Browse code

removed github old

Emanuel Soda authored on 13/05/2022 17:01:16
Showing2105 changed files

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-a
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-fb0cc84e95850ce27cdf7800328faa941221d518		branch 'master' of github.com:EmanuelSoda/ScreenR
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-ref: refs/heads/master
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-95e2b5b0659687183dbc320f19aa9cd8c2a2a289
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-[core]
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-	repositoryformatversion = 0
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-	filemode = true
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-	bare = false
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-	logallrefupdates = true
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-	ignorecase = true
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-	precomposeunicode = true
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-[remote "origin"]
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-	url = git@github.com:EmanuelSoda/ScreenR.git
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-	fetch = +refs/heads/*:refs/remotes/origin/*
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-[branch "master"]
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-	remote = origin
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-	merge = refs/heads/master
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-[remote "upstream"]
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-	url = git@git.bioconductor.org:packages/ScreenR.git
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-	fetch = +refs/heads/*:refs/remotes/upstream/*
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-Unnamed repository; edit this file 'description' to name the repository.
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-#!/bin/sh
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-#
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-# An example hook script to check the commit log message taken by
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-# applypatch from an e-mail message.
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-#
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-# The hook should exit with non-zero status after issuing an
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-# appropriate message if it wants to stop the commit.  The hook is
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-# allowed to edit the commit message file.
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-#
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-# To enable this hook, rename this file to "applypatch-msg".
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-
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-. git-sh-setup
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-commitmsg="$(git rev-parse --git-path hooks/commit-msg)"
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-test -x "$commitmsg" && exec "$commitmsg" ${1+"$@"}
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-:
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-#!/bin/sh
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-#
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-# An example hook script to check the commit log message.
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-# Called by "git commit" with one argument, the name of the file
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-# that has the commit message.  The hook should exit with non-zero
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-# status after issuing an appropriate message if it wants to stop the
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-# commit.  The hook is allowed to edit the commit message file.
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-#
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-# To enable this hook, rename this file to "commit-msg".
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-
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-# Uncomment the below to add a Signed-off-by line to the message.
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-# Doing this in a hook is a bad idea in general, but the prepare-commit-msg
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-# hook is more suited to it.
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-#
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-# SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p')
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-# grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"
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-
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-# This example catches duplicate Signed-off-by lines.
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-
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-test "" = "$(grep '^Signed-off-by: ' "$1" |
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-	 sort | uniq -c | sed -e '/^[ 	]*1[ 	]/d')" || {
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-	echo >&2 Duplicate Signed-off-by lines.
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-	exit 1
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-}
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-#!/usr/bin/perl
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-
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-use strict;
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-use warnings;
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-use IPC::Open2;
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-
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-# An example hook script to integrate Watchman
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-# (https://facebook.github.io/watchman/) with git to speed up detecting
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-# new and modified files.
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-#
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-# The hook is passed a version (currently 2) and last update token
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-# formatted as a string and outputs to stdout a new update token and
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-# all files that have been modified since the update token. Paths must
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-# be relative to the root of the working tree and separated by a single NUL.
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-#
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-# To enable this hook, rename this file to "query-watchman" and set
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-# 'git config core.fsmonitor .git/hooks/query-watchman'
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-#
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-my ($version, $last_update_token) = @ARGV;
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-
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-# Uncomment for debugging
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-# print STDERR "$0 $version $last_update_token\n";
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-
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-# Check the hook interface version
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-if ($version ne 2) {
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-	die "Unsupported query-fsmonitor hook version '$version'.\n" .
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-	    "Falling back to scanning...\n";
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-}
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-
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-my $git_work_tree = get_working_dir();
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-
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-my $retry = 1;
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-
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-my $json_pkg;
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-eval {
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-	require JSON::XS;
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-	$json_pkg = "JSON::XS";
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-	1;
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-} or do {
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-	require JSON::PP;
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-	$json_pkg = "JSON::PP";
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-};
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-
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-launch_watchman();
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-
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-sub launch_watchman {
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-	my $o = watchman_query();
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-	if (is_work_tree_watched($o)) {
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-		output_result($o->{clock}, @{$o->{files}});
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-	}
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-}
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-
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-sub output_result {
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-	my ($clockid, @files) = @_;
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-
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-	# Uncomment for debugging watchman output
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-	# open (my $fh, ">", ".git/watchman-output.out");
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-	# binmode $fh, ":utf8";
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-	# print $fh "$clockid\n@files\n";
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-	# close $fh;
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-
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-	binmode STDOUT, ":utf8";
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-	print $clockid;
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-	print "\0";
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-	local $, = "\0";
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-	print @files;
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-}
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-
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-sub watchman_clock {
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-	my $response = qx/watchman clock "$git_work_tree"/;
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-	die "Failed to get clock id on '$git_work_tree'.\n" .
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-		"Falling back to scanning...\n" if $? != 0;
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-
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-	return $json_pkg->new->utf8->decode($response);
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-}
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-
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-sub watchman_query {
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-	my $pid = open2(\*CHLD_OUT, \*CHLD_IN, 'watchman -j --no-pretty')
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-	or die "open2() failed: $!\n" .
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-	"Falling back to scanning...\n";
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-
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-	# In the query expression below we're asking for names of files that
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-	# changed since $last_update_token but not from the .git folder.
