Repository: ExoCTK/exoctk (language: python)

Issue:
Forward model bug fix and unit tests
A simple import error was breaking the forward models. This fixes it.


Discussion / hints:

Fix patch:
diff --git a/env/environment-3.7.yml b/env/environment-3.7.yml
index ef45a93e..b031d1e9 100644
--- a/env/environment-3.7.yml
+++ b/env/environment-3.7.yml
@@ -4,7 +4,7 @@ channels:
   - http://ssb.stsci.edu/astroconda
 dependencies:
   - astropy<4.1
-  - bokeh=2.3.0
+  - bokeh=2.3.2
   - boto3
   - cython=0.29.22
   - docopt=0.6.2
diff --git a/env/environment-3.8.yml b/env/environment-3.8.yml
index 2005900d..002bdd42 100644
--- a/env/environment-3.8.yml
+++ b/env/environment-3.8.yml
@@ -4,7 +4,7 @@ channels:
   - http://ssb.stsci.edu/astroconda
 dependencies:
   - astropy<4.1
-  - bokeh=2.3.0
+  - bokeh=2.3.2
   - boto3
   - cython=0.29.22
   - docopt=0.6.2
diff --git a/env/environment-3.9.yml b/env/environment-3.9.yml
index f65145a6..5f2bfa69 100644
--- a/env/environment-3.9.yml
+++ b/env/environment-3.9.yml
@@ -4,7 +4,7 @@ channels:
   - http://ssb.stsci.edu/astroconda
 dependencies:
   - astropy=4.2
-  - bokeh=2.3.0
+  - bokeh=2.3.2
   - boto3
   - cython=0.29.22
   - docopt=0.6.2
diff --git a/exoctk/data/throughputs/NIRSpec.CLEAR.PRISM.S200A1.txt b/exoctk/data/throughputs/NIRSpec.CLEAR.PRISM.S200A1.txt
new file mode 100644
index 00000000..615b49f6
--- /dev/null
+++ b/exoctk/data/throughputs/NIRSpec.CLEAR.PRISM.S200A1.txt
@@ -0,0 +1,500 @@
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diff --git a/exoctk/data/throughputs/NIRSpec.F070LP.G140H.S200A1.txt b/exoctk/data/throughputs/NIRSpec.F070LP.G140H.S200A1.txt
new file mode 100644
index 00000000..1b014f95
--- /dev/null
+++ b/exoctk/data/throughputs/NIRSpec.F070LP.G140H.S200A1.txt
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diff --git a/exoctk/data/throughputs/NIRSpec.F070LP.G140M.S200A1.txt b/exoctk/data/throughputs/NIRSpec.F070LP.G140M.S200A1.txt
new file mode 100644
index 00000000..75c97f6c
--- /dev/null
+++ b/exoctk/data/throughputs/NIRSpec.F070LP.G140M.S200A1.txt
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diff --git a/exoctk/data/throughputs/NIRSpec.F100LP.G140H.S200A1.txt b/exoctk/data/throughputs/NIRSpec.F100LP.G140H.S200A1.txt
new file mode 100644
index 00000000..dd0ae7a3
--- /dev/null
+++ b/exoctk/data/throughputs/NIRSpec.F100LP.G140H.S200A1.txt
@@ -0,0 +1,500 @@
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diff --git a/exoctk/data/throughputs/NIRSpec.F100LP.G140M.S200A1.txt b/exoctk/data/throughputs/NIRSpec.F100LP.G140M.S200A1.txt
new file mode 100644
index 00000000..395d2f06
--- /dev/null
+++ b/exoctk/data/throughputs/NIRSpec.F100LP.G140M.S200A1.txt
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diff --git a/exoctk/data/throughputs/NIRSpec.F170LP.G235H.S200A1.txt b/exoctk/data/throughputs/NIRSpec.F170LP.G235H.S200A1.txt
new file mode 100644
index 00000000..a596e56a
--- /dev/null
+++ b/exoctk/data/throughputs/NIRSpec.F170LP.G235H.S200A1.txt
@@ -0,0 +1,500 @@
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diff --git a/exoctk/data/throughputs/NIRSpec.F170LP.G235M.S200A1.txt b/exoctk/data/throughputs/NIRSpec.F170LP.G235M.S200A1.txt
new file mode 100644
index 00000000..a7a995a6
--- /dev/null
+++ b/exoctk/data/throughputs/NIRSpec.F170LP.G235M.S200A1.txt
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diff --git a/exoctk/data/throughputs/NIRSpec.F290LP.G395H.S200A1.txt b/exoctk/data/throughputs/NIRSpec.F290LP.G395H.S200A1.txt
new file mode 100644
index 00000000..e3ac74ea
--- /dev/null
+++ b/exoctk/data/throughputs/NIRSpec.F290LP.G395H.S200A1.txt
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diff --git a/exoctk/data/throughputs/NIRSpec.F290LP.G395M.S200A1.txt b/exoctk/data/throughputs/NIRSpec.F290LP.G395M.S200A1.txt
new file mode 100644
index 00000000..fb62c4e0
--- /dev/null
+++ b/exoctk/data/throughputs/NIRSpec.F290LP.G395M.S200A1.txt
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diff --git a/exoctk/exoctk_app/templates/base.html b/exoctk/exoctk_app/templates/base.html
index a9f44a2f..aa544972 100644
--- a/exoctk/exoctk_app/templates/base.html
+++ b/exoctk/exoctk_app/templates/base.html
@@ -146,7 +146,7 @@
                         <div style="float:right; width:120px;text-align:center;">
                             <p>
                                 Running<br>
-                                <a href='https://github.com/ExoCTK/exoctk/releases/tag/v1.2.0'>exoctk v1.2.0</a>{{version|safe}}
+                                <a href='https://github.com/ExoCTK/exoctk/releases/tag/v1.2.1'>exoctk v1.2.1</a>{{version|safe}}
                             </p>
                             <p style='font-size:0.8em'>
                                 <a href='admin' style='color:#aaaaaa;'>Admin Area</a>
diff --git a/exoctk/forward_models/forward_models.py b/exoctk/forward_models/forward_models.py
index 0e865def..260835a7 100644
--- a/exoctk/forward_models/forward_models.py
+++ b/exoctk/forward_models/forward_models.py
@@ -34,7 +34,7 @@
 import pandas as pd
 from sqlalchemy import create_engine
 
