From e63e2be7b4cb30dc94134ca078390a918e0b1a66 Mon Sep 17 00:00:00 2001
From: muryanto1 <muryanto1@llnl.gov>
Date: Wed, 1 Jul 2020 13:32:07 -0700
Subject: [PATCH 01/15] replace numpy.rank() with numpy.ndim(), and add
 testPercentiles()

---
 Lib/statistics.py                | 2 +-
 tests/test_genutil_statistics.py | 5 +++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/Lib/statistics.py b/Lib/statistics.py
index fd12988..90cdbd9 100644
--- a/Lib/statistics.py
+++ b/Lib/statistics.py
@@ -1696,7 +1696,7 @@ def _percentiles(out, percent):
             pass
         Aii = numpy.where(numpy.equal(ns, 1), 100., tmp)
         ii = numpy.where(numpy.equal(ii, ns), ns - 1, ii)
-        if numpy.rank(ii) > 0:
+        if numpy.ndim(ii) > 0:
             ii = ii.astype(numpy.int)
 # tmp = (p-Ai)/(Aii-Ai)*array_indexing.extract(out,ii) + \
 # (Aii-p)/(Aii-Ai)*array_indexing.extract(out,i)
diff --git a/tests/test_genutil_statistics.py b/tests/test_genutil_statistics.py
index bd87283..e6501c9 100644
--- a/tests/test_genutil_statistics.py
+++ b/tests/test_genutil_statistics.py
@@ -17,6 +17,11 @@ def assertArraysEqual(self,A,nm,skip=False, dump=dump):
         if not skip:
             self.assertTrue(numpy.ma.allclose(A,B))
 
+    def testPercentiles(self):
+        a = numpy.array([1.0,2.0,3.0,4.0,5.0])
+        p = genutil.statistics.percentiles(a,percentiles=[1])
+        # REVISIT
+
     def testStatisitcs(self):
         f=cdms2.open(os.path.join(cdat_info.get_sampledata_path(),'clt.nc'))
 

From 872b55f00f8c9d086d7686b52b9df614fa304783 Mon Sep 17 00:00:00 2001
From: Jason Boutte <boutte.jason@gmail.com>
Date: Wed, 1 Jul 2020 20:02:52 -0700
Subject: [PATCH 02/15] Cleans up setup.py formatting

---
 setup.py | 66 ++++++++++++++++++++++++++++++--------------------------
 1 file changed, 35 insertions(+), 31 deletions(-)

diff --git a/setup.py b/setup.py
index f555538..e9001b0 100755
--- a/setup.py
+++ b/setup.py
@@ -1,36 +1,40 @@
-from distutils.core import setup, Extension
-import os,sys
+from setuptools import setup, Extension
+
+# from distutils.core import setup, Extension
+import os
+import sys
 import numpy
+
 try:
     import cdat_info
-    Version=cdat_info.Version
-except:
-    Version="???"
-print("VERSION:",Version)
-setup (name = "genutil",
-       version=Version,
-       author='LLNL',
-       description = "General utilities for scientific computing",
-       url = "http://uvcdat.llnl.gov/software",
-       packages = ['genutil','unidata'],
-       package_dir = {'genutil': 'Lib', 'unidata':"unidata"},
-       include_dirs = ['Include', numpy.lib.utils.get_include()],
-       ext_modules = [
-    Extension('genutil.array_indexing',
-              ['Src/array_indexing.c',]
-              ),
-    Extension('genutil.udunits_wrap',
-        ['Src/udunits_wrap.c',
-            ## 'Src/utparse.c',
-            ## 'Src/utlib.c',
-            ## 'Src/utscan.c',
-            ],
-        include_dirs = [os.path.join(sys.prefix,'include')],
-        library_dirs = [os.path.join(sys.prefix,'lib')],
-        libraries=['udunits2','expat']
-        )
 
-    
+    Version = cdat_info.Version
+except Exception:
+    Version = "???"
+print("VERSION:", Version)
+setup(
+    name="genutil",
+    version=Version,
+    author="LLNL",
+    description="General utilities for scientific computing",
+    url="http://uvcdat.llnl.gov/software",
+    packages=["genutil", "unidata"],
+    package_dir={"genutil": "Lib", "unidata": "unidata"},
+    include_dirs=["Include", numpy.lib.utils.get_include()],
+    ext_modules=[
+        Extension("genutil.array_indexing", ["Src/array_indexing.c"]),
+        Extension(
+            "genutil.udunits_wrap",
+            [
+                "Src/udunits_wrap.c",
+                # 'Src/utparse.c',
+                # 'Src/utlib.c',
+                # 'Src/utscan.c',
+            ],
+            include_dirs=[os.path.join(sys.prefix, "include")],
+            library_dirs=[os.path.join(sys.prefix, "lib")],
+            libraries=["udunits2", "expat"],
+        ),
     ],
-      data_files=[('share/genutil', ('share/test_data_files.txt',))]
-      )
+    data_files=[("share/genutil", ("share/test_data_files.txt",))],
+)

From a483a45e758b12b0967882274f9bf57f1199e8e6 Mon Sep 17 00:00:00 2001
From: Jason Boutte <boutte.jason@gmail.com>
Date: Thu, 2 Jul 2020 21:03:41 -0700
Subject: [PATCH 03/15] Fixes converting 1d to 2d array

---
 Lib/statistics.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/Lib/statistics.py b/Lib/statistics.py
index 90cdbd9..7affef3 100644
--- a/Lib/statistics.py
+++ b/Lib/statistics.py
@@ -1668,6 +1668,10 @@ def geometricmean(x, axis=0, max_pct_missing=100.):
 
 
 def _percentiles(out, percent):
+    # change 1d to 2d array
+    if out.ndim == 1:
+        out = out.reshape((1,)+out.shape)
+
     if cdms2.isVariable(out):
         out = MV2.sort(out, axis=0).asma()
         ns = MV2.count(out, axis=0).asma()
@@ -1698,8 +1702,6 @@ def _percentiles(out, percent):
         ii = numpy.where(numpy.equal(ii, ns), ns - 1, ii)
         if numpy.ndim(ii) > 0:
             ii = ii.astype(numpy.int)
-# tmp = (p-Ai)/(Aii-Ai)*array_indexing.extract(out,ii) + \
-# (Aii-p)/(Aii-Ai)*array_indexing.extract(out,i)
 
         tmp = (p - Ai) / (Aii - Ai) * arrayindexing.get(out, ii) + \
             (Aii - p) / (Aii - Ai) * arrayindexing.get(out, i)

From bed83554d6e09feed79625b93d7f06036164ca56 Mon Sep 17 00:00:00 2001
From: Jason Boutte <boutte.jason@gmail.com>
Date: Thu, 2 Jul 2020 21:05:27 -0700
Subject: [PATCH 04/15] Fixes raising error when axis is out of bounds and adds
 some unittests for percentile

---
 Lib/stats_checker.py             | 102 ++++++++++++++++--------
 tests/test_genutil_statistics.py | 129 ++++++++++++++++++++++---------
 2 files changed, 162 insertions(+), 69 deletions(-)

diff --git a/Lib/stats_checker.py b/Lib/stats_checker.py
index 4740337..4b8eff1 100644
--- a/Lib/stats_checker.py
+++ b/Lib/stats_checker.py
@@ -4,7 +4,7 @@
 from .averager import __check_weightoptions
 
 
-class StatisticsError (Exception):
+class StatisticsError(Exception):
     def __init__(self, args=None):
         """Create an exception"""
         self.args = args
@@ -12,6 +12,7 @@ def __init__(self, args=None):
     def __str__(self):
         """Calculate the string representation"""
         return str(self.args)
+
     __repr__ = __str__
 
