Revert "Netcdf46 (#249)"

This reverts commit a9e29ea.

.travis.yml

@@ -20,7 +20,7 @@ before_install:
 script:
 #- conda install -c uvcdat/label/nightly -c conda-forge -c uvcdat libcf distarray cdtime libcdms cdat_info numpy esmf esmpy libdrs_f pyopenssl nose requests flake8
 - conda create -n py3 python=3.6
-- conda install -n py3 -c conda-forge -c cdat libcf distarray cdtime libcdms cdat_info numpy libdrs_f pyopenssl=17.2.0 nose requests flake8 myproxyclient 
+- conda install -n py3 -c conda-forge -c uvcdat libcf distarray cdtime libcdms cdat_info numpy libdrs_f pyopenssl=17.2.0 nose requests flake8 myproxyclient 
 - source activate py3
 - if [ "$TRAVIS_OS_NAME" = "linux" ]; then conda install -n py3 -c nesii/channel/dev-esmf -c conda-forge esmpy ; fi
 - export UVCDAT_ANONYMOUS_LOG=False
@@ -37,7 +37,7 @@ script:
 - conda create -n py2 python=2.7
 - source activate py2
 - which python
-- conda install -c nesii/channel/dev-esmf -c conda-forge -c cdat libcf distarray cdtime libcdms cdat_info numpy esmf esmpy libdrs_f pyopenssl nose requests flake8
+- conda install -c nesii/channel/dev-esmf -c conda-forge -c uvcdat libcf distarray cdtime libcdms cdat_info numpy esmf esmpy libdrs_f pyopenssl nose requests flake8
 - export UVCDAT_ANONYMOUS_LOG=False
 - python setup.py install
 - python run_tests.py -v2 -s

ci-support/circleci_mac.sh

@@ -0,0 +1,15 @@
+export UVCDAT_ANONYMOUS_LOG=False
+export PATH=${HOME}/miniconda/bin:${PATH}
+echo "CIRCLE CI BRANCH:"$CIRCLE_BRANCH
+echo "CI_PULL_REQUESTS"$CI_PULL_REQUESTS
+echo "CI_PULL_REQUEST"$CI_PULL_REQUEST
+source activate py2
+python run_tests.py -v2 -s
+RESULT=$?
+source activate py3
+python run_tests.py -v2 -s
+RESULT=$(( $RESULT + $? ))
+echo "RESULT:"${RESULT}
+if [ $RESULT -eq 0 -a $CIRCLE_BRANCH != "master" ]; then LABEL='unstable' bash ./ci-support/conda_upload.sh ; fi
+if [ $RESULT -eq 0 -a $CIRCLE_BRANCH == "master" ]; then LABEL='nightly' bash ./ci-support/conda_upload.sh ; fi
+exit $RESULT

