Refactor of LineList tables

.travis.yml

@@ -1,126 +1,125 @@
-language: python
-
-# The apt packages below are needed for sphinx builds, which can no longer
-# be installed with sudo apt-get.
-addons:
-    apt:
-        packages:
-            - graphviz
-            - texlive-latex-extra
-            - dvipng
-
-python:
-    - 2.7
-    - 3.5
-    - 3.6
-
-    # This is just for "egg_info".  All other builds are explicitly given in the matrix
+# We set the language to c because python isn't supported on the MacOS X nodes
+# on Travis. However, the language ends up being irrelevant anyway, since we
+# install Python ourselves using conda.
+language: c
+
+os:
+    - linux
+
+# Setting sudo to false opts in to Travis-CI container-based builds.
+sudo: false
+
 env:
     global:
+
         # The following versions are the 'default' for tests, unless
-        # overidden underneath. They are defined here in order to save having
+        # overridden underneath. They are defined here in order to save having
         # to repeat them for all configurations.
-        - NUMPY_VERSION=1.11
+        - FOLDERNAME='linetools'
+        - PYTHON_VERSION=3.6
         - ASTROPY_VERSION=stable
-        - CONDA_INSTALL='conda install -c astropy-ci-extras --yes'
-        - PIP_INSTALL='pip install'
+        - NUMPY_VERSION=stable
+        - MAIN_CMD='python setup.py'
+        - SETUP_CMD='test'
+        - CONDA_DEPENDENCIES='scipy h5py pyyaml matplotlib'
+        - PIP_DEPENDENCIES=''
+        - EVENT_TYPE='pull_request push'
+        - TASK='test'
+
+        # Conda packages for affiliated packages are hosted in channel
+        # "astropy" while builds for astropy LTS with recent numpy versions
+        # are in astropy-ci-extras. If your package uses either of these,
+        # add the channels to CONDA_CHANNELS along with any other channels
+        # you want to use.
+        - CONDA_CHANNELS='astropy-ci-extras'
+
+        # If there are matplotlib or other GUI tests, uncomment the following
+        # line to use the X virtual framebuffer.
+        - SETUP_XVFB=True
 
     matrix:
-        - SETUP_CMD='egg_info'
+      # Extra context is a way to override options that the user normally
+      # specifies during the questions phase of the cookiecutter setup. The keys
+      # being overridden here must exist in the cookiecutter.json
+      # See https://cookiecutter.readthedocs.io/en/0.9.1/advanced_usage.html#injecting-extra-context
+      #- EXTRA_CONTEXT=''
+      #- EXTRA_CONTEXT='include_example_cython_code=y'
+      #- EXTRA_CONTEXT="package_name=AstropyProject" FOLDERNAME='AstropyProject'
+      #- EXTRA_CONTEXT='_parent_project=sunpy'
+      #- TASK='render' EXTRA_CONTEXT='include_example_cython_code=y initialize_git_repo=n'
+      - PYTHON_VERSION=2.7 SETUP_CMD='egg_info'
+      - PYTHON_VERSION=3.6 SETUP_CMD='egg_info'
 
 matrix:
+
+    # Don't wait for allowed failures
+    fast_finish: true
+
     include:
+        # Try MacOS X
+        #- os: osx
+        #  env: SETUP_CMD='test'
 
-        # Do a coverage test in Python 2.
-        - python: 2.7
+        # Do a coverage test.
+        - os: linux
           env: SETUP_CMD='test --coverage'
 