 
@@ -32,10 +33,10 @@ def __makeweights(x, w, axes):
     if not numpy.ma.isarray(w):
         # Ok Krishna returned a list of 1D arrays.... Let's put it together
         axs = x.getAxisList()
-        axes = cdms2.order2index(axs, axes)[:len(cdms2.orderparse(axes))]
+        axes = cdms2.order2index(axs, axes)[: len(cdms2.orderparse(axes))]
         endax = []
         for i in range(len(axes)):
-            if w[i] == 'unweighted':
+            if w[i] == "unweighted":
                 w[i] = numpy.ma.ones(len(axs[axes[i]]), dtype=x.dtype.char)
             if i == 0:
                 wo = w[i]
@@ -45,8 +46,8 @@ def __makeweights(x, w, axes):
                 endax.append(axs[axes[i]])
         w = cdms2.MV2.array(wo)
         w.setAxisList(endax)
-# else:
-# w.setAxisList(x.getAxisList())
+    # else:
+    # w.setAxisList(x.getAxisList())
     return w
 
 
@@ -64,20 +65,21 @@ def __checker(x, y, w, axes, smally=0):
         x = numpy.ma.array(x, copy=0)
     if not numpy.ma.isarray(y) and y is not None:
         y = numpy.ma.array(y, copy=0)
-    if not numpy.ma.isarray(
-            w) and w is not None and not isinstance(w, type('')):
-        if not isinstance(w[0], type('')):
+    if not numpy.ma.isarray(w) and w is not None and not isinstance(w, type("")):
+        if not isinstance(w[0], type("")):
             w = numpy.ma.array(w, copy=0)
         else:
             if not xismv:
                 raise StatisticsError(
-                    'Error if weights are a list then x must be an MV2 !!!')
+                    "Error if weights are a list then x must be an MV2 !!!"
+                )
             w = __makeweights(x, w, axes)
             wismv = 1
     elif w is not None:
         if not xismv:
             raise StatisticsError(
-                'Error if weights are a list then x must be an MV2 !!!')
+                "Error if weights are a list then x must be an MV2 !!!"
+            )
         w = __makeweights(x, w, axes)
         wismv = 1
 
@@ -85,8 +87,12 @@ def __checker(x, y, w, axes, smally=0):
         # We didn't pass all MV2s shapes have to match (unless None)
         if smally == 0:
             if x.shape != numpy.ma.shape(y) and y is not None:
-                raise StatisticsError('Error x and y shape do not match !' +
-                                      str(x.shape) + ',' + str(numpy.ma.shape(y)))
+                raise StatisticsError(
+                    "Error x and y shape do not match !"
+                    + str(x.shape)
+                    + ","
+                    + str(numpy.ma.shape(y))
+                )
         else:
             shy = list(y.shape)
             shy2 = y.shape
@@ -96,7 +102,9 @@ def __checker(x, y, w, axes, smally=0):
                 for i in axes:
                     myaxes.append(eval(i))
             elif isinstance(axes, int):
-                myaxes = [axes, ]
+                myaxes = [
+                    axes,
+                ]
             else:
                 myaxes = list(axes)
             for anaxis in myaxes[::-1]:
@@ -109,25 +117,42 @@ def __checker(x, y, w, axes, smally=0):
                     sh[i] = myaxes[i]
                 y = numpy.ma.transpose(y, sh)
             if x.shape != numpy.ma.shape(y) and y is not None:
-                raise StatisticsError('Error x and y shape do not match (y shouldbe 1D less than x) !' +
-                                      str(x.shape) + ',' + str(shy2) + ' Remember y must be 1D less than x')
+                raise StatisticsError(
+                    "Error x and y shape do not match (y shouldbe 1D less than x) !"
+                    + str(x.shape)
+                    + ","
+                    + str(shy2)
+                    + " Remember y must be 1D less than x"
+                )
         if x.shape != numpy.ma.shape(w) and w is not None:
-            raise StatisticsError('Error x and weights shape do not match !' +
-                                  str(x.shape) + ',' + str(numpy.ma.shape(w)) +
-                                  ' ATTENTION if you are trynig to pass a list of 1D arrays' +
-                                  'for each dim, then x must be an MV2 !!!')
+            raise StatisticsError(
+                "Error x and weights shape do not match !"
+                + str(x.shape)
+                + ","
+                + str(numpy.ma.shape(w))
+                + " ATTENTION if you are trynig to pass a list of 1D arrays"
+                + "for each dim, then x must be an MV2 !!!"
+            )
         if not isinstance(axes, type([])):
             axes = cdms2.orderparse(str(axes))
         for i in axes:
             if len(x.shape) < i:
-                raise StatisticsError('Error you have ' + str(len(x.shape)) +
-                                      ' dimensions and try to work on dim:' + str(i))
+                raise StatisticsError(
+                    "Error you have "
+                    + str(len(x.shape))
+                    + " dimensions and try to work on dim:"
+                    + str(i)
+                )
     else:
         if y is not None:
             x, y = grower(x, y)
             if x.shape != y.shape:
                 raise StatisticsError(
-                    'Error x and y have different shapes' + str(x.shape) + ', ' + str(y.shape))
+                    "Error x and y have different shapes"
+                    + str(x.shape)
+                    + ", "
+                    + str(y.shape)
+                )
         ax = x.getAxisList()
         xorder = x.getOrder(ids=1)
         # Now grows w
@@ -136,11 +161,16 @@ def __checker(x, y, w, axes, smally=0):
             for o in worder:
                 if o not in xorder:
                     raise StatisticsError(
-                        'Error weights have a dimension that is neither in x or y:' + o)
+                        "Error weights have a dimension that is neither in x or y:" + o
+                    )
             x, w = grower(x, w)
             if x.shape != w.shape:
                 raise StatisticsError(
-                    'Error x and weights have different shapes' + str(x.shape) + ', ' + str(w.shape))
+                    "Error x and weights have different shapes"
+                    + str(x.shape)
+                    + ", "
+                    + str(w.shape)
+                )
         # Last thing convert the axes input to numbers
         if isinstance(axes, type(1)):
             axes = str(axes)
@@ -149,24 +179,24 @@ def __checker(x, y, w, axes, smally=0):
             naxes = len(axesparse)
             for i in range(naxes):
                 o = axesparse[i]
-                if isinstance(o, type('')):
+                if isinstance(o, type("")):
                     for j in range(len(xorder)):
                         if xorder[j] == o:
                             axesparse[i] = j
                     # Well it must be a name for x y t....
-                    if isinstance(axesparse[i], type('')):
+                    if isinstance(axesparse[i], type("")):
                         for j in range(len(x.shape)):
                             if o[1:-1] == x.getAxis(j).id:
                                 axesparse[i] = j
                     # Everything failed the axis id must be not existing in the
                     # slab...
-                    if isinstance(axesparse[i], type('')):
+                    if isinstance(axesparse[i], type("")):
                         raise StatisticsError(
-                            'Error axis id :' +
-                            o +
-                            ' not found in first slab: ' +
-                            x.getOrder(
-                                ids=1))
+                            "Error axis id :"
+                            + o
+                            + " not found in first slab: "
+                            + x.getOrder(ids=1)
+                        )
             axes = axesparse
     # Now we have array those shape match, and a nice list of axes let's keep
     # going
@@ -176,8 +206,12 @@ def __checker(x, y, w, axes, smally=0):
     xorder = list(range(len(x.shape)))
     forder = []
     for i in range(naxes):
-        forder.append(axes[i])
-        n0 = n0 * xsh[axes[i]]
+        a = axes[i]
+        forder.append(a)
+        try:
+            n0 = n0 * xsh[a]
+        except IndexError:
+            raise Exception("Axis {} is out of bounds for dimension {}".format(a, len(xsh)))
     fsh = [n0]
     ax2 = []
     for i in range(len(x.shape)):
diff --git a/tests/test_genutil_statistics.py b/tests/test_genutil_statistics.py
index e6501c9..fb6f888 100644
--- a/tests/test_genutil_statistics.py
+++ b/tests/test_genutil_statistics.py
@@ -1,63 +1,122 @@
 from __future__ import print_function
-import cdms2,genutil,os,sys
+import cdms2
+import genutil
+import os
 import unittest
 import cdat_info
 import numpy
+
 dump = False
 
