removed build directory from repo, merged master in

CDAT · May 3, 2017 · 39b9798 · 39b9798
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diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,24 @@
+os:
+    - osx
+    - linux
+sudo: false
+before_install:
+- if [ "$TRAVIS_OS_NAME" = "linux" ]; then wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh; fi
+- if [ "$TRAVIS_OS_NAME" = "osx" ]; then wget https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh -O miniconda.sh; fi
+- export PATH="$HOME/miniconda/bin:$PATH"
+- bash miniconda.sh -b -p $HOME/miniconda
+- conda config --set always_yes yes --set changeps1 no
+- conda update -y -q conda
+- conda install gcc
+script:
+- conda install -c uvcdat/label/nightly -c conda-forge -c uvcdat nose cdms2 genutil cdat_info
+- export UVCDAT_ANONYMOUS_LOG=False
+- echo $TRAVIS_BRANCH
+- export TRAVIS_PR_BRANCH=$TRAVIS_BRANCH
+- echo $TRAVIS_EVENT_TYPE
+- echo $TRAVIS_PULL_REQUEST
+- python setup.py install 
+- pip install dropbox
+- python run_tests.py --dropbox -v2
+after_success:
+    - if [ "$TRAVIS_BRANCH" == "master" -a "$TRAVIS_PULL_REQUEST" == "false" ]; then conda install conda-build && conda install anaconda-client && bash scripts/conda_upload.sh ; fi
diff --git a/LEGAL.htm b/LEGAL.htm
@@ -0,0 +1,137 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+  <title>CDAT Legal Statement</title>
+</head>
+<body lang="EN-US" style="">
+<h1 align="center" style="text-align: center;">Climate Data Analysis
+Tools (CDAT)</h1>
+<h2 align="center" style="text-align: center;">UCRL-CODE-2002-0021</h2>
+This work was produced at the University of California, Lawrence
+Livermore
+National Laboratory (UC LLNL) under contract no. W-7405-ENG-48
+(Contract 48) between the U.S. Department of Energy (DOE) and The
+Regents of
+the University of California (University) for the operation of UC LLNL.
+The rights of
+the Federal Government are reserved under Contract 48 subject to the
+restrictions agreed upon by the DOE and University as allowed under DOE
+Acquisition Letter 97-1.
+<h2 align="center">DISCLAIMER</h2>
+<p>This work was prepared as an account of work sponsored by an
+agency of the United States Government. Neither the United States
+Government
+nor the University of California
+nor any of their employees, makes any warranty, express or implied, or
+assumes
+any liability or responsibility for the accuracy, completeness, or
+usefulness
+of any information, apparatus, product, or process disclosed, or
+represents
+that its use would not infringe privately-owned rights.
+Reference herein to any specific commercial
+products, process, or service by trade name, trademark, manufacturer or
+otherwise does not necessarily constitute or imply its endorsement,
+recommendation, or favoring by the United States Government or the
+University
+of California. The views and opinions of authors expressed herein do
+not necessarily
+state or reflect those of the United States Government or the
+University of California, and shall not be
+used for advertising or product endorsement purposes.</p>
+<h2 align="center" style="text-align: center;">NOTIFICATION OF
+COMMERCIAL USE</h2>
+<p>Commercialization of this product is prohibited without
+notifying the Department of Energy (DOE) or Lawrence Livermore National
+Laboratory (LLNL).</p>
+<h2 align="center">NOTE</h2>
+<p>Portions of this software, including especially portions
+of the contents of subdirectories pysrc, contrib, and cdat/Tars, were
+not written by us and are redistributed here under the terms of their
+own licenses.</p>
+<h2 align="center">External License Agreements</h2>
+<p>This release of CDAT incorporates modules from other organizations
+besides LLNL some of which are distributed under software licenses
+of their choosing, and therefore may be subject to different terms and
+conditions. We ask that users respect these all terms and conditions as
+well as any copyright notices requirements. <br>
+</p>
+<p>This release is subject to different terms and conditions associated
+with some component parts.
+By installing software components covered by third party licenses you
+are agreeing to their terms and conditions. (Terms and Conditions can
+be found below.) </p>
+<h2 align="center">CCLRC License for CCLRC Software forming part of the
+Climate Data Analysis Tools Package</h2>
+<p> The Council for the Central Laboratory of the Research Councils
+(CCLRC) grants any person who obtains a copy of this software (the
+Software), free of charge, the non-exclusive, worldwide right to use,
+copy, modify, distribute and sub-license the use of the Software on the
+terms and conditions appearing below:
+<br>
+1)The Software may be used only as part of the Climate Data Analysis
+Tools Package, made available to users free of charge.
+<br>
+2)The CCLRC copyright notice and any other notice placed by CCLRC on
+the Software must be reproduced on every copy of the Software, and on
+every Derived Work. A Derived Work means any modification of, or
+enhancement or improvement to, any of the Software, and any software or
+other work developed or derived from any of the Software.
+3)CCLRC gives no warranty and makes no representation in relation to
+the Software. The Licensee and anyone to whom the Licensee makes the
+Software or any Derived Work available, use the Software at their own
+risk. <br>
+4)All warranties, conditions, terms, undertakings and obligations on
+the part of CCLRC, implied by statute, common law, custom, trade usage,
+course of dealing or in any other way are excluded to the fullest
+extent permitted by law.&nbsp;
+<br>
+5)Subject to condition 6, CCLRC will not be liable for:
+<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+a)any loss of profits, loss of revenue, loss or corruption of data,
