v0.0.4

Makefile

@@ -2,6 +2,7 @@
 
 help:
 	@echo "pypi - submit package to the PyPI server"
+	@echo "pypi-test - submit package to the TestPyPI server"
 	@echo "docs - generate Sphinx documentation"
 	@echo "coverage - check code coverage"
 	@echo "test - run test cases"
@@ -11,6 +12,10 @@ pypi:
 	python setup.py sdist bdist_wheel
 	twine upload dist/*
 
+pypi-test:
+	python setup.py sdist bdist_wheel
+	twine upload --repository-url https://test.pypi.org/legacy/ dist/*
+
 docs:
 	rm -f docs/species.*rst
 	sphinx-apidoc -o docs/ species

README.rst

@@ -41,4 +41,4 @@ License
 
 Copyright 2018 Tomas Stolker
 
-SPECIES is free software and distributed under the GNU General Public License v3.
+SPECIES is distributed under the GNU General Public License v3. See the LICENSE file for the terms and conditions.

setup.py

@@ -12,13 +12,18 @@
 
 setup(
     name='species',
-    version='0.0.3',
+    version='0.0.4',
     description='Toolkit for analyzing spectral and photometric data of planetary and substellar atmospheres',
     long_description=open('README.rst').read(),
     author='Tomas Stolker',
     author_email='[email protected]',
     url='https://github.com/tomasstolker/species',
-    packages=['species'],
+    packages=['species',
+              'species.analysis',
+              'species.core',
+              'species.data',
+              'species.plot',
+              'species.read'],
     package_dir={'species':'species'},
     include_package_data=True,
     install_requires=reqs,

species/__init__.py

@@ -34,7 +34,7 @@
 
 __author__ = 'Tomas Stolker'
 __license__ = 'GPLv3'
-__version__ = '0.0.3'
+__version__ = '0.0.4'
 __maintainer__ = 'Tomas Stolker'
 __email__ = '[email protected]'
 __status__ = 'Development'

species/analysis/fit.py

@@ -12,9 +12,9 @@
 import progress.bar
 import numpy as np
 
-from . import photometry
-from .. data import database
-from .. read import read_model, read_object
+from species.analysis import photometry
+from species.data import database
+from species.read import read_model, read_object
 
 
 MIN_CHISQ = np.inf

species/analysis/photometry.py

@@ -10,8 +10,8 @@
 
 from scipy.integrate import simps
 
-from .. data import database
-from .. read import read_filter, read_spectrum
+from species.data import database
+from species.read import read_filter, read_spectrum
 
 
 def apparent_to_absolute(app_mag, distance):

species/data/btnextgen.py

@@ -13,7 +13,7 @@
 
 from scipy.interpolate import interp1d
 
-from . import util
+from species.data import util
 
 
 def add_btnextgen(input_path,

species/data/database.py

@@ -12,19 +12,11 @@
 
 from astropy.io import votable
 
-from .. analysis import photometry
-from .. core import box
-from .. read import read_model
-from . import drift_phoenix
-from . import btnextgen
-from . import vega
-from . import irtf
-from . import spex
-from . import vlm_plx
-from . import leggett
-from . import companions
-from . import filters
-from . import util
+from species.analysis import photometry
+from species.core import box
+from species.read import read_model
+from species.data import drift_phoenix, btnextgen, vega, irtf, spex, vlm_plx, leggett, \
+                         companions, filters, util
 
 
 warnings.simplefilter('ignore', UserWarning)

species/data/drift_phoenix.py

@@ -10,7 +10,7 @@
 
 import numpy as np
 
-from . import util
+from species.data import util
 
 
 def add_drift_phoenix(input_path,

species/data/irtf.py

@@ -12,8 +12,7 @@
 
 from astropy.io import fits
 
-from . import queries
-from . import util
+from species.data import queries, util
 
 
 def add_irtf(input_path, database):

species/data/leggett.py

@@ -11,7 +11,7 @@
 import numpy as np
 import pandas as pd
 
-from . import util
+from species.data import util
 
 
 def add_leggett(input_path,

species/data/spex.py

@@ -13,10 +13,9 @@
 from astropy.io.votable import parse_single_table
 from astropy.utils.exceptions import AstropyWarning
 