+
 class GENUTIL(unittest.TestCase):
-    def assertArraysEqual(self,A,nm,skip=False, dump=dump):
+    def assertArraysEqual(self, A, nm, skip=False, dump=dump):
         B = self.good(nm)
-        print("A-B max difference", numpy.abs(A-B).max(), skip)
-        print("A-B % difference", numpy.abs((A-B)/A).max(), skip)
+        print("A-B max difference", numpy.abs(A - B).max(), skip)
+        print("A-B % difference", numpy.abs((A - B) / A).max(), skip)
         if dump:
             self.out.write(A, id=nm)
             self.out.sync()
 
         if not skip:
-            self.assertTrue(numpy.ma.allclose(A,B))
+            self.assertTrue(numpy.ma.allclose(A, B))
 
     def testPercentiles(self):
-        a = numpy.array([1.0,2.0,3.0,4.0,5.0])
-        p = genutil.statistics.percentiles(a,percentiles=[1])
-        # REVISIT
+        a = numpy.arange(1.0, 6.0)
+        p = genutil.statistics.percentiles(a)
+
+        assert (p == a).all()
+
+        with self.assertRaises(Exception):
+            p = genutil.statistics.percentiles(a, axis=1)
+
+        aa = numpy.array([a for _ in range(10)])
+
+        p = genutil.statistics.percentiles(aa)
+
+        assert (p == aa).all()
+
+        p = genutil.statistics.percentiles(aa, axis=1)
+
+        assert (p == numpy.full((1, 10), 3.0)).all()
+
+        p = genutil.statistics.percentiles(aa, [0, 50, 100], axis=1)
+
+        assert (p == numpy.array([numpy.full((10,), x) for x in (1.0, 3.0, 5.0)])).all()
+
+        a = numpy.arange(1.0, 6.0).reshape((5, 1))
+
+        p = genutil.statistics.percentiles(a)
+
+        assert (p == numpy.array([[3.0]])).all()
 
     def testStatisitcs(self):
-        f=cdms2.open(os.path.join(cdat_info.get_sampledata_path(),'clt.nc'))
+        f = cdms2.open(os.path.join(cdat_info.get_sampledata_path(), "clt.nc"))
 
-        u=f('u',time=slice(0,1),level=slice(0,1),squeeze=1)
-        v=f('v',time=slice(0,1),plev1=slice(0,1),squeeze=1)
+        u = f("u", time=slice(0, 1), level=slice(0, 1), squeeze=1)
+        v = f("v", time=slice(0, 1), plev1=slice(0, 1), squeeze=1)
 
-        self.good = cdms2.open(os.path.join(cdat_info.get_sampledata_path(),"genutil_statistics.nc"))
+        self.good = cdms2.open(
+            os.path.join(cdat_info.get_sampledata_path(), "genutil_statistics.nc")
+        )
         if dump:
-            self.out = cdms2.open("genutil_statistics_new.nc","w")
-        print('Lagged correlation')
+            self.out = cdms2.open("genutil_statistics_new.nc", "w")
+        print("Lagged correlation")
         nm = "lagged_corr"
-        self.assertArraysEqual(genutil.statistics.laggedcorrelation(u,v,axis=0),  nm+"_1")
-        self.assertArraysEqual(genutil.statistics.laggedcorrelation(u,v,axis=0,lag=4), nm+"_2")
-        self.assertArraysEqual(genutil.statistics.laggedcorrelation(u,v,axis=0,lag=4,noloop=1), nm+"_3")
-        self.assertArraysEqual(genutil.statistics.laggedcorrelation(u,v,axis=0,lag=[4,8,10]), nm+"_4")
+        self.assertArraysEqual(
+            genutil.statistics.laggedcorrelation(u, v, axis=0), nm + "_1"
+        )
+        self.assertArraysEqual(
+            genutil.statistics.laggedcorrelation(u, v, axis=0, lag=4), nm + "_2"
+        )
+        self.assertArraysEqual(
+            genutil.statistics.laggedcorrelation(u, v, axis=0, lag=4, noloop=1),
+            nm + "_3",
+        )
+        self.assertArraysEqual(
+            genutil.statistics.laggedcorrelation(u, v, axis=0, lag=[4, 8, 10]),
+            nm + "_4",
+        )
 
-
-        print('Lagged covariance')
+        print("Lagged covariance")
         nm = "lagged_cov"
-        self.assertArraysEqual(genutil.statistics.laggedcovariance(u,v,axis=0), nm+"_1")
-        self.assertArraysEqual(genutil.statistics.laggedcovariance(u,v,axis=0,lag=4), nm+"_2")
-        self.assertArraysEqual(genutil.statistics.laggedcovariance(u,v,axis=0,lag=4,noloop=1), nm+"_3")
-        self.assertArraysEqual(genutil.statistics.laggedcovariance(u,v,axis=0,lag=[4,8,10]), nm+"_4")
+        self.assertArraysEqual(
+            genutil.statistics.laggedcovariance(u, v, axis=0), nm + "_1"
+        )
+        self.assertArraysEqual(
+            genutil.statistics.laggedcovariance(u, v, axis=0, lag=4), nm + "_2"
+        )
+        self.assertArraysEqual(
+            genutil.statistics.laggedcovariance(u, v, axis=0, lag=4, noloop=1),
+            nm + "_3",
+        )
+        self.assertArraysEqual(
+            genutil.statistics.laggedcovariance(u, v, axis=0, lag=[4, 8, 10]), nm + "_4"
+        )
 
-        print('Auto correlation')
+        print("Auto correlation")
         nm = "auto_corr"
-        self.assertArraysEqual(genutil.statistics.autocorrelation(u,axis=0), nm+"_1")
-        self.assertArraysEqual(genutil.statistics.autocorrelation(u,axis=0,lag=4), nm+"_2")
-        self.assertArraysEqual(genutil.statistics.autocorrelation(u,axis=0,lag=4,noloop=1), nm+"_3")
-        self.assertArraysEqual(genutil.statistics.autocorrelation(u,axis=0,lag=[4,8,10]), nm+"_4")
+        self.assertArraysEqual(genutil.statistics.autocorrelation(u, axis=0), nm + "_1")
+        self.assertArraysEqual(
+            genutil.statistics.autocorrelation(u, axis=0, lag=4), nm + "_2"
+        )
+        self.assertArraysEqual(
+            genutil.statistics.autocorrelation(u, axis=0, lag=4, noloop=1), nm + "_3"
+        )
+        self.assertArraysEqual(
+            genutil.statistics.autocorrelation(u, axis=0, lag=[4, 8, 10]), nm + "_4"
+        )
 
-        print('Auto covariance')
+        print("Auto covariance")
         nm = "auto_cov"
-        self.assertArraysEqual(genutil.statistics.autocovariance(u,axis=0), nm+"_1")
-        self.assertArraysEqual(genutil.statistics.autocovariance(u,axis=0,lag=4), nm+"_2")
-        self.assertArraysEqual(genutil.statistics.autocovariance(u,axis=0,lag=4,noloop=1), nm+"_3")
-        self.assertArraysEqual(genutil.statistics.autocovariance(u,axis=0,lag=[4,8,10]), nm+"_4")
+        self.assertArraysEqual(genutil.statistics.autocovariance(u, axis=0), nm + "_1")
+        self.assertArraysEqual(
+            genutil.statistics.autocovariance(u, axis=0, lag=4), nm + "_2"
+        )
+        self.assertArraysEqual(
+            genutil.statistics.autocovariance(u, axis=0, lag=4, noloop=1), nm + "_3"
+        )
+        self.assertArraysEqual(
+            genutil.statistics.autocovariance(u, axis=0, lag=[4, 8, 10]), nm + "_4"
+        )
         f.close()
-

From 78599fdc20e4d7f79ebe03814945a1af947ad74a Mon Sep 17 00:00:00 2001
From: Jason Boutte <boutte.jason@gmail.com>
Date: Thu, 2 Jul 2020 23:31:17 -0700
Subject: [PATCH 05/15] Adds a few targets and documents all targets