ci-support/circleci_mac_dep.sh

@@ -0,0 +1,102 @@
+#!/usr/bin/env bash
+cmd="ls"
+echo $cmd
+$cmd
+
+cmd="pwd"
+echo $cmd
+$cmd
+
+cmd="export PATH=${HOME}/miniconda/bin:${PATH}"
+echo $cmd
+$cmd
+
+# Create Python 3 environment
+cmd="conda create -n py3 -c uvcdat/label/nightly -c conda-forge -c uvcdat libcf distarray cdtime libcdms cdat_info numpy libdrs_f pyopenssl nose requests flake8 myproxyclient netcdf-fortran=4.4.4=5"
+echo $cmd
+$cmd
+
+# update openssl for myproxyclient
+cmd="conda install -n py3 pyopenssl"
+echo $cmd
+$cmd
+
+
+cmd="conda install -n py3 -c nesii/label/dev-esmf -c conda-forge esmf esmpy netcdf-fortran=4.4.4=5"
+echo $cmd
+$cmd
+
+# Create Python 2 environment
+cmd="conda create -n py2 python=2.7"
+echo $cmd
+$cmd
+
+# Activate python 2 environment
+cmd="source activate py2"
+echo $cmd
+$cmd 
+
+cmd="conda install -n py2 -c nesii/label/dev-esmf -c uvcdat/label/nightly -c conda-forge -c uvcdat libcf distarray cdtime libcdms cdat_info numpy esmf esmpy libdrs_f pyopenssl nose requests flake8 myproxyclient netcdf-fortran=4.4.4=5"
+echo $cmd
+$cmd
+
+# update openssl for myproxyclient
+cmd="conda install -n py2 pyopenssl"
+echo $cmd
+$cmd
+:
+
+# add relative path to ncdump
+#cmd="install_name_tool -change /usr/lib/libcurl.4.dylib @rpath/libcurl.4.dylib ${HOME}/miniconda/envs/py2/bin/ncdump"
+#echo $cmd
+#$cmd 
+
+#cmd="install_name_tool -change /usr/lib/libcurl.4.dylib @rpath/libcurl.4.dylib ${HOME}/miniconda/envs/py3/bin/ncdump"
+#echo $cmd
+#$cmd 
+
+cmd="export UVCDAT_ANONYMOUS_LOG=False"
+echo $cmd
+$cmd
+
+# Retrieve certificates from ESGF
+cmd="mkdir /Users/distiller/.esg"
+echo $cmd
+$cmd
+
+cmd="echo ${ESGF_PWD} | myproxyclient logon -s esgf-node.llnl.gov -p 7512 -t 12 -S -b -l ${ESGF_USER} -o /Users/distiller/.esg/esgf.cert "
+eval $cmd
+
+echo "Create .dods_cookies"
+cmd="curl -L  -v   -c /Users/distiller/.esg/.dods_cookies --cert /Users/distiller/.esg/esgf.cert  --key /Users/distiller/.esg/esgf.cert https://aims3.llnl.gov/thredds/dodsC/cmip5_css02_data/cmip5/output1/CMCC/CMCC-CM/decadal2005/mon/atmos/Amon/r1i1p1/cct/1/cct_Amon_CMCC-CM_decadal2005_r1i1p1_202601-203512.nc.dds"
+echo $cmd
+$cmd
+
+#cmd="openssl pkcs12 -export -inkey /Users/distiller/.esg/esgf.cert -in /Users/distiller/.esg/esgf.cert -name esgf  -out /Users/distiller/.esg/esgf.p12 -passout pass:esgf"
+#$cmd
+
+#cmd="sudo security import /Users/distiller/.esg/esgf.p12 -A -P esgf -k /Library/Keychains/System.keychain"
+#echo $cmd
+#$cmd
+
+#cmd="sudo security add-trusted-cert -d -r trustRoot -k '/Library/Keychains/System.keychain' /Users/distiller/.esg/esgf.cert" 
+#echo $cmd
+#$cmd
+
+#cmd="cp tests/dodsrccircleci /Users/distiller/.dodsrc"
+#echo $cmd
+#$cmd
+
+# compile cdms on py2 and py3 environemt.
+
+cmd="python setup.py install"
+echo $cmd
+$cmd
+
+cmd="source activate py3"
+echo $cmd
+$cmd 
+
+cmd="python setup.py install"
+echo $cmd
+$cmd

ci-support/circleci_mac_machine_pre.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+curl https://repo.continuum.io/miniconda/Miniconda3-4.3.30.1-MacOSX-x86_64.sh -o miniconda.sh
+bash miniconda.sh -b -p $HOME/miniconda
+export PATH=${HOME}/miniconda/bin:${PATH}
+conda config --set always_yes yes --set changeps1 no
+conda update -y -q conda
+conda config --set anaconda_upload no
+#git clone git://github.com/uv-cdat/uvcdat-testdata