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-	#
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-	# To accomplish this, we're using the "since" generator to use the
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-	# recency index to select candidate nodes and "fields" to limit the
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-	# output to file names only. Then we're using the "expression" term to
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-	# further constrain the results.
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-	if (substr($last_update_token, 0, 1) eq "c") {
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-		$last_update_token = "\"$last_update_token\"";
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-	}
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-	my $query = <<"	END";
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-		["query", "$git_work_tree", {
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-			"since": $last_update_token,
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-			"fields": ["name"],
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-			"expression": ["not", ["dirname", ".git"]]
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-		}]
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-	END
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-
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-	# Uncomment for debugging the watchman query
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-	# open (my $fh, ">", ".git/watchman-query.json");
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-	# print $fh $query;
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-	# close $fh;
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-
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-	print CHLD_IN $query;
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-	close CHLD_IN;
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-	my $response = do {local $/; <CHLD_OUT>};
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-
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-	# Uncomment for debugging the watch response
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-	# open ($fh, ">", ".git/watchman-response.json");
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-	# print $fh $response;
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-	# close $fh;
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-
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-	die "Watchman: command returned no output.\n" .
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-	"Falling back to scanning...\n" if $response eq "";
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-	die "Watchman: command returned invalid output: $response\n" .
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-	"Falling back to scanning...\n" unless $response =~ /^\{/;
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-
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-	return $json_pkg->new->utf8->decode($response);
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-}
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-
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-sub is_work_tree_watched {
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-	my ($output) = @_;
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-	my $error = $output->{error};
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-	if ($retry > 0 and $error and $error =~ m/unable to resolve root .* directory (.*) is not watched/) {
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-		$retry--;
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-		my $response = qx/watchman watch "$git_work_tree"/;
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-		die "Failed to make watchman watch '$git_work_tree'.\n" .
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-		    "Falling back to scanning...\n" if $? != 0;
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-		$output = $json_pkg->new->utf8->decode($response);
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-		$error = $output->{error};
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-		die "Watchman: $error.\n" .
133
-		"Falling back to scanning...\n" if $error;
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-
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-		# Uncomment for debugging watchman output
136
-		# open (my $fh, ">", ".git/watchman-output.out");
137
-		# close $fh;
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-
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-		# Watchman will always return all files on the first query so
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-		# return the fast "everything is dirty" flag to git and do the
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-		# Watchman query just to get it over with now so we won't pay
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-		# the cost in git to look up each individual file.
143
-		my $o = watchman_clock();
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-		$error = $output->{error};
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-
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-		die "Watchman: $error.\n" .
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-		"Falling back to scanning...\n" if $error;
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-
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-		output_result($o->{clock}, ("/"));
150
-		$last_update_token = $o->{clock};
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-
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-		eval { launch_watchman() };
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-		return 0;
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-	}
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-
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-	die "Watchman: $error.\n" .
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-	"Falling back to scanning...\n" if $error;
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-
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-	return 1;
160
-}
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-
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-sub get_working_dir {
163
-	my $working_dir;
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-	if ($^O =~ 'msys' || $^O =~ 'cygwin') {
165
-		$working_dir = Win32::GetCwd();
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-		$working_dir =~ tr/\\/\//;
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-	} else {
168
-		require Cwd;
169
-		$working_dir = Cwd::cwd();
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-	}
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-
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-	return $working_dir;
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-}
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-#!/bin/sh
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-#
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-# An example hook script to prepare a packed repository for use over
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-# dumb transports.
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-#
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-# To enable this hook, rename this file to "post-update".
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-
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-exec git update-server-info
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-#!/bin/sh
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-#
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-# An example hook script to verify what is about to be committed
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-# by applypatch from an e-mail message.
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-#
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-# The hook should exit with non-zero status after issuing an
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-# appropriate message if it wants to stop the commit.
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-#
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-# To enable this hook, rename this file to "pre-applypatch".
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-
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-. git-sh-setup
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-precommit="$(git rev-parse --git-path hooks/pre-commit)"
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-test -x "$precommit" && exec "$precommit" ${1+"$@"}
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-:
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-#!/bin/bash
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-README=($(git diff --cached --name-only | grep -Ei '^README\.[R]?md$'))
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-MSG="use 'git commit --no-verify' to override this check"
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-
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-if [[ ${#README[@]} == 0 ]]; then
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-  exit 0
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-fi
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-
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-if [[ README.Rmd -nt README.md ]]; then
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-  echo -e "README.md is out of date; please re-knit README.Rmd\n$MSG"
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-  exit 1
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-elif [[ ${#README[@]} -lt 2 ]]; then
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-  echo -e "README.Rmd and README.md should be both staged\n$MSG"
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-  exit 1
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-fi
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-#!/bin/sh
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-#
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-# An example hook script to verify what is about to be committed.
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-# Called by "git commit" with no arguments.  The hook should
5
-# exit with non-zero status after issuing an appropriate message if
6
-# it wants to stop the commit.
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-#
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-# To enable this hook, rename this file to "pre-commit".
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-
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-if git rev-parse --verify HEAD >/dev/null 2>&1
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-then
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-	against=HEAD
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-else
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-	# Initial commit: diff against an empty tree object
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-	against=$(git hash-object -t tree /dev/null)
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-fi
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-
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-# If you want to allow non-ASCII filenames set this variable to true.