---
 Makefile | 48 +++++++++++++++++++++++++++++++++++-------------
 1 file changed, 35 insertions(+), 13 deletions(-)

diff --git a/Makefile b/Makefile
index e5e2a4b..4a470c7 100644
--- a/Makefile
+++ b/Makefile
@@ -1,8 +1,8 @@
 .PHONY: conda-info conda-list setup-build setup-tests conda-rerender \
 	conda-build conda-upload conda-dump-env \
-	run-tests run-coveralls
+	run-tests run-coveralls dev-install dev-environment help
 
-SHELL = /bin/bash
+.DEFAULT_GOAL: help
 
 os = $(shell uname)
 pkg_name = genutil
@@ -36,48 +36,70 @@ ifndef $(local_repo)
 local_repo = $(dir $(realpath $(firstword $(MAKEFILE_LIST))))
 endif
 
-conda-info:
+help: ## Prints help
+	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | \
+		sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
+
+dev-environment: export conda_env := build-genutil
+dev-environment: export numpy_ver := 1.18
+dev-environment: export py_ver := 3.7
+dev-environment: ## Creates development environment using local conda
+	source $(conda_activate) base; conda create -y -n $(conda_env) \
+		$(foreach x,$(extra_channels),-c $(x)) \
+		"python=$(py_ver)" "numpy=$(numpy_ver)" gcc_$(os)-64 \
+		cdat_info udunits2 cdms2 cdutil testsrunner
+
+	source $(conda_activate) $(conda_env); \
+		conda remove genutil --force
+
+	$(MAKE) dev-install
+
+dev-install: ## Installs package in development environment
+	source $(conda_activate) $(conda_env); \
+		python setup.py build -g; \
+		python setup.py install --record files.txt --force
+
+conda-info: ## Prints conda info for environment
 	source $(conda_activate) $(conda_env); conda info
 
-conda-list:
+conda-list: ## Prints packages installed in environment
 	source $(conda_activate) $(conda_env); conda list
 
-setup-build:
+setup-build: ## Setup build
 ifeq ($(wildcard $(workdir)/conda-recipes),)
 	git clone -b $(conda_recipes_branch) https://github.com/CDAT/conda-recipes $(workdir)/conda-recipes
 else
 	cd $(workdir)/conda-recipes; git pull
 endif
 
-setup-tests:
+setup-tests: ## Setup test environment
 	source $(conda_activate) base; conda create -y -n $(conda_env) --use-local \
 		$(foreach x,$(extra_channels),-c $(x)) $(pkg_name) $(foreach x,$(test_pkgs),"$(x)") \
 		$(foreach x,$(extra_pkgs),"$(x)")
 
-conda-rerender: setup-build 
+conda-rerender: setup-build ## Rerender conda recipe using conda-smithy
 	python $(workdir)/$(build_script) -w $(workdir) -l $(last_stable) -B 0 -p $(pkg_name) -r $(repo_name) \
 		-b $(branch) --do_rerender --conda_env $(conda_env) --ignore_conda_missmatch \
 		--conda_activate $(conda_activate)
 
-conda-build:
+conda-build: ## Builds conda recipe
 	mkdir -p $(artifact_dir)
 
 	python $(workdir)/$(build_script) -w $(workdir) -p $(pkg_name) --build_version $(build_version) \
 		--do_build --conda_env $(conda_env) --extra_channels $(extra_channels) \
 		--conda_activate $(conda_activate) $(conda_build_extra)
 
-conda-upload:
+conda-upload: ## Upload conda packages in artifcat directory
 	source $(conda_activate) $(conda_env); \
 		anaconda -t $(conda_upload_token) upload -u $(user) -l $(label) --force $(artifact_dir)/*.tar.bz2
 
-
-conda-dump-env:
+conda-dump-env: ## Dumps conda environment
 	mkdir -p $(artifact_dir)
 
 	source $(conda_activate) $(conda_env); conda list --explicit > $(artifact_dir)/$(conda_env_filename).txt
 
-run-tests:
+run-tests: ## Runs the tests using environment
 	source $(conda_activate) $(conda_env); python run_tests.py -H -v2 $(coverage)
 
-run-coveralls:
+run-coveralls: ## Runs coveralls using environment
 	source $(conda_activate) $(conda_env); coveralls;

From 1831b724c016fad847ffe1f5e1aa3e5bacb3e8c8 Mon Sep 17 00:00:00 2001
From: muryanto1 <muryanto1@llnl.gov>
Date: Mon, 6 Jul 2020 10:04:42 -0700
Subject: [PATCH 06/15] fixed flake8 failures and temporarily upload from this
 branch

---
 .circleci/config.yml |  6 +++---
 Lib/stats_checker.py | 46 +++++++++++---------------------------------
 2 files changed, 14 insertions(+), 38 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index ac7f944..b36af64 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -197,6 +197,6 @@ workflows:
          - upload:
               requires:
                  - test
-              filters:
-                 branches:
-                    only: master
+#              filters:
+#                 branches:
+#                    only: master
diff --git a/Lib/stats_checker.py b/Lib/stats_checker.py
index 4b8eff1..b663919 100644
--- a/Lib/stats_checker.py
+++ b/Lib/stats_checker.py
@@ -88,10 +88,7 @@ def __checker(x, y, w, axes, smally=0):
         if smally == 0:
             if x.shape != numpy.ma.shape(y) and y is not None:
                 raise StatisticsError(
-                    "Error x and y shape do not match !"
-                    + str(x.shape)
-                    + ","
-                    + str(numpy.ma.shape(y))
+                    "Error x and y shape do not match !" + str(x.shape) + "," + str(numpy.ma.shape(y))
                 )
         else:
             shy = list(y.shape)
@@ -117,41 +114,26 @@ def __checker(x, y, w, axes, smally=0):
                     sh[i] = myaxes[i]
                 y = numpy.ma.transpose(y, sh)
             if x.shape != numpy.ma.shape(y) and y is not None:
+                err_msg = "Error x and y shape do not match (y shouldbe 1D less than x) !"
                 raise StatisticsError(
-                    "Error x and y shape do not match (y shouldbe 1D less than x) !"
-                    + str(x.shape)
-                    + ","
-                    + str(shy2)
-                    + " Remember y must be 1D less than x"
+                    err_msg + str(x.shape) + "," + str(shy2) + " Remember y must be 1D less than x"
                 )
         if x.shape != numpy.ma.shape(w) and w is not None:
-            raise StatisticsError(
-                "Error x and weights shape do not match !"
-                + str(x.shape)
-                + ","
-                + str(numpy.ma.shape(w))
-                + " ATTENTION if you are trynig to pass a list of 1D arrays"
-                + "for each dim, then x must be an MV2 !!!"
-            )
+            msg1 = "Error x and weights shape do not match !"
+            msg2 = " ATTENTION if you are trying to pass a list of 1D arrays for each dim, then x must be an MV2 !!!"
+            raise StatisticsError(msg1 + str(x.shape) + "," + str(numpy.ma.shape(w)) + msg2)
         if not isinstance(axes, type([])):
             axes = cdms2.orderparse(str(axes))
         for i in axes:
             if len(x.shape) < i:
-                raise StatisticsError(
-                    "Error you have "
-                    + str(len(x.shape))
-                    + " dimensions and try to work on dim:"
-                    + str(i)
-                )
+                err_msg = "Error you have " + str(len(x.shape)) + " dimensions and try to work on dim:" + str(i)
+                raise StatisticsError(err_msg)
     else:
         if y is not None:
             x, y = grower(x, y)
             if x.shape != y.shape:
                 raise StatisticsError(
-                    "Error x and y have different shapes"
-                    + str(x.shape)
-                    + ", "
-                    + str(y.shape)
+                    "Error x and y have different shapes" + str(x.shape) + ", " + str(y.shape)
                 )
         ax = x.getAxisList()
         xorder = x.getOrder(ids=1)
@@ -166,10 +148,7 @@ def __checker(x, y, w, axes, smally=0):
             x, w = grower(x, w)
             if x.shape != w.shape:
                 raise StatisticsError(
-                    "Error x and weights have different shapes"
-                    + str(x.shape)
-                    + ", "
-                    + str(w.shape)
+                    "Error x and weights have different shapes" + str(x.shape) + ", " + str(w.shape)
                 )
         # Last thing convert the axes input to numbers
         if isinstance(axes, type(1)):
@@ -192,10 +171,7 @@ def __checker(x, y, w, axes, smally=0):
                     # slab...
                     if isinstance(axesparse[i], type("")):
                         raise StatisticsError(
-                            "Error axis id :"
-                            + o
-                            + " not found in first slab: "
-                            + x.getOrder(ids=1)
+                            "Error axis id :" + o + " not found in first slab: " + x.getOrder(ids=1)
                         )
             axes = axesparse
     # Now we have array those shape match, and a nice list of axes let's keep

