Updating the latest commit(19 Oct 2020) of pyglow in setup_pyglow.sh …

…that fixes an iri2016 issue for dates after year 2010.

resen-core/resources/helpers/setup_davitpy.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+#######################################################################################
+#
+#    A helper script for installing davitpy
+#
+#    Assumes you have a py27 python virtual environment
+#
+#######################################################################################
+
+source ${HOME}/envs/py27/bin/activate
+CURDIR=$(pwd)
+DAVITPY_BUILD_DIR=${CURDIR}/davitpy_build
+
+git clone https://github.com/vtsuperdarn/davitpy.git $DAVITPY_BUILD_DIR
+cd $DAVITPY_BUILD_DIR
+git checkout tags/0.8-master -b 0.8-master
+
+pip install .
+
+# get hdw.dat and radar.dat - needed so davitpy can get radar information locally
+mkdir -p ${HOME}/cache
+cd ${HOME}/cache
+git clone https://github.com/vtsuperdarn/hdw.dat.git
+wget https://raw.githubusercontent.com/SuperDARN/rst/v4.2/tables/superdarn/radar.dat
+
+deactivate
+
+# cleanup
+cd ${CURDIR}
+rm -rf $DAVITPY_BUILD_DIR
+rm ${HOME}/.wget-hsts
+
+# set nessisary environment variables
+echo "SD_HDWPATH=${HOME}/cache/hdw.dat" >> ${HOME}/.bashrc
+echo "SD_RADAR=${HOME}/cache/radar.dat" >> ${HOME}/.bashrc

resen-core/resources/helpers/setup_hdf5viewer.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+#######################################################################################
+#
+#    A helper script for installing pyglow
+#
+#    Assumes you have conda installed with a py27 virtual environment
+#    and another environment with the name py36
+#
+#######################################################################################
+
+echo "**** Installing hdf5 viewer ****"
+
+cd $BUILD
+HDF5VIEWER_BUILD_DIR=hdf5viewer_build
+
+git clone https://github.com/pmreyes2/jupyterlab-hdf5.git $HDF5VIEWER_BUILD_DIR
+
+cd $HDF5VIEWER_BUILD_DIR
+
+git checkout a8a0e9bb1771ffa630cd8ead940ac7b258e1ad8b -b master_20190921
+
+source /home/$NB_USER/envs/py36/bin/activate
+
+export PATH=/usr/local/lib/nodejs/node-v10.16.3-linux-x64/bin:$PATH
+pip install .
+jupyter labextension install jupyterlab-hdf
+
+deactivate
+
+# cleanup
+cd $BUILD
+rm -r $HDF5VIEWER_BUILD_DIR

resen-core/resources/helpers/setup_mangopy.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+#######################################################################################
+#
+#    A helper script for installing mangopy
+#
+#    Assumes you have a py27 virtual environment
+#    and another environment with the name py36
+#
+#######################################################################################
+
+echo "**** Installing mangopy ****"
+
+CWD=$(pwd)
+
+MANGOPY_BUILD_DIR=$CWD/mangopy_build
+mkdir -p $MANGOPY_BUILD_DIR
+
+cd $MANGOPY_BUILD_DIR
+git clone https://github.com/astib/MANGO.git
+cd MANGO
+#If we wanted a specific commit:
+#git checkout b25cba78e58197394809cb8323656a1d636c3e3d -b master_06jun2019
+
+source /home/$NB_USER/envs/py27/bin/activate
+LDFLAGS="-shared" pip install .
+
+deactivate
+
+source /home/$NB_USER/envs/py36/bin/activate
+LDFLAGS="-shared" pip install .
+
+deactivate
+
+# cleanup
+cd $CWD
+rm -r $MANGOPY_BUILD_DIR

resen-core/resources/helpers/setup_py27_env.sh

@@ -0,0 +1,69 @@
+#!/bin/bash
+#######################################################################################
+#
+#    A helper script for setting up a python 2.7 environment
+#
+#######################################################################################
+
+echo "**** Installing python 2.7 packages ****"
+
+# upgrade pip
+pip install pip==20.1.1
+
+# Now use pip to install everything we can
+# Notes: pyproj==1.9.6 required for basemap, 2.0.0 breaks basemap
+pip install -U paramiko==2.4.2 \
+               ipython==5.8.0 \
+               prompt_toolkit==1.0.16 \
+               pymongo==3.7.2 \
+               mechanize==0.4.1 \
+               cryptography==2.6.1 \
+               pytest==3.0.5 \
+               nbformat==4.4.0 \
+               numpy==1.16.2 \
+               matplotlib==2.2.4 \
+               scipy==1.2.1 \
+               tables==3.5.1 \
+               sgp4==1.4 \
+               pandas==0.24.2 \
+               sympy==1.1.0 \
+               sqlalchemy==1.3.1 \
+               h5py==2.9.0 \
+               pytz==2018.9 \
+               netcdf4==1.4.3 \
+               bokeh==1.0.4 \
+               pyyaml==5.1 \
+               cython==0.29.6 \
+               sciunit2==0.4.post3.dev95073526 \
+               madrigalweb==3.1.10 \
+               pyproj==1.9.6 \
+               bsddb3==6.2.6 \
+               aacgmv2==2.5.2 \
+               pymap3d==1.8.1 \
+               astropy==2.0.14 \
+               ipympl==0.5.6 \
+               # sunpy==0.9.10
+
+# Custom pip installation for any package that needs it
+pip install apexpy==1.0.3  # have to install after installing numpy
+
+pip install  cartopy==0.17.0
+
+pip install spacepy==0.2.1
+source /usr/local/bin/definitions.B # to set the CDF definitios including $CDF_LIB
+# only update omni and qin-denton since maia.usno.navy.mil/ser7/tai-utc.dat leapseconds website was down at the time...
+python -uc "import spacepy.toolbox; spacepy.toolbox.update(QDomni=True)"
+# spacepy 0.2.1 doesn't clean up this file. Submitted issue and PR to spacepy, see https://github.com/spacepy/spacepy/pull/219
+rm OMNI_OMNI2_merged_20120213-v1.cdf
+
+# Installing mangopy (14 June 2018)
+pip install git+https://github.com/astib/MANGO.git@2dd4ca5380dca54cac8d2180c3ad63fc041a5c67
+
+# Install visuamisr
+pip install git+https://github.com/asreimer/visuamisr.git@v2.0.3
+
+# Install citationhelper
+pip install git+https://github.com/EarthCubeInGeo/citationhelper.git@v0.2
+
+# cleanup
+rm -rf ~/.cache/pip/*

