[yt-svn] commit/yt: 3 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Tue Jun 27 11:00:44 PDT 2017
3 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/d856cd571005/
Changeset: d856cd571005
User: ngoldbaum
Date: 2017-06-20 20:29:04+00:00
Summary: Remove INST_CONDA option from install script
Affected #: 5 files
diff -r 60a10fe93978952d4959283312badb40cd4f5a72 -r d856cd57100577863c14b5e87d936024c5ee84db doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -13,62 +13,23 @@
# If you do not have a working compiler environment, use the following
# configuration:
-INST_CONDA=1 # Should yt's dependencies be installed using miniconda?
INST_YT_SOURCE=0 # Should yt itself be installed from source?
-# If you want to install yt's dependencies using conda but want to build yt
-# itself from source, use the following configuration:
-
-# INST_CONDA=1
-# INST_YT_SOURCE=1
-
-# If you would like to build yt and all dependencies from source, then
-# use the following configuration by uncommenting the lines below.
-# NOTE: Building yt's dependencies from source will cause the install script
-# to require substantially more time to finish.
-
-# INST_CONDA=0
-# INST_YT_SOURCE=1
-
-BRANCH="master" # This is the branch we will install from for source installs
-
# What follows are some other options that you may or may not need to change.
-# Here's where you put the HDF5 path if you like; otherwise it'll download it
-# and install it on its own
-#HDF5_DIR=
-
-# If you've got yt some other place, set this to point to it. The script will
-# already check the current directory and the one above it in the tree.
+# If you've got a clone of the yt repository some other place, set this to
+# point to it. The script will already check the current directory and the one
+# above it in the tree.
YT_DIR=""
# These options can be set to customize the installation.
-INST_PY3=1 # Install Python 3 instead of Python 2. If this is turned
- # on, all Python packages (including yt) will be installed
- # in Python 3.
-INST_GIT=1 # Install git or not? If git is not already installed, yt
- # cannot be installed from source. Ignored if INST_CONDA=0
-INST_HG=0 # Install Mercurial or not? Ignored if INST_CONDA=0.
-INST_EMBREE=0 # Install dependencies needed for Embree-accelerated
- # ray tracing
-
-# These options control whether low-level system libraries are installed
-# they are necessary for building yt's dependencies from source and are
-# ignored when INST_CONDA=1
-
-INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with
- # the system zlib, which is compiled statically.
- # If need be, you can turn this off.
-INST_BZLIB=1 # On some systems, libbzip2 is missing. This can
- # lead to broken mercurial installations.
-INST_PNG=1 # Install a local libpng? Same things apply as with zlib.
-INST_FTYPE=1 # Install FreeType2 locally?
-INST_SQLITE3=1 # Install a local version of SQLite3?
-INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings?
-
-# These variables control whether optional dependencies are installed
-
+INST_PY3=1 # Install Python 3 instead of Python 2. If this is turned on,
+ # all Python packages (including yt) will be installed
+ # in Python 3.
+INST_GIT=1 # Install git or not? If git is not already installed, yt
+ # cannot be installed from source.
+INST_EMBREE=0 # Install dependencies needed for Embree-accelerated ray tracing
INST_PYX=0 # Install PyX? Sometimes PyX can be problematic without a
# working TeX installation.
INST_ROCKSTAR=0 # Install the Rockstar halo finder?
@@ -77,83 +38,47 @@
INST_ASTROPY=0 # Install astropy?
INST_NOSE=1 # Install nose?
INST_NETCDF4=1 # Install netcdf4 and its python bindings?
-
-# These options allow you to customize the builds of yt dependencies.
-# They are only used if INST_CONDA=0.
-
-# If you need to pass anything to the matplotlib build, do so here.
-MPL_SUPP_LDFLAGS=""
-MPL_SUPP_CFLAGS=""
-MPL_SUPP_CXXFLAGS=""
+INST_HG=0 # Install Mercurial or not?
-# If you need to supply arguments to the NumPy or SciPy build, supply them here
-# This one turns on gfortran manually:
-#NUMPY_ARGS="--fcompiler=gnu95"
-# If you absolutely can't get the fortran to work, try this:
-#NUMPY_ARGS="--fcompiler=fake"
+# This is the branch we will install from for INST_YT_SOURCE=1
+BRANCH="master"
-# If you want to spawn multiple Make jobs, here's the place to set the
-# arguments. For instance, "-j4"
-MAKE_PROCS=""
-
-# These variables control which miniconda version and yt recipe are used
-# when INST_CONDA=1.
+# These variables control which miniconda version is used
MINICONDA_URLBASE="http://repo.continuum.io/miniconda"
MINICONDA_VERSION="latest"
-if [ ${REINST_YT} ] && [ ${REINST_YT} -eq 1 ] && [ -n ${YT_DEST} ]
+if [ ! -z "${CONDA_DEFAULT_ENV}" ]
then
- DEST_DIR=${YT_DEST}
- INST_CONDA=0
+ echo "Aborting the yt installation because you appear to already"
+ echo "have a conda environment activated. Either deactivate it with:"
+ echo
+ echo " $ source deactivate"
+ echo
+ echo "or install yt into your current environment with:"
+ echo
+ echo " $ conda install -c conda-forge yt"
+ echo
+ exit 1
fi
-
-if [ $INST_CONDA -ne 0 ]
+DEST_SUFFIX="yt-conda"
+if [ -n "${PYTHONPATH}" ]
then
- if [ ! -z "${CONDA_DEFAULT_ENV}" ]
- then
- echo "Aborting the yt installation because you appear to already"
- echo "have a conda environment activated. Either deactivate it with:"
- echo
- echo " $ source deactivate"
- echo
- echo "or install yt into your current environment with:"
- echo
- echo " $ conda install -c conda-forge yt"
- echo
- exit 1
- fi
- DEST_SUFFIX="yt-conda"
- if [ -n "${PYTHONPATH}" ]
- then
- echo "WARNING WARNING WARNING WARNING WARNING WARNING WARNING"
- echo "*******************************************************"
- echo
- echo "The PYTHONPATH environment variable is set to:"
- echo
- echo " $PYTHONPATH"
- echo
- echo "If dependencies of yt (numpy, scipy, matplotlib) are installed"
- echo "to this path, this may cause issues. Exit the install script"
- echo "with Ctrl-C and unset PYTHONPATH if you are unsure."
- echo "Hit enter to continue."
- echo
- echo "WARNING WARNING WARNING WARNING WARNING WARNING WARNING"
- echo "*******************************************************"
- read -p "[hit enter]"
- fi
-else
- if [ $INST_YT_SOURCE -eq 0 ]
- then
- echo "yt must be compiled from source if INST_CONDA is set to 0"
- echo "Please set INST_YT_SOURCE to 1 and re-run."
- exit 1
- fi
- if [ $INST_GIT -eq 1 ]
- then
- INST_GIT=0
- fi
- DEST_SUFFIX="yt-`uname -m`"
+ echo "WARNING WARNING WARNING WARNING WARNING WARNING WARNING"
+ echo "*******************************************************"
+ echo
+ echo "The PYTHONPATH environment variable is set to:"
+ echo
+ echo " $PYTHONPATH"
+ echo
+ echo "If dependencies of yt (numpy, scipy, matplotlib) are installed"
+ echo "to this path, this may cause issues. Exit the install script"
+ echo "with Ctrl-C and unset PYTHONPATH if you are unsure."
+ echo "Hit enter to continue."
+ echo
+ echo "WARNING WARNING WARNING WARNING WARNING WARNING WARNING"
+ echo "*******************************************************"
+ read -p "[hit enter]"
fi
if [ -z "${DEST_DIR}" ]
@@ -204,31 +129,18 @@
function write_config
{
CONFIG_FILE=${DEST_DIR}/.yt_config
-
- echo INST_GIT=${INST_GIT} > ${CONFIG_FILE}
- echo INST_ZLIB=${INST_ZLIB} >> ${CONFIG_FILE}
- echo INST_BZLIB=${INST_BZLIB} >> ${CONFIG_FILE}
- echo INST_PNG=${INST_PNG} >> ${CONFIG_FILE}
- echo INST_FTYPE=${INST_FTYPE} >> ${CONFIG_FILE}
- echo INST_SQLITE3=${INST_SQLITE3} >> ${CONFIG_FILE}
+ echo INST_YT_SOURCE=${INST_YT_SOURCE} > ${CONFIG_FILE}
+ echo INST_GIT=${INST_GIT} >> ${CONFIG_FILE}
echo INST_PYX=${INST_PYX} >> ${CONFIG_FILE}
- echo INST_0MQ=${INST_0MQ} >> ${CONFIG_FILE}
echo INST_PY3=${INST_PY3} >> ${CONFIG_FILE}
echo INST_ROCKSTAR=${INST_ROCKSTAR} >> ${CONFIG_FILE}
echo INST_SCIPY=${INST_SCIPY} >> ${CONFIG_FILE}
+ echo INST_EMBREE=${INST_EMBREE} >> ${CONFIG_FILE}
+ echo INST_H5PY=${INST_H5PY} >> ${CONFIG_FILE}
+ echo INST_ASTROPY=${INST_ASTROPY} >> ${CONFIG_FILE}
+ echo INST_NOSE=${INST_NOSE} >> ${CONFIG_FILE}
+
echo YT_DIR=${YT_DIR} >> ${CONFIG_FILE}
- echo MPL_SUPP_LDFLAGS=${MPL_SUPP_LDFLAGS} >> ${CONFIG_FILE}
- echo MPL_SUPP_CFLAGS=${MPL_SUPP_CFLAGS} >> ${CONFIG_FILE}
- echo MPL_SUPP_CXXFLAGS=${MPL_SUPP_CXXFLAGS} >> ${CONFIG_FILE}
- echo MAKE_PROCS=${MAKE_PROCS} >> ${CONFIG_FILE}
- if [ ${HDF5_DIR} ]
- then
- echo ${HDF5_DIR} >> ${CONFIG_FILE}
- fi
- if [ ${NUMPY_ARGS} ]
- then
- echo ${NUMPY_ARGS} >> ${CONFIG_FILE}
- fi
}
function get_willwont
@@ -246,147 +158,22 @@
MYHOST=`hostname -s` # just give the short one, not FQDN
MYHOSTLONG=`hostname` # FQDN, for Ranger
MYOS=`uname -s` # A guess at the OS
- if [ "${MYHOST##kraken}" != "${MYHOST}" ]
- then
- echo "Looks like you're on Kraken."
- echo
- echo " ******************************************"
- echo " * It may be better to use the yt module! *"
- echo " * *"
- echo " * $ module load yt *"
- echo " * *"
- echo " ******************************************"
- echo
- echo "IF YOU CHOOSE TO PROCEED:"
- echo "YOU MUST BE IN THE GNU PROGRAMMING ENVIRONMENT"
- echo " $ module swap PrgEnv-pgi PrgEnv-gnu"
- echo
- return
- fi
- if [ "${MYHOST##nautilus}" != "${MYHOST}" ]
- then
- echo "Looks like you're on Nautilus."
- echo
- echo " ******************************************"
- echo " * It may be better to use the yt module! *"
- echo " * *"
- echo " * $ module load yt *"
- echo " * *"
- echo " ******************************************"
- echo
- echo "NOTE: YOU MUST BE IN THE GNU PROGRAMMING ENVIRONMENT"
- echo " $ module swap PE-intel PE-gnu"
- echo
- echo "Additionally, note that by default, yt will OVERWRITE"
- echo "any existing installations from Kraken! You might want"
- echo "to adjust the variable DEST_SUFFIX in the install script."
- echo
- return
- fi
- if [ "${MYHOST##verne}" != "${MYHOST}" ]
- then
- echo "Looks like you're on Verne."
- echo
- echo "NOTE: YOU MUST BE IN THE GNU PROGRAMMING ENVIRONMENT"
- echo "This command will take care of that for you:"
- echo
- echo " $ module swap PE-pgi PE-gnu"
- echo
- fi
- if [ "${MYHOST##steele}" != "${MYHOST}" ]
- then
- echo "Looks like you're on Steele."
- echo
- echo "NOTE: YOU MUST BE IN THE GNU PROGRAMMING ENVIRONMENT"
- echo "These commands should take care of that for you:"
- echo
- echo " $ module purge"
- echo " $ module load gcc"
- echo
- fi
- if [ "${MYHOST##midway}" != "${MYHOST}" ]
- then
- echo "Looks like you're on Midway."
- echo
- echo " ******************************************"
- echo " * It may be better to use the yt module! *"
- echo " * *"
- echo " * $ module load yt *"
- echo " * *"
- echo " ******************************************"
- echo
- return
- fi
if [ "${MYOS##Darwin}" != "${MYOS}" ]
then
- echo "Looks like you're running on Mac OSX."
+ echo "Looks like you're running on MacOS."
echo
echo "NOTE: you must have the Xcode command line tools installed."
echo
- echo "The instructions for obtaining these tools varies according"
- echo "to your exact OS version. On older versions of OS X, you"
- echo "must register for an account on the apple developer tools"
- echo "website: https://developer.apple.com/downloads to obtain the"
- echo "download link."
- echo
- echo "We have gathered some additional instructions for each"
- echo "version of OS X below. If you have trouble installing yt"
- echo "after following these instructions, don't hesitate to contact"
- echo "the yt user's e-mail list."
- echo
- echo "You can see which version of OSX you are running by clicking"
- echo "'About This Mac' in the apple menu on the left hand side of"
- echo "menu bar. We're assuming that you've installed all operating"
- echo "system updates; if you have an older version, we suggest"
- echo "running software update and installing all available updates."
- echo
- echo "OS X 10.5.8: search for and download Xcode 3.1.4 from the"
- echo "Apple developer tools website."
- echo
- echo "OS X 10.6.8: search for and download Xcode 3.2 from the Apple"
- echo "developer tools website. You can either download the"
- echo "Xcode 3.2.2 Developer Tools package (744 MB) and then use"
- echo "Software Update to update to XCode 3.2.6 or"
- echo "alternatively, you can download the Xcode 3.2.6/iOS SDK"
- echo "bundle (4.1 GB)."
- echo
- echo "OS X 10.7.5: download Xcode 4.2 from the mac app store"
- echo "(search for Xcode)."
- echo "Alternatively, download the Xcode command line tools from"
- echo "the Apple developer tools website."
- echo
- echo "OS X 10.8.4, 10.9, 10.10, and 10.11:"
- echo "download the appropriate version of Xcode from the"
- echo "mac app store (search for Xcode)."
+ echo "Download the appropriate version of Xcode from the"
+ echo "Mac App Store (search for Xcode)."
echo
echo "Additionally, you will have to manually install the Xcode"
echo "command line tools."
echo
- echo "For OS X 10.8, see:"
- echo "http://stackoverflow.com/questions/9353444"
- echo
- echo "For OS X 10.9 and newer the command line tools can be installed"
+ echo "For MacOS 10.10 and newer the command line tools can be installed"
echo "with the following command:"
echo " xcode-select --install"
echo
- if [ $INST_CONDA -eq 0 ]
- then
- echo "For OS X 10.11, you will additionally need to install the"
- echo "OpenSSL library using a package manager like homebrew or"
- echo "macports."
- echo
- echo "If your install fails with a message like"
- echo " ImportError: cannot import HTTPSHandler"
- echo "then you do not have the OpenSSL headers available in a"
- echo "location visible to your C compiler. Consider setting"
- echo "INST_CONDA=1 instead, as conda's python bundles OpenSSL."
- fi
- OSX_VERSION=`sw_vers -productVersion`
- if [ "${OSX_VERSION##10.8}" != "${OSX_VERSION}" ]
- then
- MPL_SUPP_CFLAGS="${MPL_SUPP_CFLAGS} -mmacosx-version-min=10.7"
- MPL_SUPP_CXXFLAGS="${MPL_SUPP_CXXFLAGS} -mmacosx-version-min=10.7"
- fi
fi
if [ -f /etc/redhat-release ]
then
@@ -462,31 +249,6 @@
echo " to avoid conflicts with other command-line programs "
echo " (like eog and evince, for example)."
fi
- if [ $INST_SCIPY -eq 1 ]
- then
- echo
- echo "Looks like you've requested that the install script build SciPy."
- echo
- echo "If the SciPy build fails, please uncomment one of the the lines"
- echo "at the top of the install script that sets NUMPY_ARGS, delete"
- echo "any broken installation tree, and re-run the install script"
- echo "verbatim."
- echo
- echo "If that doesn't work, don't hesitate to ask for help on the yt"
- echo "user's mailing list."
- echo
- fi
- if [ ! -z "${CFLAGS}" ]
- then
- echo "******************************************"
- echo "******************************************"
- echo "** **"
- echo "** Your CFLAGS is not empty. **"
- echo "** This can break h5py compilation. **"
- echo "** **"
- echo "******************************************"
- echo "******************************************"
- fi
}
function log_cmd
@@ -506,11 +268,6 @@
echo "Please set INST_YT_SOURCE to 1 and re-run the install script."
exit 1
fi
- if [ $INST_CONDA -eq 0 ]
- then
- echo "Embree support has not yet been implemented for INST_CONDA=0."
- exit 1
- fi
if [ `uname` = "Darwin" ]
then
EMBREE="embree-2.8.0.x86_64.macosx"
@@ -538,17 +295,6 @@
fi
fi
-if [ $INST_NETCDF4 -ne 0 ]
-then
- if [ $INST_CONDA -eq 0 ]
- then
- echo "This script can only install netcdf4 through conda."
- echo "Please set INST_CONDA to 1 to install netcdf4"
- echo "Setting INST_NETCDF4=0"
- INST_NETCDF4=0
- fi
-fi
-
echo
echo
echo "========================================================================"
@@ -562,10 +308,6 @@
echo "the script if you aren't such a fan."
echo
-printf "%-18s = %s so I " "INST_CONDA" "${INST_CONDA}"
-get_willwont ${INST_CONDA}
-echo "be installing a conda-based python environment"
-
printf "%-18s = %s so I " "INST_YT_SOURCE" "${INST_YT_SOURCE}"
get_willwont ${INST_YT_SOURCE}
echo "be compiling yt from source"
@@ -582,29 +324,6 @@
get_willwont ${INST_EMBREE}
echo "be installing Embree"
-if [ $INST_CONDA -eq 0 ]
-then
- printf "%-18s = %s so I " "INST_ZLIB" "${INST_ZLIB}"
- get_willwont ${INST_ZLIB}
- echo "be installing zlib"
-
- printf "%-18s = %s so I " "INST_BZLIB" "${INST_BZLIB}"
- get_willwont ${INST_BZLIB}
- echo "be installing bzlib"
-
- printf "%-18s = %s so I " "INST_PNG" "${INST_PNG}"
- get_willwont ${INST_PNG}
- echo "be installing libpng"
-
- printf "%-18s = %s so I " "INST_FTYPE" "${INST_FTYPE}"
- get_willwont ${INST_FTYPE}
- echo "be installing freetype2"
-
- printf "%-18s = %s so I " "INST_SQLITE3" "${INST_SQLITE3}"
- get_willwont ${INST_SQLITE3}
- echo "be installing SQLite3"
-fi
-
printf "%-18s = %s so I " "INST_PYX" "${INST_PYX}"
get_willwont ${INST_PYX}
echo "be installing PyX"
@@ -627,16 +346,6 @@
echo
-if [ $INST_CONDA -eq 0 ]
-then
- if [ -z "$HDF5_DIR" ]
- then
- echo "HDF5_DIR is not set, so I will be installing HDF5"
- else
- echo "HDF5_DIR=${HDF5_DIR} , so I will not be installing HDF5"
- fi
-fi
-
echo
echo "Installation will be to"
echo " ${DEST_DIR}"
@@ -654,21 +363,13 @@
host_specific
fi
-if [ $INST_CONDA -eq 0 ]
-then
- if [ ${USED_CONFIG} ]
- then
- echo "Settings were loaded from ${CONFIG_FILE}."
- echo "Remove this file if you wish to return to the default settings."
