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ExoCTK · Feb 10, 2022 · 9e46e65 · 9e46e65
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,18 @@ This file tracks all major changes in each `exoctk` release.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.2.3] - 2022-02-01
+
+### Fixed
+
+- Date format in hover tool of contam visibility plots
+- Logging issue with production server.
+
+### Changed
+
+- Removed support for "uniform" (constant) limb-darkening law.
+- Removed lmfit from requirements.
+
 ## [1.2.2] - 2021-07-09
 
 ### Added

diff --git a/env/environment-3.7.yml b/env/environment-3.7.yml
@@ -4,16 +4,16 @@ channels:
   - http://ssb.stsci.edu/astroconda
 dependencies:
   - astropy<4.1
-  - bokeh=2.3.3
+  - bokeh=2.4.2
   - boto3
   - cython=0.29.24
   - docopt=0.6.2
-  - docutils=0.16
+  - docutils=0.17.1
   - flake8=3.9.0
   - flask=1.1.2
   - gunicorn=20.1.0
-  - h5py=3.2.1
-  - ipython=7.26.0
+  - h5py=3.6.0
+  - ipython=7.29.0
   - jupyter=1.0.0
   - matplotlib=3.1.3
   - numpy=1.19.2
@@ -25,26 +25,26 @@ dependencies:
   - python=3.7.1
   - pyyaml
   - scipy=1.6.2
-  - scp=0.13.6
-  - sphinx=4.0.2
-  - sqlalchemy=1.4.22
+  - scp=0.14.1
+  - sphinx=4.2.0
+  - sqlalchemy=1.4.27
   - twine=3.4.1
   - wtforms=2.3.3
   - pip:
     - asteval==0.9.25
     - awscli
-    - bandit==1.7.0
+    - bandit==1.7.1
     - batman-package==2.4.8
     - bibtexparser==1.2.0
     - corner==2.2.1
-    - ddtrace==0.52.1
-    - flask_wtf==0.14.3
+    - ddtrace==0.57.0
+    - flask_wtf==1.0.0
     - lmfit==1.0.1
     - platon==4.0
     - pysiaf==0.10.0
-    - pysynphot==1.0.0
+    - pysynphot==2.0.0
     - PyYAML>=5.4
-    - sphinx_astropy==1.5
+    - sphinx_astropy==1.6.0
     - svo-filters==0.4.1
     - werkzeug>=2.0
     - git+https://github.com/spacetelescope/jwst_gtvt.git@cd6bc76f66f478eafbcc71834d3e735c73e03ed5

diff --git a/env/environment-3.8.yml b/env/environment-3.8.yml
@@ -8,12 +8,12 @@ dependencies:
   - boto3
   - cython=0.29.24
   - docopt=0.6.2
-  - docutils=0.16
+  - docutils=0.17.1
   - flake8=3.9.0
   - flask=1.1.2
   - gunicorn=20.1.0
-  - h5py=3.2.1
-  - ipython=7.26.0
+  - h5py=3.6.0
+  - ipython=7.29.0
   - jupyter=1.0.0
   - matplotlib=3.3.4
   - numpy=1.19.2
@@ -25,25 +25,25 @@ dependencies:
   - python=3.8.5
   - pyyaml
   - scipy=1.6.2
-  - scp=0.13.6
-  - sphinx=4.0.2
-  - sqlalchemy=1.4.22
+  - scp=0.14.1
+  - sphinx=4.2.0
+  - sqlalchemy=1.4.27
   - twine=3.2.0
   - wtforms=2.3.3
   - pip:
     - asteval==0.9.25
     - awscli
-    - bandit==1.7.0
+    - bandit==1.7.1
     - batman-package==2.4.8
     - bibtexparser==1.2.0
     - corner==2.2.1
-    - ddtrace==0.52.1
-    - flask_wtf==0.14.3
+    - ddtrace==0.57.0
+    - flask_wtf==1.0.0
     - lmfit==1.0.2
     - platon==4.0
     - pysiaf==0.10.0
-    - pysynphot==1.0.0
-    - sphinx_astropy==1.5
+    - pysynphot==2.0.0
+    - sphinx_astropy==1.6.0
     - svo-filters==0.4.1
     - werkzeug>=2.0
     - git+https://github.com/spacetelescope/jwst_gtvt.git@cd6bc76f66f478eafbcc71834d3e735c73e03ed5