resen-core/resources/helpers/setup_py36_env.sh

@@ -0,0 +1,74 @@
+#!/bin/bash
+#######################################################################################
+#
+#    A helper script for setting up a python 3.6 environment
+#
+#######################################################################################
+
+echo "**** Installing python 3.6 packages ****"
+
+# upgrade pip
+pip install pip==20.1.1
+
+# Now use pip to install everything we can
+# Notes: pyproj==1.9.6 required for basemap, 2.0.0 breaks basemap
+pip install -U jupyterhub==1.0.0 \
+               jupyterlab==2.1.2 \
+               notebook==6.0.3 \
+               paramiko==2.7.1 \
+               ipython==7.14.0 \
+               pymongo==3.10.1 \
+               mechanize==0.4.5 \
+               cryptography==2.9.2 \
+               pytest==5.4.2 \
+               nbformat==5.0.6 \
+               numpy==1.18.4 \
+               matplotlib==3.2.1 \
+               scipy==1.4.1 \
+               tables==3.6.1 \
+               sgp4==2.8 \
+               pandas==1.0.3 \
+               sympy==1.5.1 \
+               sqlalchemy==1.3.17 \
+               h5py==2.10.0 \
+               pytz==2020.1 \
+               netcdf4==1.5.3 \
+               bokeh==2.0.2 \
+               pyyaml==5.3.1 \
+               cython==0.29.18 \
+               pyproj==2.6.1.post1 \
+               madrigalweb==3.1.12 \
+               bsddb3==6.2.7 \
+               aacgmv2==2.6.0 \
+               pymap3d==2.4.1 \
+               astropy==3.2.1 \
+               plasmapy==0.3.1 \
+               pydarn==1.0.0.1 \
+               viresclient==0.6.1 \
+               ipympl==0.5.6 \
+               hdfviewer==0.11.0 \
+               watermark==2.0.2
+
+# Custom pip installation for any package that needs it
+pip install apexpy==1.0.3  # have to install after installing numpy
+
+pip install cartopy==0.18.0 # have to install after installing numpy
+
+pip install spacepy==0.2.1
+source /usr/local/bin/definitions.B # to set the CDF definitios including $CDF_LIB
+# only update omni and qin-denton since maia.usno.navy.mil/ser7/tai-utc.dat leapseconds website was down at the time...
+python -uc "import spacepy.toolbox; spacepy.toolbox.update(QDomni=True)"
+# spacepy 0.2.1 doesn't clean up this file. Submitted issue and PR to spacepy, see https://github.com/spacepy/spacepy/pull/219
+rm OMNI_OMNI2_merged_20120213-v1.cdf
+
+# Installing mangopy (14 June 2018)
+pip install git+https://github.com/astib/MANGO.git@2dd4ca5380dca54cac8d2180c3ad63fc041a5c67
+
+# Install visuamisr
+pip install git+https://github.com/asreimer/visuamisr.git@v2.0.3
+
+# Install citationhelper
+pip install git+https://github.com/EarthCubeInGeo/citationhelper.git@v0.2
+
+# cleanup
+rm -rf ~/.cache/pip/*

resen-core/resources/helpers/setup_pyglow.sh

@@ -13,7 +13,7 @@ PYGLOW_BUILD_DIR=pyglow_build
 
 git clone https://github.com/timduly4/pyglow.git $PYGLOW_BUILD_DIR
 cd $PYGLOW_BUILD_DIR
-git checkout 054bf800263c01ecfa783741c9cfe8d3d6c259ca -b master_20190904
+git checkout 36e998524cf603cf61ca7d98ced61e2f945ab1df -b master_20201019
 
 source ${HOME}/envs/py38/bin/activate
 

resen-core/resources/helpers/setup_spacepy.sh

@@ -0,0 +1,41 @@
+#!/bin/bash
+#######################################################################################
+#
+#    A helper script for installing spacepy
+#
+#    Assumes you have conda installed with a py27 virtual environment
+#    and another environment with the name py36
+#
+#######################################################################################
+
+echo "**** Installing spacepy ****"
+
+cd $BUILD
+SPACEPY_BUILD_DIR=spacepy_build
+
+git clone https://github.com/spacepy/spacepy.git $SPACEPY_BUILD_DIR
+cd $SPACEPY_BUILD_DIR
+git checkout 8b8c2d56ebdcb1d3a59fd868a1c92f34ce16ec64 -b 0.1.6_withfix
+
+source /home/$NB_USER/envs/py27/bin/activate
+pip install .
+
+deactivate
+
+source /home/$NB_USER/envs/py36/bin/activate
+pip install .
+
+# some post-pip initialization of packages
+cd $BUILD
+source /usr/local/bin/definitions.B # to set the CDF definitios including $CDF_LIB
+python -c "import spacepy.toolbox; spacepy.toolbox.update()"
+# a file about 195 MB called OMNI_OMNI2_merged_20120213-v1.cdf
+# has been created and will be removed later on. The data is kept
+# inside ~/.spacepy
+echo "support_notice: False" >> /home/$NB_USER/.spacepy/spacepy.rc
+
+deactivate
+
+# cleanup
+cd $BUILD
+rm -r $SPACEPY_BUILD_DIR