From 7226d7189cf391cb011cbf841b36b9ff3766a263 Mon Sep 17 00:00:00 2001
From: Jason Boutte <boutte.jason@gmail.com>
Date: Wed, 8 Jul 2020 22:22:50 -0700
Subject: [PATCH 07/15] Updates dev-environment and dev-install targets

---
 Makefile | 25 +++++++++++--------------
 1 file changed, 11 insertions(+), 14 deletions(-)

diff --git a/Makefile b/Makefile
index 4a470c7..704f590 100644
--- a/Makefile
+++ b/Makefile
@@ -4,6 +4,7 @@
 
 .DEFAULT_GOAL: help
 
+SHELL := /bin/bash
 os = $(shell uname)
 pkg_name = genutil
 repo_name = genutil
@@ -40,24 +41,20 @@ help: ## Prints help
 	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | \
 		sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
 
-dev-environment: export conda_env := build-genutil
-dev-environment: export numpy_ver := 1.18
-dev-environment: export py_ver := 3.7
-dev-environment: ## Creates development environment using local conda
-	source $(conda_activate) base; conda create -y -n $(conda_env) \
-		$(foreach x,$(extra_channels),-c $(x)) \
-		"python=$(py_ver)" "numpy=$(numpy_ver)" gcc_$(os)-64 \
-		cdat_info udunits2 cdms2 cdutil testsrunner
-
-	source $(conda_activate) $(conda_env); \
-		conda remove genutil --force
+dev-environment: conda_channels := -c conda-forge
+dev-environment: gcc := $(or $(if $(findstring $(shell uname),Darwin),clang_osx-64), gcc_linux-64)
+dev-environment: conda_pkgs := $(gcc) "numpy>=1.18" udunits expat pytest ipython cdms2
+dev-environment: export conda_env := genutil-dev
+dev-environment: ## Creates dev environment and installs genutil in "Development Mode". If you modify c code you will need to run "make dev-install".
+	source $(conda_activate) base; conda create -n $(conda_env) \
+		$(conda_channels) $(conda_pkgs)
 
 	$(MAKE) dev-install
 
-dev-install: ## Installs package in development environment
+dev-install: ## Installs genutil in "Development Mode", will recompile c code each invocation."
 	source $(conda_activate) $(conda_env); \
-		python setup.py build -g; \
-		python setup.py install --record files.txt --force
+		python setup.py build -gf; \
+		python setup.py develop 
 
 conda-info: ## Prints conda info for environment
 	source $(conda_activate) $(conda_env); conda info

From 76e4e15ebec40dcda8ec8f2589d9f209203b7f6c Mon Sep 17 00:00:00 2001
From: Jason Boutte <boutte.jason@gmail.com>
Date: Thu, 9 Jul 2020 01:09:29 -0700
Subject: [PATCH 08/15] Disables dev-evnironment for OSX and adds dev-docker
 that will create dev-environment in docker container.

---
 Makefile | 23 ++++++++++++++++++-----
 1 file changed, 18 insertions(+), 5 deletions(-)

diff --git a/Makefile b/Makefile
index 704f590..317563d 100644
--- a/Makefile
+++ b/Makefile
@@ -13,11 +13,11 @@ build_script = conda-recipes/build_tools/conda_build.py
 test_pkgs = testsrunner
 last_stable ?= 8.2
 
-conda_env ?= base
+conda_env ?= genutil-build
 workdir ?= $(PWD)/workspace
 branch ?= $(shell git rev-parse --abbrev-ref HEAD)
 extra_channels ?= cdat/label/nightly conda-forge
-conda ?= $(or $(CONDA_EXE),$(shell find /opt/*conda*/bin $(HOME)/*conda* -type f -iname conda))
+conda ?= $(or $(CONDA_EXE),$(shell find /opt/*conda*/bin $(HOME)/*conda*/bin -type f -iname conda))
 artifact_dir ?= $(PWD)/artifacts
 conda_env_filename ?= spec-file
 build_version ?= 3.7
@@ -41,20 +41,33 @@ help: ## Prints help
 	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | \
 		sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
 
+dev-docker:
+	docker run -d --name genutil-dev -v $(PWD):/src -w /src continuumio/miniconda3 /bin/sleep infinity || exit 0
+	docker start genutil-dev
+	docker exec -it genutil-dev /bin/bash -c "apt update; apt install -y make"
+	docker exec -it genutil-dev /bin/bash -c "make dev-environment"
+	docker exec -it genutil-dev /bin/bash -c "conda init bash; echo 'conda activate genutil-dev' >> ~/.bashrc"
+	docker exec -it genutil-dev /bin/bash
+
 dev-environment: conda_channels := -c conda-forge
-dev-environment: gcc := $(or $(if $(findstring $(shell uname),Darwin),clang_osx-64), gcc_linux-64)
+dev-environment: gcc := $(or $(if $(findstring os,Darwin),clang_osx-64), gcc_linux-64)
 dev-environment: conda_pkgs := $(gcc) "numpy>=1.18" udunits expat pytest ipython cdms2
 dev-environment: export conda_env := genutil-dev
 dev-environment: ## Creates dev environment and installs genutil in "Development Mode". If you modify c code you will need to run "make dev-install".
-	source $(conda_activate) base; conda create -n $(conda_env) \
+ifeq ($(os),Darwin)
+	$(error dev-environment on OSX is not support)
+endif
+
+	source $(conda_activate) base; conda create -y -n $(conda_env) \
 		$(conda_channels) $(conda_pkgs)
 
 	$(MAKE) dev-install
 
+dev-install: export conda_env := genutil-dev
 dev-install: ## Installs genutil in "Development Mode", will recompile c code each invocation."
 	source $(conda_activate) $(conda_env); \
 		python setup.py build -gf; \
-		python setup.py develop 
+		python setup.py install
 
 conda-info: ## Prints conda info for environment
 	source $(conda_activate) $(conda_env); conda info

From 8cbbff309cfb23b1aabb4120614bc597ac021053 Mon Sep 17 00:00:00 2001
From: Jason Boutte <boutte.jason@gmail.com>
Date: Thu, 9 Jul 2020 17:38:33 -0700
Subject: [PATCH 09/15] Updates makefile

---
 Makefile | 51 ++++++++++++++++++++++++++++++++++-----------------
 1 file changed, 34 insertions(+), 17 deletions(-)

diff --git a/Makefile b/Makefile
index 317563d..2368155 100644
--- a/Makefile
+++ b/Makefile
@@ -13,8 +13,9 @@ build_script = conda-recipes/build_tools/conda_build.py
 test_pkgs = testsrunner
 last_stable ?= 8.2
 
-conda_env ?= genutil-build
-workdir ?= $(PWD)/workspace
+conda_build_env = genutil-build
+conda_test_env = genutil-test
+
 branch ?= $(shell git rev-parse --abbrev-ref HEAD)
 extra_channels ?= cdat/label/nightly conda-forge
 conda ?= $(or $(CONDA_EXE),$(shell find /opt/*conda*/bin $(HOME)/*conda*/bin -type f -iname conda))
@@ -22,6 +23,18 @@ artifact_dir ?= $(PWD)/artifacts
 conda_env_filename ?= spec-file
 build_version ?= 3.7
 