-from . import queries
-from . import util
-from .. analysis import photometry
-from .. read import read_filter
+from species.analysis import photometry
+from species.data import queries, util
+from species.read import read_filter
 
 
 warnings.simplefilter('ignore', category=AstropyWarning)

species/data/vlm_plx.py

@@ -12,8 +12,7 @@
 
 from astropy.io import fits
 
-from . import queries
-from . import util
+from species.data import queries, util
 
 
 def add_vlm_plx(input_path,

species/plot/plot_mcmc.py

@@ -10,8 +10,8 @@
 import matplotlib as mpl
 import matplotlib.pyplot as plt
 
-from . util import update_labels
-from .. data import database
+from species.data import database
+from species.plot import util
 
 
 mpl.rcParams['font.serif'] = ['Bitstream Vera Serif']
@@ -37,7 +37,7 @@ def plot_walkers(tag,
     box = species_db.get_samples(tag)
 
     samples = box.samples
-    labels = update_labels(box.parameters)
+    labels = util.update_labels(box.parameters)
 
     plt.figure(1, figsize=(6, 5))
     gridsp = mpl.gridspec.GridSpec(4, 1)
@@ -136,7 +136,7 @@ def plot_posterior(tag,
     box = species_db.get_samples(tag)
 
     samples = box.samples
-    labels = update_labels(box.parameters)
+    labels = util.update_labels(box.parameters)
 
     ndim = samples.shape[2]
 

species/plot/plot_photometry.py

@@ -11,7 +11,7 @@
 
 from matplotlib.colorbar import Colorbar
 
-from .. read import read_object
+from species.read import read_object
 
 
 mpl.rcParams['font.serif'] = ['Bitstream Vera Serif']

species/plot/plot_spectrum.py

@@ -11,9 +11,9 @@
 import matplotlib as mpl
 import matplotlib.pyplot as plt
 
-from . util import quantity_unit
-from .. core import box
-from .. read import read_filter
+from species.core import box
+from species.plot import util
+from species.read import read_filter
 
 
 mpl.rcParams['font.serif'] = ['Bitstream Vera Serif']
@@ -219,9 +219,8 @@ def plot_spectrum(boxes,
                 if isinstance(boxitem, box.ModelBox):
                     param = boxitem.parameters
                     #TODO fix luminosity
-                    print(param)
 
-                    par_key, par_unit = quantity_unit(list(param.keys()))
+                    par_key, par_unit = util.quantity_unit(list(param.keys()))
                     par_val = list(param.values())
 
                     label = ''

species/read/read_colormag.py

@@ -8,8 +8,8 @@
 import h5py
 import numpy as np
 
-from .. data import database
-from .. analysis import photometry
+from species.analysis import photometry
+from species.data import database
 
 
 class ReadColorMagnitude:

species/read/read_filter.py

@@ -10,7 +10,7 @@
 
 from scipy.interpolate import interp1d, InterpolatedUnivariateSpline
 
-from .. data import database
+from species.data import database
 
 
 class ReadFilter:

species/read/read_model.py

@@ -13,10 +13,10 @@
 from scipy.interpolate import RegularGridInterpolator
 from PyAstronomy.pyasl import instrBroadGaussFast
 
-from . import read_filter
-from .. analysis import photometry
-from .. core import box
-from .. data import database
+from species.analysis import photometry
+from species.core import box
+from species.data import database
+from species.read import read_filter
 
 
 def multi_photometry(model,

species/read/read_spectrum.py

@@ -8,9 +8,9 @@
 import h5py
 import numpy as np
 
-from . import read_filter
-from .. core import box
-from .. data import database
+from species.core import box
+from species.data import database
+from species.read import read_filter
 
 
 class ReadSpectrum: