desiutil 3.5.0__tar.gz

desiutil-3.5.0/LICENSE.rst

@@ -0,0 +1,25 @@
+Copyright (c) 2014-2019, DESI Collaboration <desi-data@desi.lbl.gov>
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+* Neither the name of the DESI Collaboration nor the names of its contributors
+  may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

desiutil-3.5.0/MANIFEST.in

@@ -0,0 +1,2 @@
+prune .github
+global-exclude .gitignore .readthedocs.yml

desiutil-3.5.0/PKG-INFO

@@ -0,0 +1,77 @@
+Metadata-Version: 2.4
+Name: desiutil
+Version: 3.5.0
+Summary: DESI utilities package
+Home-page: https://github.com/desihub/desiutil
+Author: DESI Collaboration
+Author-email: desi-data@desi.lbl.gov
+License: BSD 3-Clause License
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: System :: Software Distribution
+Classifier: Topic :: Utilities
+Requires-Python: >=3.10
+Description-Content-Type: text/x-rst
+License-File: LICENSE.rst
+Requires-Dist: requests
+Requires-Dist: pyyaml
+Requires-Dist: astropy<7
+Provides-Extra: all
+Requires-Dist: healpy; extra == "all"
+Requires-Dist: matplotlib; extra == "all"
+Requires-Dist: scipy; extra == "all"
+Requires-Dist: speclite; extra == "all"
+Provides-Extra: test
+Requires-Dist: desiutil[all]; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Provides-Extra: coverage
+Requires-Dist: desiutil[all]; extra == "coverage"
+Requires-Dist: pytest-cov; extra == "coverage"
+Requires-Dist: coveralls; extra == "coverage"
+Provides-Extra: doc
+Requires-Dist: Sphinx; extra == "doc"
+Requires-Dist: sphinx-rtd-theme; extra == "doc"
+Dynamic: license-file
+
+========
+desiutil
+========
+
+|Actions Status| |Coveralls Status| |Documentation Status|
+
+.. |Actions Status| image:: https://github.com/desihub/desiutil/workflows/CI/badge.svg
+    :target: https://github.com/desihub/desiutil/actions
+    :alt: GitHub Actions CI Status
+
+.. |Coveralls Status| image:: https://coveralls.io/repos/desihub/desiutil/badge.svg
+    :target: https://coveralls.io/github/desihub/desiutil
+    :alt: Test Coverage Status
+
+.. |Documentation Status| image:: https://readthedocs.org/projects/desiutil/badge/?version=latest
+    :target: https://desiutil.readthedocs.io/en/latest/
+    :alt: Documentation Status
+
+Introduction
+============
+
+`desiutil` contains general purpose tools for use by any and all other `DESI packages`_.
+
+.. _`DESI packages`: https://github.com/desihub
+
+Full Documentation
+==================
+
+Please visit `desiutil on Read the Docs`_.
+
+.. _`desiutil on Read the Docs`: https://desiutil.readthedocs.io/en/latest/
+
+License
+=======
+
+desiutil is free software licensed under a 3-clause BSD-style license. For details see
+the ``LICENSE.rst`` file.

desiutil-3.5.0/README.rst

@@ -0,0 +1,37 @@
+========
+desiutil
+========
+
+|Actions Status| |Coveralls Status| |Documentation Status|
+
+.. |Actions Status| image:: https://github.com/desihub/desiutil/workflows/CI/badge.svg
+    :target: https://github.com/desihub/desiutil/actions
+    :alt: GitHub Actions CI Status
+
+.. |Coveralls Status| image:: https://coveralls.io/repos/desihub/desiutil/badge.svg
+    :target: https://coveralls.io/github/desihub/desiutil
+    :alt: Test Coverage Status
+
+.. |Documentation Status| image:: https://readthedocs.org/projects/desiutil/badge/?version=latest
+    :target: https://desiutil.readthedocs.io/en/latest/
+    :alt: Documentation Status
+
+Introduction
+============
+
+`desiutil` contains general purpose tools for use by any and all other `DESI packages`_.
+
+.. _`DESI packages`: https://github.com/desihub
+
+Full Documentation
+==================
+
+Please visit `desiutil on Read the Docs`_.
+
+.. _`desiutil on Read the Docs`: https://desiutil.readthedocs.io/en/latest/
+
+License
+=======
+
+desiutil is free software licensed under a 3-clause BSD-style license. For details see
+the ``LICENSE.rst`` file.