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-allownonascii=$(git config --type=bool hooks.allownonascii)
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-
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-# Redirect output to stderr.
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-exec 1>&2
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-
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-# Cross platform projects tend to avoid non-ASCII filenames; prevent
25
-# them from being added to the repository. We exploit the fact that the
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-# printable range starts at the space character and ends with tilde.
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-if [ "$allownonascii" != "true" ] &&
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-	# Note that the use of brackets around a tr range is ok here, (it's
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-	# even required, for portability to Solaris 10's /usr/bin/tr), since
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-	# the square bracket bytes happen to fall in the designated range.
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-	test $(git diff --cached --name-only --diff-filter=A -z $against |
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-	  LC_ALL=C tr -d '[ -~]\0' | wc -c) != 0
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-then
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-	cat <<\EOF
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-Error: Attempt to add a non-ASCII file name.
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-
37
-This can cause problems if you want to work with people on other platforms.
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-
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-To be portable it is advisable to rename the file.
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-
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-If you know what you are doing you can disable this check using:
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-
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-  git config hooks.allownonascii true
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-EOF
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-	exit 1
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-fi
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-
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-# If there are whitespace errors, print the offending file names and fail.
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-exec git diff-index --check --cached $against --
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-#!/bin/sh
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-#
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-# An example hook script to verify what is about to be committed.
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-# Called by "git merge" with no arguments.  The hook should
5
-# exit with non-zero status after issuing an appropriate message to
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-# stderr if it wants to stop the merge commit.
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-#
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-# To enable this hook, rename this file to "pre-merge-commit".
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-
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-. git-sh-setup
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-test -x "$GIT_DIR/hooks/pre-commit" &&
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-        exec "$GIT_DIR/hooks/pre-commit"
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-:
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-#!/bin/sh
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-
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-# An example hook script to verify what is about to be pushed.  Called by "git
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-# push" after it has checked the remote status, but before anything has been
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-# pushed.  If this script exits with a non-zero status nothing will be pushed.
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-#
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-# This hook is called with the following parameters:
8
-#
9
-# $1 -- Name of the remote to which the push is being done
10
-# $2 -- URL to which the push is being done
11
-#
12
-# If pushing without using a named remote those arguments will be equal.
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-#
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-# Information about the commits which are being pushed is supplied as lines to
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-# the standard input in the form:
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-#
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-#   <local ref> <local oid> <remote ref> <remote oid>
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-#
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-# This sample shows how to prevent push of commits where the log message starts
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-# with "WIP" (work in progress).
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-
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-remote="$1"
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-url="$2"
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-
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-zero=$(git hash-object --stdin </dev/null | tr '[0-9a-f]' '0')
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-
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-while read local_ref local_oid remote_ref remote_oid
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-do
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-	if test "$local_oid" = "$zero"
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-	then
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-		# Handle delete
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-		:
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-	else
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-		if test "$remote_oid" = "$zero"
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-		then
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-			# New branch, examine all commits
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-			range="$local_oid"
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-		else
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-			# Update to existing branch, examine new commits
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-			range="$remote_oid..$local_oid"
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-		fi
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-
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-		# Check for WIP commit
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-		commit=$(git rev-list -n 1 --grep '^WIP' "$range")
45
-		if test -n "$commit"
46
-		then
47
-			echo >&2 "Found WIP commit in $local_ref, not pushing"
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-			exit 1
49
-		fi
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-	fi
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-done
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-
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-exit 0
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-#!/bin/sh
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-#
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-# Copyright (c) 2006, 2008 Junio C Hamano
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-#
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-# The "pre-rebase" hook is run just before "git rebase" starts doing
6
-# its job, and can prevent the command from running by exiting with
7
-# non-zero status.
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-#
9
-# The hook is called with the following parameters:
10
-#
11
-# $1 -- the upstream the series was forked from.
12
-# $2 -- the branch being rebased (or empty when rebasing the current branch).
13
-#
14
-# This sample shows how to prevent topic branches that are already
15
-# merged to 'next' branch from getting rebased, because allowing it
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-# would result in rebasing already published history.
17
-
18
-publish=next
19
-basebranch="$1"
20
-if test "$#" = 2
21
-then
22
-	topic="refs/heads/$2"
23
-else
24
-	topic=`git symbolic-ref HEAD` ||
25
-	exit 0 ;# we do not interrupt rebasing detached HEAD
26
-fi
27
-
28
-case "$topic" in
29
-refs/heads/??/*)
30
-	;;
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-*)
32
-	exit 0 ;# we do not interrupt others.
33
-	;;
34
-esac
35
-
36
-# Now we are dealing with a topic branch being rebased
37
-# on top of master.  Is it OK to rebase it?
38
-
39
-# Does the topic really exist?
40
-git show-ref -q "$topic" || {
41
-	echo >&2 "No such branch $topic"
42
-	exit 1
43
-}
44
-
45
-# Is topic fully merged to master?
46
-not_in_master=`git rev-list --pretty=oneline ^master "$topic"`
47
-if test -z "$not_in_master"
48
-then
49
-	echo >&2 "$topic is fully merged to master; better remove it."
50
-	exit 1 ;# we could allow it, but there is no point.