- echo
- fi
-fi
-echo "========================================================================"
echo
+
if [[ $1 != "--yes" ]]
then
read -p "[hit enter] "
fi
+
echo
echo "Awesome! Here we go."
echo
@@ -694,49 +395,6 @@
PYTHON_EXEC='python2.7'
fi
-function do_setup_py
-{
- [ -e $1/done ] && return
- LIB=$1
- shift
- if [ -z "$@" ]
- then
- echo "Installing $LIB"
- else
- echo "Installing $LIB (arguments: '$@')"
- fi
- [ ! -e $LIB/extracted ] && tar xfz $LIB.tar.gz
- touch $LIB/extracted
- BUILD_ARGS=""
- PYEXE=${PYTHON_EXEC}
- case $LIB in
- *h5py*)
- pushd $LIB &> /dev/null
- ( ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py configure --hdf5=${HDF5_DIR} 2>&1 ) 1>> ${LOG_FILE} || do_exit
- popd &> /dev/null
- ;;
- *numpy*)
- if [ -e ${DEST_DIR}/lib/${PYTHON_EXEC}/site-packages/numpy/__init__.py ]
- then
- VER=$(${DEST_DIR}/bin/${PYTHON_EXEC} -c 'from distutils.version import StrictVersion as SV; \
- import numpy; print SV(numpy.__version__) < SV("1.8.0")')
- if [ $VER == "True" ]
- then
- echo "Removing previous NumPy instance (see issue #889)"
- rm -rf ${DEST_DIR}/lib/${PYTHON_EXEC}/site-packages/{numpy*,*.pth}
- fi
- fi
- ;;
- *)
- ;;
- esac
- cd $LIB
- ( ${DEST_DIR}/bin/${PYEXE} setup.py build ${BUILD_ARGS} $* 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( ${DEST_DIR}/bin/${PYEXE} setup.py install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
-}
-
if type -P curl &>/dev/null
then
echo "Using curl"
@@ -746,40 +404,6 @@
export GETFILE="wget -nv"
fi
-if type -P sha512sum &> /dev/null
-then
- echo "Using sha512sum"
- export SHASUM="sha512sum"
-elif type -P shasum &> /dev/null
-then
- echo "Using shasum -a 512"
- export SHASUM="shasum -a 512"
-else
- echo
- echo "I am unable to locate any shasum-like utility."
- echo "ALL FILE INTEGRITY IS NOT VERIFIABLE."
- echo "THIS IS PROBABLY A BIG DEAL."
- echo
- echo "(I'll hang out for a minute for you to consider this.)"
- sleep 60
-fi
-
-function get_ytproject
-{
- [ -e $1 ] && return
- echo "Downloading $1 from yt-project.org"
- ${GETFILE} "http://yt-project.org/dependencies/$1" || do_exit
- ( ${SHASUM} -c $1.sha512 2>&1 ) 1>> ${LOG_FILE} || do_exit
-}
-
-function get_ytdata
-{
- echo "Downloading $1 from yt-project.org"
- [ -e $1 ] && return
- ${GETFILE} "http://yt-project.org/data/$1" || do_exit
- ( ${SHASUM} -c $1.sha512 2>&1 ) 1>> ${LOG_FILE} || do_exit
-}
-
function test_install
{
echo "Testing that yt can be imported"
@@ -788,298 +412,206 @@
ORIG_PWD=`pwd`
-if [ -z "${DEST_DIR}" ]
+MYARCH=`uname -m`
+MYOS=`uname -s`
+
+if [ $MYOS = "Darwin" ]
+then
+ MINICONDA_OS="MacOSX"
+ MINICONDA_ARCH="x86_64"
+elif [ $MYOS = "Linux" ]
then
- echo "Edit this script, set the DEST_DIR parameter and re-run."
+ MINICONDA_OS="Linux"
+ if [ $MYARCH = "i386" ]
+ then
+ MINICONDA_ARCH="x86"
+ elif [ $MYARCH = "i686" ]
+ then
+ MINICONDA_ARCH="x86"
+ elif [ $MYARCH = "x86_64" ]
+ then
+ MINICONDA_ARCH="x86_64"
+ else
+ echo "Not sure which architecture you are running."
+ echo "Going with x86_64 architecture."
+ MINICONDA_OS="Linux-x86_64"
+ fi
+else
+ echo "The yt install script is not supported on the ${MYOS}"
+ echo "operating system."
exit 1
fi
-# Set paths to what they should be when yt is activated.
-if [ $INST_CONDA -eq 0 ]
+if [ $INST_PY3 -eq 1 ]
then
- export PATH=${DEST_DIR}/bin:$PATH
- export LD_LIBRARY_PATH=${DEST_DIR}/lib:$LD_LIBRARY_PATH
- export PYTHONPATH=${DEST_DIR}/lib/${PYTHON_EXEC}/site-packages
+ PY_VERSION='3'
+else
+ PY_VERSION='2'
+fi
+
+MINICONDA_PKG="Miniconda${PY_VERSION}-${MINICONDA_VERSION}-${MINICONDA_OS}-${MINICONDA_ARCH}.sh"
- # Write config settings to file.
- CONFIG_FILE=${DEST_DIR}/.yt_config
- mkdir -p ${DEST_DIR}
- if [ -z ${REINST_YT} ] || [ ${REINST_YT} -neq 1 ]
- then
- write_config
- elif [ ${REINST_YT} ] && [ ${REINST_YT} -eq 1 ] && [ -f ${CONFIG_FILE} ]
- then
- USED_CONFIG=1
- source ${CONFIG_FILE}
- fi
-
- # Get supplemental data.
+echo
+echo "Downloading ${MINICONDA_URLBASE}/${MINICONDA_PKG}"
+echo
- mkdir -p ${DEST_DIR}/data
- cd ${DEST_DIR}/data
- echo 'de6d8c6ea849f0206d219303329a0276b3cce7c051eec34377d42aacbe0a4f47ac5145eb08966a338ecddd2b83c8f787ca9956508ad5c39ee2088ad875166410 cloudy_emissivity.h5' > cloudy_emissivity.h5.sha512
- [ ! -e cloudy_emissivity.h5 ] && get_ytdata cloudy_emissivity.h5
- echo '0f714ae2eace0141b1381abf1160dc8f8a521335e886f99919caf3beb31df1fe271d67c7b2a804b1467949eb16b0ef87a3d53abad0e8160fccac1e90d8d9e85f apec_emissivity.h5' > apec_emissivity.h5.sha512
- [ ! -e apec_emissivity.h5 ] && get_ytdata apec_emissivity.h5
-
- mkdir -p ${DEST_DIR}/src
- cd ${DEST_DIR}/src
+if [ -f ${MINICONDA_PKG} ]
+then
+ rm $MINICONDA_PKG
+fi
- PYTHON2='Python-2.7.11'
- PYTHON3='Python-3.5.1'
- CYTHON='Cython-0.23.5'
- if [ $INST_PY3 -eq 0 ]
- then
- PYX='PyX-0.12.1'
- else
- PYX='PyX-0.14.1'
- fi
- BZLIB='bzip2-1.0.6'
- FREETYPE_VER='freetype-2.4.12'
- H5PY='h5py-2.5.0'
- HDF5='hdf5-1.8.14'
- LAPACK='lapack-3.4.2'
- PNG='libpng-1.6.3'
- MATPLOTLIB='matplotlib-1.5.1'
- NOSE='nose-1.3.7'
- NUMPY='numpy-1.11.0'
- GITPYTHON='GitPython-2.1.3'
- ROCKSTAR='rockstar-0.99.6'
- SCIPY='scipy-0.17.0'
- SQLITE='sqlite-autoconf-3071700'
- SYMPY='sympy-1.0'
- ZLIB='zlib-1.2.8'
- SETUPTOOLS='setuptools-20.6.7'
- ASTROPY='astropy-1.1.2'
-
- # Now we dump all our SHA512 files out.
- echo '9052d74bbd0c93757fd916939cc3c39eb1aba6c9692b48887ae577256bec64b39b1fd25b6c751e6c8fe723de4c0ddf9a1a207de39f75b0839500dfcdde69f925 Cython-0.23.5.tar.gz' > Cython-0.23.5.tar.gz.sha512
- if [ $INST_PY3 -eq 0 ]
- then
- echo '4941f5aa21aff3743546495fb073c10d2657ff42b2aff401903498638093d0e31e344cce778980f28a7170c6d29eab72ac074277b9d4088376e8692dc71e55c1 PyX-0.12.1.tar.gz' > PyX-0.12.1.tar.gz.sha512
- else
- echo '16265bbdcaf28ce194189a2987b32952f296c850b829454bcccce0abd23838bfca0276c3e9c8e96b8cbfaf1473bf14669f9b7f2032ee039b61ae59ea3aa45a20 PyX-0.14.1.tar.gz' > PyX-0.14.1.tar.gz.sha512
- fi
- echo 'f21df53da87e9e3c14599a34388976e7dd09b951dff3c4b978fe224beeff07e749c0059ffd94f68ca9b75ecaef142b285d579b8dfaad4eab85aca33957114937 Python-2.7.11.tgz' > Python-2.7.11.tgz.sha512
- echo '73f1477f3d3f5bd978c4ea1d1b679467b45e9fd2f443287b88c5c107a9ced580c56e0e8f33acea84e06b11a252e2a4e733120b721a9b6e1bb3d34493a3353bfb Python-3.5.1.tgz' > Python-3.5.1.tgz.sha512
- echo 'b83c4a1415a3eb8c016507705d0d2f22971e4da937bb97953eec08f8f856933d8fa76ce8c536122235b19e7879b16add2e20fd2fee3e488f9b2b4bf1b9f4dbdb astropy-1.1.2.tar.gz' > astropy-1.1.2.tar.gz.sha512
- echo '276bd9c061ec9a27d478b33078a86f93164ee2da72210e12e2c9da71dcffeb64767e4460b93f257302b09328eda8655e93c4b9ae85e74472869afbeae35ca71e blas.tar.gz' > blas.tar.gz.sha512
- echo '00ace5438cfa0c577e5f578d8a808613187eff5217c35164ffe044fbafdfec9e98f4192c02a7d67e01e5a5ccced630583ad1003c37697219b0f147343a3fdd12 bzip2-1.0.6.tar.gz' > bzip2-1.0.6.tar.gz.sha512
- echo '609a68a3675087e0cc95268574f31e104549daa48efe15a25a33b8e269a93b4bd160f4c3e8178dca9c950ef5ca514b039d6fd1b45db6af57f25342464d0429ce freetype-2.4.12.tar.gz' > freetype-2.4.12.tar.gz.sha512
- echo '4a83f9ae1855a7fad90133b327d426201c8ccfd2e7fbe9f39b2d61a2eee2f3ebe2ea02cf80f3d4e1ad659f8e790c173df8cc99b87d0b7ce63d34aa88cfdc7939 h5py-2.5.0.tar.gz' > h5py-2.5.0.tar.gz.sha512
- echo '4073fba510ccadaba41db0939f909613c9cb52ba8fb6c1062fc9118edc601394c75e102310be1af4077d07c9b327e6bbb1a6359939a7268dc140382d0c1e0199 hdf5-1.8.14.tar.gz' > hdf5-1.8.14.tar.gz.sha512
- echo '8770214491e31f0a7a3efaade90eee7b0eb20a8a6ab635c5f854d78263f59a1849133c14ef5123d01023f0110cbb9fc6f818da053c01277914ae81473430a952 lapack-3.4.2.tar.gz' > lapack-3.4.2.tar.gz.sha512
- echo '887582e5a22e4cde338aa8fec7a89f6dd31f2f02b8842735f00f970f64582333fa03401cea6d01704083403c7e8b7ebc26655468ce930165673b33efa4bcd586 libpng-1.6.3.tar.gz' > libpng-1.6.3.tar.gz.sha512
- echo 'a0e78b5027a3a49cf8e77dc0d26f5f380dcd80f7b309b6121199acd5e1d94f48482864a9eee3bd397f7ac6f07fe1d3c21bf517217df3c72e8e3d105b7c2ae58e matplotlib-1.5.1.tar.gz' > matplotlib-1.5.1.tar.gz.sha512
- echo 'e65c914f621f8da06b9ab11a0ff2763d6e29b82ce2aaed56da0e3773dc899d9deb1f20015789d44c65a5dad7214520f5b659b3f8d7695fb207ad3f78e5cf1b62 nose-1.3.7.tar.gz' > nose-1.3.7.tar.gz.sha512
- echo '92c1889397ad013e25da3a0657fc01e787d528fc19c29cc2acd286c3f07d41b984252583457b1b9259fc303afbe9694565cdcf5752eb4ecb950cc7a99ec1ad8b numpy-1.11.0.tar.gz' > numpy-1.11.0.tar.gz.sha512
- echo '918ff1765a85a818619165c2bcbb0d417f35c979c2f42f1bb7e41636696c0cb4d6837725f3655fbdfebea966476d1255ee18adabe9ed5536455b63336a1f399d GitPython-2.1.3.tar.gz' > GitPython-2.1.3.tar.gz.sha512
- echo 'de6409d75a3ff3cf1e5391d3b09126f0bc7e1a40a15f9bee244195638fe2f8481fca032896d8534623e6122ff59aaf669664e27ff89cf1b094a5ce7312f220b7 scipy-0.17.0.tar.gz' > scipy-0.17.0.tar.gz.sha512
- echo '96f3e51b46741450bc6b63779c10ebb4a7066860fe544385d64d1eda52592e376a589ef282ace2e1df73df61c10eab1a0d793abbdaf770e60289494d4bf3bcb4 sqlite-autoconf-3071700.tar.gz' > sqlite-autoconf-3071700.tar.gz.sha512
- echo '977db6e9bc6a5918cceb255981a57e85e7060c0922aefd2968b004d25d704e25a5cb5bbe09eb387e8695581e23e2825d9c40310068fe25ece7e9c23037a21f39 sympy-1.0.tar.gz' > sympy-1.0.tar.gz.sha512
- echo 'ece209d4c7ec0cb58ede791444dc754e0d10811cbbdebe3df61c0fd9f9f9867c1c3ccd5f1827f847c005e24eef34fb5bf87b5d3f894d75da04f1797538290e4a zlib-1.2.8.tar.gz' > zlib-1.2.8.tar.gz.sha512
- echo '91a212b5007f9fdfacb4341e06dc0355c5c29897eb8ea407dd4864091f845ba1417bb0d33b5ed6897869d0233e2d0ec6548898d3dbe9eda23f751829bd51a104 setuptools-20.6.7.tar.gz' > setuptools-20.6.7.tar.gz.sha512
- # Individual processes
- [ -z "$HDF5_DIR" ] && get_ytproject $HDF5.tar.gz
- [ $INST_ZLIB -eq 1 ] && get_ytproject $ZLIB.tar.gz
- [ $INST_BZLIB -eq 1 ] && get_ytproject $BZLIB.tar.gz
- [ $INST_PNG -eq 1 ] && get_ytproject $PNG.tar.gz
- [ $INST_FTYPE -eq 1 ] && get_ytproject $FREETYPE_VER.tar.gz
- [ $INST_SQLITE3 -eq 1 ] && get_ytproject $SQLITE.tar.gz
- [ $INST_PYX -eq 1 ] && get_ytproject $PYX.tar.gz
- [ $INST_SCIPY -eq 1 ] && get_ytproject $SCIPY.tar.gz
- [ $INST_SCIPY -eq 1 ] && get_ytproject blas.tar.gz
- [ $INST_SCIPY -eq 1 ] && get_ytproject $LAPACK.tar.gz
- if [ $INST_PY3 -eq 1 ]
- then
- get_ytproject $PYTHON3.tgz
- else
- get_ytproject $PYTHON2.tgz
- fi
- [ $INST_H5PY -eq 1 ] && get_ytproject $H5PY.tar.gz
- [ $INST_NOSE -eq 1 ] && get_ytproject $NOSE.tar.gz
- [ $INST_ASTROPY -eq 1 ] && get_ytproject $ASTROPY.tar.gz
- get_ytproject $NUMPY.tar.gz
- get_ytproject $MATPLOTLIB.tar.gz
- get_ytproject $CYTHON.tar.gz
- get_ytproject $GITPYTHON.tar.gz
- get_ytproject $SYMPY.tar.gz
- get_ytproject $SETUPTOOLS.tar.gz
+echo "Installing the Miniconda python environment."
+
+if [ -e ${DEST_DIR} ]
+then
+ rm -rf $DEST_DIR/*
+else
+ mkdir $DEST_DIR
+fi
- if [ $INST_BZLIB -eq 1 ]
- then
- if [ ! -e $BZLIB/done ]
- then
- [ ! -e $BZLIB ] && tar xfz $BZLIB.tar.gz
- echo "Installing BZLIB"
- cd $BZLIB
- if [ `uname` = "Darwin" ]
- then
- if [ -z "${CC}" ]
- then
- sed -i.bak 's/soname/install_name/' Makefile-libbz2_so
- else
- sed -i.bak -e 's/soname/install_name/' -e "s|CC=gcc|CC=${CC}|" Makefile-libbz2_so
- fi
- fi
- ( make install CFLAGS=-fPIC LDFLAGS=-fPIC PREFIX=${DEST_DIR} 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make -f Makefile-libbz2_so CFLAGS=-fPIC LDFLAGS=-fPIC PREFIX=${DEST_DIR} 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( cp -v libbz2.so.1.0.6 ${DEST_DIR}/lib 2>&1 ) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- BZLIB_DIR=${DEST_DIR}
- export LDFLAGS="${LDFLAGS} -L${BZLIB_DIR}/lib/ -L${BZLIB_DIR}/lib64/"
- LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BZLIB_DIR}/lib/"
- fi
+log_cmd ${GETFILE} ${MINICONDA_URLBASE}/${MINICONDA_PKG} || do_exit
+
+log_cmd bash ./${MINICONDA_PKG} -b -p $DEST_DIR -f
+
+# Need to set PATH so we use miniconda's python environment
+export PATH=${DEST_DIR}/bin:$PATH
+
+echo "Installing the necessary packages for yt."
+echo "This may take a while, but don't worry. yt loves you."
- if [ $INST_ZLIB -eq 1 ]
- then
- if [ ! -e $ZLIB/done ]
- then
- [ ! -e $ZLIB ] && tar xfz $ZLIB.tar.gz
- echo "Installing ZLIB"
- cd $ZLIB
- ( ./configure --shared --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make clean 2>&1 ) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- ZLIB_DIR=${DEST_DIR}
- export LDFLAGS="${LDFLAGS} -L${ZLIB_DIR}/lib/ -L${ZLIB_DIR}/lib64/"
- LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${ZLIB_DIR}/lib/"
- fi
-
- if [ $INST_PNG -eq 1 ]
- then
- if [ ! -e $PNG/done ]
- then
- [ ! -e $PNG ] && tar xfz $PNG.tar.gz
- echo "Installing PNG"
- cd $PNG
- ( ./configure CPPFLAGS=-I${DEST_DIR}/include CFLAGS=-I${DEST_DIR}/include --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- PNG_DIR=${DEST_DIR}
- export LDFLAGS="${LDFLAGS} -L${PNG_DIR}/lib/ -L${PNG_DIR}/lib64/"
- LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${PNG_DIR}/lib/"
- fi
-
- if [ $INST_FTYPE -eq 1 ]
- then
- if [ ! -e $FREETYPE_VER/done ]
- then
- [ ! -e $FREETYPE_VER ] && tar xfz $FREETYPE_VER.tar.gz
- echo "Installing FreeType2"
- cd $FREETYPE_VER
- ( ./configure CFLAGS=-I${DEST_DIR}/include --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- FTYPE_DIR=${DEST_DIR}
- export LDFLAGS="${LDFLAGS} -L${FTYPE_DIR}/lib/ -L${FTYPE_DIR}/lib64/"
- LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${FTYPE_DIR}/lib/"
- fi
+declare -a YT_DEPS
+YT_DEPS+=('python')
+YT_DEPS+=('setuptools')
+YT_DEPS+=('numpy')
+YT_DEPS+=('jupyter')
+YT_DEPS+=('ipython')
+YT_DEPS+=('sphinx')
+if [ ${INST_GIT} -eq 1 ]
+then
+ YT_DEPS+=('git')
+ YT_DEPS+=('gitpython')
+fi
+if [ $INST_H5PY -ne 0 ]
+then
+ YT_DEPS+=('h5py')
+fi
+YT_DEPS+=('matplotlib')
+YT_DEPS+=('cython')
+if [ $INST_NOSE -ne 0 ]
+then
+ YT_DEPS+=('nose')
+fi
+if [ $INST_SCIPY -ne 0 ]
+then
+ YT_DEPS+=('scipy')
+fi
+if [ $INST_ASTROPY -ne 0 ]
+then
+ YT_DEPS+=('astropy')
+fi
+YT_DEPS+=('conda-build')
+if [ $INST_PY3 -eq 0 ] && [ $INST_HG -eq 1 ]
+then
+ YT_DEPS+=('mercurial')
+fi
+YT_DEPS+=('sympy')
- if [ -z "$HDF5_DIR" ]
- then
- if [ ! -e $HDF5/done ]
- then
- [ ! -e $HDF5 ] && tar xfz $HDF5.tar.gz
- echo "Installing HDF5"
- cd $HDF5
- ( ./configure --prefix=${DEST_DIR}/ --enable-shared 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make ${MAKE_PROCS} install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- export HDF5_DIR=${DEST_DIR}
- else
- export HDF5_DIR=${HDF5_DIR}
- fi
- export HDF5_API=16
-
- if [ $INST_SQLITE3 -eq 1 ]
- then
- if [ ! -e $SQLITE/done ]
- then
- [ ! -e $SQLITE ] && tar xfz $SQLITE.tar.gz
- echo "Installing SQLite3"
- cd $SQLITE
- ( ./configure --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make ${MAKE_PROCS} install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- fi
+if [ $INST_NETCDF4 -eq 1 ]
+then
+ YT_DEPS+=('netcdf4')
+fi
- if [ $INST_PY3 -eq 1 ]
- then
- if [ ! -e $PYTHON3/done ]
- then
- echo "Installing Python 3"
- [ ! -e $PYTHON3 ] && tar xfz $PYTHON3.tgz
- cd $PYTHON3
- ( ./configure --prefix=${DEST_DIR}/ ${PYCONF_ARGS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
-
- ( make ${MAKE_PROCS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( ln -sf ${DEST_DIR}/bin/python3.5 ${DEST_DIR}/bin/pyyt 2>&1 ) 1>> ${LOG_FILE}
- ( ln -sf ${DEST_DIR}/bin/python3.5 ${DEST_DIR}/bin/python 2>&1 ) 1>> ${LOG_FILE}
- ( ln -sf ${DEST_DIR}/bin/python3-config ${DEST_DIR}/bin/python-config 2>&1 ) 1>> ${LOG_FILE}
- ( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- else
- if [ ! -e $PYTHON2/done ]
- then
- echo "Installing Python 2. This may take a while, but don't worry. yt loves you."