         # Check for sphinx doc build warnings - we do this first because it
-        # may run for a long time. Add -w flag to fail on any warning.
-        #- python: 3.4
-        #  env: SETUP_CMD='build_sphinx -w'
-
-        # Try Astropy development version
-        #- python: 2.7
-        #  env: ASTROPY_VERSION=development SETUP_CMD='test'
-        #- python: 3.5
-        #  env: ASTROPY_VERSION=development SETUP_CMD='test'
-
-        # Try all python versions with the latest numpy
-        - python: 2.7
-          env: SETUP_CMD='test'
-        - python: 3.5
-          env: SETUP_CMD='test'
-        - python: 3.6
-          env: SETUP_CMD='test'
-
-        # Try older numpy versions.
-        # - python: 2.7
-        # env: NUMPY_VERSION=1.9 SETUP_CMD='test'
-
-before_install:
-
-    # Use utf8 encoding. Should be default, but this is insurance against
-    # future changes
-    - export PYTHONIOENCODING=UTF8
-    - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
-    - chmod +x miniconda.sh
-    - ./miniconda.sh -b -p $HOME/miniconda
-    - export PATH=$HOME/miniconda/bin:$PATH
-    - hash -r
-    - conda config --set always_yes yes --set changeps1 no
-    - conda update --yes conda
-
-    # UPDATE APT-GET LISTINGS
-    #- sudo apt-get update
-
-    # DOCUMENTATION DEPENDENCIES
-    # - if [[ $SETUP_CMD == build_sphinx* ]]; then sudo apt-get install graphviz texlive-latex-extra dvipng; fi
+        # may run for a long time
+        #- os: linux
+        #  env: SETUP_CMD='build_docs -w'
+
+        # Now try Astropy dev and LTS vesions with the latest 3.x and 2.7.
+        - os: linux
+          env: PYTHON_VERSION=2.7 ASTROPY_VERSION=development
+               EVENT_TYPE='pull_request push cron'
+        - os: linux
+          env: ASTROPY_VERSION=development
+               EVENT_TYPE='pull_request push cron'
+        #- os: linux
+        #  env: PYTHON_VERSION=2.7 ASTROPY_VERSION=lts
+        #- os: linux
+        #  env: ASTROPY_VERSION=lts
+
+        # Try all python versions and Numpy versions. Since we can assume that
+        # the Numpy developers have taken care of testing Numpy with different
+        # versions of Python, we can vary Python and Numpy versions at the same
+        # time.
+
+        - os: linux
+          env: PYTHON_VERSION=2.7 NUMPY_VERSION=1.11
+        #- os: linux
+        #  env: PYTHON_VERSION=3.3 NUMPY_VERSION=1.8
+        #- os: linux
+        #  env: PYTHON_VERSION=3.4 NUMPY_VERSION=1.9
+        #- os: linux
+        #  env: PYTHON_VERSION=3.5 NUMPY_VERSION=1.10
+        - os: linux
+          env: NUMPY_VERSION=1.11
+
+        # Try numpy pre-release
+        - os: linux
+          env: NUMPY_VERSION=prerelease
+               EVENT_TYPE='pull_request push cron'
+
+        # Do a PEP8 test with pycodestyle
+        - os: linux
+          env: MAIN_CMD='pycodestyle packagename --count' SETUP_CMD=''
+
+    allow_failures:
+        # Do a PEP8 test with pycodestyle
+        # (allow to fail unless your code completely compliant)
+        - os: linux
+          env: MAIN_CMD='pycodestyle packagename --count' SETUP_CMD=''
 
 install:
 
-    # CONDA
-    - conda create --yes -n test -c astropy-ci-extras python=$TRAVIS_PYTHON_VERSION pyqt=5 qtpy
-    - source activate test
-
-    # CORE DEPENDENCIES
-    - if [[ $SETUP_CMD != egg_info ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION pytest pip Cython jinja2; fi
-    - if [[ $SETUP_CMD != egg_info ]]; then $PIP_INSTALL pytest-xdist; fi
-
-    # ASTROPY
-    - if [[ $SETUP_CMD != egg_info ]] && [[ $ASTROPY_VERSION == development ]]; then $PIP_INSTALL git+http://github.com/astropy/astropy.git#egg=astropy; fi
-    - if [[ $SETUP_CMD != egg_info ]] && [[ $ASTROPY_VERSION == stable ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION astropy; fi
-
-    # OPTIONAL DEPENDENCIES
-    # Here you can add any dependencies your package may have. You can use
-    # conda for packages available through conda, or pip for any other
-    # packages. You should leave the `numpy=$NUMPY_VERSION` in the `conda`
-    # install since this ensures Numpy does not get automatically upgraded.
-    - if [[ $SETUP_CMD != egg_info ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION scipy; fi
-    - if [[ $SETUP_CMD != egg_info ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION h5py; fi
-    - if [[ $SETUP_CMD != egg_info ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION pyyaml; fi
-    - if [[ $SETUP_CMD != egg_info ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION matplotlib; fi
-
-    # DOCUMENTATION DEPENDENCIES
-    # build_sphinx needs sphinx and matplotlib (for plot_directive). Note that
-    # this matplotlib will *not* work with py 3.x, but our sphinx build is
-    # currently 2.7, so that's fine
-    - if [[ $SETUP_CMD == build_sphinx* ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION Sphinx=1.3; fi
-
-    # COVERAGE DEPENDENCIES
-    #- if [[ $SETUP_CMD == 'test --coverage' ]]; then $PIP_INSTALL coverage coveralls; fi
-    - if [[ $SETUP_CMD == 'test --coverage' ]]; then $PIP_INSTALL coverage==3.7.1 coveralls; fi
-
-before_script:   # Required for plotting tests
-  - "export DISPLAY=:99.0"
-  - "sh -e /etc/init.d/xvfb start"
-  - sleep 3 # give xvfb some time to start
+    - git clone git://github.com/astropy/ci-helpers.git
+    - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh
 