51
-fi
52
-
53
-# Is topic ever merged to next?  If so you should not be rebasing it.
54
-only_next_1=`git rev-list ^master "^$topic" ${publish} | sort`
55
-only_next_2=`git rev-list ^master           ${publish} | sort`
56
-if test "$only_next_1" = "$only_next_2"
57
-then
58
-	not_in_topic=`git rev-list "^$topic" master`
59
-	if test -z "$not_in_topic"
60
-	then
61
-		echo >&2 "$topic is already up to date with master"
62
-		exit 1 ;# we could allow it, but there is no point.
63
-	else
64
-		exit 0
65
-	fi
66
-else
67
-	not_in_next=`git rev-list --pretty=oneline ^${publish} "$topic"`
68
-	/usr/bin/perl -e '
69
-		my $topic = $ARGV[0];
70
-		my $msg = "* $topic has commits already merged to public branch:\n";
71
-		my (%not_in_next) = map {
72
-			/^([0-9a-f]+) /;
73
-			($1 => 1);
74
-		} split(/\n/, $ARGV[1]);
75
-		for my $elem (map {
76
-				/^([0-9a-f]+) (.*)$/;
77
-				[$1 => $2];
78
-			} split(/\n/, $ARGV[2])) {
79
-			if (!exists $not_in_next{$elem->[0]}) {
80
-				if ($msg) {
81
-					print STDERR $msg;
82
-					undef $msg;
83
-				}
84
-				print STDERR " $elem->[1]\n";
85
-			}
86
-		}
87
-	' "$topic" "$not_in_next" "$not_in_master"
88
-	exit 1
89
-fi
90
-
91
-<<\DOC_END
92
-
93
-This sample hook safeguards topic branches that have been
94
-published from being rewound.
95
-
96
-The workflow assumed here is:
97
-
98
- * Once a topic branch forks from "master", "master" is never
99
-   merged into it again (either directly or indirectly).
100
-
101
- * Once a topic branch is fully cooked and merged into "master",
102
-   it is deleted.  If you need to build on top of it to correct
103
-   earlier mistakes, a new topic branch is created by forking at
104
-   the tip of the "master".  This is not strictly necessary, but
105
-   it makes it easier to keep your history simple.
106
-
107
- * Whenever you need to test or publish your changes to topic
108
-   branches, merge them into "next" branch.
109
-
110
-The script, being an example, hardcodes the publish branch name
111
-to be "next", but it is trivial to make it configurable via
112
-$GIT_DIR/config mechanism.
113
-
114
-With this workflow, you would want to know:
115
-
116
-(1) ... if a topic branch has ever been merged to "next".  Young
117
-    topic branches can have stupid mistakes you would rather
118
-    clean up before publishing, and things that have not been
119
-    merged into other branches can be easily rebased without
120
-    affecting other people.  But once it is published, you would
121
-    not want to rewind it.
122
-
123
-(2) ... if a topic branch has been fully merged to "master".
124
-    Then you can delete it.  More importantly, you should not
125
-    build on top of it -- other people may already want to
126
-    change things related to the topic as patches against your
127
-    "master", so if you need further changes, it is better to
128
-    fork the topic (perhaps with the same name) afresh from the
129
-    tip of "master".
130
-
131
-Let's look at this example:
132
-
133
-		   o---o---o---o---o---o---o---o---o---o "next"
134
-		  /       /           /           /
135
-		 /   a---a---b A     /           /
136
-		/   /               /           /
137
-	       /   /   c---c---c---c B         /
138
-	      /   /   /             \         /
139
-	     /   /   /   b---b C     \       /
140
-	    /   /   /   /             \     /
141
-    ---o---o---o---o---o---o---o---o---o---o---o "master"
142
-
143
-
144
-A, B and C are topic branches.
145
-
146
- * A has one fix since it was merged up to "next".
147
-
148
- * B has finished.  It has been fully merged up to "master" and "next",
149
-   and is ready to be deleted.
150
-
151
- * C has not merged to "next" at all.
152
-
153
-We would want to allow C to be rebased, refuse A, and encourage
154
-B to be deleted.
155
-
156
-To compute (1):
157
-
158
-	git rev-list ^master ^topic next
159
-	git rev-list ^master        next
160
-
161
-	if these match, topic has not merged in next at all.
162
-
163
-To compute (2):
164
-
165
-	git rev-list master..topic
166
-
167
-	if this is empty, it is fully merged to "master".
168
-
169
-DOC_END
170 0
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@@ -1,24 +0,0 @@
1
-#!/bin/sh
2
-#
3
-# An example hook script to make use of push options.
4
-# The example simply echoes all push options that start with 'echoback='
5
-# and rejects all pushes when the "reject" push option is used.
6
-#
7
-# To enable this hook, rename this file to "pre-receive".
8
-
9
-if test -n "$GIT_PUSH_OPTION_COUNT"
10
-then
11
-	i=0
12
-	while test "$i" -lt "$GIT_PUSH_OPTION_COUNT"
13
-	do
14
-		eval "value=\$GIT_PUSH_OPTION_$i"
15
-		case "$value" in
16
-		echoback=*)
17
-			echo "echo from the pre-receive-hook: ${value#*=}" >&2
18
-			;;
19
-		reject)
20
-			exit 1
21
-		esac
22
-		i=$((i + 1))
23
-	done
24
-fi
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... ...
