expunging attrib['z']

linetools · Nov 24, 2016 · 3617d55 · 3617d55
1 parent 09a50e1
commit 3617d55
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diff --git a/docs/examples/AbsSightline.ipynb b/docs/examples/AbsSightline.ipynb
@@ -83,7 +83,10 @@
       "/Users/xavier/local/Python/linetools/linetools/lists/linelist.py:374: RuntimeWarning: divide by zero encountered in log10\n",
       "  self._data['log(w*f)'] = np.log10(qm_strength)\n",
       "/Users/xavier/anaconda/lib/python2.7/site-packages/numpy/ma/core.py:827: RuntimeWarning: invalid value encountered in less_equal\n",
-      "  return umath.less_equal(x, self.critical_value)\n"
+      "  return umath.less_equal(x, self.critical_value)\n",
+      "/Users/xavier/anaconda/lib/python2.7/site-packages/astropy/table/column.py:1095: MaskedArrayFutureWarning: setting an item on a masked array which has a shared mask will not copy the mask and also change the original mask array in the future.\n",
+      "Check the NumPy 1.11 release notes for more information.\n",
+      "  ma.MaskedArray.__setitem__(self, index, value)\n"
      ]
     },
     {
@@ -93,22 +96,12 @@
       "Loading abundances from Asplund2009\n",
       "Abundances are relative by number on a logarithmic scale with H=12\n"
      ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/xavier/anaconda/lib/python2.7/site-packages/astropy/table/column.py:1095: MaskedArrayFutureWarning: setting an item on a masked array which has a shared mask will not copy the mask and also change the original mask array in the future.\n",
-      "Check the NumPy 1.11 release notes for more information.\n",
-      "  ma.MaskedArray.__setitem__(self, index, value)\n"
-     ]
     }
    ],
    "source": [
-    "lya = AbsLine('HI 1215')\n",
+    "lya = AbsLine('HI 1215', z=2.3)\n",
     "lya.limits.set([-300.,300.]*u.km/u.s)  # vlim\n",
-    "lya.attrib['z'] = 2.3\n",
-    "lyb = AbsLine(1025.7222*u.AA, z=lya.attrib['z'])\n",
+    "lyb = AbsLine(1025.7222*u.AA, z=2.3)\n",
     "lyb.limits.set([-300.,300.]*u.km/u.s)  # vlim\n",
     "abscomp = AbsComponent.from_abslines([lya,lyb])\n",
     "abscomp.coord = ltu.radec_to_coord((10.*u.deg, 45*u.deg))\n",
@@ -190,7 +183,7 @@
      "data": {
       "text/html": [
        "&lt;Table length=1&gt;\n",
-       "<table id=\"table4656546192\" class=\"table-striped table-bordered table-condensed\">\n",
+       "<table id=\"table4608359888\" class=\"table-striped table-bordered table-condensed\">\n",
        "<thead><tr><th>Z</th><th>ion</th><th>A</th><th>Ej</th><th>z</th><th>vmin</th><th>vmax</th><th>flag_N</th><th>logN</th><th>sig_logN</th></tr></thead>\n",
        "<thead><tr><th></th><th></th><th></th><th>1 / cm</th><th></th><th>km / s</th><th>km / s</th><th></th><th></th><th></th></tr></thead>\n",
        "<thead><tr><th>int64</th><th>int64</th><th>int64</th><th>float64</th><th>float64</th><th>float64</th><th>float64</th><th>int64</th><th>float64</th><th>float64</th></tr></thead>\n",
@@ -214,15 +207,6 @@
    "source": [
     "tbl"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

diff --git a/linetools/isgm/tests/test_init_abssightline.py b/linetools/isgm/tests/test_init_abssightline.py
@@ -12,46 +12,14 @@
 from astropy.coordinates import SkyCoord
 
 from linetools.isgm.abssightline import GenericAbsSightline
-from linetools.isgm.abscomponent import AbsComponent
-from linetools.spectralline import AbsLine
+from .utils import lyman_comp, si2_comp
 
 
 def data_path(filename):
     data_dir = os.path.join(os.path.dirname(__file__), 'files')
     return os.path.join(data_dir, filename)
 
 
-def lyman_comp(radec):
-    # HI Lya, Lyb
-    lya = AbsLine(1215.670*u.AA)
-    lya.analy['vlim'] = [-300.,300.]*u.km/u.s
-    lya.attrib['z'] = 2.92939
-    lya.attrib['N'] = 1e17 /  u.cm**2
-    lya.attrib['coord'] = radec
-    lyb = AbsLine(1025.7222*u.AA)
-    lyb.analy['vlim'] = [-300.,300.]*u.km/u.s
-    lyb.attrib['z'] = lya.attrib['z']
-    lyb.attrib['coord'] = radec
-    abscomp = AbsComponent.from_abslines([lya,lyb])
-    return abscomp
-
-
-def si2_comp(radec):
-    # SiII
-    SiIItrans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
-    abslines = []
-    for trans in SiIItrans:
-        iline = AbsLine(trans)
-        iline.attrib['z'] = 2.92939
-        iline.attrib['coord'] = radec
-        iline.analy['vlim'] = [-250.,80.]*u.km/u.s
-        abslines.append(iline)
-    #
-    SiII_comp = AbsComponent.from_abslines(abslines)
-    #
-    return SiII_comp
-
-
 def test_from_components():
     radec = SkyCoord(ra=123.1143*u.deg, dec=-12.4321*u.deg)
     # HI

diff --git a/linetools/isgm/tests/utils.py b/linetools/isgm/tests/utils.py
@@ -20,15 +20,13 @@ def data_path(filename):
 
 def lyman_comp(radec):
     # HI Lya, Lyb
-    lya = AbsLine(1215.670*u.AA)
-    lya.analy['vlim'] = [-300.,300.]*u.km/u.s
-    lya.attrib['z'] = 2.92939
+    lya = AbsLine(1215.670*u.AA, z=2.92939)
+    lya.limits.set([-300.,300.]*u.km/u.s)
     lya.attrib['flag_N'] = 1
     lya.attrib['N'] = 1e17 /  u.cm**2
     lya.attrib['coord'] = radec
-    lyb = AbsLine(1025.7222*u.AA)
-    lyb.analy['vlim'] = [-300.,300.]*u.km/u.s
-    lyb.attrib['z'] = lya.attrib['z']
+    lyb = AbsLine(1025.7222*u.AA, z=2.92939)
+    lyb.limits.set([-300.,300.]*u.km/u.s)
     lyb.attrib['coord'] = radec
     abscomp = AbsComponent.from_abslines([lya,lyb])
     abscomp.synthesize_colm()
@@ -41,10 +39,9 @@ def si2_comp(radec):
     SiIItrans = ['SiII 1260', 'SiII 1304', 'SiII 1526', 'SiII 1808']
     abslines = []
     for trans in SiIItrans:
-        iline = AbsLine(trans)
-        iline.attrib['z'] = 2.92939
+        iline = AbsLine(trans, z=2.92939)
         iline.attrib['coord'] = radec
-        iline.analy['vlim'] = [-250.,80.]*u.km/u.s
+        iline.limits.set([-250.,80.]*u.km/u.s)
         abslines.append(iline)
     #
     SiII_comp = AbsComponent.from_abslines(abslines)