- [ ! -e $PYTHON2 ] && tar xfz $PYTHON2.tgz
- cd $PYTHON2
- ( ./configure --prefix=${DEST_DIR}/ ${PYCONF_ARGS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make ${MAKE_PROCS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( ln -sf ${DEST_DIR}/bin/python2.7 ${DEST_DIR}/bin/pyyt 2>&1 ) 1>> ${LOG_FILE}
- ( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- fi
+log_cmd ${DEST_DIR}/bin/conda update --yes conda
- ( ${DEST_DIR}/bin/python -c "import _ssl" 2>&1 ) 1>> ${LOG_FILE}
- RESULT=$?
- if [ $RESULT -ne 0 ]
- then
- echo "Unable to import the python SSL bindings."
- echo "This means that OpenSSL is not installed or your system's OpenSSL"
- echo "installation is out of date."
- echo "Please install OpenSSL or set INST_CONDA=1"
- do_exit
- fi
-
- export PYTHONPATH=${DEST_DIR}/lib/${PYTHON_EXEC}/site-packages/
-
- # Install setuptools
- do_setup_py $SETUPTOOLS
-
+if [ $INST_GIT -eq 1 ]
+then
+ GIT_EXE=${DEST_DIR}/bin/git
+else
if type -P git &>/dev/null
then
GIT_EXE="git"
else
- echo "Cannot find git. Please install git."
- do_exit
+ if [ $INST_YT_SOURCE -eq 1 ]
+ then
+ echo "Cannot find git. Please install git or set INST_GIT=1."
+ do_exit
+ fi
+ fi
+fi
+
+log_cmd echo "DEPENDENCIES" ${YT_DEPS[@]}
+for YT_DEP in "${YT_DEPS[@]}"; do
+ echo "Installing $YT_DEP"
+ log_cmd ${DEST_DIR}/bin/conda install -c conda-forge --yes ${YT_DEP}
+done
+
+if [ $INST_PY3 -eq 1 ] && [ $INST_HG -eq 1 ]
+then
+ echo "Installing mercurial"
+ log_cmd ${DEST_DIR}/bin/conda create -y -n py27 python=2.7 mercurial
+ log_cmd ln -s ${DEST_DIR}/envs/py27/bin/hg ${DEST_DIR}/bin
+fi
+
+if [ $INST_YT_SOURCE -eq 1 ]
+then
+ log_cmd ${GIT_EXE} clone https://github.com/yt-project/yt_conda ${DEST_DIR}/src/yt_conda
+fi
+
+if [ $INST_EMBREE -eq 1 ]
+then
+ echo "Installing Embree"
+ if [ ! -d ${DEST_DIR}/src ]
+ then
+ mkdir ${DEST_DIR}/src
fi
+ cd ${DEST_DIR}/src
+ ( ${GETFILE} "$EMBREE_URL" 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ log_cmd tar xfz ${EMBREE}.tar.gz
+ log_cmd mv ${DEST_DIR}/src/${EMBREE}/include/embree2 ${DEST_DIR}/include
+ log_cmd mv ${DEST_DIR}/src/${EMBREE}/lib/lib*.* ${DEST_DIR}/lib
+ if [ `uname` = "Darwin" ]
+ then
+ ln -s ${DEST_DIR}/lib/libembree.2.dylib ${DEST_DIR}/lib/libembree.dylib
+ install_name_tool -id ${DEST_DIR}/lib/libembree.2.dylib ${DEST_DIR}/lib/libembree.2.dylib
+ else
+ ln -s ${DEST_DIR}/lib/libembree.so.2 ${DEST_DIR}/lib/libembree.so
+ fi
+
+ echo "Installing pyembree from source"
+ ( ${GETFILE} "$PYEMBREE_URL" 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ log_cmd unzip ${DEST_DIR}/src/master.zip
+ pushd ${DEST_DIR}/src/pyembree-master &> /dev/null
+ log_cmd ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py install build_ext -I${DEST_DIR}/include -L${DEST_DIR}/lib
+ popd &> /dev/null
+fi
+if [ $INST_ROCKSTAR -eq 1 ]
+then
+ echo "Building Rockstar"
+ ( ${GIT_EXE} clone https://github.com/yt-project/rockstar ${DEST_DIR}/src/rockstar/ 2>&1 ) 1>> ${LOG_FILE}
+ ROCKSTAR_PACKAGE=$(${DEST_DIR}/bin/conda build ${DEST_DIR}/src/yt_conda/rockstar --output)
+ log_cmd ${DEST_DIR}/bin/conda build ${DEST_DIR}/src/yt_conda/rockstar
+ log_cmd ${DEST_DIR}/bin/conda install $ROCKSTAR_PACKAGE
+ ROCKSTAR_DIR=${DEST_DIR}/src/rockstar
+fi
+
+# conda doesn't package pyx, so we install manually with pip
+if [ $INST_PYX -eq 1 ]
+then
+ if [ $INST_PY3 -eq 1 ]
+ then
+ log_cmd ${DEST_DIR}/bin/pip install pyx
+ else
+ log_cmd ${DEST_DIR}/bin/pip install pyx==0.12.1
+ fi
+fi
+
+if [ $INST_YT_SOURCE -eq 0 ]
+then
+ echo "Installing yt"
+ log_cmd ${DEST_DIR}/bin/conda install -c conda-forge --yes yt
+else
+ echo "Building yt from source"
if [ -z "$YT_DIR" ]
then
if [ -e $ORIG_PWD/yt/mods.py ]
@@ -1088,512 +620,86 @@
elif [ -e $ORIG_PWD/../yt/mods.py ]
then
YT_DIR=$(dirname $ORIG_PWD)
- elif [ ! -e yt-git ]
- then
- echo "Cloning yt"
- YT_DIR="$PWD/yt-git/"
- ( ${GIT_EXE} clone https://github.com/yt-project/yt/ ${YT_DIR} 2>&1 ) 1>> ${LOG_FILE}
- elif [ -e yt-git ]
- then
- YT_DIR="$PWD/yt-git/"
+ else
+ YT_DIR="${DEST_DIR}/src/yt-git"
+ log_cmd ${GIT_EXE} clone https://github.com/yt-project/yt ${YT_DIR}
+ log_cmd ${GIT_EXE} -C ${YT_DIR} checkout ${BRANCH}
fi
echo Setting YT_DIR=${YT_DIR}
- fi
-
- # This fixes problems with gfortran linking.
- unset LDFLAGS
-
- echo "Installing pip"
- ( ${GETFILE} https://bootstrap.pypa.io/get-pip.py 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( ${DEST_DIR}/bin/${PYTHON_EXEC} get-pip.py 2>&1 ) 1>> ${LOG_FILE} || do_exit
-
- if [ $INST_SCIPY -eq 0 ]
- then
- do_setup_py $NUMPY ${NUMPY_ARGS}
else
- if [ ! -e $SCIPY/done ]
- then
- if [ ! -e BLAS/done ]
- then
- tar xfz blas.tar.gz
- echo "Building BLAS"
- cd BLAS
- gfortran -O2 -fPIC -fno-second-underscore -c *.f
- ( ar r libfblas.a *.o 2>&1 ) 1>> ${LOG_FILE}
- ( ranlib libfblas.a 2>&1 ) 1>> ${LOG_FILE}
- rm -rf *.o
- touch done
- cd ..
- fi
- if [ ! -e $LAPACK/done ]
- then
- tar xfz $LAPACK.tar.gz
- echo "Building LAPACK"
- cd $LAPACK/
- cp INSTALL/make.inc.gfortran make.inc
- ( make lapacklib OPTS="-fPIC -O2" NOOPT="-fPIC -O0" CFLAGS=-fPIC LDFLAGS=-fPIC 2>&1 ) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- fi
- export BLAS=$PWD/BLAS/libfblas.a
- export LAPACK=$PWD/$LAPACK/liblapack.a
- do_setup_py $NUMPY ${NUMPY_ARGS}
- do_setup_py $SCIPY ${NUMPY_ARGS}
- fi
-
- if [ -n "${MPL_SUPP_LDFLAGS}" ]
- then
- OLD_LDFLAGS=${LDFLAGS}
- export LDFLAGS="${MPL_SUPP_LDFLAGS}"
- echo "Setting LDFLAGS ${LDFLAGS}"
- fi
- if [ -n "${MPL_SUPP_CXXFLAGS}" ]
- then
- OLD_CXXFLAGS=${CXXFLAGS}
- export CXXFLAGS="${MPL_SUPP_CXXFLAGS}"
- echo "Setting CXXFLAGS ${CXXFLAGS}"
- fi
- if [ -n "${MPL_SUPP_CFLAGS}" ]
- then
- OLD_CFLAGS=${CFLAGS}
- export CFLAGS="${MPL_SUPP_CFLAGS}"
- echo "Setting CFLAGS ${CFLAGS}"
- fi
- # Now we set up the basedir for matplotlib:
- mkdir -p ${DEST_DIR}/src/$MATPLOTLIB
- echo "[directories]" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
- echo "basedirlist = ${DEST_DIR}" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
- if [ `uname` = "Darwin" ]
- then
- echo "[gui_support]" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
- echo "macosx = False" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
- fi
-
- _user_DISPLAY=$DISPLAY
- unset DISPLAY # see (yt-user link missing: "Installation failure" 01/29/15)
- do_setup_py $MATPLOTLIB
- export DISPLAY=${_user_DISPLAY}
- if [ -n "${OLD_LDFLAGS}" ]
- then
- export LDFLAG=${OLD_LDFLAGS}
- fi
- [ -n "${OLD_LDFLAGS}" ] && export LDFLAGS=${OLD_LDFLAGS}
- [ -n "${OLD_CXXFLAGS}" ] && export CXXFLAGS=${OLD_CXXFLAGS}
- [ -n "${OLD_CFLAGS}" ] && export CFLAGS=${OLD_CFLAGS}
-
- echo "Installing Jupyter"
- ( ${DEST_DIR}/bin/pip install "jupyter<2.0.0" 2>&1 ) 1>> ${LOG_FILE}
-
- do_setup_py $CYTHON
- if [ $INST_H5PY -eq 1 ]
- then
- do_setup_py $H5PY
- fi
- if [ $INST_NOSE -eq 1 ]
- then
- do_setup_py $NOSE
- fi
- if [ $INST_ASTROPY -eq 1 ]
- then
- do_setup_py $ASTROPY
- fi
- do_setup_py $GITPYTHON
- do_setup_py $SYMPY
- [ $INST_PYX -eq 1 ] && do_setup_py $PYX
-
- ( ${DEST_DIR}/bin/pip install jinja2 2>&1 ) 1>> ${LOG_FILE}
-
- # Now we build Rockstar and set its environment variable.
- if [ $INST_ROCKSTAR -eq 1 ]
- then
- if [ ! -e rockstar/done ]
- then
- echo "Building Rockstar"
- if [ ! -e rockstar ]
- then
- ( ${GIT_EXE} clone https://github.com/yt-project/rockstar 2>&1 ) 1>> ${LOG_FILE}
- fi
- cd rockstar
- ( make lib 2>&1 ) 1>> ${LOG_FILE} || do_exit
- cp librockstar.so ${DEST_DIR}/lib
- ROCKSTAR_DIR=${DEST_DIR}/src/rockstar
- echo $ROCKSTAR_DIR > ${YT_DIR}/rockstar.cfg
- touch done
- cd ..
- fi
- fi
-
- MY_PWD=`pwd`
- cd $YT_DIR
- ( ${GIT_EXE} pull 2>1 && ${GIT_EXE} checkout ${BRANCH} 2>&1 ) 1>> ${LOG_FILE}
-
- echo "Installing yt"
- [ $INST_PNG -eq 1 ] && echo $PNG_DIR > png.cfg
- ( export PATH=$DEST_DIR/bin:$PATH ; ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py develop 2>&1 ) 1>> ${LOG_FILE} || do_exit
- touch done
- cd $MY_PWD
-
- if !( ( ${DEST_DIR}/bin/${PYTHON_EXEC} -c "import readline" 2>&1 )>> ${LOG_FILE}) || \
- [[ "${MYOS##Darwin}" != "${MYOS}" && $INST_PY3 -eq 1 ]]
- then
- if !( ( ${DEST_DIR}/bin/${PYTHON_EXEC} -c "import gnureadline" 2>&1 )>> ${LOG_FILE})
+ if [ ! -e $YT_DIR/.git ]
then
- echo "Installing pure-python readline"
- ( ${DEST_DIR}/bin/pip install gnureadline 2>&1 ) 1>> ${LOG_FILE}
- fi
- fi
-
- if [ -e $HOME/.matplotlib/fontList.cache ] && \
- ( grep -q python2.6 $HOME/.matplotlib/fontList.cache )
- then
- echo "WARNING WARNING WARNING WARNING WARNING WARNING WARNING"
- echo "*******************************************************"
- echo
- echo " You likely need to remove your old fontList.cache!"
- echo " You can do this with this command:"
- echo ""
- echo " rm $HOME/.matplotlib/fontList.cache"
- echo
- echo "*******************************************************"
- fi
-
- # Add the environment scripts
- ( cp ${YT_DIR}/doc/activate ${DEST_DIR}/bin/activate 2>&1 ) 1>> ${LOG_FILE}
- sed -i.bak -e "s,__YT_DIR__,${DEST_DIR}," ${DEST_DIR}/bin/activate
- ( cp ${YT_DIR}/doc/activate.csh ${DEST_DIR}/bin/activate.csh 2>&1 ) 1>> ${LOG_FILE}
- sed -i.bak -e "s,__YT_DIR__,${DEST_DIR}," ${DEST_DIR}/bin/activate.csh
-
- test_install
-
- function print_afterword
- {
- echo
- echo
- echo "========================================================================"
- echo
- echo "yt is now installed in $DEST_DIR ."
- echo
- echo "To run from this new installation, use the activate script for this "
- echo "environment."
- echo
- echo " $ source $DEST_DIR/bin/activate"
- echo
- echo "This modifies the environment variables YT_DEST, PATH, PYTHONPATH, and"
- echo "LD_LIBRARY_PATH to match your new yt install. If you use csh, just"
- echo "append .csh to the above."
- echo
- echo "To get started with yt, check out the orientation:"
- echo
- echo " http://yt-project.org/doc/quickstart/"
- echo
- echo "The source for yt is located at:"
- echo " $YT_DIR"
- echo
- echo "For support, see the website and join the mailing list:"
- echo
- echo " http://yt-project.org/"
- echo " http://yt-project.org/data/ (Sample data)"
- echo " http://yt-project.org/doc/ (Docs)"
- echo
- echo " http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org"
- echo
- echo "========================================================================"
- echo
- echo "Oh, look at me, still talking when there's science to do!"
- echo "Good luck, and email the user list if you run into any problems."
- }
-
- print_afterword
- print_afterword >> ${LOG_FILE}
-
- echo "yt dependencies were last updated on" > ${DEST_DIR}/.yt_update
- date >> ${DEST_DIR}/.yt_update
-else # INST_CONDA -eq 1
- MYARCH=`uname -m` # A guess at the OS
- MYOS=`uname -s`
-
- if [ $MYOS = "Darwin" ]
- then
- MINICONDA_OS="MacOSX"
- MINICONDA_ARCH="x86_64"
- elif [ $MYOS = "Linux" ]
- then
- MINICONDA_OS="Linux"
- if [ $MYARCH = "i386" ]
- then
- MINICONDA_ARCH="x86"
- elif [ $MYARCH = "i686" ]
- then
- MINICONDA_ARCH="x86"
- elif [ $MYARCH = "x86_64" ]
- then
- MINICONDA_ARCH="x86_64"
- else
- echo "Not sure which architecture you are running."
- echo "Going with x86_64 architecture."
- MINICONDA_OS="Linux-x86_64"
- fi
- else
- echo "The yt install script is not supported on the ${MYOS}"
- echo "operating system."
- exit 1
- fi
-
- if [ $INST_PY3 -eq 1 ]
- then
- PY_VERSION='3'
- else
- PY_VERSION='2'
- fi
-
- MINICONDA_PKG="Miniconda${PY_VERSION}-${MINICONDA_VERSION}-${MINICONDA_OS}-${MINICONDA_ARCH}.sh"
-
- echo
- echo "Downloading ${MINICONDA_URLBASE}/${MINICONDA_PKG}"
- echo
-
- if [ -f ${MINICONDA_PKG} ]
- then
- rm $MINICONDA_PKG
- fi
-
- echo "Installing the Miniconda python environment."
-
- if [ -e ${DEST_DIR} ]
- then
- rm -rf $DEST_DIR/*
- else
- mkdir $DEST_DIR
- fi
-
- log_cmd ${GETFILE} ${MINICONDA_URLBASE}/${MINICONDA_PKG} || do_exit
-
- log_cmd bash ./${MINICONDA_PKG} -b -p $DEST_DIR -f
-
- # Need to set PATH so we use miniconda's python environment
- export PATH=${DEST_DIR}/bin:$PATH
-
- echo "Installing the necessary packages for yt."
- echo "This may take a while, but don't worry. yt loves you."
-
- declare -a YT_DEPS
- YT_DEPS+=('python')
- YT_DEPS+=('setuptools')
- YT_DEPS+=('numpy')
- YT_DEPS+=('jupyter')
- YT_DEPS+=('ipython')
- YT_DEPS+=('sphinx')
- if [ ${INST_GIT} -eq 1 ]
- then
- YT_DEPS+=('git')
- YT_DEPS+=('gitpython')
- fi
- if [ $INST_H5PY -ne 0 ]
- then
- YT_DEPS+=('h5py')
- fi
- YT_DEPS+=('matplotlib')
- YT_DEPS+=('cython')
- if [ $INST_NOSE -ne 0 ]
- then
- YT_DEPS+=('nose')
- fi
- if [ $INST_SCIPY -ne 0 ]
- then
- YT_DEPS+=('scipy')
- fi
- if [ $INST_ASTROPY -ne 0 ]
- then
- YT_DEPS+=('astropy')
- fi
- YT_DEPS+=('conda-build')
- if [ $INST_PY3 -eq 0 ] && [ $INST_HG -eq 1 ]
- then
- YT_DEPS+=('mercurial')
- fi
- YT_DEPS+=('sympy')
-
- if [ $INST_NETCDF4 -eq 1 ]
- then
- YT_DEPS+=('netcdf4')
- fi
-
- log_cmd ${DEST_DIR}/bin/conda update --yes conda
-
- if [ $INST_GIT -eq 1 ]
- then
- GIT_EXE=${DEST_DIR}/bin/git
- else
- if type -P git &>/dev/null
- then
- GIT_EXE="git"
- else
- echo "Cannot find git. Please install git or set INST_GIT=1."