desiutil-3.5.0/bin/annotate_fits

@@ -0,0 +1,6 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+from sys import exit
+from desiutil.annotate import main
+exit(main())

desiutil-3.5.0/bin/desiBootstrap.sh

@@ -0,0 +1,112 @@
+#!/bin/bash
+#
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+#
+function usage() {
+    local execName=$(basename $0)
+    (
+    echo "${execName} [-a VERSION] [-b BRANCH] [-c CONFIG] [-h] [-m MODULESHOME] [-p PYTHON] [-t] [-v]"
+    echo ""
+    echo "Install desiutil on a bare system."
+    echo ""
+    echo "    -a = Version of DESI+Anaconda software stack."
+    echo "    -b = Switch to desiutil BRANCH before installing."
+    echo "    -c = Pass CONFIG to desiInstall."
+    echo "    -h = Print this message and exit."
+    echo "    -m = Look for the Modules install in MODULESHOME."
+    echo "    -p = Use the Python executable PYTHON (e.g. /opt/local/bin/python2.7)."
+    echo "    -t = Test mode.  Do not make any changes.  Implies -v."
+    echo "    -v = Verbose mode. Print lots of extra information."
+    ) >&2
+}
+#
+# Get options
+#
+anaconda='current'
+branch=''
+config=''
+modules=''
+py=''
+test=''
+verbose=''
+while getopts a:b:c:hm:p:tv argname; do
+    case ${argname} in
+        a) anaconda=${OPTARG} ;;
+        b) branch=${OPTARG} ;;
+        c) config="-c ${OPTARG}" ;;
+        h) usage; exit 0 ;;
+        m) modules=${OPTARG} ;;
+        p) py=${OPTARG} ;;
+        t) test='-t'; verbose='-v' ;;
+        v) verbose='-v' ;;
+        *) usage; exit 1 ;;
+    esac
+done
+shift $((OPTIND-1))
+#
+# Validate options
+#
+if [[ -z "${DESI_PRODUCT_ROOT}" && -z "${NERSC_HOST}" ]]; then
+    echo "You haven't set the DESI_PRODUCT_ROOT environment variable."
+    echo "I'm not going to try to guess where you want to install things."
+    exit 1
+fi
+if [[ -n "${modules}" ]]; then
+    export MODULESHOME=${modules}
+fi
+if [[ -z "${MODULESHOME}" ]]; then
+    echo "You do not appear to have Modules installed."
+    exit 1
+fi
+if [[ -n "${NERSC_HOST}" && -z "${py}" ]]; then
+    #
+    # Make certain we are using the Python version associated with the
+    # specified DESI+Anaconda stack.
+    #
+    desiconda=/global/common/software/desi/${NERSC_HOST}/desiconda/${anaconda}
+    if [[ -d ${desiconda} ]]; then
+        if [[ "${anaconda}" == "current" ]]; then
+            anaconda=$(readlink ${desiconda})
+            dd=$(dirname ${desiconda})/${anaconda}
+        else
+            dd=${desiconda}
+        fi
+        py=${dd}/conda/bin/python
+        if [[ ! -x ${py} ]]; then
+            echo "Python executable ${py} not found!"
+            exit 1
+        fi
+    fi
+    if [[ -z "${py}" ]]; then
+        echo "Could not find Python executable associated with '${anaconda}' on ${NERSC_HOST}!"
+        exit 1
+    fi
+fi
+#
+# Export
+#
+checkout=desiutil-checkout
+[[ -n "${verbose}" ]] && echo git clone https://github.com/desihub/desiutil.git ${checkout}
+git clone https://github.com/desihub/desiutil.git ${checkout}
+if [[ -n "${branch}" ]]; then
+    cd ${checkout}
+    [[ -n "${verbose}" ]] && echo git checkout ${branch}
+    git checkout ${branch}
+    cd ..
+fi
+export DESIUTIL=$(pwd)/${checkout}
+export PATH=${DESIUTIL}/bin:${PATH}
+if [[ -z "${PYTHONPATH}" ]]; then
+    export PYTHONPATH=${DESIUTIL}/py
+else
+    export PYTHONPATH=${DESIUTIL}/py:${PYTHONPATH}
+fi
+if [[ -z "${py}" ]]; then
+    [[ -n "${verbose}" ]] && echo desiInstall -a ${anaconda} -b ${config} ${test} ${verbose}
+    desiInstall -a ${anaconda} -b ${config} ${test} ${verbose}
+else
+    [[ -n "${verbose}" ]] && echo ${py} ${DESIUTIL}/bin/desiInstall -a ${anaconda} -b ${config} ${test} ${verbose}
+    ${py} ${DESIUTIL}/bin/desiInstall -a ${anaconda} -b ${config} ${test} ${verbose}
+fi
+[[ -n "${verbose}" ]] && echo /bin/rm -rf ${DESIUTIL}
+/bin/rm -rf ${DESIUTIL}