diff --git a/env/environment-3.9.yml b/env/environment-3.9.yml
@@ -10,8 +10,8 @@ dependencies:
   - docopt=0.6.2
   - flake8=3.9.0
   - flask=1.1.2
-  - h5py=2.10.0
-  - ipython=7.26.0
+  - h5py=3.6.0
+  - ipython=7.29.0
   - jupyter=1.0.0
   - matplotlib=3.3.4
   - numpy=1.19.2
@@ -23,27 +23,26 @@ dependencies:
   - python=3.9.1
   - pyyaml
   - scipy=1.6.2
-  - scp=0.13.6
-  - sphinx=4.0.2
-  - sqlalchemy=1.4.22
+  - scp=0.14.1
+  - sphinx=4.2.0
+  - sqlalchemy=1.4.27
   - twine=3.2.0
   - wtforms=2.3.3
   - pip:
     - asteval==0.9.25
     - awscli
-    - bandit==1.7.0
+    - bandit==1.7.1
     - batman-package==2.4.8
     - bibtexparser==1.2.0
     - corner==2.2.1
-    - ddtrace==0.52.1
-    - docutils==0.15.2
-    - flask_wtf==0.14.3
+    - ddtrace==0.57.0
+    - docutils==0.17.1
+    - flask_wtf==1.0.0
     - gunicorn==20.0.4
-    - lmfit==1.0.2
-    - platon==4.0
+    - platon==5.3
     - pysiaf==0.10.0
-    - pysynphot==1.0.0
-    - sphinx_astropy==1.5
+    - pysynphot==2.0.0
+    - sphinx_astropy==1.6.0
     - svo-filters==0.4.1
     - werkzeug>=2.0
     - git+https://github.com/spacetelescope/jwst_gtvt.git@cd6bc76f66f478eafbcc71834d3e735c73e03ed5

diff --git a/exoctk/contam_visibility/visibilityPA.py b/exoctk/contam_visibility/visibilityPA.py
@@ -302,10 +302,6 @@ def using_gtvt(
                                         panom=paNom,
                                         pamax=paMax,
                                         date=gd))
-    TOOLTIPS = [('Date', '@date{%F}'),
-                ('Maximum Aperture PA', '@pamax'),
-                ('Nominal Aperture PA', '@panom'),
-                ('Minimum Aperture PA', '@pamin')]
 
     # Time to plot
     if output == 'bokeh':
@@ -334,10 +330,11 @@ def using_gtvt(
     fig.circle('date', 'pamax', color=COLOR, size=1, source=SOURCE)
 
     # Adding HoverTool
-    fig.add_tools(HoverTool(renderers=[nom],
-                            tooltips=TOOLTIPS,
-                            formatters={'date': 'datetime'},
-                            mode='vline'))
+    fig.add_tools(HoverTool(tooltips=[('Date', '@date{%F}'),
+                                      ('Maximum Aperture PA', '@pamax'),
+                                      ('Nominal Aperture PA', '@panom'),
+                                      ('Minimum Aperture PA', '@pamin')],
+                            formatters={'@date': 'datetime'}))
 
     # Plot formatting
     fig.xaxis.axis_label = 'Date'

diff --git a/exoctk/exoctk_app/app_exoctk.py b/exoctk/exoctk_app/app_exoctk.py
@@ -37,13 +37,13 @@
 
 # Load the database to log all form submissions
 if get_env_variables()['exoctklog_dir'] is None:
-    dbpath = ':memory:'
+    DBPATH = ':memory:'
 else:
-    dbpath = os.path.realpath(os.path.join(get_env_variables()['exoctklog_dir'], 'exoctk_log.db'))
-    if not os.path.isfile(dbpath):
-        log_exoctk.create_db(dbpath)
+    DBPATH = os.path.realpath(os.path.join(get_env_variables()['exoctklog_dir'], 'exoctk_log.db'))
+    if not os.path.isfile(DBPATH):
+        log_exoctk.create_db(DBPATH)
 try:
-    DB = log_exoctk.load_db(dbpath)
+    DB = log_exoctk.load_db(DBPATH)
 except IOError:
     DB = None
 