+ echo "$YT_DIR is not a clone of the yt git repository, exiting"
do_exit
fi
fi
-
- log_cmd echo "DEPENDENCIES" ${YT_DEPS[@]}
- for YT_DEP in "${YT_DEPS[@]}"; do
- echo "Installing $YT_DEP"
- log_cmd ${DEST_DIR}/bin/conda install -c conda-forge --yes ${YT_DEP}
- done
-
- if [ $INST_PY3 -eq 1 ] && [ $INST_HG -eq 1 ]
- then
- echo "Installing mercurial"
- log_cmd ${DEST_DIR}/bin/conda create -y -n py27 python=2.7 mercurial
- log_cmd ln -s ${DEST_DIR}/envs/py27/bin/hg ${DEST_DIR}/bin
- fi
-
- log_cmd ${GIT_EXE} clone https://github.com/yt-project/yt_conda ${DEST_DIR}/src/yt_conda
-
if [ $INST_EMBREE -eq 1 ]
then
-
- echo "Installing Embree"
- if [ ! -d ${DEST_DIR}/src ]
- then
- mkdir ${DEST_DIR}/src
- fi
- cd ${DEST_DIR}/src
- ( ${GETFILE} "$EMBREE_URL" 2>&1 ) 1>> ${LOG_FILE} || do_exit
- log_cmd tar xfz ${EMBREE}.tar.gz
- log_cmd mv ${DEST_DIR}/src/${EMBREE}/include/embree2 ${DEST_DIR}/include
- log_cmd mv ${DEST_DIR}/src/${EMBREE}/lib/lib*.* ${DEST_DIR}/lib
- if [ `uname` = "Darwin" ]
- then
- ln -s ${DEST_DIR}/lib/libembree.2.dylib ${DEST_DIR}/lib/libembree.dylib
- install_name_tool -id ${DEST_DIR}/lib/libembree.2.dylib ${DEST_DIR}/lib/libembree.2.dylib
- else
- ln -s ${DEST_DIR}/lib/libembree.so.2 ${DEST_DIR}/lib/libembree.so
- fi
-
- echo "Installing pyembree from source"
- ( ${GETFILE} "$PYEMBREE_URL" 2>&1 ) 1>> ${LOG_FILE} || do_exit
- log_cmd unzip ${DEST_DIR}/src/master.zip
- pushd ${DEST_DIR}/src/pyembree-master &> /dev/null
- log_cmd ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py install build_ext -I${DEST_DIR}/include -L${DEST_DIR}/lib
- popd &> /dev/null
+ echo $DEST_DIR > ${YT_DIR}/embree.cfg
fi
-
if [ $INST_ROCKSTAR -eq 1 ]
then
- echo "Building Rockstar"
- ( ${GIT_EXE} clone https://github.com/yt-project/rockstar ${DEST_DIR}/src/rockstar/ 2>&1 ) 1>> ${LOG_FILE}
- ROCKSTAR_PACKAGE=$(${DEST_DIR}/bin/conda build ${DEST_DIR}/src/yt_conda/rockstar --output)
- log_cmd ${DEST_DIR}/bin/conda build ${DEST_DIR}/src/yt_conda/rockstar
- log_cmd ${DEST_DIR}/bin/conda install $ROCKSTAR_PACKAGE
- ROCKSTAR_DIR=${DEST_DIR}/src/rockstar
- fi
-
- # conda doesn't package pyx, so we install manually with pip
- if [ $INST_PYX -eq 1 ]
- then
- if [ $INST_PY3 -eq 1 ]
- then
- log_cmd ${DEST_DIR}/bin/pip install pyx
- else
- log_cmd ${DEST_DIR}/bin/pip install pyx==0.12.1
- fi
- fi
-
- if [ $INST_YT_SOURCE -eq 0 ]
- then
- echo "Installing yt"
- log_cmd ${DEST_DIR}/bin/conda install -c conda-forge --yes yt
- else
- echo "Building yt from source"
- if [ -z "$YT_DIR" ]
- then
- if [ -e $ORIG_PWD/yt/mods.py ]
- then
- YT_DIR="$ORIG_PWD"
- elif [ -e $ORIG_PWD/../yt/mods.py ]
- then
- YT_DIR=$(dirname $ORIG_PWD)
- else
- YT_DIR="${DEST_DIR}/src/yt-git"
- log_cmd ${GIT_EXE} clone https://github.com/yt-project/yt ${YT_DIR}
- log_cmd ${GIT_EXE} -C ${YT_DIR} checkout ${BRANCH}
- fi
- echo Setting YT_DIR=${YT_DIR}
- else
- if [ ! -e $YT_DIR/.git ]
- then
- echo "$YT_DIR is not a clone of the yt git repository, exiting"
- do_exit
- fi
- fi
- if [ $INST_EMBREE -eq 1 ]
- then
- echo $DEST_DIR > ${YT_DIR}/embree.cfg
- fi
- if [ $INST_ROCKSTAR -eq 1 ]
- then
- echo $ROCKSTAR_DIR > ${YT_DIR}/rockstar.cfg
- ROCKSTAR_LIBRARY_PATH=${DEST_DIR}/lib
- fi
- pushd ${YT_DIR} &> /dev/null
- ( LIBRARY_PATH=$ROCKSTAR_LIBRARY_PATH ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py develop 2>&1) 1>> ${LOG_FILE} || do_exit
- popd &> /dev/null
+ echo $ROCKSTAR_DIR > ${YT_DIR}/rockstar.cfg
+ ROCKSTAR_LIBRARY_PATH=${DEST_DIR}/lib
fi
+ pushd ${YT_DIR} &> /dev/null
+ ( LIBRARY_PATH=$ROCKSTAR_LIBRARY_PATH ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py develop 2>&1) 1>> ${LOG_FILE} || do_exit
+ popd &> /dev/null
+fi
- test_install
+test_install
- echo
- echo
- echo "========================================================================"
- echo
- echo "yt and the Conda system are now installed in $DEST_DIR"
- echo
- echo "To get started with yt, check out the orientation:"
- echo
- echo " http://yt-project.org/doc/orientation/"
- echo
- echo "For support, see the website and join the mailing list:"
- echo
- echo " http://yt-project.org/"
- echo " http://yt-project.org/data/ (Sample data)"
- echo " http://yt-project.org/doc/ (Docs)"
- echo
- echo " http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org"
- echo
- echo "You must now prepend the following folder to your PATH environment variable:"
- echo
- echo " $DEST_DIR/bin"
- echo
- echo "On Bash-style shells you can copy/paste the following command to "
- echo "temporarily activate the yt installation:"
+echo
+echo
+echo "========================================================================"
+echo
+echo "yt and the Conda system are now installed in $DEST_DIR"
+echo
+echo "To get started with yt, check out the orientation:"
+echo
+echo " http://yt-project.org/doc/orientation/"
+echo
+echo "For support, see the website and join the mailing list:"
+echo
+echo " http://yt-project.org/"
+echo " http://yt-project.org/data/ (Sample data)"
+echo " http://yt-project.org/doc/ (Docs)"
+echo
+echo " http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org"
+echo
+echo "You must now prepend the following folder to your PATH environment variable:"
+echo
+echo " $DEST_DIR/bin"
+echo
+echo "On Bash-style shells you can copy/paste the following command to "
+echo "temporarily activate the yt installation:"
+echo
+echo " export PATH=$DEST_DIR/bin:\$PATH"
+echo
+echo "and on csh-style shells:"
+echo
+echo " setenv PATH $DEST_DIR/bin:\$PATH"
+echo
+echo "You can also update the init file appropriate for your shell"
+echo "(e.g. .bashrc, .bash_profile, .cshrc, or .zshrc) to include"
+echo "the same command."
+echo
+if [ $INST_ROCKSTAR -eq 1 ]
+then
+ if [ $MYOS = "Darwin" ]
+ then
+ LD_NAME="DYLD_LIBRARY_PATH"
+ else
+ LD_NAME="LD_LIBRARY_PATH"
+ fi
echo
- echo " export PATH=$DEST_DIR/bin:\$PATH"
- echo
- echo "and on csh-style shells:"
+ echo "For rockstar to work, you must also set $LD_NAME:"
echo
- echo " setenv PATH $DEST_DIR/bin:\$PATH"
- echo
- echo "You can also update the init file appropriate for your shell"
- echo "(e.g. .bashrc, .bash_profile, .cshrc, or .zshrc) to include"
- echo "the same command."
+ echo " export $LD_NAME=$DEST_DIR/lib:\$$LD_NAME"
echo
- if [ $INST_ROCKSTAR -eq 1 ]
- then
- if [ $MYOS = "Darwin" ]
- then
- LD_NAME="DYLD_LIBRARY_PATH"
- else
- LD_NAME="LD_LIBRARY_PATH"
- fi
- echo
- echo "For rockstar to work, you must also set $LD_NAME:"
- echo
- echo " export $LD_NAME=$DEST_DIR/lib:\$$LD_NAME"
- echo
- echo "or whichever invocation is appropriate for your shell."
- fi
- echo "========================================================================"
- echo
- echo "Oh, look at me, still talking when there's science to do!"
- echo "Good luck, and email the mailing list if you run into any problems."
+ echo "or whichever invocation is appropriate for your shell."
fi
+echo "========================================================================"
+echo
+echo "Oh, look at me, still talking when there's science to do!"
+echo "Good luck, and email the mailing list if you run into any problems."
diff -r 60a10fe93978952d4959283312badb40cd4f5a72 -r d856cd57100577863c14b5e87d936024c5ee84db doc/source/installing.rst
--- a/doc/source/installing.rst
+++ b/doc/source/installing.rst
@@ -121,10 +121,6 @@
yt git repository and build yt form source. The default is
``INST_YT_SOURCE=0``, which installs yt from a binary conda package.
-The install script can also build python and all yt dependencies from source. To
-switch to this mode, set ``INST_CONDA=0`` at the top of the install script. If
-you choose this mode, you must also set ``INST_YT_SOURCE=1``.
-
In addition, you can tell the install script to download and install some
additional packages --- currently these include
`PyX <http://pyx.sourceforge.net/>`_, the `Rockstar halo
@@ -144,8 +140,8 @@
Because the installer is downloading and building a variety of packages from
source, this will likely take a few minutes, especially if you have a slow
-internet connection or have ``INST_CONDA=0`` set. You will get updates of its
-status at the command prompt throughout.
+internet connection. You will get updates of its status at the command prompt
+throughout.
If you receive errors during this process, the installer will provide you
with a large amount of information to assist in debugging your problems. The
@@ -155,15 +151,6 @@
potentially figure out what went wrong. If you have problems, though, do not
hesitate to :ref:`contact us <asking-for-help>` for assistance.
-If the install script errors out with a message about being unable to import the
-python SSL bindings, this means that the Python built by the install script was
-unable to link against the OpenSSL library. This likely means that you installed
-with ``INST_CONDA=0`` on a recent version of OSX, or on a cluster that has a
-very out of date installation of OpenSSL. In both of these cases you will either
-need to install OpenSSL yourself from the system package manager or consider
-using ``INST_CONDA=1``, since conda-based installs can install the conda package
-for OpenSSL.
-
.. _activating-yt:
Activating Your Installation
@@ -172,11 +159,8 @@
Once the installation has completed, there will be instructions on how to set up
your shell environment to use yt.
-Activating Conda-based installs (``INST_CONDA=1``)
-""""""""""""""""""""""""""""""""""""""""""""""""""
-
-For conda-based installs, you will need to ensure that the installation's
-``yt-conda/bin`` directory is prepended to your ``PATH`` environment variable.
+In particular, you will need to ensure that the installation's ``yt-conda/bin``
+directory is prepended to your ``PATH`` environment variable.
For Bash-style shells, you can use the following command in a terminal session
to temporarily activate the yt installation:
@@ -195,31 +179,6 @@
appropriate for your shell and OS (e.g. .bashrc, .bash_profile, .cshrc, .zshrc)
to include the same command.
-Activating source-based installs (``INST_CONDA=0``)
-"""""""""""""""""""""""""""""""""""""""""""""""""""
-
-For this installation method, you must run an ``activate`` script to activate
-the yt environment in a terminal session. You must run this script in order to
-have yt properly recognized by your system. You can either add it to your login
-script, or you must execute it in each shell session prior to working with yt.
-
-.. code-block:: bash
-
- $ source <yt installation directory>/bin/activate
-
-If you use csh or tcsh as your shell, activate that version of the script:
-
-.. code-block:: bash
-
- $ source <yt installation directory>/bin/activate.csh
-
-If you don't like executing outside scripts on your computer, you can set
-the shell variables manually. ``YT_DEST`` needs to point to the root of the
-directory containing the install. By default, this will be ``yt-<arch>``, where
-``<arch>`` is your machine's architecture (usually ``x86_64`` or ``i386``). You
-will also need to set ``LD_LIBRARY_PATH`` and ``PYTHONPATH`` to contain
-``$YT_DEST/lib`` and ``$YT_DEST/python2.7/site-packages``, respectively.
-
.. _updating-yt:
Updating yt and Its Dependencies
@@ -231,21 +190,20 @@
.. code-block:: bash
- $ yt update
+ $ conda update yt
-Additionally, if you ran the install script with ``INST_CONDA=0`` and want to
-make sure you have the latest dependencies associated with yt and update the
-codebase simultaneously, type this:
+If you want to update your dependencies, run:
.. code-block:: bash
- $ yt update --all
+ $ conda update --all
-If you ran the install script with ``INST_CONDA=1`` and want to update your dependencies, run:
+If you have installed yt from source, you can use the following command to get
+the latest development version of yt:
.. code-block:: bash
- $ conda update --all
+ $ yt update
.. _removing-yt:
@@ -254,10 +212,14 @@
Because yt and its dependencies are installed in an isolated directory when
you use the script installer, you can easily remove yt and all of its
-dependencies cleanly. Simply remove the install directory and its
-subdirectories and you're done. If you *really* had problems with the
-code, this is a last defense for solving: remove and then fully
-:ref:`re-install <installing-yt>` from the install script again.
+dependencies cleanly. Simply remove the install directory and its
+subdirectories::
+
+ $ rm -rf yt-conda
+
+If you *really* had problems with the installation process, this is a last
+defense for solving: remove and then fully :ref:`re-install <installing-yt>`
+from the install script again.
.. _anaconda-installation:
@@ -335,13 +297,11 @@
This will make sure you are running a version of yt corresponding to the
most up-to-date source code.
-.. _rockstar-conda:
-
-Rockstar Halo Finder for Conda-based installations
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Installing Support for the Rockstar Halo Finder
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The easiest way to set rockstar up in a conda-based python envrionment is to run
-the install script with both ``INST_CONDA=1`` and ``INST_ROCKSTAR=1``.
+the install script with ``INST_ROCKSTAR=1``.
If you want to do this manually, you will need to follow these
instructions. First, clone Matt Turk's fork of rockstar and compile it:
diff -r 60a10fe93978952d4959283312badb40cd4f5a72 -r d856cd57100577863c14b5e87d936024c5ee84db doc/source/visualizing/unstructured_mesh_rendering.rst
--- a/doc/source/visualizing/unstructured_mesh_rendering.rst
+++ b/doc/source/visualizing/unstructured_mesh_rendering.rst
@@ -22,9 +22,9 @@
conda install -c http://use.yt/with_conda/ yt
-Alternatively, you can install yt from source using the ``install_script.sh``
-script. Be sure to set the INST_CONDA, INST_YT_SOURCE, INST_EMBREE,
-and INST_NETCDF4 flags to 1 at the top of the script. The ``install_script.sh``
+Alternatively, you can install yt from source using the ``install_script.sh``
+script. Be sure to set the ``INST_YT_SOURCE``, ``INST_EMBREE``, and
+``INST_NETCDF4`` flags to 1 at the top of the script. The ``install_script.sh``
script can be downloaded by doing:
.. code-block:: bash
diff -r 60a10fe93978952d4959283312badb40cd4f5a72 -r d856cd57100577863c14b5e87d936024c5ee84db tests/test_install_script.py
--- a/tests/test_install_script.py
+++ b/tests/test_install_script.py
@@ -1,6 +1,7 @@
import contextlib
import glob
import os
+import platform
import shutil
import subprocess
import sys
@@ -34,12 +35,6 @@
'rockstar'
]
-# dependencies that are only installable when yt is built from source under
-# conda
-YT_SOURCE_CONDA_ONLY_DEPS = [
- 'embree'
-]
-
DEPENDENCY_IMPORT_TESTS = {
'embree': "from yt.utilities.lib import mesh_traversal",
'rockstar': ("from yt.analysis_modules.halo_finding.rockstar "
@@ -56,7 +51,7 @@
except subprocess.CalledProcessError as er:
raise RuntimeError(
'Command \'%s\' failed with return code \'%s\' and error:\n\n%s' %
- (command, er.returncode, er.output))
+ (command, er.returncode, er.output.decode('utf-8')))
finally:
if len(output.splitlines()) > 25:
print ('truncated output:')
@@ -80,10 +75,9 @@
shutil.rmtree(path)
-def run_install_script(install_script_path, inst_py3,
- conda=False, binary_yt=False):
- msg = 'Testing installation with conda={}, inst_py3={}, and binary_yt={}'
- print (msg.format(conda, inst_py3, binary_yt))
+def run_install_script(install_script_path, inst_py3, binary_yt=False):
+ msg = 'Testing installation with inst_py3={} and binary_yt={}'
+ print (msg.format(inst_py3, binary_yt))
shutil.copy(install_script_path, os.curdir)
with open('install_script.sh', 'r') as source:
with open('install_script_edited.sh', 'w') as target:
@@ -91,14 +85,14 @@
for dep in OPTIONAL_DEPS:
if binary_yt is True and dep in YT_SOURCE_ONLY_DEPS:
continue
- if conda is False and dep in YT_SOURCE_CONDA_ONLY_DEPS:
- continue
+ if dep == 'rockstar':
+ # compiling rockstar is broken on newer MacOS releases
+ if platform.mac_ver()[0].startswith(('10.12', '10.13')):
+ continue
dname = 'INST_%s' % dep.upper()
data = data.replace(dname + '=0', dname + '=1')
if inst_py3 is True:
data = data.replace('INST_PY3=0', 'INST_PY3=1')
- if conda is False:
- data = data.replace('INST_CONDA=1', 'INST_CONDA=0')
if binary_yt is False:
data = data.replace('INST_YT_SOURCE=0', 'INST_YT_SOURCE=1')
target.write(data)
@@ -106,7 +100,7 @@
call_unix_command('bash install_script.sh --yes')
-def verify_yt_installation(binary_yt, conda):
+def verify_yt_installation(binary_yt):
yt_dir = glob.glob('yt-*')
ndirs = len(yt_dir)
if ndirs != 1:
@@ -117,14 +111,15 @@
for dep in OPTIONAL_DEPS + REQUIRED_DEPS:
if binary_yt is True and dep in YT_SOURCE_ONLY_DEPS:
continue
- if conda is False and dep in YT_SOURCE_CONDA_ONLY_DEPS:
- continue
if dep == 'git':
git_path = os.sep.join([yt_dir, 'bin', 'git'])
call_unix_command('{} --version'.format(git_path))
if dep in DEPENDENCY_IMPORT_TESTS:
cmd = "{} -c '{}'"
if dep == 'rockstar':
+ # compiling rockstar is broken on newer MacOS releases
+ if platform.mac_ver()[0].startswith(('10.12', '10.13')):
+ continue
cmd = 'LD_LIBRARY_PATH={} '.format(
os.sep.join([os.curdir, yt_dir, 'lib'])) + cmd
if sys.platform == 'darwin':
@@ -142,20 +137,10 @@
for inst_py3 in [False, True]:
tmpdir = tempfile.mkdtemp()
with working_directory(tmpdir):
- run_install_script(
- install_script_path, inst_py3, conda=True, binary_yt=True)
- conda_binary_path = verify_yt_installation(
- binary_yt=True, conda=True)
+ run_install_script(install_script_path, inst_py3, binary_yt=True)
+ conda_binary_path = verify_yt_installation(binary_yt=True)
shutil.rmtree(conda_binary_path)
- run_install_script(
- install_script_path, inst_py3, conda=True, binary_yt=False)
- conda_source_path = verify_yt_installation(
- binary_yt=False, conda=True)
+ run_install_script(install_script_path, inst_py3, binary_yt=False)
+ conda_source_path = verify_yt_installation(binary_yt=False)
shutil.rmtree(conda_source_path)
-
- run_install_script(
- install_script_path, inst_py3, conda=False, binary_yt=False)
- source_path = verify_yt_installation(
- binary_yt=False, conda=False)
- shutil.rmtree(source_path)
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/yt_analysis/yt/commits/a9a8acacb9cf/
Changeset: a9a8acacb9cf
User: ngoldbaum
Date: 2017-06-20 23:34:53+00:00
Summary: removing mentions of 'yt update --all' from docs
Affected #: 3 files
diff -r d856cd57100577863c14b5e87d936024c5ee84db -r a9a8acacb9cfe7bacac3dd127ac63f08234b93b9 doc/source/faq/index.rst
--- a/doc/source/faq/index.rst
+++ b/doc/source/faq/index.rst
@@ -28,25 +28,16 @@
$ yt version
yt module located at:
- /Users/username/src/yt-x86_64/src/yt-hg
- The supplemental repositories are located at:
- /Users/username/src/yt-x86_64/src/yt-supplemental
+ /Users/username/src/yt-conda/src/yt-git
- The current version and changeset for the code is:
+ The current version of yt is:
---
- Version = 2.7-dev
- Changeset = 6bffc737a67a
+ Version = 3.4-dev
+ Changeset = 94033fca00e5
---
This installation CAN be automatically updated.