+# Only populate if workdir is not defined
+ifeq ($(origin workdir),undefined)
+# Create .tempdir if it doesn't exist
+ifeq ($(wildcard $(PWD)/.tempdir),)
+workdir := $(shell mktemp -d -t "build_$(pkg_name).XXXXXXXX")
+$(shell echo $(workdir) > $(PWD)/.tempdir)
+endif
+
+# Read tempdir
+workdir := $(shell cat $(PWD)/.tempdir)
+endif
+
 ifneq ($(coverage),)
 coverage = -c tests/coverage.json --coverage-from-egg
 endif
@@ -33,9 +46,10 @@ conda_activate = $(conda_base)/bin/activate
 
 conda_build_extra = --copy_conda_package $(artifact_dir)/
 
-ifndef $(local_repo)
-local_repo = $(dir $(realpath $(firstword $(MAKEFILE_LIST))))
-endif
+# Is this needed?
+# ifndef $(local_repo)
+# local_repo = $(dir $(realpath $(firstword $(MAKEFILE_LIST))))
+# endif
 
 help: ## Prints help
 	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | \
@@ -51,9 +65,9 @@ dev-docker:
 
 dev-environment: conda_channels := -c conda-forge
 dev-environment: gcc := $(or $(if $(findstring os,Darwin),clang_osx-64), gcc_linux-64)
-dev-environment: conda_pkgs := $(gcc) "numpy>=1.18" udunits expat pytest ipython cdms2
+dev-environment: conda_pkgs := $(gcc) "numpy>=1.18" udunits expat pytest ipython cdms2 $(test_pkgs)
 dev-environment: export conda_env := genutil-dev
-dev-environment: ## Creates dev environment and installs genutil in "Development Mode". If you modify c code you will need to run "make dev-install".
+dev-environment: ## Creates dev environment and installs genutil. Will need to run dev-install after any code change.
 ifeq ($(os),Darwin)
 	$(error dev-environment on OSX is not support)
 endif
@@ -64,16 +78,19 @@ endif
 	$(MAKE) dev-install
 
 dev-install: export conda_env := genutil-dev
-dev-install: ## Installs genutil in "Development Mode", will recompile c code each invocation."
+dev-install: ## Installs genutil in conda environment "genutil-dev"
 	source $(conda_activate) $(conda_env); \
 		python setup.py build -gf; \
 		python setup.py install
 
+dev-conda-build: conda_build_extra := --local_repo $(PWD)
+dev-conda-build: setup-build conda-rerender conda-build ## Build conda package
+
 conda-info: ## Prints conda info for environment
-	source $(conda_activate) $(conda_env); conda info
+	source $(conda_activate) base; conda info
 
 conda-list: ## Prints packages installed in environment
-	source $(conda_activate) $(conda_env); conda list
+	source $(conda_activate) $(conda_test_env); conda list
 
 setup-build: ## Setup build
 ifeq ($(wildcard $(workdir)/conda-recipes),)
@@ -83,33 +100,33 @@ else
 endif
 
 setup-tests: ## Setup test environment
-	source $(conda_activate) base; conda create -y -n $(conda_env) --use-local \
+	source $(conda_activate) base; conda create -y -n $(conda_test_env) --use-local \
 		$(foreach x,$(extra_channels),-c $(x)) $(pkg_name) $(foreach x,$(test_pkgs),"$(x)") \
 		$(foreach x,$(extra_pkgs),"$(x)")
 
 conda-rerender: setup-build ## Rerender conda recipe using conda-smithy
 	python $(workdir)/$(build_script) -w $(workdir) -l $(last_stable) -B 0 -p $(pkg_name) -r $(repo_name) \
-		-b $(branch) --do_rerender --conda_env $(conda_env) --ignore_conda_missmatch \
+		-b $(branch) --do_rerender --conda_env $(conda_build_env) --ignore_conda_missmatch \
 		--conda_activate $(conda_activate)
 
 conda-build: ## Builds conda recipe
 	mkdir -p $(artifact_dir)
 
 	python $(workdir)/$(build_script) -w $(workdir) -p $(pkg_name) --build_version $(build_version) \
-		--do_build --conda_env $(conda_env) --extra_channels $(extra_channels) \
+		--do_build --conda_env $(conda_build_env) --extra_channels $(extra_channels) \
 		--conda_activate $(conda_activate) $(conda_build_extra)
 
 conda-upload: ## Upload conda packages in artifcat directory
-	source $(conda_activate) $(conda_env); \
+	source $(conda_activate) $(conda_build_env); \
 		anaconda -t $(conda_upload_token) upload -u $(user) -l $(label) --force $(artifact_dir)/*.tar.bz2
 
 conda-dump-env: ## Dumps conda environment
 	mkdir -p $(artifact_dir)
 
-	source $(conda_activate) $(conda_env); conda list --explicit > $(artifact_dir)/$(conda_env_filename).txt
+	source $(conda_activate) $(conda_test_env); conda list --explicit > $(artifact_dir)/$(conda_env_filename).txt
 
 run-tests: ## Runs the tests using environment
-	source $(conda_activate) $(conda_env); python run_tests.py -H -v2 $(coverage)
+	source $(conda_activate) $(conda_test_env); python run_tests.py -H -v2 $(coverage)
 
 run-coveralls: ## Runs coveralls using environment
-	source $(conda_activate) $(conda_env); coveralls;
+	source $(conda_activate) $(conda_test_env); coveralls;

From b568452ae212e3ed4ee3762c4795324372aac85d Mon Sep 17 00:00:00 2001
From: muryanto1 <muryanto1@llnl.gov>
Date: Fri, 10 Jul 2020 11:05:25 -0700
Subject: [PATCH 10/15] cleanup Makefile and .circleci/config.yml

---
 .circleci/config.yml | 49 +++++++-------------------------------------
 Makefile             | 20 +++++++++++-------
 2 files changed, 20 insertions(+), 49 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index b36af64..a0f8877 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -1,25 +1,5 @@
 version: 2.1
 
-parameters:
-   pkg_name:
-      type: string
-      default: "genutil"
-   repo_name:
-      type: string
-      default: "genutil"
-   last_stable:
-      type: string
-      default: "8.2"
-   user:
-      type: string
-      default: "cdat"
-   label:
-      type: string
-      default: "nightly"
-   env_name:
-      type: string
-      default: "test_genutil"
-
 aliases:
   - &setup_env
     name: setup_env
@@ -31,7 +11,6 @@ aliases:
           export PROJECT_DIR=/home/circleci/project/workdir/linux
        fi
        echo "export WORKDIR=$PROJECT_DIR/$PY_VER" >> $BASH_ENV
-       cat $BASH_ENV
        source $BASH_ENV
        mkdir -p $WORKDIR
 
@@ -39,20 +18,17 @@ aliases:
     name: setup_miniconda
     command: |
        source $BASH_ENV
-       mkdir -p $WORKDIR
        git clone https://github.com/CDAT/cdat.git $WORKDIR/cdat
        # install_miniconda.py installs miniconda3 under $WORKDIR/miniconda
        python $WORKDIR/cdat/scripts/install_miniconda.py -w $WORKDIR -p 'py3'
 
-
   - &conda_rerender
     name: conda_rerender
     command: |
        source $BASH_ENV
        source $WORKDIR/miniconda/etc/profile.d/conda.sh
        conda activate base
-       echo "make conda-rerender conda=$WORKDIR/miniconda/bin/conda workdir=$WORKDIR last_stable=$LAST_STABLE branch=$CIRCLE_BRANCH"
-       make conda-rerender conda=$WORKDIR/miniconda/bin/conda workdir=$WORKDIR last_stable=$LAST_STABLE branch=$CIRCLE_BRANCH
+       make conda-rerender workdir=$WORKDIR branch=$CIRCLE_BRANCH
 