-from exoctk.utils import get_env_variables
+from exoctk.utils import get_env_variables, check_for_data
 
 ## -- FUNCTIONS
 
@@ -69,7 +69,7 @@ def fortney_grid(args, write_plot=False, write_table=False):
     temp_out : list of str of int
         The list of temperatures in the model grid.
     """
-    utils.check_for_data('fortney')
+    check_for_data('fortney')
 
     # Check for Fortney Grid database
     print(os.path.join(get_env_variables()['exoctk_data'], 'fortney/fortney_models.db'))
@@ -206,7 +206,7 @@ def generic_grid(input_args, write_plot=False, write_table=False):
     error_message : str
         An error message, or lack therof.
     """
-    utils.check_for_data('generic')
+    check_for_data('generic')
 
     # Find path to the database.
     database_path = os.path.join(get_env_variables()['exoctk_data'], 'generic/generic_grid_db.hdf5')
diff --git a/exoctk/throughputs.py b/exoctk/throughputs.py
index a4b9c69e..36b3cfb8 100644
--- a/exoctk/throughputs.py
+++ b/exoctk/throughputs.py
@@ -42,7 +42,7 @@ def __init__(self, name, **kwargs):
             super().__init__(name, **kwargs)
 
 
-def get_pce(instrument='niriss', mode='soss', filter='clear', disperser='gr700xd', aperture='soss'):
+def get_pce(instrument='niriss', mode='soss', filter='clear', disperser='gr700xd', aperture='soss', detector=None):
     """
     Use pandeia to generate the JWST throughputs
 
@@ -66,7 +66,7 @@ def get_pce(instrument='niriss', mode='soss', filter='clear', disperser='gr700xd
     """
     # Get optical element configuration
     obsmode = {'instrument': instrument, 'mode': mode, 'filter': filter, 'aperture': aperture, 'disperser': disperser}
-    conf = {'instrument': obsmode}
+    conf = {'instrument': obsmode, 'detector': detector}
     i = InstrumentFactory(config=conf)
 
     # Determine wavelength range
@@ -92,8 +92,8 @@ def generate_JWST_throughputs(path=None, data_dir=None):
 
     else:
 
-        # Iterate over science instruments
-        for inst in ['niriss', 'nircam', 'nirspec', 'miri']:
+        # Iterate over science instruments (NIRSpec separated out below)
+        for inst in ['niriss', 'nircam', 'miri']:
 
             # Get all valid configurations from pandeia config file
             cfgfile = open(os.path.join(path, 'jwst/{}/config.json'.format(inst)))
@@ -147,4 +147,26 @@ def generate_JWST_throughputs(path=None, data_dir=None):
                             print("{} file created!".format(datafile_path))
 
