Compatibility with Python 3.8

tomasstolker · Dec 19, 2020 · 3cf6aed · 3cf6aed
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diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -7,7 +7,7 @@ build:
     image: latest
 
 python:
-   version: 3.7
+   version: 3.8
    install:
       - requirements: requirements.txt
       - requirements: docs/requirements.txt
diff --git a/.travis.yml b/.travis.yml
@@ -5,6 +5,7 @@ dist: xenial
 python:
   - 3.6
   - 3.7
+  - 3.8
 
 before_install:
   - sudo apt-get install pandoc

diff --git a/README.rst b/README.rst
@@ -6,7 +6,7 @@
 .. image:: https://badge.fury.io/py/species.svg
     :target: https://badge.fury.io/py/species
 
-.. image:: https://img.shields.io/badge/Python-3.6%2C%203.7-yellow.svg?style=flat
+.. image:: https://img.shields.io/badge/Python-3.6%2C%203.7%2C%203.8-yellow.svg?style=flat
     :target: https://pypi.python.org/pypi/species
 
 .. image:: https://travis-ci.org/tomasstolker/species.svg?branch=master
@@ -37,7 +37,7 @@ Documentation can be found at `http://species.readthedocs.io <http://species.rea
 Attribution
 -----------
 
-Please cite `Stolker et al. (2020) <https://ui.adsabs.harvard.edu/abs/2020A%26A...635A.182S/abstract>`_ whenever results from *species* are used in a publication. Please also make sure to give credit to the relevant papers regarding the use of the publicly available data that *species* benefits from. The *species* logo is `available <https://people.phys.ethz.ch/~stolkert/species/species_logo.zip>`_ for use in presentations.
+Please cite `Stolker et al. (2020) <https://ui.adsabs.harvard.edu/abs/2020A%26A...635A.182S/abstract>`_ whenever results from *species* are used in a publication. Please also make sure to give credit to the relevant papers regarding the use of the publicly available data that *species* benefits from. The *species* logo is `available <https://home.strw.leidenuniv.nl/~stolker/species/species_logo.zip>`_ for use in presentations.
 
 Contributing
 ------------

diff --git a/docs/about.rst b/docs/about.rst
@@ -6,7 +6,7 @@ About
 Questions & feedback
 --------------------
 
-*species* is developed by Tomas Stolker (tomas.stolker@phys.ethz.ch). Feel free to send an email for questions, comments, or suggestions.
+*species* is developed by Tomas Stolker (stolker@strw.leidenuniv.nl). Feel free to send an email for questions, comments, or suggestions.
 
 Attribution
 -----------
@@ -16,4 +16,4 @@ Please cite `Stolker et al. (2020) <https://ui.adsabs.harvard.edu/abs/2020A%26A.
 Logo
 ----
 
-Are you presenting results obtained with `species` in a talk or poster? Please consider using the `logo <https://people.phys.ethz.ch/~stolkert/species/species_logo.zip>`_ that is available in PDF and PNG format.
+Are you presenting results obtained with `species` in a talk or poster? Please consider using the `logo <https://home.strw.leidenuniv.nl/~stolker/species/species_logo.zip>`_ that is available in PDF and PNG format.
diff --git a/docs/index.rst b/docs/index.rst
@@ -3,11 +3,11 @@
 Documentation for *species*
 ===========================
 
-*species* is a toolkit for atmospheric characterization of self-luminous exoplanets and brown dwarfs. The package has been developed and is maintained by |stolker|.
+*species* is a toolkit for atmospheric characterization of directly imaged exoplanets. The package has been developed and is maintained by |stolker|.
 