@@ -1,42 +0,0 @@
1
-#!/bin/sh
2
-#
3
-# An example hook script to prepare the commit log message.
4
-# Called by "git commit" with the name of the file that has the
5
-# commit message, followed by the description of the commit
6
-# message's source.  The hook's purpose is to edit the commit
7
-# message file.  If the hook fails with a non-zero status,
8
-# the commit is aborted.
9
-#
10
-# To enable this hook, rename this file to "prepare-commit-msg".
11
-
12
-# This hook includes three examples. The first one removes the
13
-# "# Please enter the commit message..." help message.
14
-#
15
-# The second includes the output of "git diff --name-status -r"
16
-# into the message, just before the "git status" output.  It is
17
-# commented because it doesn't cope with --amend or with squashed
18
-# commits.
19
-#
20
-# The third example adds a Signed-off-by line to the message, that can
21
-# still be edited.  This is rarely a good idea.
22
-
23
-COMMIT_MSG_FILE=$1
24
-COMMIT_SOURCE=$2
25
-SHA1=$3
26
-
27
-/usr/bin/perl -i.bak -ne 'print unless(m/^. Please enter the commit message/..m/^#$/)' "$COMMIT_MSG_FILE"
28
-
29
-# case "$COMMIT_SOURCE,$SHA1" in
30
-#  ,|template,)
31
-#    /usr/bin/perl -i.bak -pe '
32
-#       print "\n" . `git diff --cached --name-status -r`
33
-# 	 if /^#/ && $first++ == 0' "$COMMIT_MSG_FILE" ;;
34
-#  *) ;;
35
-# esac
36
-
37
-# SOB=$(git var GIT_COMMITTER_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p')
38
-# git interpret-trailers --in-place --trailer "$SOB" "$COMMIT_MSG_FILE"
39
-# if test -z "$COMMIT_SOURCE"
40
-# then
41
-#   /usr/bin/perl -i.bak -pe 'print "\n" if !$first_line++' "$COMMIT_MSG_FILE"
42
-# fi
43 0
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... ...
@@ -1,78 +0,0 @@
1
-#!/bin/sh
2
-
3
-# An example hook script to update a checked-out tree on a git push.
4
-#
5
-# This hook is invoked by git-receive-pack(1) when it reacts to git
6
-# push and updates reference(s) in its repository, and when the push
7
-# tries to update the branch that is currently checked out and the
8
-# receive.denyCurrentBranch configuration variable is set to
9
-# updateInstead.
10
-#
11
-# By default, such a push is refused if the working tree and the index
12
-# of the remote repository has any difference from the currently
13
-# checked out commit; when both the working tree and the index match
14
-# the current commit, they are updated to match the newly pushed tip
15
-# of the branch. This hook is to be used to override the default
16
-# behaviour; however the code below reimplements the default behaviour
17
-# as a starting point for convenient modification.
18
-#
19
-# The hook receives the commit with which the tip of the current
20
-# branch is going to be updated:
21
-commit=$1
22
-
23
-# It can exit with a non-zero status to refuse the push (when it does
24
-# so, it must not modify the index or the working tree).
25
-die () {
26
-	echo >&2 "$*"
27
-	exit 1
28
-}
29
-
30
-# Or it can make any necessary changes to the working tree and to the
31
-# index to bring them to the desired state when the tip of the current
32
-# branch is updated to the new commit, and exit with a zero status.
33
-#
34
-# For example, the hook can simply run git read-tree -u -m HEAD "$1"
35
-# in order to emulate git fetch that is run in the reverse direction
36
-# with git push, as the two-tree form of git read-tree -u -m is
37
-# essentially the same as git switch or git checkout that switches
38
-# branches while keeping the local changes in the working tree that do
39
-# not interfere with the difference between the branches.
40
-
41
-# The below is a more-or-less exact translation to shell of the C code
42
-# for the default behaviour for git's push-to-checkout hook defined in
43
-# the push_to_deploy() function in builtin/receive-pack.c.
44
-#
45
-# Note that the hook will be executed from the repository directory,
46
-# not from the working tree, so if you want to perform operations on
47
-# the working tree, you will have to adapt your code accordingly, e.g.
48
-# by adding "cd .." or using relative paths.
49
-
50
-if ! git update-index -q --ignore-submodules --refresh
51
-then
52
-	die "Up-to-date check failed"
53
-fi
54
-
55
-if ! git diff-files --quiet --ignore-submodules --
56
-then
57
-	die "Working directory has unstaged changes"
58
-fi
59
-
60
-# This is a rough translation of:
61
-#
62
-#   head_has_history() ? "HEAD" : EMPTY_TREE_SHA1_HEX
63
-if git cat-file -e HEAD 2>/dev/null
64
-then
65
-	head=HEAD
66
-else
67
-	head=$(git hash-object -t tree --stdin </dev/null)
68
-fi
69
-
70
-if ! git diff-index --quiet --cached --ignore-submodules $head --
71
-then
72
-	die "Working directory has staged changes"
73
-fi
74
-
75
-if ! git read-tree -u -m "$commit"
76
-then
77
-	die "Could not update working tree to new HEAD"
78
-fi
79 0
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@@ -1,128 +0,0 @@
1
-#!/bin/sh
2
-#
3
-# An example hook script to block unannotated tags from entering.