+loss of contracts or opportunity, loss of savings or third party claims
+(in each case whether direct or
+indirect);
+<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+b)any indirect loss or damage arising out of or in connection with the
+Software;
+<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+c)any direct loss or damage arising out of, or in connection with, the
+Software
+in each case, whether that loss arises as a result of CCLRC&acirc;&#8364;&#8482;s
+negligence, or in any other way, even if CCLRC has been advised of the
+possibility of that loss arising, or if it was within CCLRC's
+contemplation.
+<br>
+6)None of these conditions limits or excludes CCLRC's liability for
+death or personal injury caused by its negligence or for any fraud, or
+for any sort of liability that, by law, cannot be limited or excluded.
+<br>
+7)These conditions set out the entire agreement relating to the
+Software. The licensee acknowledges that it has not relied on any
+warranty, representation, statement, agreement or undertaking given by
+CCLRC, and waives any claim in respect of any of the same.
+<br>
+8)The rights granted above will cease immediately on any breach of
+these conditions and the licensee will destroy all copies of the
+Software and any Derived Work in its control or possession. Conditions
+3, 4, 5, 6, 7, 8, 9 and 10 will survive termination and continue
+indefinitely.
+<br>
+9)The licence and these conditions are governed by, and are to be
+construed in accordance with, English law. The English Courts will have
+exclusive jurisdiction to deal with any dispute which has arisen or may
+arise out of or in connection with the Software, the rights granted and
+these conditions, except that CCLRC may bring proceedings for an
+injunction in any jurisdiction.
+<br>
+10)If the whole or any part of these conditions are void or
+unenforceable in any jurisdiction, the other provisions, and the rest
+of the void or unenforceable provision, will continue in force in that
+jurisdiction, and the validity and enforceability of that provision in
+any other jurisdiction will not be affected.</p>
+</body>
+</html>
diff --git a/LEGAL.txt b/LEGAL.txt
@@ -0,0 +1,51 @@
+Climate Data Analysis Tools (CDAT)
+
+
+UCRL-CODE-2002-0021
+
+ This work was produced at the University of California, Lawrence Livermore National Laboratory (UC LLNL) under contract no. W-7405-ENG-48 (Contract 48) between the U.S. Department of Energy (DOE) and The Regents of the University of California (University) for the operation of UC LLNL. The rights of the Federal Government are reserved under Contract 48 subject to the restrictions agreed upon by the DOE and University as allowed under DOE Acquisition Letter 97-1. 
+
+DISCLAIMER
+
+
+This work was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the University of California nor any of their employees, makes any warranty, express or implied, or assumes any liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately-owned rights. Reference herein to any specific commercial products, process, or service by trade name, trademark, manufacturer or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or the University of California, and shall not be used for advertising or product endorsement purposes.
+
+
+NOTIFICATION OF COMMERCIAL USE
+
+
+Commercialization of this product is prohibited without notifying the Department of Energy (DOE) or Lawrence Livermore National Laboratory (LLNL).
+
+
+NOTE
+
+
+Portions of this software, including especially portions of the contents of subdirectories pysrc, contrib, and cdat/Tars, were not written by us and are redistributed here under the terms of their own licenses.
+
+
+External License Agreements
+
+
+This release of CDAT incorporates modules from other organizations besides LLNL some of which are distributed under software licenses of their choosing, and therefore may be subject to different terms and conditions. We ask that users respect these all terms and conditions as well as any copyright notices requirements. 
+
+
+
+This release is subject to different terms and conditions associated with some component parts. By installing software components covered by third party licenses you are agreeing to their terms and conditions. (Terms and Conditions can be found below.) 
+
+
+CCLRC Licence for CCLRC Software forming part of the Climate Data Analysis Tools Package
+
+
+ The Council for the Central Laboratory of the Research Councils (CCLRC) grants any person who obtains a copy of this software (the Software), free of charge, the non-exclusive, worldwide right to use, copy, modify, distribute and sub-license the use of the Software on the terms and conditions appearing below: 
+ 1)The Software may be used only as part of the Climate Data Analysis Tools Package, made available to users free of charge. 
+ 2)The CCLRC copyright notice and any other notice placed by CCLRC on the Software must be reproduced on every copy of the Software, and on every Derived Work. A Derived Work means any modification of, or enhancement or improvement to, any of the Software, and any software or other work developed or derived from any of the Software. 3)CCLRC gives no warranty and makes no representation in relation to the Software. The Licensee and anyone to whom the Licensee makes the Software or any Derived Work available, use the Software at their own risk. 
+ 4)All warranties, conditions, terms, undertakings and obligations on the part of CCLRC, implied by statute, common law, custom, trade usage, course of dealing or in any other way are excluded to the fullest extent permitted by law.  
+ 5)Subject to condition 6, CCLRC will not be liable for: 