- yt dependencies were last updated on
- Wed Dec 4 15:47:40 MST 2013
-
- To update all dependencies, run "yt update --all".
-
-If the changeset is displayed followed by a "+", it means you have made
-modifications to the code since the last changeset.
For more information on this topic, see :ref:`updating-yt`.
diff -r d856cd57100577863c14b5e87d936024c5ee84db -r a9a8acacb9cfe7bacac3dd127ac63f08234b93b9 doc/source/help/index.rst
--- a/doc/source/help/index.rst
+++ b/doc/source/help/index.rst
@@ -36,19 +36,24 @@
Sometimes the pace of development is pretty fast on yt, particularly in the
development branch, so a fix to your problem may have already been developed
by the time you encounter it. Many users' problems can simply be corrected
-by updating to the latest version of the code and/or its dependencies. You
-can update yt's source by running:
+by updating to the latest version of the code and/or its dependencies. If you
+have installed the latest stable release of yt then you should update yt using
+the package manager appropriate for your python installation. For example, with
+``pip``::
+
+ $ pip install -U yt
+
+Or with conda::
+
+ $ conda update yt
+
+If you installed yt from a checkout of the git repository, you can update to
+the latest development version by issuing the following command:
.. code-block:: bash
$ yt update
-or you could update yt's source as well as any software dependencies by running:
-
-.. code-block:: bash
-
- $ yt update --all
-
.. _update-errors:
Update errors
diff -r d856cd57100577863c14b5e87d936024c5ee84db -r a9a8acacb9cfe7bacac3dd127ac63f08234b93b9 doc/source/yt3differences.rst
--- a/doc/source/yt3differences.rst
+++ b/doc/source/yt3differences.rst
@@ -24,7 +24,7 @@
.. code-block:: bash
- $ yt update --all
+ $ yt update
This will update yt to the most recent version and rebuild the source base.
If you installed using the installer script, it will assure you have all of the
https://bitbucket.org/yt_analysis/yt/commits/272125cbb417/
Changeset: 272125cbb417
User: jzuhone
Date: 2017-06-27 18:00:20+00:00
Summary: Merge pull request #1461 from ngoldbaum/rm-inst-conda-0
Remove INST_CONDA option from install script
Affected #: 8 files
diff -r fc58054806fe06993c0fc585939e8fd48552c117 -r 272125cbb417b446f20fec4d38e3c1e4efa54375 doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -13,62 +13,23 @@
# If you do not have a working compiler environment, use the following
# configuration:
-INST_CONDA=1 # Should yt's dependencies be installed using miniconda?
INST_YT_SOURCE=0 # Should yt itself be installed from source?
-# If you want to install yt's dependencies using conda but want to build yt
-# itself from source, use the following configuration:
-
-# INST_CONDA=1
-# INST_YT_SOURCE=1
-
-# If you would like to build yt and all dependencies from source, then
-# use the following configuration by uncommenting the lines below.
-# NOTE: Building yt's dependencies from source will cause the install script
-# to require substantially more time to finish.
-
-# INST_CONDA=0
-# INST_YT_SOURCE=1
-
-BRANCH="master" # This is the branch we will install from for source installs
-
# What follows are some other options that you may or may not need to change.
-# Here's where you put the HDF5 path if you like; otherwise it'll download it
-# and install it on its own
-#HDF5_DIR=
-
-# If you've got yt some other place, set this to point to it. The script will
-# already check the current directory and the one above it in the tree.
+# If you've got a clone of the yt repository some other place, set this to
+# point to it. The script will already check the current directory and the one
+# above it in the tree.
YT_DIR=""
# These options can be set to customize the installation.
-INST_PY3=1 # Install Python 3 instead of Python 2. If this is turned
- # on, all Python packages (including yt) will be installed
- # in Python 3.
-INST_GIT=1 # Install git or not? If git is not already installed, yt
- # cannot be installed from source. Ignored if INST_CONDA=0
-INST_HG=0 # Install Mercurial or not? Ignored if INST_CONDA=0.
-INST_EMBREE=0 # Install dependencies needed for Embree-accelerated
- # ray tracing
-
-# These options control whether low-level system libraries are installed
-# they are necessary for building yt's dependencies from source and are
-# ignored when INST_CONDA=1
-
-INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with
- # the system zlib, which is compiled statically.
- # If need be, you can turn this off.
-INST_BZLIB=1 # On some systems, libbzip2 is missing. This can
- # lead to broken mercurial installations.
-INST_PNG=1 # Install a local libpng? Same things apply as with zlib.
-INST_FTYPE=1 # Install FreeType2 locally?
-INST_SQLITE3=1 # Install a local version of SQLite3?
-INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings?
-
-# These variables control whether optional dependencies are installed
-
+INST_PY3=1 # Install Python 3 instead of Python 2. If this is turned on,
+ # all Python packages (including yt) will be installed
+ # in Python 3.
+INST_GIT=1 # Install git or not? If git is not already installed, yt
+ # cannot be installed from source.
+INST_EMBREE=0 # Install dependencies needed for Embree-accelerated ray tracing
INST_PYX=0 # Install PyX? Sometimes PyX can be problematic without a
# working TeX installation.
INST_ROCKSTAR=0 # Install the Rockstar halo finder?
@@ -77,83 +38,47 @@
INST_ASTROPY=0 # Install astropy?
INST_NOSE=1 # Install nose?
INST_NETCDF4=1 # Install netcdf4 and its python bindings?
-
-# These options allow you to customize the builds of yt dependencies.
-# They are only used if INST_CONDA=0.
-
-# If you need to pass anything to the matplotlib build, do so here.
-MPL_SUPP_LDFLAGS=""
-MPL_SUPP_CFLAGS=""
-MPL_SUPP_CXXFLAGS=""
+INST_HG=0 # Install Mercurial or not?
-# If you need to supply arguments to the NumPy or SciPy build, supply them here
-# This one turns on gfortran manually:
-#NUMPY_ARGS="--fcompiler=gnu95"
-# If you absolutely can't get the fortran to work, try this:
-#NUMPY_ARGS="--fcompiler=fake"
+# This is the branch we will install from for INST_YT_SOURCE=1
+BRANCH="master"
-# If you want to spawn multiple Make jobs, here's the place to set the
-# arguments. For instance, "-j4"
-MAKE_PROCS=""
-
-# These variables control which miniconda version and yt recipe are used
-# when INST_CONDA=1.
+# These variables control which miniconda version is used
MINICONDA_URLBASE="http://repo.continuum.io/miniconda"
MINICONDA_VERSION="latest"
-if [ ${REINST_YT} ] && [ ${REINST_YT} -eq 1 ] && [ -n ${YT_DEST} ]
+if [ ! -z "${CONDA_DEFAULT_ENV}" ]
then
- DEST_DIR=${YT_DEST}
- INST_CONDA=0
+ echo "Aborting the yt installation because you appear to already"
+ echo "have a conda environment activated. Either deactivate it with:"
+ echo
+ echo " $ source deactivate"
+ echo
+ echo "or install yt into your current environment with:"
+ echo
+ echo " $ conda install -c conda-forge yt"
+ echo
+ exit 1
fi
-
-if [ $INST_CONDA -ne 0 ]
+DEST_SUFFIX="yt-conda"
+if [ -n "${PYTHONPATH}" ]
then
- if [ ! -z "${CONDA_DEFAULT_ENV}" ]
- then
- echo "Aborting the yt installation because you appear to already"
- echo "have a conda environment activated. Either deactivate it with:"
- echo
- echo " $ source deactivate"
- echo
- echo "or install yt into your current environment with:"
- echo
- echo " $ conda install -c conda-forge yt"
- echo
- exit 1
- fi
- DEST_SUFFIX="yt-conda"
- if [ -n "${PYTHONPATH}" ]
- then
- echo "WARNING WARNING WARNING WARNING WARNING WARNING WARNING"
- echo "*******************************************************"
- echo
- echo "The PYTHONPATH environment variable is set to:"
- echo
- echo " $PYTHONPATH"
- echo
- echo "If dependencies of yt (numpy, scipy, matplotlib) are installed"
- echo "to this path, this may cause issues. Exit the install script"
- echo "with Ctrl-C and unset PYTHONPATH if you are unsure."
- echo "Hit enter to continue."
- echo
- echo "WARNING WARNING WARNING WARNING WARNING WARNING WARNING"
- echo "*******************************************************"
- read -p "[hit enter]"
- fi
-else
- if [ $INST_YT_SOURCE -eq 0 ]
- then
- echo "yt must be compiled from source if INST_CONDA is set to 0"
- echo "Please set INST_YT_SOURCE to 1 and re-run."
- exit 1
- fi
- if [ $INST_GIT -eq 1 ]
- then
- INST_GIT=0
- fi
- DEST_SUFFIX="yt-`uname -m`"
+ echo "WARNING WARNING WARNING WARNING WARNING WARNING WARNING"
+ echo "*******************************************************"
+ echo
+ echo "The PYTHONPATH environment variable is set to:"
+ echo
+ echo " $PYTHONPATH"
+ echo
+ echo "If dependencies of yt (numpy, scipy, matplotlib) are installed"
+ echo "to this path, this may cause issues. Exit the install script"
+ echo "with Ctrl-C and unset PYTHONPATH if you are unsure."
+ echo "Hit enter to continue."
+ echo
+ echo "WARNING WARNING WARNING WARNING WARNING WARNING WARNING"
+ echo "*******************************************************"
+ read -p "[hit enter]"
fi
if [ -z "${DEST_DIR}" ]
@@ -204,31 +129,18 @@
function write_config
{
CONFIG_FILE=${DEST_DIR}/.yt_config
-
- echo INST_GIT=${INST_GIT} > ${CONFIG_FILE}
- echo INST_ZLIB=${INST_ZLIB} >> ${CONFIG_FILE}
- echo INST_BZLIB=${INST_BZLIB} >> ${CONFIG_FILE}
- echo INST_PNG=${INST_PNG} >> ${CONFIG_FILE}
- echo INST_FTYPE=${INST_FTYPE} >> ${CONFIG_FILE}
- echo INST_SQLITE3=${INST_SQLITE3} >> ${CONFIG_FILE}
+ echo INST_YT_SOURCE=${INST_YT_SOURCE} > ${CONFIG_FILE}
+ echo INST_GIT=${INST_GIT} >> ${CONFIG_FILE}
echo INST_PYX=${INST_PYX} >> ${CONFIG_FILE}
- echo INST_0MQ=${INST_0MQ} >> ${CONFIG_FILE}
echo INST_PY3=${INST_PY3} >> ${CONFIG_FILE}
echo INST_ROCKSTAR=${INST_ROCKSTAR} >> ${CONFIG_FILE}
echo INST_SCIPY=${INST_SCIPY} >> ${CONFIG_FILE}
+ echo INST_EMBREE=${INST_EMBREE} >> ${CONFIG_FILE}
+ echo INST_H5PY=${INST_H5PY} >> ${CONFIG_FILE}
+ echo INST_ASTROPY=${INST_ASTROPY} >> ${CONFIG_FILE}
+ echo INST_NOSE=${INST_NOSE} >> ${CONFIG_FILE}
+
echo YT_DIR=${YT_DIR} >> ${CONFIG_FILE}
- echo MPL_SUPP_LDFLAGS=${MPL_SUPP_LDFLAGS} >> ${CONFIG_FILE}
- echo MPL_SUPP_CFLAGS=${MPL_SUPP_CFLAGS} >> ${CONFIG_FILE}
- echo MPL_SUPP_CXXFLAGS=${MPL_SUPP_CXXFLAGS} >> ${CONFIG_FILE}
- echo MAKE_PROCS=${MAKE_PROCS} >> ${CONFIG_FILE}
- if [ ${HDF5_DIR} ]
- then
- echo ${HDF5_DIR} >> ${CONFIG_FILE}
- fi
- if [ ${NUMPY_ARGS} ]
- then
- echo ${NUMPY_ARGS} >> ${CONFIG_FILE}
- fi
}
function get_willwont
@@ -246,147 +158,22 @@
MYHOST=`hostname -s` # just give the short one, not FQDN
MYHOSTLONG=`hostname` # FQDN, for Ranger
MYOS=`uname -s` # A guess at the OS
- if [ "${MYHOST##kraken}" != "${MYHOST}" ]
- then
- echo "Looks like you're on Kraken."
- echo
- echo " ******************************************"
- echo " * It may be better to use the yt module! *"
- echo " * *"
- echo " * $ module load yt *"
- echo " * *"
- echo " ******************************************"
- echo
- echo "IF YOU CHOOSE TO PROCEED:"
- echo "YOU MUST BE IN THE GNU PROGRAMMING ENVIRONMENT"
- echo " $ module swap PrgEnv-pgi PrgEnv-gnu"
- echo
- return
- fi
- if [ "${MYHOST##nautilus}" != "${MYHOST}" ]
- then
- echo "Looks like you're on Nautilus."
- echo
- echo " ******************************************"
- echo " * It may be better to use the yt module! *"
- echo " * *"
- echo " * $ module load yt *"
- echo " * *"
- echo " ******************************************"
- echo
- echo "NOTE: YOU MUST BE IN THE GNU PROGRAMMING ENVIRONMENT"
- echo " $ module swap PE-intel PE-gnu"
- echo
- echo "Additionally, note that by default, yt will OVERWRITE"
- echo "any existing installations from Kraken! You might want"
- echo "to adjust the variable DEST_SUFFIX in the install script."
- echo
- return
- fi
- if [ "${MYHOST##verne}" != "${MYHOST}" ]
- then
- echo "Looks like you're on Verne."
- echo
- echo "NOTE: YOU MUST BE IN THE GNU PROGRAMMING ENVIRONMENT"
- echo "This command will take care of that for you:"
- echo
- echo " $ module swap PE-pgi PE-gnu"
- echo
- fi
- if [ "${MYHOST##steele}" != "${MYHOST}" ]
- then
- echo "Looks like you're on Steele."
- echo
- echo "NOTE: YOU MUST BE IN THE GNU PROGRAMMING ENVIRONMENT"
- echo "These commands should take care of that for you:"
- echo
- echo " $ module purge"
- echo " $ module load gcc"
- echo
- fi
- if [ "${MYHOST##midway}" != "${MYHOST}" ]
- then
- echo "Looks like you're on Midway."
- echo
- echo " ******************************************"
- echo " * It may be better to use the yt module! *"
- echo " * *"
- echo " * $ module load yt *"
- echo " * *"
- echo " ******************************************"
- echo
- return
- fi
if [ "${MYOS##Darwin}" != "${MYOS}" ]
then
- echo "Looks like you're running on Mac OSX."
+ echo "Looks like you're running on MacOS."
echo
echo "NOTE: you must have the Xcode command line tools installed."
echo
- echo "The instructions for obtaining these tools varies according"
- echo "to your exact OS version. On older versions of OS X, you"
- echo "must register for an account on the apple developer tools"
- echo "website: https://developer.apple.com/downloads to obtain the"
- echo "download link."
- echo
- echo "We have gathered some additional instructions for each"
- echo "version of OS X below. If you have trouble installing yt"
- echo "after following these instructions, don't hesitate to contact"
- echo "the yt user's e-mail list."
- echo
- echo "You can see which version of OSX you are running by clicking"
- echo "'About This Mac' in the apple menu on the left hand side of"
- echo "menu bar. We're assuming that you've installed all operating"
- echo "system updates; if you have an older version, we suggest"
- echo "running software update and installing all available updates."
- echo
- echo "OS X 10.5.8: search for and download Xcode 3.1.4 from the"
- echo "Apple developer tools website."
- echo
- echo "OS X 10.6.8: search for and download Xcode 3.2 from the Apple"
- echo "developer tools website. You can either download the"
- echo "Xcode 3.2.2 Developer Tools package (744 MB) and then use"
- echo "Software Update to update to XCode 3.2.6 or"
- echo "alternatively, you can download the Xcode 3.2.6/iOS SDK"
- echo "bundle (4.1 GB)."
- echo
- echo "OS X 10.7.5: download Xcode 4.2 from the mac app store"
- echo "(search for Xcode)."
- echo "Alternatively, download the Xcode command line tools from"
- echo "the Apple developer tools website."
- echo
- echo "OS X 10.8.4, 10.9, 10.10, and 10.11:"
- echo "download the appropriate version of Xcode from the"
- echo "mac app store (search for Xcode)."
+ echo "Download the appropriate version of Xcode from the"
+ echo "Mac App Store (search for Xcode)."
echo
echo "Additionally, you will have to manually install the Xcode"
echo "command line tools."
echo
- echo "For OS X 10.8, see:"
- echo "http://stackoverflow.com/questions/9353444"
- echo
- echo "For OS X 10.9 and newer the command line tools can be installed"
+ echo "For MacOS 10.10 and newer the command line tools can be installed"
echo "with the following command:"
echo " xcode-select --install"
echo
- if [ $INST_CONDA -eq 0 ]
- then
- echo "For OS X 10.11, you will additionally need to install the"
- echo "OpenSSL library using a package manager like homebrew or"
- echo "macports."
- echo
- echo "If your install fails with a message like"
- echo " ImportError: cannot import HTTPSHandler"
- echo "then you do not have the OpenSSL headers available in a"
- echo "location visible to your C compiler. Consider setting"
- echo "INST_CONDA=1 instead, as conda's python bundles OpenSSL."
- fi
- OSX_VERSION=`sw_vers -productVersion`
- if [ "${OSX_VERSION##10.8}" != "${OSX_VERSION}" ]
- then
- MPL_SUPP_CFLAGS="${MPL_SUPP_CFLAGS} -mmacosx-version-min=10.7"
- MPL_SUPP_CXXFLAGS="${MPL_SUPP_CXXFLAGS} -mmacosx-version-min=10.7"
- fi
fi
if [ -f /etc/redhat-release ]
then
@@ -462,31 +249,6 @@
echo " to avoid conflicts with other command-line programs "
echo " (like eog and evince, for example)."
fi
- if [ $INST_SCIPY -eq 1 ]
- then
- echo
- echo "Looks like you've requested that the install script build SciPy."
- echo
- echo "If the SciPy build fails, please uncomment one of the the lines"
- echo "at the top of the install script that sets NUMPY_ARGS, delete"
- echo "any broken installation tree, and re-run the install script"
- echo "verbatim."
- echo
- echo "If that doesn't work, don't hesitate to ask for help on the yt"
- echo "user's mailing list."
- echo
- fi
- if [ ! -z "${CFLAGS}" ]
- then
- echo "******************************************"
- echo "******************************************"
- echo "** **"
- echo "** Your CFLAGS is not empty. **"
- echo "** This can break h5py compilation. **"
- echo "** **"
- echo "******************************************"
- echo "******************************************"
- fi
}
function log_cmd
@@ -506,11 +268,6 @@
echo "Please set INST_YT_SOURCE to 1 and re-run the install script."
exit 1
fi
- if [ $INST_CONDA -eq 0 ]
- then
- echo "Embree support has not yet been implemented for INST_CONDA=0."
- exit 1
- fi
if [ `uname` = "Darwin" ]
then
EMBREE="embree-2.8.0.x86_64.macosx"
@@ -538,17 +295,6 @@
fi
fi
-if [ $INST_NETCDF4 -ne 0 ]
-then
- if [ $INST_CONDA -eq 0 ]
- then
- echo "This script can only install netcdf4 through conda."