4
-# Called by "git receive-pack" with arguments: refname sha1-old sha1-new
5
-#
6
-# To enable this hook, rename this file to "update".
7
-#
8
-# Config
9
-# ------
10
-# hooks.allowunannotated
11
-#   This boolean sets whether unannotated tags will be allowed into the
12
-#   repository.  By default they won't be.
13
-# hooks.allowdeletetag
14
-#   This boolean sets whether deleting tags will be allowed in the
15
-#   repository.  By default they won't be.
16
-# hooks.allowmodifytag
17
-#   This boolean sets whether a tag may be modified after creation. By default
18
-#   it won't be.
19
-# hooks.allowdeletebranch
20
-#   This boolean sets whether deleting branches will be allowed in the
21
-#   repository.  By default they won't be.
22
-# hooks.denycreatebranch
23
-#   This boolean sets whether remotely creating branches will be denied
24
-#   in the repository.  By default this is allowed.
25
-#
26
-
27
-# --- Command line
28
-refname="$1"
29
-oldrev="$2"
30
-newrev="$3"
31
-
32
-# --- Safety check
33
-if [ -z "$GIT_DIR" ]; then
34
-	echo "Don't run this script from the command line." >&2
35
-	echo " (if you want, you could supply GIT_DIR then run" >&2
36
-	echo "  $0 <ref> <oldrev> <newrev>)" >&2
37
-	exit 1
38
-fi
39
-
40
-if [ -z "$refname" -o -z "$oldrev" -o -z "$newrev" ]; then
41
-	echo "usage: $0 <ref> <oldrev> <newrev>" >&2
42
-	exit 1
43
-fi
44
-
45
-# --- Config
46
-allowunannotated=$(git config --type=bool hooks.allowunannotated)
47
-allowdeletebranch=$(git config --type=bool hooks.allowdeletebranch)
48
-denycreatebranch=$(git config --type=bool hooks.denycreatebranch)
49
-allowdeletetag=$(git config --type=bool hooks.allowdeletetag)
50
-allowmodifytag=$(git config --type=bool hooks.allowmodifytag)
51
-
52
-# check for no description
53
-projectdesc=$(sed -e '1q' "$GIT_DIR/description")
54
-case "$projectdesc" in
55
-"Unnamed repository"* | "")
56
-	echo "*** Project description file hasn't been set" >&2
57
-	exit 1
58
-	;;
59
-esac
60
-
61
-# --- Check types
62
-# if $newrev is 0000...0000, it's a commit to delete a ref.
63
-zero=$(git hash-object --stdin </dev/null | tr '[0-9a-f]' '0')
64
-if [ "$newrev" = "$zero" ]; then
65
-	newrev_type=delete
66
-else
67
-	newrev_type=$(git cat-file -t $newrev)
68
-fi
69
-
70
-case "$refname","$newrev_type" in
71
-	refs/tags/*,commit)
72
-		# un-annotated tag
73
-		short_refname=${refname##refs/tags/}
74
-		if [ "$allowunannotated" != "true" ]; then
75
-			echo "*** The un-annotated tag, $short_refname, is not allowed in this repository" >&2
76
-			echo "*** Use 'git tag [ -a | -s ]' for tags you want to propagate." >&2
77
-			exit 1
78
-		fi
79
-		;;
80
-	refs/tags/*,delete)
81
-		# delete tag
82
-		if [ "$allowdeletetag" != "true" ]; then
83
-			echo "*** Deleting a tag is not allowed in this repository" >&2
84
-			exit 1
85
-		fi
86
-		;;
87
-	refs/tags/*,tag)
88
-		# annotated tag
89
-		if [ "$allowmodifytag" != "true" ] && git rev-parse $refname > /dev/null 2>&1
90
-		then
91
-			echo "*** Tag '$refname' already exists." >&2
92
-			echo "*** Modifying a tag is not allowed in this repository." >&2
93
-			exit 1
94
-		fi
95
-		;;
96
-	refs/heads/*,commit)
97
-		# branch
98
-		if [ "$oldrev" = "$zero" -a "$denycreatebranch" = "true" ]; then
99
-			echo "*** Creating a branch is not allowed in this repository" >&2
100
-			exit 1
101
-		fi
102
-		;;
103
-	refs/heads/*,delete)
104
-		# delete branch
105
-		if [ "$allowdeletebranch" != "true" ]; then
106
-			echo "*** Deleting a branch is not allowed in this repository" >&2
107
-			exit 1
108
-		fi
109
-		;;
110
-	refs/remotes/*,commit)
111
-		# tracking branch
112
-		;;
113
-	refs/remotes/*,delete)
114
-		# delete tracking branch
115
-		if [ "$allowdeletebranch" != "true" ]; then
116
-			echo "*** Deleting a tracking branch is not allowed in this repository" >&2
117
-			exit 1
118
-		fi
119
-		;;
120
-	*)
121
-		# Anything else (is there anything else?)
122
-		echo "*** Update hook: unknown type of update to ref $refname of type $newrev_type" >&2
123
-		exit 1
124
-		;;
125
-esac
126
-
127
-# --- Finished
128
-exit 0
129 0
deleted file mode 100644
130 1
Binary files a/.git_old/index and /dev/null differ
131 2
deleted file mode 100644
... ...