+             a)any loss of profits, loss of revenue, loss or corruption of data, loss of contracts or opportunity, loss of savings or third party claims (in each case whether direct or indirect); 
+             b)any indirect loss or damage arising out of or in connection with the Software; 
+             c)any direct loss or damage arising out of, or in connection with, the Software in each case, whether that loss arises as a result of CCLRCâ€™s negligence, or in any other way, even if CCLRC has been advised of the possibility of that loss arising, or if it was within CCLRC's contemplation. 
+ 6)None of these conditions limits or excludes CCLRC's liability for death or personal injury caused by its negligence or for any fraud, or for any sort of liability that, by law, cannot be limited or excluded. 
+ 7)These conditions set out the entire agreement relating to the Software. The licensee acknowledges that it has not relied on any warranty, representation, statement, agreement or undertaking given by CCLRC, and waives any claim in respect of any of the same. 
+ 8)The rights granted above will cease immediately on any breach of these conditions and the licensee will destroy all copies of the Software and any Derived Work in its control or possession. Conditions 3, 4, 5, 6, 7, 8, 9 and 10 will survive termination and continue indefinitely. 
+ 9)The licence and these conditions are governed by, and are to be construed in accordance with, English law. The English Courts will have exclusive jurisdiction to deal with any dispute which has arisen or may arise out of or in connection with the Software, the rights granted and these conditions, except that CCLRC may bring proceedings for an injunction in any jurisdiction. 
+ 10)If the whole or any part of these conditions are void or unenforceable in any jurisdiction, the other provisions, and the rest of the void or unenforceable provision, will continue in force in that jurisdiction, and the validity and enforceability of that provision in any other jurisdiction will not be affected.
diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,66 @@
+CCLRC License for CCLRC Software forming part of the Ultrascale Visualization
+Climate Data Analysis Tools Package.
+
+The Council for the Central Laboratory of the Research Councils (CCLRC)
+grants any person who obtains a copy of this software (the Software),
+free of charge, the non-exclusive, worldwide right to use, copy, modify,
+distribute and sub-license the use of the Software on the terms and
+conditions appearing below:
+
+1)The Software may be used only as part of the Climate Data Analysis
+Tools Package, made available to users free of charge.
+
+2)The CCLRC copyright notice and any other notice placed by CCLRC on the
+Software must be reproduced on every copy of the Software, and on every
+Derived Work. A Derived Work means any modification of, or enhancement
+or improvement to, any of the Software, and any software or other work
+developed or derived from any of the Software.
+
+3)CCLRC gives no warranty and makes no representation in relation to
+the Software. The Licensee and anyone to whom the Licensee makes the
+Software or any Derived Work available, use the Software at their own
+risk.
+
+4)All warranties, conditions, terms, undertakings and obligations on the
+part of CCLRC, implied by statute, common law, custom, trade usage,
+course of dealing or in any other way are excluded to the fullest extent
+permitted by law.
+
+5)Subject to condition 6, CCLRC will not be liable for:
+  a)any loss of profits, loss of revenue, loss or corruption
+    of data, loss of contracts or opportunity, loss of savings or third
+    party claims (in each case whether direct or indirect);
+  b)any indirect loss or damage arising out of or in
+    connection with the Software;
+  c)any direct loss or damage arising out of, or in connection
+    with, the Software in each case, whether that loss arises as a result of
+    CCLRC's negligence, or in any other way, even if CCLRC has been
+    advised of the possibility of that loss arising, or if it was within
+    CCLRC's contemplation.
+
+6)None of these conditions limits or excludes CCLRC's liability for
+death or personal injury caused by its negligence or for any fraud, or
+for any sort of liability that, by law, cannot be limited or excluded.
+
+7)These conditions set out the entire agreement relating to the
+Software. The licensee acknowledges that it has not relied on any
+warranty, representation, statement, agreement or undertaking given by
+CCLRC, and waives any claim in respect of any of the same.
+
+8)The rights granted above will cease immediately on any breach of these
+conditions and the licensee will destroy all copies of the Software and
+any Derived Work in its control or possession. Conditions 3, 4, 5, 6, 7,
+8, 9 and 10 will survive termination and continue indefinitely.
+
+9)The licence and these conditions are governed by, and are to be
+construed in accordance with, English law. The English Courts will have
+exclusive jurisdiction to deal with any dispute which has arisen or may
+arise out of or in connection with the Software, the rights granted and
+these conditions, except that CCLRC may bring proceedings for an
+injunction in any jurisdiction.
+
+10)If the whole or any part of these conditions are void or
+unenforceable in any jurisdiction, the other provisions, and the rest of
+the void or unenforceable provision, will continue in force in that
+jurisdiction, and the validity and enforceability of that provision in
+any other jurisdiction will not be affected.
diff --git a/Lib/region.py b/Lib/region.py
@@ -223,7 +223,7 @@ def post(self,fetched,slab,axes,specifications,confined_by,aux,axismap):
                         ax.designateLatitude()
                     faxes[axismap[i]]=ax
 