 .. |stolker| raw:: html
 
-	<a href="https://people.phys.ethz.ch/~stolkert/" target="_blank">Tomas Stolker</a>
+	<a href="https://home.strw.leidenuniv.nl/~stolker/" target="_blank">Tomas Stolker</a>
 
 .. toctree::
    :maxdepth: 2

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -3,7 +3,8 @@
 Installation
 ============
 
-*species* is compatible with Python 3.6/3.7 and is available in the |pypi| and on |github|.
+*species* is compatible with Python 3.6/3.7/3.8 and is available in the |pypi| and on |github|.
+
 
 Installation from PyPI
 ----------------------

diff --git a/docs/species.analysis.rst b/docs/species.analysis.rst
@@ -28,7 +28,6 @@ species.analysis.photometry module
    :undoc-members:
    :show-inheritance:
 
-
 Module contents
 ---------------
 

diff --git a/docs/species.core.rst b/docs/species.core.rst
@@ -28,7 +28,6 @@ species.core.setup module
    :undoc-members:
    :show-inheritance:
 
-
 Module contents
 ---------------
 

diff --git a/docs/species.data.rst b/docs/species.data.rst
@@ -180,7 +180,6 @@ species.data.vlm\_plx module
    :undoc-members:
    :show-inheritance:
 
-
 Module contents
 ---------------
 

diff --git a/docs/species.plot.rst b/docs/species.plot.rst
@@ -28,7 +28,6 @@ species.plot.plot\_spectrum module
    :undoc-members:
    :show-inheritance:
 
-
 Module contents
 ---------------
 

diff --git a/docs/species.read.rst b/docs/species.read.rst
@@ -68,7 +68,6 @@ species.read.read\_spectrum module
    :undoc-members:
    :show-inheritance:
 
-
 Module contents
 ---------------
 

diff --git a/docs/species.util.rst b/docs/species.util.rst
@@ -60,7 +60,6 @@ species.util.test\_util module
    :undoc-members:
    :show-inheritance:
 
-
 Module contents
 ---------------
 

diff --git a/setup.py b/setup.py
@@ -11,11 +11,11 @@
 setup(
     name='species',
     version='0.3.2',
-    description='Toolkit for atmospheric characterization of exoplanets and brown dwarfs',
+    description='Toolkit for atmospheric characterization of directly imaged exoplanets',
     long_description=open('README.rst').read(),
     long_description_content_type='text/x-rst',
     author='Tomas Stolker',
-    author_email='tomas.stolker@phys.ethz.ch',
+    author_email='stolker@strw.leidenuniv.nl',
     url='https://github.com/tomasstolker/species',
     project_urls={'Documentation': 'https://species.readthedocs.io'},
     packages=['species',
@@ -25,7 +25,7 @@
               'species.plot',
               'species.read',
               'species.util'],
-    package_dir={'species':'species'},
+    package_dir={'species': 'species'},
     include_package_data=True,
     install_requires=reqs,
     license='MIT',
@@ -39,5 +39,6 @@
         'Natural Language :: English',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
     ],
 )
diff --git a/species/__init__.py b/species/__init__.py
@@ -65,5 +65,5 @@
 __license__ = 'MIT'
 __version__ = '0.3.2'
 __maintainer__ = 'Tomas Stolker'
-__email__ = 'tomas.stolker@phys.ethz.ch'
+__email__ = 'stolker@strw.leidenuniv.nl'
 __status__ = 'Development'
diff --git a/species/data/dust.py b/species/data/dust.py
@@ -36,7 +36,7 @@ def add_optical_constants(input_path: str,
     if not os.path.exists(input_path):
         os.makedirs(input_path)
 
-    url = 'https://people.phys.ethz.ch/~stolkert/species/optical_constants.zip'
+    url = 'https://home.strw.leidenuniv.nl/~stolker/species/optical_constants.zip'
 
     data_file = os.path.join(input_path, 'optical_constants.zip')
 
@@ -116,7 +116,7 @@ def add_cross_sections(input_path: str,
     if not os.path.exists(input_path):
         os.makedirs(input_path)
 
-    url = 'https://people.phys.ethz.ch/~stolkert/species/lognorm_mgsio3_c_ext.fits'
+    url = 'https://home.strw.leidenuniv.nl/~stolker/species/lognorm_mgsio3_c_ext.fits'
 
     data_file = os.path.join(input_path, 'lognorm_mgsio3_c_ext.fits')
 
