xmmpysas 1.4.2__tar.gz

xmmpysas-1.4.2/PKG-INFO

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+Metadata-Version: 2.1
+Name: xmmpysas
+Version: 1.4.2
+Summary: Python wrapper for XMM-Newton SAS
+Author: Ryan Tanner
+Author-email: ryan.tanner@nasa.gov
+Requires-Python: >=3.10,<4.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: astropy (>=6.1.5,<7.0.0)
+Requires-Dist: astroquery (>=0.4.7,<0.5.0)
+Requires-Dist: beautifultable (>=1.1.0,<2.0.0)
+Requires-Dist: matplotlib (>=3.9.2,<4.0.0)
+Requires-Dist: notebook (>=7.2.2,<8.0.0)
+Requires-Dist: numpy (>=2.1.3,<3.0.0)
+Requires-Dist: pyds9 (>=1.8.1,<2.0.0)
+Requires-Dist: pypdf (>=5.1.0,<6.0.0)
+Requires-Dist: pyqt5 (>=5.15.11,<6.0.0)
+Requires-Dist: pytest (>=8.3.3,<9.0.0)
+Requires-Dist: requests (>=2.32.3,<3.0.0)
+Requires-Dist: scipy (>=1.14.1,<2.0.0)
+Description-Content-Type: text/markdown
+
+### Installing pySAS
+
+This development version of pySAS can be used with versions 20 and up of XMM-Newton SAS. After installing SAS [following the installation instructions](https://www.cosmos.esa.int/web/xmm-newton/sas-installation) you can then install the development version of pySAS using
+```
+pip install xmmpysas
+```
+Before you use pySAS for the first time you will need to configure pySAS so that it knows where you have SAS installed, and where the XMM calibration files are located. After installing pySAS using pip, in Python just run:
+```python
+import pysas
+pysas.config_pysas.run_config()
+```
+This will step you through connecting pySAS to SAS. After pySAS has been configured you can import pySAS like normal.
+```python
+import pysas
+```
+You can update pySAS using
+```
+pip install xmmpysas --upgrade
+```
+
+### Cloning This Repository
+
+*Alternatively*, this repository can be cloned by going into the directory where pySAS is installed to remove the current version of pySAS using 
+```
+cd /path/to/sas/install/xmmsas_202XXXXXX_YYYY/lib/python/
+rm -rf ./pysas
+```
+and then clone this version of pySAS by executing the command,
+```
+git clone https://github.com/XMMGOF/pysas.git
+```
+You can then use pySAS like normal.
+
+To incorporate new changes to pySAS from GitHub, from the pysas directory use the following command,
+```
+git pull https://github.com/XMMGOF/pysas.git
+```
+
+### Running pySAS for the First Time
+
+The very first time you run this version of pySAS you will have to set SAS defaults that will be used by pySAS. To set the defaults run the following commands in python:
+```python
+import pysas
+pysas.config_pysas.run_config()
+```
+This script will set:
+
+- sas_dir: The directory where SAS is installed. If you are running the script from inside the SAS directory this will be auto-detected.
+- sas_ccfpath: The directory where the calibration files are stored. If you already have them downloaded, just enter the directory where they are. But if you have not downloaded them yet, you will be given the option to download them after the setup. The script will even create the directory for you.
+- data_dir: You will have the option of designating a defaut data directory. All observation data files will be downloaded into this directory. If the data directory does not exist it will be created for you.
+
+**Note:** If you installed pySAS by cloning it from GitHub you must add the pySAS directory to your PYTHONPATH environment variable. For example:
+```
+export PYTHONPATH=/path/to/sas/install/xmmsas_202XXXXXX_YYYY/lib/python:$PYTHONPATH
+```
+It is recommended that you add this line to your .bash_profile file (or equivelent shell file).
+**This is not necessary if pySAS was installed using `pip install xmmpysas`.**
+
+### Example Scripts
+
+There are example scripts and Jupyter notebooks available on [GitHub demonstrating how to use pySAS](https://github.com/XMMGOF/pysas/tree/main/documentation). We are expanding the number of example scripts and Jupyter notebooks.
+
+### FAQ
+
+Q: Will this break my SAS inatallation?
+
+A: No. All changes have been made to keep this developmental version of pySAS working with SAS.
+
+Q: I have already been working with pySAS and I have several Python scripts already written. Will this make them break?
+
+A: No. This developmental version of pySAS is fully backwards compatible with the standard pySAS distributed with SAS. The develomental version only adds capabilites. The features included here will eventually work their way into the standard version of pySAS.
+
+Q: Can I contribute changes to pySAS?
+
+A: YES! That is the purpose of this repository! The whole idea is to provide a place where changes can be made and tested, issues can be raised, and features can be requested for pySAS. User input is greatly encouraged.
+
+Q: Can I use pip to install pySAS?
+
+A: Yes! Install using
+```
+pip install xmmpysas
+```
+
+Q: What about using conda to install pySAS?
+
+A: We are working on it!
+
+Q: Can I use pySAS to update the XMM-Newton calibration files?
+
+A: Yes! Just start a Python session and run the following commands:
+
+```python
+import pysas
+pysas.sasutils.update_calibration_files()
+```
+
+This will download new calibration files.
+
+Q: What version of pySAS is installed on SciServer?
+
+A: The version 1.4.1a. Some changes to pySAS have been made since the HEASARC image was created for SciServer. The next time a new HEASARC image is created for SciServer all new changes to pySAS will be incorporated.
+
+Q: Why have this version of pySAS separate from the standard version you can download from ESA when you download SAS?
+
+A: Because of the realities of developing across multiple systems. Changes were needed to make pySAS run on systems such as SciServer (and other future online systems that are in the works, stay tuned!). The development timetable for SciServer did not match up with the development timetable for SAS. This allows us to continuously develop pySAS to match *all* of the development timetables. This also allows us to get feedback from the XMM-Newton user community about what they want to see in pySAS.
+