 script:
-   - python setup.py $SETUP_CMD
+    - $MAIN_CMD $SETUP_CMD
+
 
 after_success:
-    # If coveralls.io is set up for this package, uncomment the line
-    # below and replace "packagename" with the name of your package.
-    # The coveragerc file may be customized as needed for your package.
     - if [[ $SETUP_CMD == 'test --coverage' ]]; then coveralls --rcfile='linetools/tests/coveragerc'; fi

docs/linelist.rst

@@ -204,7 +204,7 @@ Which give us the information of all the 6 transitions of `MgII`::
     262500000.0   0   0   0     1 MgII 2796 35760.848 ... 0.0  12   4   2 262500000.0   --   --
     259500000.0   0   0   0     1 MgII 2803 35669.298 ... 0.0  12   2   2 259500000.0   --   --
 
-In this case ``mgii`` is a QTable because more than 1
+In this case ``mgii`` is a Table because more than 1
 transition was found. In cases were only 1 transition
 exists, the output of `all_transitions()` is a dictionary
 with the same keywords as the columns of ``ism._data`` QTable::

linetools/abund/ions.py

@@ -23,22 +23,6 @@
 from linetools.abund import roman
 
 ########################## ##########################
-########################## ##########################
-def ion_name(ion, flg=0, nspace=None):
-    """ Wrapper to ion_to_name for backwards compatability
-    WILL BE DEPRECATED
-    Parameters
-    ----------
-    ion
-    flg
-    nspace
-
-    Returns
-    -------
-
-    """
-    warnings.warn("This method will be DEPRECATED.  Use ion_to_name")
-    return ion_to_name(ion, flg=flg, nspace=nspace)
 
 def ion_to_name(ion, flg=0, nspace=None):
     """ Convert ion tuple into a string
@@ -66,7 +50,7 @@ def ion_to_name(ion, flg=0, nspace=None):
         elm = ELEMENTS[ion[0]]
         str_elm = elm.symbol
     else:
-        return ion_name( (ion['Z'], ion['ion']) )
+        return ion_to_name((ion['Z'], ion['ion']))
 
     # Ion state
     if flg == 0: # Roman

linetools/analysis/utils.py

@@ -103,7 +103,7 @@ def gaussian_ew(spec, ltype, initial_guesses=None):
     # Use only good values (i.e. with meaningful errors)
     cond = (sig > 0.) & (np.isfinite(sig))
     # Actual fit
-    g = fit_g(g_init, wv[cond], fx[cond], weights=1./sig[cond])
+    g = fit_g(g_init, wv[cond].value, fx[cond].value, weights=1./sig[cond].value)
 
     #Check whether the final fit is sensible
     fit_info = fit_g.fit_info

linetools/data/lines/EUV_lines.ascii

@@ -1,9 +1,9 @@
 ; Lines by hand from Tripp list
 ; Will update with atomic data before too long
 ; Ref column added by hand by N. Tejos (Dec 28, 2015)
-|  wrest   |    name     |  f   |   Z | ion | Ref   |
-| 551.3621 |  ArVI  551  | 0.00 |  18 |  6  | Tripp |
-| 562.711  |  NeVI* 562a | 0.00 |  10 |  6  | Tripp |
-| 562.803  |  NeVI* 562b | 0.00 |  10 |  6  | Tripp |
-| 569.758  |  NeV* 659a  | 0.00 |  10 |  5  | Tripp |
-| 569.830  |  NeV* 659b  | 0.00 |  10 |  5  | Tripp |
+ wrest   |    name     |  f   |   Z | ion | Ref   
+551.3621 |  ArVI  551  | 0.00 |  18 |  6  | Tripp 
+562.711  |  NeVI* 562a | 0.00 |  10 |  6  | Tripp 
+562.803  |  NeVI* 562b | 0.00 |  10 |  6  | Tripp 
+569.758  |  NeV* 659a  | 0.00 |  10 |  5  | Tripp
+569.830  |  NeV* 659b  | 0.00 |  10 |  5  | Tripp