- echo "Please set INST_CONDA to 1 to install netcdf4"
- echo "Setting INST_NETCDF4=0"
- INST_NETCDF4=0
- fi
-fi
-
echo
echo
echo "========================================================================"
@@ -562,10 +308,6 @@
echo "the script if you aren't such a fan."
echo
-printf "%-18s = %s so I " "INST_CONDA" "${INST_CONDA}"
-get_willwont ${INST_CONDA}
-echo "be installing a conda-based python environment"
-
printf "%-18s = %s so I " "INST_YT_SOURCE" "${INST_YT_SOURCE}"
get_willwont ${INST_YT_SOURCE}
echo "be compiling yt from source"
@@ -582,29 +324,6 @@
get_willwont ${INST_EMBREE}
echo "be installing Embree"
-if [ $INST_CONDA -eq 0 ]
-then
- printf "%-18s = %s so I " "INST_ZLIB" "${INST_ZLIB}"
- get_willwont ${INST_ZLIB}
- echo "be installing zlib"
-
- printf "%-18s = %s so I " "INST_BZLIB" "${INST_BZLIB}"
- get_willwont ${INST_BZLIB}
- echo "be installing bzlib"
-
- printf "%-18s = %s so I " "INST_PNG" "${INST_PNG}"
- get_willwont ${INST_PNG}
- echo "be installing libpng"
-
- printf "%-18s = %s so I " "INST_FTYPE" "${INST_FTYPE}"
- get_willwont ${INST_FTYPE}
- echo "be installing freetype2"
-
- printf "%-18s = %s so I " "INST_SQLITE3" "${INST_SQLITE3}"
- get_willwont ${INST_SQLITE3}
- echo "be installing SQLite3"
-fi
-
printf "%-18s = %s so I " "INST_PYX" "${INST_PYX}"
get_willwont ${INST_PYX}
echo "be installing PyX"
@@ -627,16 +346,6 @@
echo
-if [ $INST_CONDA -eq 0 ]
-then
- if [ -z "$HDF5_DIR" ]
- then
- echo "HDF5_DIR is not set, so I will be installing HDF5"
- else
- echo "HDF5_DIR=${HDF5_DIR} , so I will not be installing HDF5"
- fi
-fi
-
echo
echo "Installation will be to"
echo " ${DEST_DIR}"
@@ -654,21 +363,13 @@
host_specific
fi
-if [ $INST_CONDA -eq 0 ]
-then
- if [ ${USED_CONFIG} ]
- then
- echo "Settings were loaded from ${CONFIG_FILE}."
- echo "Remove this file if you wish to return to the default settings."
- echo
- fi
-fi
-echo "========================================================================"
echo
+
if [[ $1 != "--yes" ]]
then
read -p "[hit enter] "
fi
+
echo
echo "Awesome! Here we go."
echo
@@ -694,49 +395,6 @@
PYTHON_EXEC='python2.7'
fi
-function do_setup_py
-{
- [ -e $1/done ] && return
- LIB=$1
- shift
- if [ -z "$@" ]
- then
- echo "Installing $LIB"
- else
- echo "Installing $LIB (arguments: '$@')"
- fi
- [ ! -e $LIB/extracted ] && tar xfz $LIB.tar.gz
- touch $LIB/extracted
- BUILD_ARGS=""
- PYEXE=${PYTHON_EXEC}
- case $LIB in
- *h5py*)
- pushd $LIB &> /dev/null
- ( ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py configure --hdf5=${HDF5_DIR} 2>&1 ) 1>> ${LOG_FILE} || do_exit
- popd &> /dev/null
- ;;
- *numpy*)
- if [ -e ${DEST_DIR}/lib/${PYTHON_EXEC}/site-packages/numpy/__init__.py ]
- then
- VER=$(${DEST_DIR}/bin/${PYTHON_EXEC} -c 'from distutils.version import StrictVersion as SV; \
- import numpy; print SV(numpy.__version__) < SV("1.8.0")')
- if [ $VER == "True" ]
- then
- echo "Removing previous NumPy instance (see issue #889)"
- rm -rf ${DEST_DIR}/lib/${PYTHON_EXEC}/site-packages/{numpy*,*.pth}
- fi
- fi
- ;;
- *)
- ;;
- esac
- cd $LIB
- ( ${DEST_DIR}/bin/${PYEXE} setup.py build ${BUILD_ARGS} $* 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( ${DEST_DIR}/bin/${PYEXE} setup.py install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
-}
-
if type -P curl &>/dev/null
then
echo "Using curl"
@@ -746,40 +404,6 @@
export GETFILE="wget -nv"
fi
-if type -P sha512sum &> /dev/null
-then
- echo "Using sha512sum"
- export SHASUM="sha512sum"
-elif type -P shasum &> /dev/null
-then
- echo "Using shasum -a 512"
- export SHASUM="shasum -a 512"
-else
- echo
- echo "I am unable to locate any shasum-like utility."
- echo "ALL FILE INTEGRITY IS NOT VERIFIABLE."
- echo "THIS IS PROBABLY A BIG DEAL."
- echo
- echo "(I'll hang out for a minute for you to consider this.)"
- sleep 60
-fi
-
-function get_ytproject
-{
- [ -e $1 ] && return
- echo "Downloading $1 from yt-project.org"
- ${GETFILE} "http://yt-project.org/dependencies/$1" || do_exit
- ( ${SHASUM} -c $1.sha512 2>&1 ) 1>> ${LOG_FILE} || do_exit
-}
-
-function get_ytdata
-{
- echo "Downloading $1 from yt-project.org"
- [ -e $1 ] && return
- ${GETFILE} "http://yt-project.org/data/$1" || do_exit
- ( ${SHASUM} -c $1.sha512 2>&1 ) 1>> ${LOG_FILE} || do_exit
-}
-
function test_install
{
echo "Testing that yt can be imported"
@@ -788,298 +412,206 @@
ORIG_PWD=`pwd`
-if [ -z "${DEST_DIR}" ]
+MYARCH=`uname -m`
+MYOS=`uname -s`
+
+if [ $MYOS = "Darwin" ]
+then
+ MINICONDA_OS="MacOSX"
+ MINICONDA_ARCH="x86_64"
+elif [ $MYOS = "Linux" ]
then
- echo "Edit this script, set the DEST_DIR parameter and re-run."
+ MINICONDA_OS="Linux"
+ if [ $MYARCH = "i386" ]
+ then
+ MINICONDA_ARCH="x86"
+ elif [ $MYARCH = "i686" ]
+ then
+ MINICONDA_ARCH="x86"
+ elif [ $MYARCH = "x86_64" ]
+ then
+ MINICONDA_ARCH="x86_64"
+ else
+ echo "Not sure which architecture you are running."
+ echo "Going with x86_64 architecture."
+ MINICONDA_OS="Linux-x86_64"
+ fi
+else
+ echo "The yt install script is not supported on the ${MYOS}"
+ echo "operating system."
exit 1
fi
-# Set paths to what they should be when yt is activated.
-if [ $INST_CONDA -eq 0 ]
+if [ $INST_PY3 -eq 1 ]
then
- export PATH=${DEST_DIR}/bin:$PATH
- export LD_LIBRARY_PATH=${DEST_DIR}/lib:$LD_LIBRARY_PATH
- export PYTHONPATH=${DEST_DIR}/lib/${PYTHON_EXEC}/site-packages
+ PY_VERSION='3'
+else
+ PY_VERSION='2'
+fi
+
+MINICONDA_PKG="Miniconda${PY_VERSION}-${MINICONDA_VERSION}-${MINICONDA_OS}-${MINICONDA_ARCH}.sh"
- # Write config settings to file.
- CONFIG_FILE=${DEST_DIR}/.yt_config
- mkdir -p ${DEST_DIR}
- if [ -z ${REINST_YT} ] || [ ${REINST_YT} -neq 1 ]
- then
- write_config
- elif [ ${REINST_YT} ] && [ ${REINST_YT} -eq 1 ] && [ -f ${CONFIG_FILE} ]
- then
- USED_CONFIG=1
- source ${CONFIG_FILE}
- fi
-
- # Get supplemental data.
+echo
+echo "Downloading ${MINICONDA_URLBASE}/${MINICONDA_PKG}"
+echo
- mkdir -p ${DEST_DIR}/data
- cd ${DEST_DIR}/data
- echo 'de6d8c6ea849f0206d219303329a0276b3cce7c051eec34377d42aacbe0a4f47ac5145eb08966a338ecddd2b83c8f787ca9956508ad5c39ee2088ad875166410 cloudy_emissivity.h5' > cloudy_emissivity.h5.sha512
- [ ! -e cloudy_emissivity.h5 ] && get_ytdata cloudy_emissivity.h5
- echo '0f714ae2eace0141b1381abf1160dc8f8a521335e886f99919caf3beb31df1fe271d67c7b2a804b1467949eb16b0ef87a3d53abad0e8160fccac1e90d8d9e85f apec_emissivity.h5' > apec_emissivity.h5.sha512
- [ ! -e apec_emissivity.h5 ] && get_ytdata apec_emissivity.h5
-
- mkdir -p ${DEST_DIR}/src
- cd ${DEST_DIR}/src
+if [ -f ${MINICONDA_PKG} ]
+then
+ rm $MINICONDA_PKG
+fi
- PYTHON2='Python-2.7.11'
- PYTHON3='Python-3.5.1'
- CYTHON='Cython-0.23.5'
- if [ $INST_PY3 -eq 0 ]
- then
- PYX='PyX-0.12.1'
- else
- PYX='PyX-0.14.1'
- fi
- BZLIB='bzip2-1.0.6'
- FREETYPE_VER='freetype-2.4.12'
- H5PY='h5py-2.5.0'
- HDF5='hdf5-1.8.14'
- LAPACK='lapack-3.4.2'
- PNG='libpng-1.6.3'
- MATPLOTLIB='matplotlib-1.5.1'
- NOSE='nose-1.3.7'
- NUMPY='numpy-1.11.0'
- GITPYTHON='GitPython-2.1.3'
- ROCKSTAR='rockstar-0.99.6'
- SCIPY='scipy-0.17.0'
- SQLITE='sqlite-autoconf-3071700'
- SYMPY='sympy-1.0'
- ZLIB='zlib-1.2.8'
- SETUPTOOLS='setuptools-20.6.7'
- ASTROPY='astropy-1.1.2'
-
- # Now we dump all our SHA512 files out.
- echo '9052d74bbd0c93757fd916939cc3c39eb1aba6c9692b48887ae577256bec64b39b1fd25b6c751e6c8fe723de4c0ddf9a1a207de39f75b0839500dfcdde69f925 Cython-0.23.5.tar.gz' > Cython-0.23.5.tar.gz.sha512
- if [ $INST_PY3 -eq 0 ]
- then
- echo '4941f5aa21aff3743546495fb073c10d2657ff42b2aff401903498638093d0e31e344cce778980f28a7170c6d29eab72ac074277b9d4088376e8692dc71e55c1 PyX-0.12.1.tar.gz' > PyX-0.12.1.tar.gz.sha512
- else
- echo '16265bbdcaf28ce194189a2987b32952f296c850b829454bcccce0abd23838bfca0276c3e9c8e96b8cbfaf1473bf14669f9b7f2032ee039b61ae59ea3aa45a20 PyX-0.14.1.tar.gz' > PyX-0.14.1.tar.gz.sha512
- fi
- echo 'f21df53da87e9e3c14599a34388976e7dd09b951dff3c4b978fe224beeff07e749c0059ffd94f68ca9b75ecaef142b285d579b8dfaad4eab85aca33957114937 Python-2.7.11.tgz' > Python-2.7.11.tgz.sha512
- echo '73f1477f3d3f5bd978c4ea1d1b679467b45e9fd2f443287b88c5c107a9ced580c56e0e8f33acea84e06b11a252e2a4e733120b721a9b6e1bb3d34493a3353bfb Python-3.5.1.tgz' > Python-3.5.1.tgz.sha512
- echo 'b83c4a1415a3eb8c016507705d0d2f22971e4da937bb97953eec08f8f856933d8fa76ce8c536122235b19e7879b16add2e20fd2fee3e488f9b2b4bf1b9f4dbdb astropy-1.1.2.tar.gz' > astropy-1.1.2.tar.gz.sha512
- echo '276bd9c061ec9a27d478b33078a86f93164ee2da72210e12e2c9da71dcffeb64767e4460b93f257302b09328eda8655e93c4b9ae85e74472869afbeae35ca71e blas.tar.gz' > blas.tar.gz.sha512
- echo '00ace5438cfa0c577e5f578d8a808613187eff5217c35164ffe044fbafdfec9e98f4192c02a7d67e01e5a5ccced630583ad1003c37697219b0f147343a3fdd12 bzip2-1.0.6.tar.gz' > bzip2-1.0.6.tar.gz.sha512
- echo '609a68a3675087e0cc95268574f31e104549daa48efe15a25a33b8e269a93b4bd160f4c3e8178dca9c950ef5ca514b039d6fd1b45db6af57f25342464d0429ce freetype-2.4.12.tar.gz' > freetype-2.4.12.tar.gz.sha512
- echo '4a83f9ae1855a7fad90133b327d426201c8ccfd2e7fbe9f39b2d61a2eee2f3ebe2ea02cf80f3d4e1ad659f8e790c173df8cc99b87d0b7ce63d34aa88cfdc7939 h5py-2.5.0.tar.gz' > h5py-2.5.0.tar.gz.sha512
- echo '4073fba510ccadaba41db0939f909613c9cb52ba8fb6c1062fc9118edc601394c75e102310be1af4077d07c9b327e6bbb1a6359939a7268dc140382d0c1e0199 hdf5-1.8.14.tar.gz' > hdf5-1.8.14.tar.gz.sha512
- echo '8770214491e31f0a7a3efaade90eee7b0eb20a8a6ab635c5f854d78263f59a1849133c14ef5123d01023f0110cbb9fc6f818da053c01277914ae81473430a952 lapack-3.4.2.tar.gz' > lapack-3.4.2.tar.gz.sha512
- echo '887582e5a22e4cde338aa8fec7a89f6dd31f2f02b8842735f00f970f64582333fa03401cea6d01704083403c7e8b7ebc26655468ce930165673b33efa4bcd586 libpng-1.6.3.tar.gz' > libpng-1.6.3.tar.gz.sha512
- echo 'a0e78b5027a3a49cf8e77dc0d26f5f380dcd80f7b309b6121199acd5e1d94f48482864a9eee3bd397f7ac6f07fe1d3c21bf517217df3c72e8e3d105b7c2ae58e matplotlib-1.5.1.tar.gz' > matplotlib-1.5.1.tar.gz.sha512
- echo 'e65c914f621f8da06b9ab11a0ff2763d6e29b82ce2aaed56da0e3773dc899d9deb1f20015789d44c65a5dad7214520f5b659b3f8d7695fb207ad3f78e5cf1b62 nose-1.3.7.tar.gz' > nose-1.3.7.tar.gz.sha512
- echo '92c1889397ad013e25da3a0657fc01e787d528fc19c29cc2acd286c3f07d41b984252583457b1b9259fc303afbe9694565cdcf5752eb4ecb950cc7a99ec1ad8b numpy-1.11.0.tar.gz' > numpy-1.11.0.tar.gz.sha512
- echo '918ff1765a85a818619165c2bcbb0d417f35c979c2f42f1bb7e41636696c0cb4d6837725f3655fbdfebea966476d1255ee18adabe9ed5536455b63336a1f399d GitPython-2.1.3.tar.gz' > GitPython-2.1.3.tar.gz.sha512
- echo 'de6409d75a3ff3cf1e5391d3b09126f0bc7e1a40a15f9bee244195638fe2f8481fca032896d8534623e6122ff59aaf669664e27ff89cf1b094a5ce7312f220b7 scipy-0.17.0.tar.gz' > scipy-0.17.0.tar.gz.sha512
- echo '96f3e51b46741450bc6b63779c10ebb4a7066860fe544385d64d1eda52592e376a589ef282ace2e1df73df61c10eab1a0d793abbdaf770e60289494d4bf3bcb4 sqlite-autoconf-3071700.tar.gz' > sqlite-autoconf-3071700.tar.gz.sha512
- echo '977db6e9bc6a5918cceb255981a57e85e7060c0922aefd2968b004d25d704e25a5cb5bbe09eb387e8695581e23e2825d9c40310068fe25ece7e9c23037a21f39 sympy-1.0.tar.gz' > sympy-1.0.tar.gz.sha512
- echo 'ece209d4c7ec0cb58ede791444dc754e0d10811cbbdebe3df61c0fd9f9f9867c1c3ccd5f1827f847c005e24eef34fb5bf87b5d3f894d75da04f1797538290e4a zlib-1.2.8.tar.gz' > zlib-1.2.8.tar.gz.sha512
- echo '91a212b5007f9fdfacb4341e06dc0355c5c29897eb8ea407dd4864091f845ba1417bb0d33b5ed6897869d0233e2d0ec6548898d3dbe9eda23f751829bd51a104 setuptools-20.6.7.tar.gz' > setuptools-20.6.7.tar.gz.sha512
- # Individual processes
- [ -z "$HDF5_DIR" ] && get_ytproject $HDF5.tar.gz
- [ $INST_ZLIB -eq 1 ] && get_ytproject $ZLIB.tar.gz
- [ $INST_BZLIB -eq 1 ] && get_ytproject $BZLIB.tar.gz
- [ $INST_PNG -eq 1 ] && get_ytproject $PNG.tar.gz
- [ $INST_FTYPE -eq 1 ] && get_ytproject $FREETYPE_VER.tar.gz
- [ $INST_SQLITE3 -eq 1 ] && get_ytproject $SQLITE.tar.gz
- [ $INST_PYX -eq 1 ] && get_ytproject $PYX.tar.gz
- [ $INST_SCIPY -eq 1 ] && get_ytproject $SCIPY.tar.gz
- [ $INST_SCIPY -eq 1 ] && get_ytproject blas.tar.gz
- [ $INST_SCIPY -eq 1 ] && get_ytproject $LAPACK.tar.gz
- if [ $INST_PY3 -eq 1 ]
- then
- get_ytproject $PYTHON3.tgz
- else
- get_ytproject $PYTHON2.tgz
- fi
- [ $INST_H5PY -eq 1 ] && get_ytproject $H5PY.tar.gz
- [ $INST_NOSE -eq 1 ] && get_ytproject $NOSE.tar.gz
- [ $INST_ASTROPY -eq 1 ] && get_ytproject $ASTROPY.tar.gz
- get_ytproject $NUMPY.tar.gz
- get_ytproject $MATPLOTLIB.tar.gz
- get_ytproject $CYTHON.tar.gz
- get_ytproject $GITPYTHON.tar.gz
- get_ytproject $SYMPY.tar.gz
- get_ytproject $SETUPTOOLS.tar.gz
+echo "Installing the Miniconda python environment."
+
+if [ -e ${DEST_DIR} ]
+then
+ rm -rf $DEST_DIR/*
+else
+ mkdir $DEST_DIR
+fi
- if [ $INST_BZLIB -eq 1 ]
- then
- if [ ! -e $BZLIB/done ]
- then
- [ ! -e $BZLIB ] && tar xfz $BZLIB.tar.gz
- echo "Installing BZLIB"
- cd $BZLIB
- if [ `uname` = "Darwin" ]
- then
- if [ -z "${CC}" ]
- then
- sed -i.bak 's/soname/install_name/' Makefile-libbz2_so
- else
- sed -i.bak -e 's/soname/install_name/' -e "s|CC=gcc|CC=${CC}|" Makefile-libbz2_so
- fi
- fi
- ( make install CFLAGS=-fPIC LDFLAGS=-fPIC PREFIX=${DEST_DIR} 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make -f Makefile-libbz2_so CFLAGS=-fPIC LDFLAGS=-fPIC PREFIX=${DEST_DIR} 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( cp -v libbz2.so.1.0.6 ${DEST_DIR}/lib 2>&1 ) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- BZLIB_DIR=${DEST_DIR}
- export LDFLAGS="${LDFLAGS} -L${BZLIB_DIR}/lib/ -L${BZLIB_DIR}/lib64/"
- LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BZLIB_DIR}/lib/"
- fi
+log_cmd ${GETFILE} ${MINICONDA_URLBASE}/${MINICONDA_PKG} || do_exit
+
+log_cmd bash ./${MINICONDA_PKG} -b -p $DEST_DIR -f
+
+# Need to set PATH so we use miniconda's python environment
+export PATH=${DEST_DIR}/bin:$PATH
+
+echo "Installing the necessary packages for yt."
+echo "This may take a while, but don't worry. yt loves you."