   - &conda_build
     name: conda_build
@@ -62,7 +38,7 @@ aliases:
        conda activate base
        os=`uname`
        artifacts_dir="artifacts/artifacts.${os}.py_${PY_VER}"
-       make conda-build conda=$WORKDIR/miniconda/bin/conda workdir=$WORKDIR artifact_dir=$PWD/$artifacts_dir build_version=$PY_VER
+       make conda-build workdir=$WORKDIR artifact_dir=$artifacts_dir build_version=$PY_VER
 
   - &setup_run_tests
     name: setup_run_tests
@@ -72,19 +48,15 @@ aliases:
        conda activate base
        export CONDA_PY_VER="python=$PY_VER"
        export LIBNETCDF_VER="libnetcdf=*=${LIBNETCDF}_*"
-
-       echo "make setup-tests conda=$WORKDIR/miniconda/bin/conda conda_env=$ENV_NAME extra_pkgs=\"$CONDA_PY_VER $LIBNETCDF_VER $COVERAGE_PKGS\""
-       make setup-tests conda=$WORKDIR/miniconda/bin/conda conda_env=$ENV_NAME extra_pkgs="$CONDA_PY_VER $LIBNETCDF_VER $COVERAGE_PKGS"
-
-       make conda-dump-env conda=$WORKDIR/miniconda/bin/conda conda_env=$ENV_NAME artifact_dir=$PWD/spec_artifacts conda_env_filename=$CIRCLE_JOB
+       make setup-tests workdir=$WORKDIR extra_pkgs="$CONDA_PY_VER $LIBNETCDF_VER $COVERAGE_PKGS"
+       make conda-dump-env workdir=$WORKDIR artifact_dir=$PWDspec_artifacts conda_env_filename=$CIRCLE_JOB
 
   - &run_tests
     name: run_tests
     command: |
        source $BASH_ENV
        source $WORKDIR/miniconda/etc/profile.d/conda.sh
-       conda activate $ENV_NAME
-       make run-tests conda=$WORKDIR/miniconda/bin/conda conda_env=$ENV_NAME workdir=$WORKDIR
+       make run-tests workdir=$WORKDIR
     no_output_timeout: 10m
 
   - &conda_upload
@@ -93,8 +65,8 @@ aliases:
        source $BASH_ENV
        source $WORKDIR/miniconda/etc/profile.d/conda.sh
        conda activate base
-       UPLOAD_OPTIONS="conda_upload_token=$CONDA_UPLOAD_TOKEN user=$USER label=$LABEL"
-       make conda-upload $UPLOAD_OPTIONS conda=$WORKDIR/miniconda/bin/conda artifact_dir="$PWD/artifacts/*/"
+       UPLOAD_OPTIONS="conda_upload_token=$CONDA_UPLOAD_TOKEN"
+       make conda-upload workdir=$WORKDIR $UPLOAD_OPTIONS artifact_dir="artifacts/*/"
 
 executors:
    linux:
@@ -113,9 +85,6 @@ jobs:
             type: string
       executor: << parameters.os >>
       environment:
-         PKG_NAME: << pipeline.parameters.pkg_name >>
-         REPO_NAME: << pipeline.parameters.repo_name >>
-         LAST_STABLE: << pipeline.parameters.last_stable >>
          PY_VER: << parameters.py_ver >>
       steps:
          - checkout
@@ -141,8 +110,6 @@ jobs:
             type: string
       executor: << parameters.os >>
       environment:
-         PKG_NAME: << pipeline.parameters.pkg_name >>
-         ENV_NAME: << pipeline.parameters.env_name >>
          PY_VER: << parameters.py_ver >>
          LIBNETCDF: << parameters.libnetcdf >>
       steps:
@@ -164,8 +131,6 @@ jobs:
       machine:
          image: circleci/classic:latest
       environment:
-         USER: << pipeline.parameters.user >>
-         LABEL: << pipeline.parameters.label >>
          PY_VER: "3.7"
       steps:
          - checkout
diff --git a/Makefile b/Makefile
index 2368155..6f61cad 100644
--- a/Makefile
+++ b/Makefile
@@ -8,18 +8,22 @@ SHELL := /bin/bash
 os = $(shell uname)
 pkg_name = genutil
 repo_name = genutil
+
+user ?= cdat
+label ?= nightly
+
 build_script = conda-recipes/build_tools/conda_build.py
 
 test_pkgs = testsrunner
 last_stable ?= 8.2
 
-conda_build_env = genutil-build
-conda_test_env = genutil-test
+conda_test_env = test-$(pkg_name)
+conda_build_env = build-$(pkg_name)
 
 branch ?= $(shell git rev-parse --abbrev-ref HEAD)
 extra_channels ?= cdat/label/nightly conda-forge
 conda ?= $(or $(CONDA_EXE),$(shell find /opt/*conda*/bin $(HOME)/*conda*/bin -type f -iname conda))
-artifact_dir ?= $(PWD)/artifacts
+
 conda_env_filename ?= spec-file
 build_version ?= 3.7
 
@@ -35,6 +39,8 @@ endif
 workdir := $(shell cat $(PWD)/.tempdir)
 endif
 
+artif_dir = $(workdir)/$(artifact_dir)
+
 ifneq ($(coverage),)
 coverage = -c tests/coverage.json --coverage-from-egg
 endif
@@ -44,7 +50,7 @@ conda_recipes_branch ?= master
 conda_base = $(patsubst %/bin/conda,%,$(conda))
 conda_activate = $(conda_base)/bin/activate
 
-conda_build_extra = --copy_conda_package $(artifact_dir)/
+conda_build_extra = --copy_conda_package $(artif_dir)/
 
 # Is this needed?
 # ifndef $(local_repo)
@@ -66,7 +72,7 @@ dev-docker:
 dev-environment: conda_channels := -c conda-forge
 dev-environment: gcc := $(or $(if $(findstring os,Darwin),clang_osx-64), gcc_linux-64)
 dev-environment: conda_pkgs := $(gcc) "numpy>=1.18" udunits expat pytest ipython cdms2 $(test_pkgs)
-dev-environment: export conda_env := genutil-dev
+dev-environment: export conda_env := dev-$(pkg_name)
 dev-environment: ## Creates dev environment and installs genutil. Will need to run dev-install after any code change.
 ifeq ($(os),Darwin)
 	$(error dev-environment on OSX is not support)
@@ -110,7 +116,7 @@ conda-rerender: setup-build ## Rerender conda recipe using conda-smithy
 		--conda_activate $(conda_activate)
 
 conda-build: ## Builds conda recipe
-	mkdir -p $(artifact_dir)
+	mkdir -p $(artif_dir)
 
 	python $(workdir)/$(build_script) -w $(workdir) -p $(pkg_name) --build_version $(build_version) \
 		--do_build --conda_env $(conda_build_env) --extra_channels $(extra_channels) \
@@ -118,7 +124,7 @@ conda-build: ## Builds conda recipe
 
 conda-upload: ## Upload conda packages in artifcat directory
 	source $(conda_activate) $(conda_build_env); \
-		anaconda -t $(conda_upload_token) upload -u $(user) -l $(label) --force $(artifact_dir)/*.tar.bz2
+		anaconda -t $(conda_upload_token) upload -u $(user) -l $(label) --force $(artif_dir)/*.tar.bz2
 
 conda-dump-env: ## Dumps conda environment
 	mkdir -p $(artifact_dir)

From 1686d51b7a662a18f54aa8397f056d7ca0e95ace Mon Sep 17 00:00:00 2001
From: Jason Boutte <boutte.jason@gmail.com>
Date: Fri, 10 Jul 2020 13:22:13 -0700
Subject: [PATCH 11/15] Fixes chenking if workdir is defined

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 6f61cad..ac7c757 100644
--- a/Makefile
+++ b/Makefile
@@ -28,7 +28,7 @@ conda_env_filename ?= spec-file
 build_version ?= 3.7
 