desiutil-3.5.0/bin/desiInstall

@@ -0,0 +1,6 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+from sys import exit
+from desiutil.install import main
+exit(main())

desiutil-3.5.0/bin/desi_api_file

@@ -0,0 +1,6 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+from sys import exit
+from desiutil.api import main
+exit(main())

desiutil-3.5.0/bin/desi_module_file

@@ -0,0 +1,6 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+from sys import exit
+from desiutil.modules import main
+exit(main())

desiutil-3.5.0/bin/desi_update_version

@@ -0,0 +1,6 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+from sys import exit
+from desiutil.setup import main
+exit(main())

desiutil-3.5.0/bin/fix_permissions.sh

@@ -0,0 +1,135 @@
+#!/bin/sh
+#
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+#
+# See https://desi.lbl.gov/trac/wiki/Computing/NerscFileSystem#FileSystemAccess
+# for the detailed requirements that motivate this script.
+#
+function usage() {
+    local execName=$(basename $0)
+    (
+    echo "${execName} [-a] [-g GROUP] [-h] [-t] [-v] DIR"
+    echo ""
+    echo "Set group-friendly permissions on a directory tree."
+    echo ""
+    echo "    -a = Include apache/www access (via ACL) when modifying permissions."
+    echo "    -g = Change group ownership to GROUP (default 'desi')."
+    echo "    -h = Print this message and exit."
+    echo "    -t = Test mode.  Do not make any changes.  Implies -v."
+    echo "    -v = Verbose mode. Print lots of extra information."
+    echo "   DIR = Directory to fix. Required."
+    ) >&2
+}
+#
+#
+#
+function run() {
+    local vrb=$1
+    local cmd=$2
+    ${vrb} && echo "${cmd}"
+    ${cmd}
+}
+#
+# Get options
+#
+apacheACL=''
+apacheUID=48
+desiGID=desi
+test=/usr/bin/false
+verbose=/usr/bin/false
+while getopts ag:htv argname; do
+    case ${argname} in
+        a) apacheACL="u:${apacheUID}:rX" ;;
+        g) desiGID=${OPTARG} ;;
+        h) usage; exit 0 ;;
+        t) test=/usr/bin/true; verbose=/usr/bin/true ;;
+        v) verbose=/usr/bin/true ;;
+        *) usage; exit 1 ;;
+    esac
+done
+shift $((OPTIND-1))
+#
+# Check for commands
+#
+find=/usr/bin/find
+if [ ! -x "${find}" ]; then
+    echo "Could not find the 'find' command (tried ${find})!" >&2
+    exit 1
+fi
+setfacl=/usr/bin/setfacl
+if [ ! -x "${setfacl}" ]; then
+    echo "Could not find the 'setfacl' command (tried ${setfacl})!" >&2
+    echo "Skipping all ACL changes." >&2
+    apacheACL=''
+fi
+#
+# Make sure directory exists, and check consistency.
+#
+if [ $# -lt 1 ]; then
+    echo "You must specify a directory!" >&2
+    usage
+    exit 1
+fi
+directory=$1
+if [ ! -d "${directory}" ]; then
+    echo "${directory} does not exist or is not a directory!" >&2
+    usage
+    exit 1
+fi
+if [ -z "${USER}" ]; then
+    echo "The USER environment variable does not appear to be set!" >&2
+    exit 1
+fi
+if [ -z "${NERSC_HOST}" ]; then
+    echo "Unable to determine NERSC environment.  Are you running this script at NERSC?" >&2
+    exit 1
+fi
+if [ $(realpath ${directory}) = $(realpath ${HOME}) ]; then
+    echo "You are attempting to change the permissions of HOME=${HOME}, which is dangerous.  Aborting." >&2
+    exit 1
+fi
+#