@@ -1,6 +0,0 @@
1
-# git ls-files --others --exclude-from=.git/info/exclude
2
-# Lines that start with '#' are comments.
3
-# For a project mostly in C, the following would be a good set of
4
-# exclude patterns (uncomment them if you want to use them):
5
-# *.[oa]
6
-# *~
7 0
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... ...
@@ -1,76 +0,0 @@
1
-0000000000000000000000000000000000000000 dee1003e81a2553a14b02ebe61d5c6d6340dd92b Emanuel Soda <emanuelsoda@gmail.com> 1646400745 +0100	clone: from github.com:EmanuelSoda/ScreenR.git
2
-dee1003e81a2553a14b02ebe61d5c6d6340dd92b 7624ce33230f9b152fd386886719ce5969487308 Emanuel Soda <emanuelsoda@gmail.com> 1646400966 +0100	checkout: moving from master to develop
3
-7624ce33230f9b152fd386886719ce5969487308 72a461a62a588f008e334fe70b90c84171264a78 Emanuel Soda <emanuelsoda@gmail.com> 1646492278 +0100	commit: changes to documentation
4
-72a461a62a588f008e334fe70b90c84171264a78 a26a66ffcbf5ec09376b6d69086f562455bad3d7 Emanuel Soda <emanuelsoda@gmail.com> 1646497080 +0100	commit: modificata vignetta
5
-a26a66ffcbf5ec09376b6d69086f562455bad3d7 98069c9b8d46911bb491bbd2bf13d3866b5cde97 Emanuel Soda <emanuelsoda@gmail.com> 1646498114 +0100	commit: ccc
6
-98069c9b8d46911bb491bbd2bf13d3866b5cde97 c66637d67d4f3d52defc472cc314e710d3ac9d06 Emanuel Soda <emanuelsoda@gmail.com> 1648206989 +0100	commit: risolved some error for bioconductor
7
-c66637d67d4f3d52defc472cc314e710d3ac9d06 5c3cc3f1794d814c6aaa9f7bd3d9eb7cb490dbc9 Emanuel Soda <emanuelsoda@gmail.com> 1649069227 +0200	commit: fixed some bugs
8
-5c3cc3f1794d814c6aaa9f7bd3d9eb7cb490dbc9 5c3cc3f1794d814c6aaa9f7bd3d9eb7cb490dbc9 Emanuel Soda <emanuelsoda@gmail.com> 1649070546 +0200	checkout: moving from develop to develop_2
9
-5c3cc3f1794d814c6aaa9f7bd3d9eb7cb490dbc9 b2783d0827f18fb1c081ec69654bb1ff11a054ed Emanuel Soda <emanuelsoda@gmail.com> 1649071594 +0200	checkout: moving from develop_2 to master
10
-b2783d0827f18fb1c081ec69654bb1ff11a054ed 53c2de862aa5a9d41af68f365b2405d67f4b4e9b Emanuel Soda <emanuelsoda@gmail.com> 1649071744 +0200	commit (merge): eliminate figure
11
-53c2de862aa5a9d41af68f365b2405d67f4b4e9b 37a1e5bb8639706b15a680238da89d50a0ce4813 Emanuel Soda <emanuelsoda@gmail.com> 1649073699 +0200	commit: Increment version number to 0.100.0
12
-37a1e5bb8639706b15a680238da89d50a0ce4813 3ed0e46df45b1765a7311b378ded59e05c2ae9a3 Emanuel Soda <emanuelsoda@gmail.com> 1649073803 +0200	commit: bug fix
13
-3ed0e46df45b1765a7311b378ded59e05c2ae9a3 56797d513c07787a09b441c5168555fed3935bde Emanuel Soda <emanuelsoda@gmail.com> 1649075405 +0200	commit: fixed bug of the previus upload
14
-56797d513c07787a09b441c5168555fed3935bde 416f8180ef27d8578c81a1665c6ab861ac055842 Emanuel Soda <emanuelsoda@gmail.com> 1649143952 +0200	commit: other bug fix
15
-416f8180ef27d8578c81a1665c6ab861ac055842 3395f3a604a07b2445505f474107de251d0a5fb8 Emanuel Soda <emanuelsoda@gmail.com> 1649145007 +0200	commit: a
16
-3395f3a604a07b2445505f474107de251d0a5fb8 16bfe01c1bcd69310a55031772ad1fce51d3eac7 Emanuel Soda <emanuelsoda@gmail.com> 1649145357 +0200	commit: trying to remove unwanted files
17
-16bfe01c1bcd69310a55031772ad1fce51d3eac7 3896ec5da42dbc146f0a654fdc70fbd9b5af4cde Emanuel Soda <emanuelsoda@gmail.com> 1649146922 +0200	commit: removed ScreenR.Rproj from git
18
-3896ec5da42dbc146f0a654fdc70fbd9b5af4cde 97f9ea2621eccea424dffb2ff1ba97c8786908fb Emanuel Soda <emanuelsoda@gmail.com> 1649146980 +0200	commit: removed ScreenR.Rproj from git 2
19
-97f9ea2621eccea424dffb2ff1ba97c8786908fb 353eaa4f5653e3e9242322efea703e9d712ecfb4 Emanuel Soda <emanuelsoda@gmail.com> 1649147724 +0200	commit: non sto capendo
20