@@ -888,6 +888,8 @@ def secret_page():
     ``flask.render_template`` obj
         The rendered template for the admin page.
     """
+    # Reload the DB when this page loads so the data is current
+    DB = log_exoctk.load_db(DBPATH)
 
     tables = [i[0] for i in DB.execute("SELECT name FROM sqlite_master WHERE type='table'").fetchall()]
 

diff --git 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/v1.2.2'>exoctk v1.2.2</a>{{version|safe}}
+                                <a href='https://github.com/ExoCTK/exoctk/releases/tag/v1.2.3'>exoctk v1.2.3</a>{{version|safe}}
                             </p>
                             <p style='font-size:0.8em'>
                                 <a href='admin' style='color:#aaaaaa;'>Admin Area</a>

diff --git a/exoctk/lightcurve_fitting/fitters.py b/exoctk/lightcurve_fitting/fitters.py
@@ -6,7 +6,7 @@
 
 import copy
 
-import lmfit
+# import lmfit
 import numpy as np
 
 from .parameters import Parameters

diff --git a/exoctk/limb_darkening/limb_darkening_fit.py b/exoctk/limb_darkening/limb_darkening_fit.py
@@ -44,7 +44,7 @@ def ld_profile(name='quadratic', latex=False):
     ----------
     name: str
         The name of the limb darkening profile function to use,
-        including 'uniform', 'linear', 'quadratic', 'square-root',
+        including 'linear', 'quadratic', 'square-root',
         'logarithmic', 'exponential', '3-parameter', and '4-parameter'
     latex: bool
         Return the function as a LaTeX formatted string
@@ -56,16 +56,11 @@ def ld_profile(name='quadratic', latex=False):
 
     """
     # Supported profiles a la BATMAN
-    names = ['uniform', 'linear', 'quadratic', 'square-root', 'logarithmic', 'exponential', '3-parameter', '4-parameter']
+    names = ['linear', 'quadratic', 'square-root', 'logarithmic', 'exponential', '3-parameter', '4-parameter']
 
     # Check that the profile is supported
     if name in names:
 
-        # Uniform
-        if name == 'uniform':
-            def profile(m, c1):
-                return c1
-
         # Linear
         if name == 'linear':
             def profile(m, c1):
@@ -155,7 +150,7 @@ def __init__(self, model_grid='ACES'):
         dtypes = ['|S20', float, float, float, '|S20', '|S20', '|S20', object, object, object, np.float16, np.float16, np.float16, object, object, np.float16, object, object, np.float16, object, object, object, '|S20']
         self.results = at.Table(names=columns, dtype=dtypes)
 
-        self.ld_color = {'quadratic': 'blue', '4-parameter': 'red', 'exponential': 'green', 'linear': 'orange', 'square-root': 'cyan', '3-parameter': 'magenta', 'logarithmic': 'pink', 'uniform': 'purple'}
+        self.ld_color = {'quadratic': 'blue', '4-parameter': 'red', 'exponential': 'green', 'linear': 'orange', 'square-root': 'cyan', '3-parameter': 'magenta', 'logarithmic': 'pink'}
 
         self.count = 1
 
@@ -214,7 +209,7 @@ def calculate(self, Teff, logg, FeH, profile, mu_min=0.05, ld_min=0.01,
             The logarithm of the metallicity
         profile: str
             The name of the limb darkening profile function to use,
-            including 'uniform', 'linear', 'quadratic', 'square-root',
+            including 'linear', 'quadratic', 'square-root',
             'logarithmic', 'exponential', and '4-parameter'
         mu_min: float
             The minimum mu value to consider

diff --git a/exoctk/log_exoctk.py b/exoctk/log_exoctk.py
@@ -77,7 +77,7 @@ def create_db(dbpath, overwrite=True):
     cur.execute("CREATE TABLE 'groups_integrations' ('id' INTEGER NOT NULL UNIQUE, 'date' TEXT NOT NULL, 'targname' TEXT, 'kmag' REAL, 'mod' TEXT, 'obs_time' REAL, 'n_group' REAL, 'ins' TEXT, 'filt' TEXT, 'filt_ta' TEXT, 'subarray' TEXT, 'subarray_ta' TEXT, 'sat_mode' TEXT, 'sat_max' REAL, PRIMARY KEY(id));")
 