-        a=cdms.createVariable(fetched.filled(),mask=fetched.mask,axes=faxes)
+        a=cdms.createVariable(fetched.filled(),mask=fetched.mask,axes=faxes,attributes=fetched.attributes)
         return a                        
 
 def domain(*args, **kargs):

diff --git a/Lib/times.py b/Lib/times.py
@@ -162,12 +162,11 @@ def isMonthly(s):
     units=tim.units
     monthly=1
     for i in range(len(tim)-1):
-      month1=cdtime.reltime(tim[i],units).torel('months since 2000').value
-      month2=cdtime.reltime(tim[i+1],units).torel('months since 2000').value
+      month1=cdtime.reltime(tim[i],units).torel('months since 2000',tim.getCalendar()).value
+      month2=cdtime.reltime(tim[i+1],units).torel('months since 2000',tim.getCalendar()).value
       if month2-month1!=1 : monthly=0
     return monthly
 
-
 def mergeTime(ds,statusbar=1,fill_value=1.e20):
     """
     Merge chronologically a bunch of slabs
@@ -500,7 +499,7 @@ def departures(self,slab,slicerarg=None,criteriaarg=None,ref=None,statusbar=None
 
         :returns: The departures of slab from the result of get
         """
-        sliced=TimeSlicer.get(self,slab,slicerarg,criteriaarg,statusbar=statusbar,sum=sum)
+        sliced=TimeSlicer.get(self, slab, slicerarg, criteriaarg, statusbar=statusbar, sum=sum)
 
         if sliced is None:
             return None
@@ -509,17 +508,20 @@ def departures(self,slab,slicerarg=None,criteriaarg=None,ref=None,statusbar=None
 
         if order[0]!='t' : sliced=sliced(order='t...')
         order2=sliced.getOrder(ids=1)
+        weights = self.slicer(sliced.getTime(), slicerarg)
         if ref is None:
             if sum is False:
-                ref=numpy.ma.average(sliced,0)
+                ref = numpy.ma.average(sliced, axis=0, weights=zip(*weights[2])[0])
             else:
-                ref = numpy.ma.sum(sliced,0)
+                ref = numpy.ma.sum(sliced, axis=0, weights=zip(*weights[2])[0])
         elif len(order2[1:])>0:
             ref=ref(order=order2[1:])
+
         if cdms2.isVariable(ref):
             out=cdms2.asVariable(sliced(raw=1)-ref(raw=1))
         else:
             out=cdms2.asVariable(sliced(raw=1)-ref)
+
         # put the axes back
         out.id=slab.id
         for i in range(len(sliced.shape)):
@@ -820,7 +822,7 @@ def dayBasedSlicer(tim,arg=None):
                         subarg='feb-29'
                     else:
                         t=cdtime.reltime(index,'month since 1997')
-                        t=t.tocomp()
+                        t=t.tocomp(tim.getCalendar())
                         subarg=str(t.month)+'-'+str(t.day)
                 except:
                     raise Exception,"Error, dayBasedSlicer args must have '-' or '/' as month/day separator"