- if [ $INST_ZLIB -eq 1 ]
- then
- if [ ! -e $ZLIB/done ]
- then
- [ ! -e $ZLIB ] && tar xfz $ZLIB.tar.gz
- echo "Installing ZLIB"
- cd $ZLIB
- ( ./configure --shared --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make clean 2>&1 ) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- ZLIB_DIR=${DEST_DIR}
- export LDFLAGS="${LDFLAGS} -L${ZLIB_DIR}/lib/ -L${ZLIB_DIR}/lib64/"
- LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${ZLIB_DIR}/lib/"
- fi
-
- if [ $INST_PNG -eq 1 ]
- then
- if [ ! -e $PNG/done ]
- then
- [ ! -e $PNG ] && tar xfz $PNG.tar.gz
- echo "Installing PNG"
- cd $PNG
- ( ./configure CPPFLAGS=-I${DEST_DIR}/include CFLAGS=-I${DEST_DIR}/include --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- PNG_DIR=${DEST_DIR}
- export LDFLAGS="${LDFLAGS} -L${PNG_DIR}/lib/ -L${PNG_DIR}/lib64/"
- LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${PNG_DIR}/lib/"
- fi
-
- if [ $INST_FTYPE -eq 1 ]
- then
- if [ ! -e $FREETYPE_VER/done ]
- then
- [ ! -e $FREETYPE_VER ] && tar xfz $FREETYPE_VER.tar.gz
- echo "Installing FreeType2"
- cd $FREETYPE_VER
- ( ./configure CFLAGS=-I${DEST_DIR}/include --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- FTYPE_DIR=${DEST_DIR}
- export LDFLAGS="${LDFLAGS} -L${FTYPE_DIR}/lib/ -L${FTYPE_DIR}/lib64/"
- LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${FTYPE_DIR}/lib/"
- fi
+declare -a YT_DEPS
+YT_DEPS+=('python')
+YT_DEPS+=('setuptools')
+YT_DEPS+=('numpy')
+YT_DEPS+=('jupyter')
+YT_DEPS+=('ipython')
+YT_DEPS+=('sphinx')
+if [ ${INST_GIT} -eq 1 ]
+then
+ YT_DEPS+=('git')
+ YT_DEPS+=('gitpython')
+fi
+if [ $INST_H5PY -ne 0 ]
+then
+ YT_DEPS+=('h5py')
+fi
+YT_DEPS+=('matplotlib')
+YT_DEPS+=('cython')
+if [ $INST_NOSE -ne 0 ]
+then
+ YT_DEPS+=('nose')
+fi
+if [ $INST_SCIPY -ne 0 ]
+then
+ YT_DEPS+=('scipy')
+fi
+if [ $INST_ASTROPY -ne 0 ]
+then
+ YT_DEPS+=('astropy')
+fi
+YT_DEPS+=('conda-build')
+if [ $INST_PY3 -eq 0 ] && [ $INST_HG -eq 1 ]
+then
+ YT_DEPS+=('mercurial')
+fi
+YT_DEPS+=('sympy')
- if [ -z "$HDF5_DIR" ]
- then
- if [ ! -e $HDF5/done ]
- then
- [ ! -e $HDF5 ] && tar xfz $HDF5.tar.gz
- echo "Installing HDF5"
- cd $HDF5
- ( ./configure --prefix=${DEST_DIR}/ --enable-shared 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make ${MAKE_PROCS} install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- export HDF5_DIR=${DEST_DIR}
- else
- export HDF5_DIR=${HDF5_DIR}
- fi
- export HDF5_API=16
-
- if [ $INST_SQLITE3 -eq 1 ]
- then
- if [ ! -e $SQLITE/done ]
- then
- [ ! -e $SQLITE ] && tar xfz $SQLITE.tar.gz
- echo "Installing SQLite3"
- cd $SQLITE
- ( ./configure --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make ${MAKE_PROCS} install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- fi
+if [ $INST_NETCDF4 -eq 1 ]
+then
+ YT_DEPS+=('netcdf4')
+fi
- if [ $INST_PY3 -eq 1 ]
- then
- if [ ! -e $PYTHON3/done ]
- then
- echo "Installing Python 3"
- [ ! -e $PYTHON3 ] && tar xfz $PYTHON3.tgz
- cd $PYTHON3
- ( ./configure --prefix=${DEST_DIR}/ ${PYCONF_ARGS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
-
- ( make ${MAKE_PROCS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( ln -sf ${DEST_DIR}/bin/python3.5 ${DEST_DIR}/bin/pyyt 2>&1 ) 1>> ${LOG_FILE}
- ( ln -sf ${DEST_DIR}/bin/python3.5 ${DEST_DIR}/bin/python 2>&1 ) 1>> ${LOG_FILE}
- ( ln -sf ${DEST_DIR}/bin/python3-config ${DEST_DIR}/bin/python-config 2>&1 ) 1>> ${LOG_FILE}
- ( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- else
- if [ ! -e $PYTHON2/done ]
- then
- echo "Installing Python 2. This may take a while, but don't worry. yt loves you."
- [ ! -e $PYTHON2 ] && tar xfz $PYTHON2.tgz
- cd $PYTHON2
- ( ./configure --prefix=${DEST_DIR}/ ${PYCONF_ARGS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make ${MAKE_PROCS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( ln -sf ${DEST_DIR}/bin/python2.7 ${DEST_DIR}/bin/pyyt 2>&1 ) 1>> ${LOG_FILE}
- ( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- fi
+log_cmd ${DEST_DIR}/bin/conda update --yes conda
- ( ${DEST_DIR}/bin/python -c "import _ssl" 2>&1 ) 1>> ${LOG_FILE}
- RESULT=$?
- if [ $RESULT -ne 0 ]
- then
- echo "Unable to import the python SSL bindings."
- echo "This means that OpenSSL is not installed or your system's OpenSSL"
- echo "installation is out of date."
- echo "Please install OpenSSL or set INST_CONDA=1"
- do_exit
- fi
-
- export PYTHONPATH=${DEST_DIR}/lib/${PYTHON_EXEC}/site-packages/
-
- # Install setuptools
- do_setup_py $SETUPTOOLS
-
+if [ $INST_GIT -eq 1 ]
+then
+ GIT_EXE=${DEST_DIR}/bin/git
+else
if type -P git &>/dev/null
then
GIT_EXE="git"
else
- echo "Cannot find git. Please install git."
- do_exit
+ if [ $INST_YT_SOURCE -eq 1 ]
+ then
+ echo "Cannot find git. Please install git or set INST_GIT=1."
+ do_exit
+ fi
+ fi
+fi
+
+log_cmd echo "DEPENDENCIES" ${YT_DEPS[@]}
+for YT_DEP in "${YT_DEPS[@]}"; do
+ echo "Installing $YT_DEP"
+ log_cmd ${DEST_DIR}/bin/conda install -c conda-forge --yes ${YT_DEP}
+done
+
+if [ $INST_PY3 -eq 1 ] && [ $INST_HG -eq 1 ]
+then
+ echo "Installing mercurial"
+ log_cmd ${DEST_DIR}/bin/conda create -y -n py27 python=2.7 mercurial
+ log_cmd ln -s ${DEST_DIR}/envs/py27/bin/hg ${DEST_DIR}/bin
+fi
+
+if [ $INST_YT_SOURCE -eq 1 ]
+then
+ log_cmd ${GIT_EXE} clone https://github.com/yt-project/yt_conda ${DEST_DIR}/src/yt_conda
+fi
+
+if [ $INST_EMBREE -eq 1 ]
+then
+ echo "Installing Embree"
+ if [ ! -d ${DEST_DIR}/src ]
+ then
+ mkdir ${DEST_DIR}/src
fi
+ cd ${DEST_DIR}/src
+ ( ${GETFILE} "$EMBREE_URL" 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ log_cmd tar xfz ${EMBREE}.tar.gz
+ log_cmd mv ${DEST_DIR}/src/${EMBREE}/include/embree2 ${DEST_DIR}/include
+ log_cmd mv ${DEST_DIR}/src/${EMBREE}/lib/lib*.* ${DEST_DIR}/lib
+ if [ `uname` = "Darwin" ]
+ then
+ ln -s ${DEST_DIR}/lib/libembree.2.dylib ${DEST_DIR}/lib/libembree.dylib
+ install_name_tool -id ${DEST_DIR}/lib/libembree.2.dylib ${DEST_DIR}/lib/libembree.2.dylib
+ else
+ ln -s ${DEST_DIR}/lib/libembree.so.2 ${DEST_DIR}/lib/libembree.so
+ fi
+
+ echo "Installing pyembree from source"
+ ( ${GETFILE} "$PYEMBREE_URL" 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ log_cmd unzip ${DEST_DIR}/src/master.zip
+ pushd ${DEST_DIR}/src/pyembree-master &> /dev/null
+ log_cmd ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py install build_ext -I${DEST_DIR}/include -L${DEST_DIR}/lib
+ popd &> /dev/null
+fi
+if [ $INST_ROCKSTAR -eq 1 ]
+then
+ echo "Building Rockstar"
+ ( ${GIT_EXE} clone https://github.com/yt-project/rockstar ${DEST_DIR}/src/rockstar/ 2>&1 ) 1>> ${LOG_FILE}
+ ROCKSTAR_PACKAGE=$(${DEST_DIR}/bin/conda build ${DEST_DIR}/src/yt_conda/rockstar --output)
+ log_cmd ${DEST_DIR}/bin/conda build ${DEST_DIR}/src/yt_conda/rockstar
+ log_cmd ${DEST_DIR}/bin/conda install $ROCKSTAR_PACKAGE
+ ROCKSTAR_DIR=${DEST_DIR}/src/rockstar
+fi
+
+# conda doesn't package pyx, so we install manually with pip
+if [ $INST_PYX -eq 1 ]
+then
+ if [ $INST_PY3 -eq 1 ]
+ then
+ log_cmd ${DEST_DIR}/bin/pip install pyx
+ else
+ log_cmd ${DEST_DIR}/bin/pip install pyx==0.12.1
+ fi
+fi
+
+if [ $INST_YT_SOURCE -eq 0 ]
+then
+ echo "Installing yt"
+ log_cmd ${DEST_DIR}/bin/conda install -c conda-forge --yes yt
+else
+ echo "Building yt from source"
if [ -z "$YT_DIR" ]
then
if [ -e $ORIG_PWD/yt/mods.py ]
@@ -1088,512 +620,86 @@
elif [ -e $ORIG_PWD/../yt/mods.py ]
then
YT_DIR=$(dirname $ORIG_PWD)
- elif [ ! -e yt-git ]
- then
- echo "Cloning yt"
- YT_DIR="$PWD/yt-git/"
- ( ${GIT_EXE} clone https://github.com/yt-project/yt/ ${YT_DIR} 2>&1 ) 1>> ${LOG_FILE}
- elif [ -e yt-git ]
- then
- YT_DIR="$PWD/yt-git/"
+ else
+ YT_DIR="${DEST_DIR}/src/yt-git"
+ log_cmd ${GIT_EXE} clone https://github.com/yt-project/yt ${YT_DIR}
+ log_cmd ${GIT_EXE} -C ${YT_DIR} checkout ${BRANCH}
fi
echo Setting YT_DIR=${YT_DIR}
- fi
-
- # This fixes problems with gfortran linking.
- unset LDFLAGS
-
- echo "Installing pip"
- ( ${GETFILE} https://bootstrap.pypa.io/get-pip.py 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( ${DEST_DIR}/bin/${PYTHON_EXEC} get-pip.py 2>&1 ) 1>> ${LOG_FILE} || do_exit
-
- if [ $INST_SCIPY -eq 0 ]
- then
- do_setup_py $NUMPY ${NUMPY_ARGS}
else
- if [ ! -e $SCIPY/done ]
- then
- if [ ! -e BLAS/done ]
- then
- tar xfz blas.tar.gz
- echo "Building BLAS"
- cd BLAS
- gfortran -O2 -fPIC -fno-second-underscore -c *.f
- ( ar r libfblas.a *.o 2>&1 ) 1>> ${LOG_FILE}
- ( ranlib libfblas.a 2>&1 ) 1>> ${LOG_FILE}
- rm -rf *.o
- touch done
- cd ..
- fi
- if [ ! -e $LAPACK/done ]
- then
- tar xfz $LAPACK.tar.gz
- echo "Building LAPACK"
- cd $LAPACK/
- cp INSTALL/make.inc.gfortran make.inc
- ( make lapacklib OPTS="-fPIC -O2" NOOPT="-fPIC -O0" CFLAGS=-fPIC LDFLAGS=-fPIC 2>&1 ) 1>> ${LOG_FILE} || do_exit
- touch done
- cd ..
- fi
- fi
- export BLAS=$PWD/BLAS/libfblas.a
- export LAPACK=$PWD/$LAPACK/liblapack.a
- do_setup_py $NUMPY ${NUMPY_ARGS}
- do_setup_py $SCIPY ${NUMPY_ARGS}
- fi
-
- if [ -n "${MPL_SUPP_LDFLAGS}" ]
- then
- OLD_LDFLAGS=${LDFLAGS}
- export LDFLAGS="${MPL_SUPP_LDFLAGS}"
- echo "Setting LDFLAGS ${LDFLAGS}"
- fi
- if [ -n "${MPL_SUPP_CXXFLAGS}" ]
- then
- OLD_CXXFLAGS=${CXXFLAGS}
- export CXXFLAGS="${MPL_SUPP_CXXFLAGS}"
- echo "Setting CXXFLAGS ${CXXFLAGS}"
- fi
- if [ -n "${MPL_SUPP_CFLAGS}" ]
- then
- OLD_CFLAGS=${CFLAGS}
- export CFLAGS="${MPL_SUPP_CFLAGS}"
- echo "Setting CFLAGS ${CFLAGS}"
- fi
- # Now we set up the basedir for matplotlib:
- mkdir -p ${DEST_DIR}/src/$MATPLOTLIB
- echo "[directories]" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
- echo "basedirlist = ${DEST_DIR}" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
- if [ `uname` = "Darwin" ]
- then
- echo "[gui_support]" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
- echo "macosx = False" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
- fi
-
- _user_DISPLAY=$DISPLAY
- unset DISPLAY # see (yt-user link missing: "Installation failure" 01/29/15)
- do_setup_py $MATPLOTLIB
- export DISPLAY=${_user_DISPLAY}
- if [ -n "${OLD_LDFLAGS}" ]
- then
- export LDFLAG=${OLD_LDFLAGS}
- fi
- [ -n "${OLD_LDFLAGS}" ] && export LDFLAGS=${OLD_LDFLAGS}
- [ -n "${OLD_CXXFLAGS}" ] && export CXXFLAGS=${OLD_CXXFLAGS}
- [ -n "${OLD_CFLAGS}" ] && export CFLAGS=${OLD_CFLAGS}
-
- echo "Installing Jupyter"
- ( ${DEST_DIR}/bin/pip install "jupyter<2.0.0" 2>&1 ) 1>> ${LOG_FILE}
-
- do_setup_py $CYTHON
- if [ $INST_H5PY -eq 1 ]
- then
- do_setup_py $H5PY
- fi
- if [ $INST_NOSE -eq 1 ]
- then
- do_setup_py $NOSE
- fi
- if [ $INST_ASTROPY -eq 1 ]
- then
- do_setup_py $ASTROPY
- fi
- do_setup_py $GITPYTHON
- do_setup_py $SYMPY
- [ $INST_PYX -eq 1 ] && do_setup_py $PYX
-
- ( ${DEST_DIR}/bin/pip install jinja2 2>&1 ) 1>> ${LOG_FILE}
-
- # Now we build Rockstar and set its environment variable.
- if [ $INST_ROCKSTAR -eq 1 ]
- then
- if [ ! -e rockstar/done ]
- then
- echo "Building Rockstar"
- if [ ! -e rockstar ]
- then
- ( ${GIT_EXE} clone https://github.com/yt-project/rockstar 2>&1 ) 1>> ${LOG_FILE}
- fi
- cd rockstar
- ( make lib 2>&1 ) 1>> ${LOG_FILE} || do_exit
- cp librockstar.so ${DEST_DIR}/lib
- ROCKSTAR_DIR=${DEST_DIR}/src/rockstar
- echo $ROCKSTAR_DIR > ${YT_DIR}/rockstar.cfg
- touch done
- cd ..
- fi
- fi
-
- MY_PWD=`pwd`
- cd $YT_DIR
- ( ${GIT_EXE} pull 2>1 && ${GIT_EXE} checkout ${BRANCH} 2>&1 ) 1>> ${LOG_FILE}
-
- echo "Installing yt"
- [ $INST_PNG -eq 1 ] && echo $PNG_DIR > png.cfg
- ( export PATH=$DEST_DIR/bin:$PATH ; ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py develop 2>&1 ) 1>> ${LOG_FILE} || do_exit
- touch done
- cd $MY_PWD
-
- if !( ( ${DEST_DIR}/bin/${PYTHON_EXEC} -c "import readline" 2>&1 )>> ${LOG_FILE}) || \
- [[ "${MYOS##Darwin}" != "${MYOS}" && $INST_PY3 -eq 1 ]]
- then
- if !( ( ${DEST_DIR}/bin/${PYTHON_EXEC} -c "import gnureadline" 2>&1 )>> ${LOG_FILE})
+ if [ ! -e $YT_DIR/.git ]
then
- echo "Installing pure-python readline"
- ( ${DEST_DIR}/bin/pip install gnureadline 2>&1 ) 1>> ${LOG_FILE}
- fi
- fi
-
- if [ -e $HOME/.matplotlib/fontList.cache ] && \
- ( grep -q python2.6 $HOME/.matplotlib/fontList.cache )
- then
- echo "WARNING WARNING WARNING WARNING WARNING WARNING WARNING"
- echo "*******************************************************"
- echo
- echo " You likely need to remove your old fontList.cache!"
- echo " You can do this with this command:"
- echo ""
- echo " rm $HOME/.matplotlib/fontList.cache"
- echo
- echo "*******************************************************"
- fi
-
- # Add the environment scripts
- ( cp ${YT_DIR}/doc/activate ${DEST_DIR}/bin/activate 2>&1 ) 1>> ${LOG_FILE}
- sed -i.bak -e "s,__YT_DIR__,${DEST_DIR}," ${DEST_DIR}/bin/activate
- ( cp ${YT_DIR}/doc/activate.csh ${DEST_DIR}/bin/activate.csh 2>&1 ) 1>> ${LOG_FILE}
- sed -i.bak -e "s,__YT_DIR__,${DEST_DIR}," ${DEST_DIR}/bin/activate.csh
-
- test_install
-
- function print_afterword
- {
- echo
- echo
- echo "========================================================================"
- echo
- echo "yt is now installed in $DEST_DIR ."
- echo
- echo "To run from this new installation, use the activate script for this "
- echo "environment."
- echo
- echo " $ source $DEST_DIR/bin/activate"
- echo
- echo "This modifies the environment variables YT_DEST, PATH, PYTHONPATH, and"
- echo "LD_LIBRARY_PATH to match your new yt install. If you use csh, just"
- echo "append .csh to the above."
- echo
- echo "To get started with yt, check out the orientation:"
- echo
- echo " http://yt-project.org/doc/quickstart/"
- echo
- echo "The source for yt is located at:"
- echo " $YT_DIR"
- echo
- echo "For support, see the website and join the mailing list:"
- echo
- echo " http://yt-project.org/"
- echo " http://yt-project.org/data/ (Sample data)"
- echo " http://yt-project.org/doc/ (Docs)"
- echo
- echo " http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org"
- echo
- echo "========================================================================"
- echo
- echo "Oh, look at me, still talking when there's science to do!"
- echo "Good luck, and email the user list if you run into any problems."
- }
-
- print_afterword
- print_afterword >> ${LOG_FILE}
-
- echo "yt dependencies were last updated on" > ${DEST_DIR}/.yt_update
- date >> ${DEST_DIR}/.yt_update
-else # INST_CONDA -eq 1
- MYARCH=`uname -m` # A guess at the OS
- MYOS=`uname -s`
-
- if [ $MYOS = "Darwin" ]
- then
- MINICONDA_OS="MacOSX"
- MINICONDA_ARCH="x86_64"
- elif [ $MYOS = "Linux" ]
- then
- MINICONDA_OS="Linux"
- if [ $MYARCH = "i386" ]
- then
- MINICONDA_ARCH="x86"
- elif [ $MYARCH = "i686" ]
- then
- MINICONDA_ARCH="x86"
- elif [ $MYARCH = "x86_64" ]
- then
- MINICONDA_ARCH="x86_64"
- else
- echo "Not sure which architecture you are running."
- echo "Going with x86_64 architecture."
- MINICONDA_OS="Linux-x86_64"
- fi
- else
- echo "The yt install script is not supported on the ${MYOS}"
- echo "operating system."
- exit 1
- fi
-
- if [ $INST_PY3 -eq 1 ]
- then
- PY_VERSION='3'
- else
- PY_VERSION='2'
- fi
-
- MINICONDA_PKG="Miniconda${PY_VERSION}-${MINICONDA_VERSION}-${MINICONDA_OS}-${MINICONDA_ARCH}.sh"
-
- echo
- echo "Downloading ${MINICONDA_URLBASE}/${MINICONDA_PKG}"
- echo
-
- if [ -f ${MINICONDA_PKG} ]
- then
- rm $MINICONDA_PKG
- fi
-
- echo "Installing the Miniconda python environment."