     # Table for limb_darkening
-    cur.execute("CREATE TABLE 'limb_darkening' ('id' INTEGER NOT NULL UNIQUE, 'date' TEXT NOT NULL, 'n_bins' INTEGER, 'teff' REAL, 'logg' REAL, 'feh' REAL, 'bandpass' TEXT, 'modeldir' TEXT, 'wave_min' REAL, 'mu_min' REAL, 'wave_max' REAL, 'local_files' TEXT, 'pixels_per_bin' INTEGER, 'uniform' TEXT, 'linear' TEXT, 'quadratic' TEXT, 'squareroot' TEXT, 'logarithmic' TEXT, 'exponential' TEXT, 'three_parameter' TEXT, 'four_parameter' TEXT, PRIMARY KEY(id));")
+    cur.execute("CREATE TABLE 'limb_darkening' ('id' INTEGER NOT NULL UNIQUE, 'date' TEXT NOT NULL, 'n_bins' INTEGER, 'teff' REAL, 'logg' REAL, 'feh' REAL, 'bandpass' TEXT, 'modeldir' TEXT, 'wave_min' REAL, 'mu_min' REAL, 'wave_max' REAL, 'local_files' TEXT, 'pixels_per_bin' INTEGER, 'linear' TEXT, 'quadratic' TEXT, 'squareroot' TEXT, 'logarithmic' TEXT, 'exponential' TEXT, 'three_parameter' TEXT, 'four_parameter' TEXT, PRIMARY KEY(id));")
 
     # Table for contam_visibility
     cur.execute("CREATE TABLE 'contam_visibility' ('id' INTEGER NOT NULL UNIQUE, 'date' TEXT NOT NULL, 'targname' TEXT, 'ra' REAL, 'dec' REAL, 'inst' TEXT, 'companion' TEXT, PRIMARY KEY(id));")

diff --git a/exoctk/tests/test_atmospheric_retrievals.py b/exoctk/tests/test_atmospheric_retrievals.py
@@ -22,10 +22,6 @@
 from platon.constants import R_sun, R_jup, M_jup
 import pytest
 
-from ..atmospheric_retrievals.aws_tools import get_config
-from ..atmospheric_retrievals.platon_wrapper import _apply_factors
-from ..atmospheric_retrievals.platon_wrapper import PlatonWrapper
-
 ON_GITHUB_ACTIONS = os.path.expanduser('~') in ['/home/runner', '/Users/runner']
 
 
@@ -42,6 +38,8 @@ def initialize_platon_wrapper_object():
         The ``PlatonWrapper`` object
     """
 
+    from ..atmospheric_retrievals.platon_wrapper import PlatonWrapper
+
     # Define the fit parameters
     params = {
         'Rs': 1.19,  # Required
@@ -79,11 +77,14 @@ def initialize_platon_wrapper_object():
     return pw
 
 
+@pytest.mark.skipif(ON_GITHUB_ACTIONS, reason='Test takes too long on Travis server.  Try testing locally.')
 def test_apply_factors():
     """Test the ``_apply_factors()`` function in ``platon_wrapper``
     module.
     """
 
+    from ..atmospheric_retrievals.platon_wrapper import _apply_factors
+
     params = {'Rs': 1.19, 'Mp': 0.73, 'Rp': 1.4}
     params = _apply_factors(params)
 
@@ -93,9 +94,11 @@ def test_apply_factors():
     assert params['Rp'] == 100088800.0
 
 
+@pytest.mark.skipif(ON_GITHUB_ACTIONS, reason='Test takes too long on Travis server.  Try testing locally.')
 def test_get_config():
     """Tests the ``get_config`` function in ``aws_tools`` module."""
 
+    from ..atmospheric_retrievals.aws_tools import get_config
     settings = get_config()
 
     assert isinstance(settings, dict)