@@ -150,7 +150,7 @@ def add_cross_sections(input_path: str,
         data_range = f'{np.amin(hdu_list[3].data)} - {np.amax(hdu_list[3].data)}'
         print(f'   - Geometric standard deviation range: {data_range}')
 
-    url = 'https://people.phys.ethz.ch/~stolkert/species/powerlaw_mgsio3_c_ext.fits'
+    url = 'https://home.strw.leidenuniv.nl/~stolker/species/powerlaw_mgsio3_c_ext.fits'
 
     data_file = os.path.join(input_path, 'powerlaw_mgsio3_c_ext.fits')
 

diff --git a/species/data/filters.py b/species/data/filters.py
@@ -86,7 +86,7 @@ def download_filter(filter_id: str) -> Tuple[Optional[np.ndarray],
         os.remove('VisAO_Ys_filter_curve.dat')
 
     elif filter_id == 'ALMA/band6':
-        url = 'https://people.phys.ethz.ch/~stolkert/species/alma_band6.dat'
+        url = 'https://home.strw.leidenuniv.nl/~stolker/species/alma_band6.dat'
         urllib.request.urlretrieve(url, 'alma_band6.dat')
 
         wavelength, transmission = np.loadtxt('alma_band6.dat', unpack=True)
@@ -96,7 +96,7 @@ def download_filter(filter_id: str) -> Tuple[Optional[np.ndarray],
         os.remove('alma_band6.dat')
 
     elif filter_id == 'ALMA/band7':
-        url = 'https://people.phys.ethz.ch/~stolkert/species/alma_band7.dat'
+        url = 'https://home.strw.leidenuniv.nl/~stolker/species/alma_band7.dat'
         urllib.request.urlretrieve(url, 'alma_band7.dat')
 
         wavelength, transmission = np.loadtxt('alma_band7.dat', unpack=True)

diff --git a/species/data/irtf.py b/species/data/irtf.py
@@ -44,7 +44,7 @@ def add_irtf(input_path: str,
     if sptypes is None:
         sptypes = ['F', 'G', 'K', 'M', 'L', 'T']
 
-    distance_url = 'https://people.phys.ethz.ch/~stolkert/species/distance.dat'
+    distance_url = 'https://home.strw.leidenuniv.nl/~stolker/species/distance.dat'
     distance_file = os.path.join(input_path, 'distance.dat')
 
     if not os.path.isfile(distance_file):

diff --git a/species/data/spex.py b/species/data/spex.py
@@ -31,7 +31,7 @@ def add_spex(input_path, database):
         None
     """
 
-    distance_url = 'https://people.phys.ethz.ch/~stolkert/species/distance.dat'
+    distance_url = 'https://home.strw.leidenuniv.nl/~stolker/species/distance.dat'
     distance_file = os.path.join(input_path, 'distance.dat')
 
     if not os.path.isfile(distance_file):

diff --git a/species/plot/plot_spectrum.py b/species/plot/plot_spectrum.py
@@ -230,7 +230,7 @@ def plot_spectrum(boxes: list,
         ax1.set_xlabel('Wavelength (µm)', fontsize=13)
 
     if filters is not None:
-        ax2.set_ylabel('T$_\lambda$', fontsize=13)
+        ax2.set_ylabel(r'T$_\lambda$', fontsize=13)
 
     if residuals is not None:
         if quantity == 'flux density':

diff --git a/test/test_read/test_isochrone.py b/test/test_read/test_isochrone.py
@@ -17,7 +17,7 @@ def setup_class(self):
 
         filename = 'model.AMES-Cond-2000.M-0.0.NaCo.Vega'
 
-        url = 'https://people.phys.ethz.ch/~stolkert/species/model.AMES-Cond-2000.M-0.0.NaCo.Vega'
+        url = 'https://home.strw.leidenuniv.nl/~stolker/species/model.AMES-Cond-2000.M-0.0.NaCo.Vega'
 
         urllib.request.urlretrieve(url, filename)