xmmpysas-1.4.2/pyproject.toml

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+[tool.poetry]
+name = "xmmpysas"
+version = "1.4.2"
+description = "Python wrapper for XMM-Newton SAS"
+authors = ["Ryan Tanner <ryan.tanner@nasa.gov>"]
+readme = "pysas/README.md"
+packages = [{ include = "pysas" }]
+
+[tool.poetry.dependencies]
+python = "^3.10"
+astropy = "^6.1.5"
+numpy = "^2.1.3"
+matplotlib = "^3.9.2"
+requests = "^2.32.3"
+pyds9 = "^1.8.1"
+pyqt5 = "^5.15.11"
+beautifultable = "^1.1.0"
+scipy = "^1.14.1"
+notebook = "^7.2.2"
+astroquery = "^0.4.7"
+pytest = "^8.3.3"
+pypdf = "^5.1.0"
+
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

xmmpysas-1.4.2/pysas/.git/FETCH_HEAD

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+1262902a30d0862d1d1cedc43fafa4b70a94f45a		branch 'main' of https://github.com/XMMGOF/pysas
+3aa50333432aa3fc3dc0c92f485555bcbe90adba	not-for-merge	branch 'dev_calibration' of https://github.com/XMMGOF/pysas
+1bdf787aadad1161616d419eea892343ebfb63ae	not-for-merge	branch 'epatplotpy' of https://github.com/XMMGOF/pysas

xmmpysas-1.4.2/pysas/.git/HEAD

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+ref: refs/heads/main

xmmpysas-1.4.2/pysas/.git/config

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+[core]
+	repositoryformatversion = 0
+	filemode = true
+	bare = false
+	logallrefupdates = true
+[remote "origin"]
+	url = https://github.com/XMMGOF/pysas.git
+	fetch = +refs/heads/*:refs/remotes/origin/*
+[branch "main"]
+	remote = origin
+	merge = refs/heads/main
+	vscode-merge-base = origin/main

xmmpysas-1.4.2/pysas/.git/description

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+Unnamed repository; edit this file 'description' to name the repository.

xmmpysas-1.4.2/pysas/.git/hooks/applypatch-msg.sample

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+#!/bin/sh
+#
+# An example hook script to check the commit log message taken by
+# applypatch from an e-mail message.
+#
+# The hook should exit with non-zero status after issuing an
+# appropriate message if it wants to stop the commit.  The hook is
+# allowed to edit the commit message file.
+#
+# To enable this hook, rename this file to "applypatch-msg".
+
+. git-sh-setup
+commitmsg="$(git rev-parse --git-path hooks/commit-msg)"
+test -x "$commitmsg" && exec "$commitmsg" ${1+"$@"}
+:

xmmpysas-1.4.2/pysas/.git/hooks/commit-msg.sample

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+#!/bin/sh
+#
+# An example hook script to check the commit log message.
+# Called by "git commit" with one argument, the name of the file
+# that has the commit message.  The hook should exit with non-zero
+# status after issuing an appropriate message if it wants to stop the
+# commit.  The hook is allowed to edit the commit message file.
+#
+# To enable this hook, rename this file to "commit-msg".
+
+# Uncomment the below to add a Signed-off-by line to the message.
+# Doing this in a hook is a bad idea in general, but the prepare-commit-msg
+# hook is more suited to it.
+#
+# SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p')
+# grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"
+
+# This example catches duplicate Signed-off-by lines.
+
+test "" = "$(grep '^Signed-off-by: ' "$1" |
+	 sort | uniq -c | sed -e '/^[ 	]*1[ 	]/d')" || {
+	echo >&2 Duplicate Signed-off-by lines.
+	exit 1
+}

xmmpysas-1.4.2/pysas/.git/hooks/fsmonitor-watchman.sample

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+#!/usr/bin/perl
+
+use strict;
+use warnings;
+use IPC::Open2;
+
+# An example hook script to integrate Watchman
+# (https://facebook.github.io/watchman/) with git to speed up detecting
+# new and modified files.
+#
+# The hook is passed a version (currently 1) and a time in nanoseconds
+# formatted as a string and outputs to stdout all files that have been
+# modified since the given time. Paths must be relative to the root of
+# the working tree and separated by a single NUL.
+#
+# To enable this hook, rename this file to "query-watchman" and set
+# 'git config core.fsmonitor .git/hooks/query-watchman'
+#
+my ($version, $time) = @ARGV;
+
+# Check the hook interface version
+
+if ($version == 1) {
+	# convert nanoseconds to seconds
+	# subtract one second to make sure watchman will return all changes
+	$time = int ($time / 1000000000) - 1;
+} else {
+	die "Unsupported query-fsmonitor hook version '$version'.\n" .
+	    "Falling back to scanning...\n";
+}
+
+my $git_work_tree;
+if ($^O =~ 'msys' || $^O =~ 'cygwin') {
+	$git_work_tree = Win32::GetCwd();
+	$git_work_tree =~ tr/\\/\//;
+} else {
+	require Cwd;
+	$git_work_tree = Cwd::cwd();
+}
+
+my $retry = 1;
+
+launch_watchman();
+
+sub launch_watchman {
+
+	my $pid = open2(\*CHLD_OUT, \*CHLD_IN, 'watchman -j --no-pretty')
+	    or die "open2() failed: $!\n" .
+	    "Falling back to scanning...\n";
+
+	# In the query expression below we're asking for names of files that
+	# changed since $time but were not transient (ie created after
+	# $time but no longer exist).
+	#
+	# To accomplish this, we're using the "since" generator to use the
+	# recency index to select candidate nodes and "fields" to limit the
+	# output to file names only.
+
+	my $query = <<"	END";
+		["query", "$git_work_tree", {
+			"since": $time,
+			"fields": ["name"]
+		}]
+	END
+
+	print CHLD_IN $query;
+	close CHLD_IN;
+	my $response = do {local $/; <CHLD_OUT>};
+
+	die "Watchman: command returned no output.\n" .
+	    "Falling back to scanning...\n" if $response eq "";
+	die "Watchman: command returned invalid output: $response\n" .
+	    "Falling back to scanning...\n" unless $response =~ /^\{/;
+
+	my $json_pkg;
+	eval {
+		require JSON::XS;
+		$json_pkg = "JSON::XS";
+		1;
+	} or do {
+		require JSON::PP;
+		$json_pkg = "JSON::PP";
+	};
+
+	my $o = $json_pkg->new->utf8->decode($response);
+
+	if ($retry > 0 and $o->{error} and $o->{error} =~ m/unable to resolve root .* directory (.*) is not watched/) {
+		print STDERR "Adding '$git_work_tree' to watchman's watch list.\n";
+		$retry--;
+		qx/watchman watch "$git_work_tree"/;
+		die "Failed to make watchman watch '$git_work_tree'.\n" .
+		    "Falling back to scanning...\n" if $? != 0;
+
+		# Watchman will always return all files on the first query so
+		# return the fast "everything is dirty" flag to git and do the
+		# Watchman query just to get it over with now so we won't pay
+		# the cost in git to look up each individual file.
+		print "/\0";
+		eval { launch_watchman() };
+		exit 0;
+	}
+
+	die "Watchman: $o->{error}.\n" .
+	    "Falling back to scanning...\n" if $o->{error};
+
+	binmode STDOUT, ":utf8";
+	local $, = "\0";
+	print @{$o->{files}};
+}

xmmpysas-1.4.2/pysas/.git/hooks/post-update.sample

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+#!/bin/sh
+#
+# An example hook script to prepare a packed repository for use over
+# dumb transports.
+#
+# To enable this hook, rename this file to "post-update".
+
+exec git update-server-info

xmmpysas-1.4.2/pysas/.git/hooks/pre-applypatch.sample

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+#!/bin/sh
+#
+# An example hook script to verify what is about to be committed
+# by applypatch from an e-mail message.
+#
+# The hook should exit with non-zero status after issuing an
+# appropriate message if it wants to stop the commit.
+#
+# To enable this hook, rename this file to "pre-applypatch".
+
+. git-sh-setup
+precommit="$(git rev-parse --git-path hooks/pre-commit)"
+test -x "$precommit" && exec "$precommit" ${1+"$@"}
+:

xmmpysas-1.4.2/pysas/.git/hooks/pre-commit.sample

@@ -0,0 +1,49 @@
+#!/bin/sh
+#
+# An example hook script to verify what is about to be committed.
+# Called by "git commit" with no arguments.  The hook should
+# exit with non-zero status after issuing an appropriate message if
+# it wants to stop the commit.
+#
+# To enable this hook, rename this file to "pre-commit".
+
+if git rev-parse --verify HEAD >/dev/null 2>&1
+then
+	against=HEAD
+else
+	# Initial commit: diff against an empty tree object
+	against=$(git hash-object -t tree /dev/null)
+fi
+
+# If you want to allow non-ASCII filenames set this variable to true.
+allownonascii=$(git config --bool hooks.allownonascii)
+
+# Redirect output to stderr.
+exec 1>&2
+
+# Cross platform projects tend to avoid non-ASCII filenames; prevent
+# them from being added to the repository. We exploit the fact that the
+# printable range starts at the space character and ends with tilde.
+if [ "$allownonascii" != "true" ] &&
+	# Note that the use of brackets around a tr range is ok here, (it's
+	# even required, for portability to Solaris 10's /usr/bin/tr), since
+	# the square bracket bytes happen to fall in the designated range.
+	test $(git diff --cached --name-only --diff-filter=A -z $against |
+	  LC_ALL=C tr -d '[ -~]\0' | wc -c) != 0
+then
+	cat <<\EOF
+Error: Attempt to add a non-ASCII file name.
+
+This can cause problems if you want to work with people on other platforms.
+
+To be portable it is advisable to rename the file.
+
+If you know what you are doing you can disable this check using:
+
+  git config hooks.allownonascii true
+EOF
+	exit 1
+fi
+
+# If there are whitespace errors, print the offending file names and fail.
+exec git diff-index --check --cached $against --

xmmpysas-1.4.2/pysas/.git/hooks/pre-merge-commit.sample

@@ -0,0 +1,13 @@
+#!/bin/sh
+#
+# An example hook script to verify what is about to be committed.
+# Called by "git merge" with no arguments.  The hook should
+# exit with non-zero status after issuing an appropriate message to
+# stderr if it wants to stop the merge commit.
+#
+# To enable this hook, rename this file to "pre-merge-commit".
+
+. git-sh-setup
+test -x "$GIT_DIR/hooks/pre-commit" &&
+        exec "$GIT_DIR/hooks/pre-commit"
+:

xmmpysas-1.4.2/pysas/.git/hooks/pre-push.sample

@@ -0,0 +1,53 @@
+#!/bin/sh
+
+# An example hook script to verify what is about to be pushed.  Called by "git
+# push" after it has checked the remote status, but before anything has been
+# pushed.  If this script exits with a non-zero status nothing will be pushed.
+#
+# This hook is called with the following parameters:
+#
+# $1 -- Name of the remote to which the push is being done
+# $2 -- URL to which the push is being done
+#
+# If pushing without using a named remote those arguments will be equal.
+#
+# Information about the commits which are being pushed is supplied as lines to
+# the standard input in the form:
+#
+#   <local ref> <local sha1> <remote ref> <remote sha1>
+#
+# This sample shows how to prevent push of commits where the log message starts
+# with "WIP" (work in progress).
+
+remote="$1"
+url="$2"
+
+z40=0000000000000000000000000000000000000000
+
+while read local_ref local_sha remote_ref remote_sha
+do
+	if [ "$local_sha" = $z40 ]
+	then
+		# Handle delete
+		:
+	else
+		if [ "$remote_sha" = $z40 ]
+		then
+			# New branch, examine all commits
+			range="$local_sha"
+		else
+			# Update to existing branch, examine new commits
+			range="$remote_sha..$local_sha"
+		fi
+
+		# Check for WIP commit
+		commit=`git rev-list -n 1 --grep '^WIP' "$range"`
+		if [ -n "$commit" ]
+		then
+			echo >&2 "Found WIP commit in $local_ref, not pushing"
+			exit 1
+		fi
+	fi
+done
+
+exit 0