                         except KeyError:
-                            print("Could not produce throughput for {}".format(conf))
\ No newline at end of file
+                            print("Could not produce throughput for {}".format(conf))
+
+        # Do NIRSpec separately because pandeia doesn't show them correctly
+        nirspec_combos = ['G140M/F070LP', 'G140M/F100LP', 'G235M/F170LP', 'G395M/F290LP', 'G140H/F070LP', 'G140H/F100LP', 'G235H/F170LP', 'G395H/F290LP', 'PRISM/CLEAR']
+
+        for disp, filt in [i.split('/') for i in nirspec_combos]:
+            inst = 'nirspec'
+            aper = 's200a1'
+            mode = 'fixed_slit'
+            detector = {"nexp": 1, "ngroup": 10, "nint": 1, "readout_pattern": "nrs", "subarray": "full"}
+
+            # Generate throughput
+            wave, thru = get_pce(inst, mode, filt.lower(), disp.lower(), aper, detector)
+            name = '.'.join(
+                [inst.upper().replace('CAM', 'Cam').replace('SPEC', 'Spec'), filt.upper(),
+                 disp.upper(), aper.upper()])
+
+            # Save to txt file
+            data = np.array([wave, thru]).T
+            datafile_path = os.path.join(data_dir, '{}.txt'.format(name))
+            with open(datafile_path, 'w+') as datafile_id:
+                np.savetxt(datafile_id, data)
+            print("{} file created!".format(datafile_path))
diff --git a/pip_requirements.txt b/pip_requirements.txt
index e703f5ed..6fa63c92 100644
--- a/pip_requirements.txt
+++ b/pip_requirements.txt
@@ -3,37 +3,37 @@ astropy==4.0.2
 bandit==1.7.0
 batman-package==2.4.6
 bibtexparser==1.2.0
-bokeh==2.3.0
-boto3==1.17.42
+bokeh==2.3.2
+boto3==1.17.84
 corner==2.2.1
-cython==0.29.22
-ddtrace==0.48.2
+cython==0.29.23
+ddtrace==0.49.2
 docopt==0.6.2
-docutils==0.16
-flake8==3.9.0
-flask==1.1.2
-flask_wtf==0.14.3
+docutils==0.17.1
+flake8==3.9.2
+flask==2.0.1
+flask_wtf==0.15.1
 gunicorn==20.1.0
 h5py==3.2.1
-ipython==7.22.0
+ipython==7.24.0
 lmfit==1.0.1
-matplotlib==3.4.1
-numpy==1.20.2
+matplotlib==3.4.2
+numpy==1.20.3
 numpydoc==1.1.0
-pandas==1.2.3
+pandas==1.2.4
 paramiko==2.7.2
 platon==5.1.2
 pysiaf==0.10.0
 pysynphot==1.0.0
-pytest==6.2.2
+pytest==6.2.4
 pyyaml==5.4.1
-scipy==1.6.2
+scipy==1.6.3
 scp==0.13.3
-sphinx==3.5.3
+sphinx==4.0.2
 sphinx_astropy==1.3
 sphinx-automodapi==0.13
 svo_filters==0.4.1
-sqlalchemy==1.4.4
+sqlalchemy==1.4.17
 twine==3.4.1
 wtforms==2.3.3
 git+https://github.com/spacetelescope/jwst_gtvt.git@cd6bc76f66f478eafbcc71834d3e735c73e03ed5
diff --git a/setup.py b/setup.py
index 532a337d..b77ab0d8 100755
--- a/setup.py
+++ b/setup.py
@@ -49,7 +49,7 @@
 
 setup(
     name='exoctk',
-    version='1.2.0',
+    version='1.2.1',
     description='Observation reduction and planning tools for exoplanet science',
     packages=find_packages(
         ".",


Test patch:
diff --git a/exoctk/tests/test_forward_models.py b/exoctk/tests/test_forward_models.py
new file mode 100644
index 00000000..9e2c72d7
--- /dev/null
+++ b/exoctk/tests/test_forward_models.py
@@ -0,0 +1,64 @@
+#! /usr/bin/env python
+
+"""Tests for the ``forward_models`` module
+
+Authors
+-------
+
+    Joe Filippazzo
+
+Use
+---
+
+    These tests can be run via the command line (omit the ``-s`` to
+    suppress verbose output to stdout):
+    ::
+
+        pytest -s test_forward_models.py
+"""
+
+import unittest
+import pytest
+import os
+
+from exoctk.forward_models.forward_models import fortney_grid, generic_grid
+
+ON_GITHUB_ACTIONS = os.path.expanduser('~') in ['/home/runner', '/Users/runner']
+
+
+class TestFortney(unittest.TestCase):
+    """Tests for the fortney_grid function"""
+    def setUp(self):
+        """Setup"""
+        temp = 1000
+        chem = 'noTiO'
+        cloud = '0'
+        pmass = '1.5'
+        m_unit = 'M_jup'
+        reference_radius = '1'
+        r_unit = 'R_jup'
+        rstar = '1'
+        rstar_unit = 'R_sun'
+
+        self.args = {'temp': temp, 'chem': chem, 'cloud': cloud, 'pmass': pmass,
+                      'm_unit': m_unit, 'reference_radius': reference_radius,
+                      'r_unit': r_unit, 'rstar': rstar, 'rstar_unit': rstar_unit}
+
+    @pytest.mark.skipif(ON_GITHUB_ACTIONS, reason='Grid data not available')
+    def test_model(self):
+        """Test that fortney_grid can be run"""
+        fig, fh, temp_out = fortney_grid(self.args, write_plot=False, write_table=False)
+
+
+class TestGeneric(unittest.TestCase):
+    """Tests for the generic_grid function"""
+    def setUp(self):
+        """Setup"""
+        self.args = {'r_star' : 1, 'r_planet' : 0.1, 'gravity': '10', 'temperature': 1000,
+                     'condensation': 'local', 'metallicity': '+1.0', 'c_o': '0.56', 'haze': '0010',
+                     'cloud': '0.00'}
+
+    @pytest.mark.skipif(ON_GITHUB_ACTIONS, reason='Grid data not available')
+    def test_model(self):
+        """Test that fortney_grid can be run"""
+        fig, fh, closest_match, error_message = generic_grid(self.args, write_plot=False, write_table=False)