-353eaa4f5653e3e9242322efea703e9d712ecfb4 4808c9650a62d8711510aed9da3d8c208cea518c Emanuel Soda <emanuelsoda@gmail.com> 1649148385 +0200	commit: .gitignore modified again
21
-4808c9650a62d8711510aed9da3d8c208cea518c d23c11ef2e29a4f0471918dfcb87dbe0e93d412a Emanuel Soda <emanuelsoda@gmail.com> 1649161910 +0200	commit: tried to removed unwanted files
22
-d23c11ef2e29a4f0471918dfcb87dbe0e93d412a ce24e60f876918e266ca21603ba9cf864d9f1374 Emanuel Soda <emanuelsoda@gmail.com> 1649166908 +0200	commit: modified the find_commond_hit function
23
-ce24e60f876918e266ca21603ba9cf864d9f1374 a0109cd08d102177567e7e5c9356181aae8f876d Emanuel Soda <emanuelsoda@gmail.com> 1649168022 +0200	commit: modified find_common_hit
24
-a0109cd08d102177567e7e5c9356181aae8f876d 2b065f50d18b69b04dfbd491715aad3f7c655132 Emanuel Soda <emanuelsoda@gmail.com> 1649171784 +0200	commit: No the warning and error, moreover rebuild the site
25
-2b065f50d18b69b04dfbd491715aad3f7c655132 dd6374ad7a82ddb289a4478f37aea923ed73295f Emanuel Soda <emanuelsoda@gmail.com> 1649172023 +0200	commit: removed .Rproj.user/
26
-dd6374ad7a82ddb289a4478f37aea923ed73295f 773ceed2f194352f05de66652b9bd3f72af65f67 Emanuel Soda <emanuelsoda@gmail.com> 1649338634 +0200	commit: updated the vignette with the new data
27
-773ceed2f194352f05de66652b9bd3f72af65f67 a15d5938250aba810191c46c0a6db92986b303a1 Emanuel Soda <emanuelsoda@gmail.com> 1649347474 +0200	commit: new data and all works
28
-a15d5938250aba810191c46c0a6db92986b303a1 576fd8e2f2d19220a4d607f996f67f4a7257565f Emanuel Soda <emanuelsoda@gmail.com> 1649349028 +0200	commit: all setted
29
-576fd8e2f2d19220a4d607f996f67f4a7257565f a354d6de8df20245274ccbf32b7dc0e10035dafe Emanuel Soda <emanuelsoda@gmail.com> 1649427781 +0200	commit: update
30
-a354d6de8df20245274ccbf32b7dc0e10035dafe 5f0382b0817abef012c865493517a1d3f9ef132c Emanuel Soda <emanuelsoda@gmail.com> 1649428044 +0200	commit: update github
31
-5f0382b0817abef012c865493517a1d3f9ef132c 35afaf59abc78f761baabfa0d986460ad87d2523 Emanuel Soda <emanuelsoda@gmail.com> 1649777896 +0200	commit: tried some blog stuff
32
-35afaf59abc78f761baabfa0d986460ad87d2523 fcfec19bb1ab2225538367081043fb9d26fe90b1 Emanuel Soda <emanuelsoda@gmail.com> 1649791272 +0200	commit: aggiunte github action
33
-fcfec19bb1ab2225538367081043fb9d26fe90b1 f75bdf3211cbd105e330f5bcd335398a3336dbea Emanuel Soda <emanuelsoda@gmail.com> 1649793901 +0200	commit: modified site
34
-f75bdf3211cbd105e330f5bcd335398a3336dbea d5a4f7558712fa509f494a70dd8f49c134285642 Emanuel Soda <emanuelsoda@gmail.com> 1649793948 +0200	pull: Fast-forward
35
-d5a4f7558712fa509f494a70dd8f49c134285642 860275eaddab4b6ab66d8f7628053aa86ed455f4 Emanuel Soda <emanuelsoda@gmail.com> 1649840525 +0200	commit: added new logo
36
-860275eaddab4b6ab66d8f7628053aa86ed455f4 ad6a582ca867a38bcba04b2e65be45a82486a9d4 Emanuel Soda <emanuelsoda@gmail.com> 1650032958 +0200	commit: Start the revision process modified plot_MDS function removing tolto check_overlap = TRUE and added show_elements = TRUE to plot_common
37
-ad6a582ca867a38bcba04b2e65be45a82486a9d4 e655ff4964845cca0512101a499975f580a40ef9 Emanuel Soda <emanuelsoda@gmail.com> 1650034275 +0200	commit: Removed lazy data
38
-e655ff4964845cca0512101a499975f580a40ef9 6ca88b001b83939b2bcf920af3e114c1f13c08d0 Emanuel Soda <emanuelsoda@gmail.com> 1650211003 +0200	commit: scoperto biocthis
39
-6ca88b001b83939b2bcf920af3e114c1f13c08d0 d157a13512a292b3a45be3952666b7ef487519d0 Emanuel Soda <emanuelsoda@gmail.com> 1650215258 +0200	commit: used styler
40
-d157a13512a292b3a45be3952666b7ef487519d0 fecb96194b7152a6dfd77aba63055965c9d1788e Emanuel Soda <emanuelsoda@gmail.com> 1650216820 +0200	commit: problem with site
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