-
- if [ -e ${DEST_DIR} ]
- then
- rm -rf $DEST_DIR/*
- else
- mkdir $DEST_DIR
- fi
-
- log_cmd ${GETFILE} ${MINICONDA_URLBASE}/${MINICONDA_PKG} || do_exit
-
- log_cmd bash ./${MINICONDA_PKG} -b -p $DEST_DIR -f
-
- # Need to set PATH so we use miniconda's python environment
- export PATH=${DEST_DIR}/bin:$PATH
-
- echo "Installing the necessary packages for yt."
- echo "This may take a while, but don't worry. yt loves you."
-
- declare -a YT_DEPS
- YT_DEPS+=('python')
- YT_DEPS+=('setuptools')
- YT_DEPS+=('numpy')
- YT_DEPS+=('jupyter')
- YT_DEPS+=('ipython')
- YT_DEPS+=('sphinx')
- if [ ${INST_GIT} -eq 1 ]
- then
- YT_DEPS+=('git')
- YT_DEPS+=('gitpython')
- fi
- if [ $INST_H5PY -ne 0 ]
- then
- YT_DEPS+=('h5py')
- fi
- YT_DEPS+=('matplotlib')
- YT_DEPS+=('cython')
- if [ $INST_NOSE -ne 0 ]
- then
- YT_DEPS+=('nose')
- fi
- if [ $INST_SCIPY -ne 0 ]
- then
- YT_DEPS+=('scipy')
- fi
- if [ $INST_ASTROPY -ne 0 ]
- then
- YT_DEPS+=('astropy')
- fi
- YT_DEPS+=('conda-build')
- if [ $INST_PY3 -eq 0 ] && [ $INST_HG -eq 1 ]
- then
- YT_DEPS+=('mercurial')
- fi
- YT_DEPS+=('sympy')
-
- if [ $INST_NETCDF4 -eq 1 ]
- then
- YT_DEPS+=('netcdf4')
- fi
-
- log_cmd ${DEST_DIR}/bin/conda update --yes conda
-
- if [ $INST_GIT -eq 1 ]
- then
- GIT_EXE=${DEST_DIR}/bin/git
- else
- if type -P git &>/dev/null
- then
- GIT_EXE="git"
- else
- echo "Cannot find git. Please install git or set INST_GIT=1."
+ echo "$YT_DIR is not a clone of the yt git repository, exiting"
do_exit
fi
fi
-
- log_cmd echo "DEPENDENCIES" ${YT_DEPS[@]}
- for YT_DEP in "${YT_DEPS[@]}"; do
- echo "Installing $YT_DEP"
- log_cmd ${DEST_DIR}/bin/conda install -c conda-forge --yes ${YT_DEP}
- done
-
- if [ $INST_PY3 -eq 1 ] && [ $INST_HG -eq 1 ]
- then
- echo "Installing mercurial"
- log_cmd ${DEST_DIR}/bin/conda create -y -n py27 python=2.7 mercurial
- log_cmd ln -s ${DEST_DIR}/envs/py27/bin/hg ${DEST_DIR}/bin
- fi
-
- log_cmd ${GIT_EXE} clone https://github.com/yt-project/yt_conda ${DEST_DIR}/src/yt_conda
-
if [ $INST_EMBREE -eq 1 ]
then
-
- echo "Installing Embree"
- if [ ! -d ${DEST_DIR}/src ]
- then
- mkdir ${DEST_DIR}/src
- fi
- cd ${DEST_DIR}/src
- ( ${GETFILE} "$EMBREE_URL" 2>&1 ) 1>> ${LOG_FILE} || do_exit
- log_cmd tar xfz ${EMBREE}.tar.gz
- log_cmd mv ${DEST_DIR}/src/${EMBREE}/include/embree2 ${DEST_DIR}/include
- log_cmd mv ${DEST_DIR}/src/${EMBREE}/lib/lib*.* ${DEST_DIR}/lib
- if [ `uname` = "Darwin" ]
- then
- ln -s ${DEST_DIR}/lib/libembree.2.dylib ${DEST_DIR}/lib/libembree.dylib
- install_name_tool -id ${DEST_DIR}/lib/libembree.2.dylib ${DEST_DIR}/lib/libembree.2.dylib
- else
- ln -s ${DEST_DIR}/lib/libembree.so.2 ${DEST_DIR}/lib/libembree.so
- fi
-
- echo "Installing pyembree from source"
- ( ${GETFILE} "$PYEMBREE_URL" 2>&1 ) 1>> ${LOG_FILE} || do_exit
- log_cmd unzip ${DEST_DIR}/src/master.zip
- pushd ${DEST_DIR}/src/pyembree-master &> /dev/null
- log_cmd ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py install build_ext -I${DEST_DIR}/include -L${DEST_DIR}/lib
- popd &> /dev/null
+ echo $DEST_DIR > ${YT_DIR}/embree.cfg
fi
-
if [ $INST_ROCKSTAR -eq 1 ]
then
- echo "Building Rockstar"
- ( ${GIT_EXE} clone https://github.com/yt-project/rockstar ${DEST_DIR}/src/rockstar/ 2>&1 ) 1>> ${LOG_FILE}
- ROCKSTAR_PACKAGE=$(${DEST_DIR}/bin/conda build ${DEST_DIR}/src/yt_conda/rockstar --output)
- log_cmd ${DEST_DIR}/bin/conda build ${DEST_DIR}/src/yt_conda/rockstar
- log_cmd ${DEST_DIR}/bin/conda install $ROCKSTAR_PACKAGE
- ROCKSTAR_DIR=${DEST_DIR}/src/rockstar
- fi
-
- # conda doesn't package pyx, so we install manually with pip
- if [ $INST_PYX -eq 1 ]
- then
- if [ $INST_PY3 -eq 1 ]
- then
- log_cmd ${DEST_DIR}/bin/pip install pyx
- else
- log_cmd ${DEST_DIR}/bin/pip install pyx==0.12.1
- fi
- fi
-
- if [ $INST_YT_SOURCE -eq 0 ]
- then
- echo "Installing yt"
- log_cmd ${DEST_DIR}/bin/conda install -c conda-forge --yes yt
- else
- echo "Building yt from source"
- if [ -z "$YT_DIR" ]
- then
- if [ -e $ORIG_PWD/yt/mods.py ]
- then
- YT_DIR="$ORIG_PWD"
- elif [ -e $ORIG_PWD/../yt/mods.py ]
- then
- YT_DIR=$(dirname $ORIG_PWD)
- else
- YT_DIR="${DEST_DIR}/src/yt-git"
- log_cmd ${GIT_EXE} clone https://github.com/yt-project/yt ${YT_DIR}
- log_cmd ${GIT_EXE} -C ${YT_DIR} checkout ${BRANCH}
- fi
- echo Setting YT_DIR=${YT_DIR}
- else
- if [ ! -e $YT_DIR/.git ]
- then
- echo "$YT_DIR is not a clone of the yt git repository, exiting"
- do_exit
- fi
- fi
- if [ $INST_EMBREE -eq 1 ]
- then
- echo $DEST_DIR > ${YT_DIR}/embree.cfg
- fi
- if [ $INST_ROCKSTAR -eq 1 ]
- then
- echo $ROCKSTAR_DIR > ${YT_DIR}/rockstar.cfg
- ROCKSTAR_LIBRARY_PATH=${DEST_DIR}/lib
- fi
- pushd ${YT_DIR} &> /dev/null
- ( LIBRARY_PATH=$ROCKSTAR_LIBRARY_PATH ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py develop 2>&1) 1>> ${LOG_FILE} || do_exit
- popd &> /dev/null
+ echo $ROCKSTAR_DIR > ${YT_DIR}/rockstar.cfg
+ ROCKSTAR_LIBRARY_PATH=${DEST_DIR}/lib
fi
+ pushd ${YT_DIR} &> /dev/null
+ ( LIBRARY_PATH=$ROCKSTAR_LIBRARY_PATH ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py develop 2>&1) 1>> ${LOG_FILE} || do_exit
+ popd &> /dev/null
+fi
- test_install
+test_install
- echo
- echo
- echo "========================================================================"
- echo
- echo "yt and the Conda system are now installed in $DEST_DIR"
- echo
- echo "To get started with yt, check out the orientation:"
- echo
- echo " http://yt-project.org/doc/orientation/"
- echo
- echo "For support, see the website and join the mailing list:"
- echo
- echo " http://yt-project.org/"
- echo " http://yt-project.org/data/ (Sample data)"
- echo " http://yt-project.org/doc/ (Docs)"
- echo
- echo " http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org"
- echo
- echo "You must now prepend the following folder to your PATH environment variable:"
- echo
- echo " $DEST_DIR/bin"
- echo
- echo "On Bash-style shells you can copy/paste the following command to "
- echo "temporarily activate the yt installation:"
+echo
+echo
+echo "========================================================================"
+echo
+echo "yt and the Conda system are now installed in $DEST_DIR"
+echo
+echo "To get started with yt, check out the orientation:"
+echo
+echo " http://yt-project.org/doc/orientation/"
+echo
+echo "For support, see the website and join the mailing list:"
+echo
+echo " http://yt-project.org/"
+echo " http://yt-project.org/data/ (Sample data)"
+echo " http://yt-project.org/doc/ (Docs)"
+echo
+echo " http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org"
+echo
+echo "You must now prepend the following folder to your PATH environment variable:"
+echo
+echo " $DEST_DIR/bin"
+echo
+echo "On Bash-style shells you can copy/paste the following command to "
+echo "temporarily activate the yt installation:"
+echo
+echo " export PATH=$DEST_DIR/bin:\$PATH"
+echo
+echo "and on csh-style shells:"
+echo
+echo " setenv PATH $DEST_DIR/bin:\$PATH"
+echo
+echo "You can also update the init file appropriate for your shell"
+echo "(e.g. .bashrc, .bash_profile, .cshrc, or .zshrc) to include"
+echo "the same command."
+echo
+if [ $INST_ROCKSTAR -eq 1 ]
+then
+ if [ $MYOS = "Darwin" ]
+ then
+ LD_NAME="DYLD_LIBRARY_PATH"
+ else
+ LD_NAME="LD_LIBRARY_PATH"
+ fi
echo
- echo " export PATH=$DEST_DIR/bin:\$PATH"
- echo
- echo "and on csh-style shells:"
+ echo "For rockstar to work, you must also set $LD_NAME:"
echo
- echo " setenv PATH $DEST_DIR/bin:\$PATH"
- echo
- echo "You can also update the init file appropriate for your shell"
- echo "(e.g. .bashrc, .bash_profile, .cshrc, or .zshrc) to include"
- echo "the same command."
+ echo " export $LD_NAME=$DEST_DIR/lib:\$$LD_NAME"
echo
- if [ $INST_ROCKSTAR -eq 1 ]
- then
- if [ $MYOS = "Darwin" ]
- then
- LD_NAME="DYLD_LIBRARY_PATH"
- else
- LD_NAME="LD_LIBRARY_PATH"
- fi
- echo
- echo "For rockstar to work, you must also set $LD_NAME:"
- echo
- echo " export $LD_NAME=$DEST_DIR/lib:\$$LD_NAME"
- echo
- echo "or whichever invocation is appropriate for your shell."
- fi
- echo "========================================================================"
- echo
- echo "Oh, look at me, still talking when there's science to do!"
- echo "Good luck, and email the mailing list if you run into any problems."
+ echo "or whichever invocation is appropriate for your shell."
fi
+echo "========================================================================"
+echo
+echo "Oh, look at me, still talking when there's science to do!"
+echo "Good luck, and email the mailing list if you run into any problems."
diff -r fc58054806fe06993c0fc585939e8fd48552c117 -r 272125cbb417b446f20fec4d38e3c1e4efa54375 doc/source/faq/index.rst
--- a/doc/source/faq/index.rst
+++ b/doc/source/faq/index.rst
@@ -28,25 +28,16 @@
$ yt version
yt module located at:
- /Users/username/src/yt-x86_64/src/yt-hg
- The supplemental repositories are located at:
- /Users/username/src/yt-x86_64/src/yt-supplemental
+ /Users/username/src/yt-conda/src/yt-git
- The current version and changeset for the code is:
+ The current version of yt is:
---
- Version = 2.7-dev
- Changeset = 6bffc737a67a
+ Version = 3.4-dev
+ Changeset = 94033fca00e5
---
This installation CAN be automatically updated.
- yt dependencies were last updated on
- Wed Dec 4 15:47:40 MST 2013
-
- To update all dependencies, run "yt update --all".
-
-If the changeset is displayed followed by a "+", it means you have made
-modifications to the code since the last changeset.
For more information on this topic, see :ref:`updating-yt`.
diff -r fc58054806fe06993c0fc585939e8fd48552c117 -r 272125cbb417b446f20fec4d38e3c1e4efa54375 doc/source/help/index.rst
--- a/doc/source/help/index.rst
+++ b/doc/source/help/index.rst
@@ -36,19 +36,24 @@
Sometimes the pace of development is pretty fast on yt, particularly in the
development branch, so a fix to your problem may have already been developed
by the time you encounter it. Many users' problems can simply be corrected
-by updating to the latest version of the code and/or its dependencies. You
-can update yt's source by running:
+by updating to the latest version of the code and/or its dependencies. If you
+have installed the latest stable release of yt then you should update yt using
+the package manager appropriate for your python installation. For example, with
+``pip``::
+
+ $ pip install -U yt
+
+Or with conda::
+
+ $ conda update yt
+
+If you installed yt from a checkout of the git repository, you can update to
+the latest development version by issuing the following command:
.. code-block:: bash
$ yt update
-or you could update yt's source as well as any software dependencies by running:
-
-.. code-block:: bash
-
- $ yt update --all
-
.. _update-errors:
Update errors
diff -r fc58054806fe06993c0fc585939e8fd48552c117 -r 272125cbb417b446f20fec4d38e3c1e4efa54375 doc/source/installing.rst
--- a/doc/source/installing.rst
+++ b/doc/source/installing.rst
@@ -121,10 +121,6 @@
yt git repository and build yt form source. The default is
``INST_YT_SOURCE=0``, which installs yt from a binary conda package.
-The install script can also build python and all yt dependencies from source. To
-switch to this mode, set ``INST_CONDA=0`` at the top of the install script. If
-you choose this mode, you must also set ``INST_YT_SOURCE=1``.
-
In addition, you can tell the install script to download and install some
additional packages --- currently these include
`PyX <http://pyx.sourceforge.net/>`_, the `Rockstar halo
@@ -144,8 +140,8 @@
Because the installer is downloading and building a variety of packages from
source, this will likely take a few minutes, especially if you have a slow
-internet connection or have ``INST_CONDA=0`` set. You will get updates of its
-status at the command prompt throughout.
+internet connection. You will get updates of its status at the command prompt
+throughout.
If you receive errors during this process, the installer will provide you
with a large amount of information to assist in debugging your problems. The
@@ -155,15 +151,6 @@
potentially figure out what went wrong. If you have problems, though, do not
hesitate to :ref:`contact us <asking-for-help>` for assistance.
-If the install script errors out with a message about being unable to import the
-python SSL bindings, this means that the Python built by the install script was
-unable to link against the OpenSSL library. This likely means that you installed
-with ``INST_CONDA=0`` on a recent version of OSX, or on a cluster that has a
-very out of date installation of OpenSSL. In both of these cases you will either
-need to install OpenSSL yourself from the system package manager or consider
-using ``INST_CONDA=1``, since conda-based installs can install the conda package
-for OpenSSL.
-
.. _activating-yt:
Activating Your Installation
@@ -172,11 +159,8 @@
Once the installation has completed, there will be instructions on how to set up
your shell environment to use yt.
-Activating Conda-based installs (``INST_CONDA=1``)
-""""""""""""""""""""""""""""""""""""""""""""""""""
-
-For conda-based installs, you will need to ensure that the installation's
-``yt-conda/bin`` directory is prepended to your ``PATH`` environment variable.
+In particular, you will need to ensure that the installation's ``yt-conda/bin``
+directory is prepended to your ``PATH`` environment variable.
For Bash-style shells, you can use the following command in a terminal session
to temporarily activate the yt installation:
@@ -195,31 +179,6 @@
appropriate for your shell and OS (e.g. .bashrc, .bash_profile, .cshrc, .zshrc)
to include the same command.
-Activating source-based installs (``INST_CONDA=0``)
-"""""""""""""""""""""""""""""""""""""""""""""""""""
-
-For this installation method, you must run an ``activate`` script to activate
-the yt environment in a terminal session. You must run this script in order to
-have yt properly recognized by your system. You can either add it to your login
-script, or you must execute it in each shell session prior to working with yt.
-
-.. code-block:: bash
-
- $ source <yt installation directory>/bin/activate
-
-If you use csh or tcsh as your shell, activate that version of the script:
-
-.. code-block:: bash
-
- $ source <yt installation directory>/bin/activate.csh
-
-If you don't like executing outside scripts on your computer, you can set
-the shell variables manually. ``YT_DEST`` needs to point to the root of the
-directory containing the install. By default, this will be ``yt-<arch>``, where
-``<arch>`` is your machine's architecture (usually ``x86_64`` or ``i386``). You
-will also need to set ``LD_LIBRARY_PATH`` and ``PYTHONPATH`` to contain
-``$YT_DEST/lib`` and ``$YT_DEST/python2.7/site-packages``, respectively.
-
.. _updating-yt:
Updating yt and Its Dependencies
@@ -231,21 +190,20 @@
.. code-block:: bash
- $ yt update
+ $ conda update yt
-Additionally, if you ran the install script with ``INST_CONDA=0`` and want to
-make sure you have the latest dependencies associated with yt and update the
-codebase simultaneously, type this:
+If you want to update your dependencies, run:
.. code-block:: bash
- $ yt update --all
+ $ conda update --all
-If you ran the install script with ``INST_CONDA=1`` and want to update your dependencies, run:
+If you have installed yt from source, you can use the following command to get
+the latest development version of yt:
.. code-block:: bash
- $ conda update --all
+ $ yt update
.. _removing-yt:
@@ -254,10 +212,14 @@
Because yt and its dependencies are installed in an isolated directory when
you use the script installer, you can easily remove yt and all of its
-dependencies cleanly. Simply remove the install directory and its
-subdirectories and you're done. If you *really* had problems with the
-code, this is a last defense for solving: remove and then fully
-:ref:`re-install <installing-yt>` from the install script again.
+dependencies cleanly. Simply remove the install directory and its
+subdirectories::
+
+ $ rm -rf yt-conda
+
+If you *really* had problems with the installation process, this is a last
+defense for solving: remove and then fully :ref:`re-install <installing-yt>`
+from the install script again.
.. _anaconda-installation:
@@ -335,13 +297,11 @@
This will make sure you are running a version of yt corresponding to the
most up-to-date source code.
-.. _rockstar-conda:
-
-Rockstar Halo Finder for Conda-based installations
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Installing Support for the Rockstar Halo Finder
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The easiest way to set rockstar up in a conda-based python envrionment is to run
-the install script with both ``INST_CONDA=1`` and ``INST_ROCKSTAR=1``.
+the install script with ``INST_ROCKSTAR=1``.
If you want to do this manually, you will need to follow these
instructions. First, clone Matt Turk's fork of rockstar and compile it:
diff -r fc58054806fe06993c0fc585939e8fd48552c117 -r 272125cbb417b446f20fec4d38e3c1e4efa54375 doc/source/visualizing/unstructured_mesh_rendering.rst
--- a/doc/source/visualizing/unstructured_mesh_rendering.rst
+++ b/doc/source/visualizing/unstructured_mesh_rendering.rst
@@ -22,9 +22,9 @@
conda install -c http://use.yt/with_conda/ yt
-Alternatively, you can install yt from source using the ``install_script.sh``
-script. Be sure to set the INST_CONDA, INST_YT_SOURCE, INST_EMBREE,
-and INST_NETCDF4 flags to 1 at the top of the script. The ``install_script.sh``
+Alternatively, you can install yt from source using the ``install_script.sh``
+script. Be sure to set the ``INST_YT_SOURCE``, ``INST_EMBREE``, and
+``INST_NETCDF4`` flags to 1 at the top of the script. The ``install_script.sh``
script can be downloaded by doing:
.. code-block:: bash
diff -r fc58054806fe06993c0fc585939e8fd48552c117 -r 272125cbb417b446f20fec4d38e3c1e4efa54375 doc/source/yt3differences.rst
--- a/doc/source/yt3differences.rst
+++ b/doc/source/yt3differences.rst
@@ -24,7 +24,7 @@
.. code-block:: bash
- $ yt update --all
+ $ yt update
This will update yt to the most recent version and rebuild the source base.
If you installed using the installer script, it will assure you have all of the
This diff is so big that we needed to truncate the remainder.
Repository URL: https://bitbucket.org/yt_analysis/yt/
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