-dusty.M-0.0.NaCo.Vega')"
+    "urllib.request.urlretrieve('https://phoenix.ens-lyon.fr/Grids/AMES-Cond/ISOCHRONES/model.AMES-Cond-2000.M-0.0.NaCo.Vega',\n",
+    "                           'data/model.AMES-Cond-2000.M-0.0.NaCo.Vega')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "urllib.request.urlretrieve('https://phoenix.ens-lyon.fr/Grids/AMES-Dusty/ISOCHRONES/model.AMES-dusty.M-0.0.NaCo.Vega',\n",
+    "                           'data/model.AMES-dusty.M-0.0.NaCo.Vega')"
    ]
   },
   {

diff --git a/docs/tutorials/data_model.ipynb b/docs/tutorials/data_model.ipynb
@@ -113,8 +113,8 @@
    "source": [
     "database.add_model(model='ames-cond',\n",
     "                   wavel_range=(0.1, 6.),\n",
-    "                   teff_range=(2800., 3000.),\n",
-    "                   spec_res=1000.)"
+    "                   spec_res=1000.\n",
+    "                   teff_range=(2800., 3000.))"
    ]
   },
   {

diff --git a/docs/tutorials/fitting_photometry.ipynb b/docs/tutorials/fitting_photometry.ipynb
@@ -74,8 +74,8 @@
    "source": [
     "database.add_model(model='drift-phoenix',\n",
     "                   wavel_range=None,\n",
-    "                   teff_range=None,\n",
-    "                   spec_res=None)"
+    "                   spec_res=None\n",
+    "                   teff_range=None)"
    ]
   },
   {

diff --git a/docs/tutorials/flux_magnitude.ipynb b/docs/tutorials/flux_magnitude.ipynb
@@ -16,7 +16,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Initiating species v0.1.0... [DONE]\n",
+      "Initiating species v0.1.2... [DONE]\n",
       "Creating species_config.ini... [DONE]\n",
       "Database: /Users/tomasstolker/applications/species/docs/tutorials/species_database.hdf5\n",
       "Data folder: /Users/tomasstolker/applications/species/docs/tutorials/data\n",
@@ -28,7 +28,7 @@
     {
      "data": {
       "text/plain": [
-       "<species.core.setup.SpeciesInit at 0x1083eff28>"
+       "<species.core.setup.SpeciesInit at 0x108831e48>"
       ]
      },
      "execution_count": 1,
@@ -61,7 +61,7 @@
      "text": [
       "Adding filter: JWST/NIRCam.F115W... [DONE]\n",
       "Downloading Vega spectrum (270 kB)... [DONE]\n",
-      "Adding Vega spectrum...[DONE]\n",
+      "Adding Vega spectrum... [DONE]\n",
       "Flux density [W m-2 micron-1] = 4.15e-15 +/- 7.69e-16\n"
      ]
     }

diff --git a/docs/tutorials/photometric_calibration.ipynb b/docs/tutorials/photometric_calibration.ipynb
@@ -34,8 +34,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import urllib.request\n",
     "import species\n",
-    "import wget\n",
     "from IPython.display import Image"
    ]
   },
@@ -187,8 +187,8 @@
     }
    ],
    "source": [
-    "wget.download('http://irtfweb.ifa.hawaii.edu/~spex/IRTF_Spectral_Library/Data/G8V_HD75732.txt',\n",
-    "              out='data/G8V_HD75732.txt')"
+    "urllib.request.urlretrieve('http://irtfweb.ifa.hawaii.edu/~spex/IRTF_Spectral_Library/Data/G8V_HD75732.txt',\n",
+    "                           'data/G8V_HD75732.txt')"
    ]
   },
   {