xmmpysas-1.4.2/pysas/.git/hooks/pre-rebase.sample

@@ -0,0 +1,169 @@
+#!/bin/sh
+#
+# Copyright (c) 2006, 2008 Junio C Hamano
+#
+# The "pre-rebase" hook is run just before "git rebase" starts doing
+# its job, and can prevent the command from running by exiting with
+# non-zero status.
+#
+# The hook is called with the following parameters:
+#
+# $1 -- the upstream the series was forked from.
+# $2 -- the branch being rebased (or empty when rebasing the current branch).
+#
+# This sample shows how to prevent topic branches that are already
+# merged to 'next' branch from getting rebased, because allowing it
+# would result in rebasing already published history.
+
+publish=next
+basebranch="$1"
+if test "$#" = 2
+then
+	topic="refs/heads/$2"
+else
+	topic=`git symbolic-ref HEAD` ||
+	exit 0 ;# we do not interrupt rebasing detached HEAD
+fi
+
+case "$topic" in
+refs/heads/??/*)
+	;;
+*)
+	exit 0 ;# we do not interrupt others.
+	;;
+esac
+
+# Now we are dealing with a topic branch being rebased
+# on top of master.  Is it OK to rebase it?
+
+# Does the topic really exist?
+git show-ref -q "$topic" || {
+	echo >&2 "No such branch $topic"
+	exit 1
+}
+
+# Is topic fully merged to master?
+not_in_master=`git rev-list --pretty=oneline ^master "$topic"`
+if test -z "$not_in_master"
+then
+	echo >&2 "$topic is fully merged to master; better remove it."
+	exit 1 ;# we could allow it, but there is no point.
+fi
+
+# Is topic ever merged to next?  If so you should not be rebasing it.
+only_next_1=`git rev-list ^master "^$topic" ${publish} | sort`
+only_next_2=`git rev-list ^master           ${publish} | sort`
+if test "$only_next_1" = "$only_next_2"
+then
+	not_in_topic=`git rev-list "^$topic" master`
+	if test -z "$not_in_topic"
+	then
+		echo >&2 "$topic is already up to date with master"
+		exit 1 ;# we could allow it, but there is no point.
+	else
+		exit 0
+	fi
+else
+	not_in_next=`git rev-list --pretty=oneline ^${publish} "$topic"`
+	/usr/bin/perl -e '
+		my $topic = $ARGV[0];
+		my $msg = "* $topic has commits already merged to public branch:\n";
+		my (%not_in_next) = map {
+			/^([0-9a-f]+) /;
+			($1 => 1);
+		} split(/\n/, $ARGV[1]);
+		for my $elem (map {
+				/^([0-9a-f]+) (.*)$/;
+				[$1 => $2];
+			} split(/\n/, $ARGV[2])) {
+			if (!exists $not_in_next{$elem->[0]}) {
+				if ($msg) {
+					print STDERR $msg;
+					undef $msg;
+				}
+				print STDERR " $elem->[1]\n";
+			}
+		}
+	' "$topic" "$not_in_next" "$not_in_master"
+	exit 1
+fi
+
+<<\DOC_END
+
+This sample hook safeguards topic branches that have been
+published from being rewound.
+
+The workflow assumed here is:
+
+ * Once a topic branch forks from "master", "master" is never
+   merged into it again (either directly or indirectly).
+
+ * Once a topic branch is fully cooked and merged into "master",
+   it is deleted.  If you need to build on top of it to correct
+   earlier mistakes, a new topic branch is created by forking at
+   the tip of the "master".  This is not strictly necessary, but
+   it makes it easier to keep your history simple.
+
+ * Whenever you need to test or publish your changes to topic
+   branches, merge them into "next" branch.
+
+The script, being an example, hardcodes the publish branch name
+to be "next", but it is trivial to make it configurable via
+$GIT_DIR/config mechanism.
+
+With this workflow, you would want to know:
+
+(1) ... if a topic branch has ever been merged to "next".  Young
+    topic branches can have stupid mistakes you would rather
+    clean up before publishing, and things that have not been
+    merged into other branches can be easily rebased without
+    affecting other people.  But once it is published, you would
+    not want to rewind it.
+
+(2) ... if a topic branch has been fully merged to "master".
+    Then you can delete it.  More importantly, you should not
+    build on top of it -- other people may already want to
+    change things related to the topic as patches against your
+    "master", so if you need further changes, it is better to
+    fork the topic (perhaps with the same name) afresh from the
+    tip of "master".
+
+Let's look at this example:
+
+		   o---o---o---o---o---o---o---o---o---o "next"
+		  /       /           /           /
+		 /   a---a---b A     /           /
+		/   /               /           /
+	       /   /   c---c---c---c B         /
+	      /   /   /             \         /
+	     /   /   /   b---b C     \       /
+	    /   /   /   /             \     /
+    ---o---o---o---o---o---o---o---o---o---o---o "master"
+
+
+A, B and C are topic branches.
+
+ * A has one fix since it was merged up to "next".
+
+ * B has finished.  It has been fully merged up to "master" and "next",
+   and is ready to be deleted.
+
+ * C has not merged to "next" at all.
+
+We would want to allow C to be rebased, refuse A, and encourage
+B to be deleted.
+
+To compute (1):
+
+	git rev-list ^master ^topic next
+	git rev-list ^master        next
+
+	if these match, topic has not merged in next at all.
+
+To compute (2):
+
+	git rev-list master..topic
+
+	if this is empty, it is fully merged to "master".
+
+DOC_END

xmmpysas-1.4.2/pysas/.git/hooks/pre-receive.sample

@@ -0,0 +1,24 @@
+#!/bin/sh
+#
+# An example hook script to make use of push options.
+# The example simply echoes all push options that start with 'echoback='
+# and rejects all pushes when the "reject" push option is used.
+#
+# To enable this hook, rename this file to "pre-receive".
+
+if test -n "$GIT_PUSH_OPTION_COUNT"
+then
+	i=0
+	while test "$i" -lt "$GIT_PUSH_OPTION_COUNT"
+	do
+		eval "value=\$GIT_PUSH_OPTION_$i"
+		case "$value" in
+		echoback=*)
+			echo "echo from the pre-receive-hook: ${value#*=}" >&2
+			;;
+		reject)
+			exit 1
+		esac
+		i=$((i + 1))
+	done
+fi