ci-support/conda_upload.sh

@@ -1,34 +1,83 @@
 #!/usr/bin/env bash
 PKG_NAME=cdms2
 USER=cdat
-export VERSION="3.0"
-echo "Trying to upload to conda"
-echo ""
-echo "Activating base env"
-source activate base
-echo "Making sure conda-build is installed"
-conda install "conda-build<3.10"
-echo "Updating conda"
-conda update -y -q conda
+echo "Trying to upload conda"
+mkdir ${HOME}/conda-bld
+export CONDA_BLD_PATH=${HOME}/conda-bld
+export VERSION="2.12"
 if [ `uname` == "Linux" ]; then
     OS=linux-64
     echo "Linux OS"
+    yum install -y wget git gcc
+    # wget --no-check https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh  -O miniconda3.sh 2> /dev/null
+    wget --no-check https://repo.continuum.io/miniconda/Miniconda2-4.3.30-Linux-x86_64.sh  -O miniconda2.sh 2> /dev/null
+    bash miniconda2.sh -b -p ${HOME}/miniconda
+    export SYSPATH=$PATH
+    export PATH=${HOME}/miniconda/bin:${SYSPATH}
+    echo $PATH
+    conda config --set always_yes yes --set changeps1 no
+    conda config --set anaconda_upload false --set ssl_verify false
+    conda install -n root -q anaconda-client "conda-build<3.3"
+    conda install -n root gcc future
+    which python
+    export UVCDAT_ANONYMOUS_LOG=False
+    BRANCH=${TRAVIS_BRANCH}
+#    echo "Creating python 3 env"
+#    conda create -n py3 python=3.6
+#    conda install -n py3 -c conda-forge -c uvcdat setuptools libcf distarray cdtime libcdms cdat_info numpy libdrs_f pyopenssl nose requests flake8 myproxyclient numpy
+#    conda install -n py3 -c nesii/channel/dev-esmf -c conda-forge esmpy
+#    echo "Creating certificate"
+#    source activate py3
+#    mkdir ${HOME}/.esg
+#    echo ${ESGF_PWD} | myproxyclient logon -s esgf-node.llnl.gov -p 7512 -t 12 -S -b -l ${ESGF_USER} -o ${HOME}/.esg/esgf.cert
+#    ls ${HOME}/.esg
+#    cd travis_home
+#    ls
+#    cp tests/dodsrc ${HOME}.dodsrc
+#    source deactivate
 else
     echo "Mac OS"
     OS=osx-64
+    BRANCH=${CIRCLE_BRANCH}
 fi
 
-mkdir ~/conda-bld
+which python
+if [ `uname` == "Linux" ]; then
+    conda install -n root -q anaconda-client "conda-build<3.3"
+else
+    conda install -n root -q anaconda-client conda-build
+fi
+# pin conda so that conda-build does not update it
+#if [ `uname` == "Darwin" ]; then
+#    echo "conda ==4.3.21" >> ~/miniconda/conda-meta/pinned  # Pin conda as workaround for conda/conda#6030
+#fi
 conda config --set anaconda_upload no
-export CONDA_BLD_PATH=${HOME}/conda-bld
 echo "Cloning recipes"
-git clone git://github.com/CDAT/conda-recipes
+cd ${HOME}
+git clone git://github.com/UV-CDAT/conda-recipes
 cd conda-recipes
 # uvcdat creates issues for build -c uvcdat confises package and channel
 rm -rf uvcdat
-export BRANCH=${CIRCLE_BRANCH}
-python ./prep_for_build.py  -b ${BRANCH}
+python ./prep_for_build.py -b ${BRANCH}
+echo "Building now"
+echo "use nesii/label/dev-esmf for esmf"
+conda build -V
+conda build $PKG_NAME -c nesii/label/dev-esmf  -c uvcdat/label/nightly -c conda-forge -c uvcdat 
+#
+# binstar config set 'false' instead of false (not quote) I have to do it manually
+# this is true for OSX.
+# binstar is changing verify_ssl to ssl_verify, but the later is not always working
+# 
+# binstar config --set verify_ssl false
+# binstar config --set ssl_verify false
+#
+mkdir -p ~/.continuum/anaconda-client/
+echo "ssl_verify: false" >> ~/.continuum/anaconda-client/config.yaml
+echo "verify_ssl: false" >> ~/.continuum/anaconda-client/config.yaml
+if [ `uname` == "Darwin" ]; then
+    # fix conda and anaconda-client conflict
+    conda install conda==4.2.16
+fi
+anaconda -t $CONDA_UPLOAD_TOKEN upload -u $USER -l ${LABEL}  ${CONDA_BLD_PATH}/$OS/$PKG_NAME-$VERSION.`date +%Y`*_0.tar.bz2 --force
+
 
-conda build ${PKG_NAME} -c cdat/label/unstable -c conda-forge  --python 3.6
-conda build ${PKG_NAME} -c cdat/label/unstable -c conda-forge  --python 2.7
-anaconda -t $CONDA_UPLOAD_TOKEN upload -u $USER -l $LABEL $CONDA_BLD_PATH/$OS/${PKG_NAME}-$VERSION.`date +%Y*`0.tar.bz2 --force