+# Proceed with permission changes.
+#
+findbase="${find} ${directory} -user ${USER}"
+${verbose} && echo "Fixing permissions on ${directory} ..."
+if ${test}; then
+    run ${verbose} "${findbase} -not -group ${desiGID} -ls"
+    run ${verbose} "${findbase} -type f -not -perm /g+r -ls"
+    run ${verbose} "${findbase} -type d -not -perm -g+rxs -ls"
+    if [ -n "${apacheACL}" ]; then
+        run ${verbose} "${findbase} -exec ${setfacl} --test --modify ${apacheACL} {} ;"
+    fi
+else
+    vflag=''
+    #
+    # Instruct chgrp & chmod to only report files that change.
+    #
+    ${verbose} && vflag='-c'
+    # Change group.
+    run ${verbose} "${findbase} -not -group ${desiGID} -exec chgrp ${vflag} -h ${desiGID} {} ;"
+    # Set group read access.
+    run ${verbose} "${findbase} -type f -not -perm /g+r -exec chmod ${vflag} g+r {} ;"
+    run ${verbose} "${findbase} -type d -not -perm -g+rxs -exec chmod ${vflag} g+rxs {} ;"
+    if [ -n "${apacheACL}" ]; then
+        run ${verbose} "${findbase} -exec ${setfacl} --modify ${apacheACL} {} ;"
+    fi
+fi
+#
+# Notes on searching for group-unreadable files.
+#
+# getfacl -R -t /global/cfs/cdirs//desi/spectro/ | grep -e '^# file:' -e '^GROUP' | sed -n 'h;n;G;p' | paste - - | awk '$3=="---" {print}'
+#
+# in a few minutes I didn't find any with "---" group ACL, but if I change to searching for things with a "r--" ACL, a sample of the output looks like:
+# sleak@cori06$ getfacl -R -t /global/cfs/cdirs//desi/spectro/ | grep -e '^# file:' -e '^GROUP' | sed -n 'h;n;G;p' | paste - - | awk '$3=="r--" {print}' | head
+# getfacl: Removing leading '/' from absolute path names
+# GROUP desi r-- # file: global/cfs/cdirs//desi/spectro//ql_calib/fiberflat-z7.fits
+# GROUP desi r-- # file: global/cfs/cdirs//desi/spectro//ql_calib/fiberflat-z3.fits
+# GROUP desi r-- # file: global/cfs/cdirs//desi/spectro//ql_calib/fiberflat-b2.fits
+# GROUP desi r-- # file: global/cfs/cdirs//desi/spectro//ql_calib/fiberflat-z4.fits
+# GROUP desi r-- # file: global/cfs/cdirs//desi/spectro//ql_calib/fiberflat-b7.fits
+# GROUP desi r-- # file: global/cfs/cdirs//desi/spectro//ql_calib/fiberflat-z6.fits
+# GROUP desi r-- # file: global/cfs/cdirs//desi/spectro//ql_calib/fiberflat-b4.fits
+# GROUP desi r-- # file: global/cfs/cdirs//desi/spectro//ql_calib/fiberflat-r7.fits
+# GROUP desi r-- # file: global/cfs/cdirs//desi/spectro//ql_calib/fiberflat-b9.fits
+# GROUP desi r-- # file: global/cfs/cdirs//desi/spectro//ql_calib/fiberflat-r0.fits

desiutil-3.5.0/bin/update_iers_frozen

@@ -0,0 +1,9 @@
+#!/usr/bin/env python
+"""Update the iers_frozen file.
+"""
+from importlib.resources import files
+from desiutil.iers import update_iers
+
+frozen = str(files('desiutil') / 'data' / 'iers_frozen.ecsv')
+print(f"Updating {frozen}.")
+update_iers(frozen)

desiutil-3.5.0/py/desiutil/__init__.py

@@ -0,0 +1,15 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+# -*- coding: utf-8 -*-
+"""
+========
+desiutil
+========
+
+This package provides low-level utilities for general use by DESI_.
+
+.. _DESI: https://www.desi.lbl.gov
+"""
+#
+# Set version string.
+#
+from ._version import __version__

desiutil-3.5.0/py/desiutil/_version.py

@@ -0,0 +1 @@
+__version__ = '3.5.0'