 # Only populate if workdir is not defined
-ifeq ($(origin workdir),undefined)
+ifeq ($(workdir),)
 # Create .tempdir if it doesn't exist
 ifeq ($(wildcard $(PWD)/.tempdir),)
 workdir := $(shell mktemp -d -t "build_$(pkg_name).XXXXXXXX")

From c27ab814e27761ba4565c516d17403f5ec0840cb Mon Sep 17 00:00:00 2001
From: Jason Boutte <boutte.jason@gmail.com>
Date: Fri, 10 Jul 2020 13:22:44 -0700
Subject: [PATCH 12/15] Fixes dev environment name

---
 Makefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index ac7c757..f9c26aa 100644
--- a/Makefile
+++ b/Makefile
@@ -66,7 +66,7 @@ dev-docker:
 	docker start genutil-dev
 	docker exec -it genutil-dev /bin/bash -c "apt update; apt install -y make"
 	docker exec -it genutil-dev /bin/bash -c "make dev-environment"
-	docker exec -it genutil-dev /bin/bash -c "conda init bash; echo 'conda activate genutil-dev' >> ~/.bashrc"
+	docker exec -it genutil-dev /bin/bash -c "conda init bash; echo 'conda activate dev-$(pkg_name)' >> ~/.bashrc"
 	docker exec -it genutil-dev /bin/bash
 
 dev-environment: conda_channels := -c conda-forge
@@ -83,7 +83,7 @@ endif
 
 	$(MAKE) dev-install
 
-dev-install: export conda_env := genutil-dev
+dev-install: export conda_env := dev-$(pkg_name)
 dev-install: ## Installs genutil in conda environment "genutil-dev"
 	source $(conda_activate) $(conda_env); \
 		python setup.py build -gf; \

From c7ab64515e580c52ddf10da76f6b7995207cad7e Mon Sep 17 00:00:00 2001
From: Jason Boutte <boutte.jason@gmail.com>
Date: Fri, 10 Jul 2020 13:23:07 -0700
Subject: [PATCH 13/15] Fixes add cdat nighly channel for test_pkgs

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index f9c26aa..6323971 100644
--- a/Makefile
+++ b/Makefile
@@ -69,7 +69,7 @@ dev-docker:
 	docker exec -it genutil-dev /bin/bash -c "conda init bash; echo 'conda activate dev-$(pkg_name)' >> ~/.bashrc"
 	docker exec -it genutil-dev /bin/bash
 
-dev-environment: conda_channels := -c conda-forge
+dev-environment: conda_channels := -c cdat/label/nightly -c conda-forge
 dev-environment: gcc := $(or $(if $(findstring os,Darwin),clang_osx-64), gcc_linux-64)
 dev-environment: conda_pkgs := $(gcc) "numpy>=1.18" udunits expat pytest ipython cdms2 $(test_pkgs)
 dev-environment: export conda_env := dev-$(pkg_name)

From de202e61664900ddbaccb21d95b3b9b85206da4b Mon Sep 17 00:00:00 2001
From: muryanto1 <muryanto1@llnl.gov>
Date: Fri, 10 Jul 2020 14:52:46 -0700
Subject: [PATCH 14/15] more cleanup on Makefile

---
 .circleci/config.yml |  2 +-
 Makefile             | 22 +++++++++++++---------
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index a0f8877..ea0c416 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -49,7 +49,7 @@ aliases:
        export CONDA_PY_VER="python=$PY_VER"
        export LIBNETCDF_VER="libnetcdf=*=${LIBNETCDF}_*"
        make setup-tests workdir=$WORKDIR extra_pkgs="$CONDA_PY_VER $LIBNETCDF_VER $COVERAGE_PKGS"
-       make conda-dump-env workdir=$WORKDIR artifact_dir=$PWDspec_artifacts conda_env_filename=$CIRCLE_JOB
+       make conda-dump-env workdir=$WORKDIR artifact_dir=$PWD/spec_artifacts conda_env_filename=$CIRCLE_JOB
 
   - &run_tests
     name: run_tests
diff --git a/Makefile b/Makefile
index 6323971..d8872c7 100644
--- a/Makefile
+++ b/Makefile
@@ -19,6 +19,7 @@ last_stable ?= 8.2
 
 conda_test_env = test-$(pkg_name)
 conda_build_env = build-$(pkg_name)
+conda_dev_env = dev-$(pkg_name)
 
 branch ?= $(shell git rev-parse --abbrev-ref HEAD)
 extra_channels ?= cdat/label/nightly conda-forge
@@ -62,17 +63,17 @@ help: ## Prints help
 		sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
 
 dev-docker:
-	docker run -d --name genutil-dev -v $(PWD):/src -w /src continuumio/miniconda3 /bin/sleep infinity || exit 0
-	docker start genutil-dev
-	docker exec -it genutil-dev /bin/bash -c "apt update; apt install -y make"
-	docker exec -it genutil-dev /bin/bash -c "make dev-environment"
-	docker exec -it genutil-dev /bin/bash -c "conda init bash; echo 'conda activate dev-$(pkg_name)' >> ~/.bashrc"
-	docker exec -it genutil-dev /bin/bash
+	docker run -d --name $(conda_dev_env) -v $(PWD):/src -w /src continuumio/miniconda3 /bin/sleep infinity || exit 0
+	docker start $(conda_dev_env)
+	docker exec -it $(conda_dev_env) /bin/bash -c "apt update; apt install -y make"
+	docker exec -it $(conda_dev_env) /bin/bash -c "make dev-environment"
+	docker exec -it $(conda_dev_env) /bin/bash -c "conda init bash; echo 'conda activate $(conda_dev_env)' >> ~/.bashrc"
+	docker exec -it $(conda_dev_env) /bin/bash
 
 dev-environment: conda_channels := -c cdat/label/nightly -c conda-forge
 dev-environment: gcc := $(or $(if $(findstring os,Darwin),clang_osx-64), gcc_linux-64)
 dev-environment: conda_pkgs := $(gcc) "numpy>=1.18" udunits expat pytest ipython cdms2 $(test_pkgs)
-dev-environment: export conda_env := dev-$(pkg_name)
+dev-environment: export conda_env := $(conda_dev_env)
 dev-environment: ## Creates dev environment and installs genutil. Will need to run dev-install after any code change.
 ifeq ($(os),Darwin)
 	$(error dev-environment on OSX is not support)
@@ -83,8 +84,8 @@ endif
 
 	$(MAKE) dev-install
 
-dev-install: export conda_env := dev-$(pkg_name)
-dev-install: ## Installs genutil in conda environment "genutil-dev"
+dev-install: export conda_env := $(conda_dev_env)
+dev-install: ## Installs genutil in conda environment "$(conda_dev_env)"
 	source $(conda_activate) $(conda_env); \
 		python setup.py build -gf; \
 		python setup.py install
@@ -92,6 +93,9 @@ dev-install: ## Installs genutil in conda environment "genutil-dev"
 dev-conda-build: conda_build_extra := --local_repo $(PWD)
 dev-conda-build: setup-build conda-rerender conda-build ## Build conda package
 
+dev-run-tests: ## Runs the tests using environment
+	source $(conda_activate) $(conda_dev_env); python run_tests.py -H -v2 $(coverage)
+
 conda-info: ## Prints conda info for environment
 	source $(conda_activate) base; conda info
 

From 9af45926e1372cb795dc2ea57cad1ec21eb57d06 Mon Sep 17 00:00:00 2001
From: muryanto1 <muryanto1@llnl.gov>
Date: Sat, 11 Jul 2020 14:38:36 -0700
Subject: [PATCH 15/15] only upload from master branch

---
 .circleci/config.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index ea0c416..532bf96 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -162,6 +162,6 @@ workflows:
          - upload:
               requires:
                  - test
-#              filters:
-#                 branches:
-#                    only: master
+              filters:
+                 branches:
+                    only: master