diff --git a/docs/tutorials/synthetic_photometry.ipynb b/docs/tutorials/synthetic_photometry.ipynb
@@ -13,9 +13,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import species\n",
-    "import wget\n",
-    "import numpy as np"
+    "import urllib.request\n",
+    "import numpy as np\n",
+    "import species"
    ]
   },
   {
@@ -27,7 +27,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Initiating species v0.1.0... [DONE]\n",
+      "Initiating species v0.1.2... [DONE]\n",
       "Creating species_config.ini... [DONE]\n",
       "Database: /Users/tomasstolker/applications/species/docs/tutorials/species_database.hdf5\n",
       "Data folder: /Users/tomasstolker/applications/species/docs/tutorials/data\n",
@@ -39,7 +39,7 @@
     {
      "data": {
       "text/plain": [
-       "<species.core.setup.SpeciesInit at 0x123ce14e0>"
+       "<species.core.setup.SpeciesInit at 0x12f882048>"
       ]
      },
      "execution_count": 2,
@@ -55,17 +55,35 @@
    "cell_type": "code",
    "execution_count": 3,
    "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "('data/plnt_Jupiter.txt', <http.client.HTTPMessage at 0x12f953f28>)"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "urllib.request.urlretrieve('http://irtfweb.ifa.hawaii.edu/~spex/IRTF_Spectral_Library/Data/plnt_Jupiter.txt',\n",
+    "                           'data/plnt_Jupiter.txt')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
    "outputs": [],
    "source": [
-    "wget.download('http://irtfweb.ifa.hawaii.edu/~spex/IRTF_Spectral_Library/Data/plnt_Jupiter.txt',\n",
-    "              out='data/plnt_Jupiter.txt')\n",
-    "\n",
     "wavelength, flux, error = np.loadtxt('data/plnt_Jupiter.txt', unpack=True)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -74,7 +92,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -83,7 +101,7 @@
      "text": [
       "Adding filter: JWST/NIRCam.F115W... [DONE]\n",
       "Downloading Vega spectrum (270 kB)... [DONE]\n",
-      "Adding Vega spectrum...[DONE]\n"
+      "Adding Vega spectrum... [DONE]\n"
      ]
     }
    ],
@@ -94,7 +112,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {

diff --git a/requirements.txt b/requirements.txt
@@ -10,4 +10,3 @@ scipy ~= 1.4
 spectres ~= 2.0
 tqdm ~= 4.42
 xlrd ~= 1.2
-wget ~= 3.2
diff --git a/species/analysis/fit_model.py b/species/analysis/fit_model.py
@@ -121,7 +121,7 @@ def lnlike(param,
             chisq += (item[0]-flux)**2 / item[1]**2
 
     if spectrum is not None:
-        model = modelspec.get_model(paramdict, None)
+        model = modelspec.get_model(paramdict)
 
         flux_new = spectres.spectres(new_spec_wavs=spectrum[:, 0],
                                      old_spec_wavs=model.wavelength,

diff --git a/species/core/setup.py b/species/core/setup.py
@@ -23,7 +23,7 @@ def __init__(self):
             None
         """
 
-        print(f'Initiating species v{species.__version__}...', end='')
+        print(f'Initiating species v{species.__version__}...', end='', flush=True)
 
         working_folder = os.path.abspath(os.getcwd())
 
@@ -33,7 +33,7 @@ def __init__(self):
 
         if not os.path.isfile(config_file):
 
-            print('Creating species_config.ini...', end='')
+            print('Creating species_config.ini...', end='', flush=True)
 
             with open(config_file, 'w') as file_obj:
                 file_obj.write('[species]\n')
@@ -53,12 +53,12 @@ def __init__(self):
         print(f'Working folder: {working_folder}')
 
         if not os.path.isfile(database_file):
-            print('Creating species_database.hdf5...', end='')
+            print('Creating species_database.hdf5...', end='', flush=True)
             h5_file = h5py.File(database_file, 'w')
             h5_file.close()
             print(' [DONE]')
 
         if not os.path.exists(data_folder):
-            print('Creating data folder...', end='')
+            print('Creating data folder...', end='', flush=True)
             os.makedirs(data_folder)
             print(' [DONE]')