Mercurial > repos > fubar > egapx_runner
changeset 3:9b1c2fb3b218 draft
planemo upload for repository https://github.com/ncbi/egapx commit 69fafcdd687884c990c7f4027aa2982df66626e6
| author | fubar |
|---|---|
| date | Sun, 04 Aug 2024 00:52:17 +0000 |
| parents | a3b158471bd3 |
| children | 6592ae57bb8b |
| files | oldgit/COMMIT_EDITMSG oldgit/HEAD oldgit/config oldgit/description oldgit/hooks/applypatch-msg.sample oldgit/hooks/commit-msg.sample oldgit/hooks/fsmonitor-watchman.sample oldgit/hooks/post-update.sample oldgit/hooks/pre-applypatch.sample oldgit/hooks/pre-commit.sample oldgit/hooks/pre-merge-commit.sample oldgit/hooks/pre-push.sample oldgit/hooks/pre-rebase.sample oldgit/hooks/pre-receive.sample oldgit/hooks/prepare-commit-msg.sample oldgit/hooks/push-to-checkout.sample oldgit/hooks/sendemail-validate.sample oldgit/hooks/update.sample oldgit/index oldgit/info/exclude oldgit/logs/HEAD oldgit/logs/refs/heads/main oldgit/objects/12/8459020d0f193a4d78338ecb7ffe24b3e58ca8 oldgit/objects/20/5230162a98e8d485d50da287dcffe6904bd4a4 oldgit/objects/2b/729cc347f48df57f5ad3627b083bba447fdcae oldgit/objects/37/5ac3ad6c77bc7efad8b0c8c3375c7157e29651 oldgit/objects/42/eb7d873cfb6e0520cd900861b003352cc289a8 oldgit/objects/50/af98953019db86a9049ca177e7eea83420628c oldgit/objects/5b/1410b05f882ec5c2f385c0706ea7fb5563e63f oldgit/objects/77/2d158f9c02d6c744e34db4215a9f5b674a53ab oldgit/objects/9c/48f18504f5f7816e05b25c557708796863051e oldgit/objects/9e/0074b1d9d6ff477362229b22ea871438e7d07f oldgit/objects/c0/46380e8916cbd3f6f8912bd12ca348b5bb7516 oldgit/objects/c6/78a02d0cd5790e72234cbd2dcd7d282a1160a3 oldgit/objects/cb/bedabad083074c9a954e724fc450dd5d617d91 oldgit/objects/f3/c08e87196592a045b940d2cb545f35237592ec oldgit/objects/fa/cf1d12577080e370217f80e47006717e910a53 oldgit/objects/pack/pack-d158b90a10a1152c5c411e670b6f9585f84b6c62.idx oldgit/objects/pack/pack-d158b90a10a1152c5c411e670b6f9585f84b6c62.pack oldgit/objects/pack/pack-d158b90a10a1152c5c411e670b6f9585f84b6c62.rev oldgit/packed-refs oldgit/refs/heads/main |
| diffstat | 42 files changed, 0 insertions(+), 911 deletions(-) [+] |
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--- a/oldgit/COMMIT_EDITMSG Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -update help -considering adding some prepackaged yaml options? -currently point to samples in egapx github repo -# Please enter the commit message for your changes. Lines starting -# with '#' will be ignored, and an empty message aborts the commit. -# -# On branch main -# Your branch is up to date with 'origin/main'. -# -# Changes to be committed: -# new file: .shed.yml -# new file: EGAPXREADME.md -# modified: README.md -# new file: assets/default_task_params.yaml -# new file: egapx_runner.xml -# new file: static/images/Pipeline_sm_ncRNA_CAGE_80pct.png -# new file: test-data/yamlconfig_sample -# modified: ui/assets/config/executor/docker_minimal.config -#
--- a/oldgit/HEAD Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -ref: refs/heads/main
--- a/oldgit/config Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -[core] - repositoryformatversion = 0 - filemode = true - bare = false - logallrefupdates = true
--- a/oldgit/description Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -Unnamed repository; edit this file 'description' to name the repository.
--- a/oldgit/hooks/applypatch-msg.sample Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -#!/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" ${1+"$@"} -:
--- a/oldgit/hooks/commit-msg.sample Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -#!/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: ' "$1" | - sort | uniq -c | sed -e '/^[ ]*1[ ]/d')" || { - echo >&2 Duplicate Signed-off-by lines. - exit 1 -}
--- a/oldgit/hooks/fsmonitor-watchman.sample Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,174 +0,0 @@ -#!/usr/bin/perl - -use strict; -use warnings; -use IPC::Open2; - -# An example hook script to integrate Watchman -# (https://facebook.github.io/watchman/) with git to speed up detecting -# new and modified files. -# -# The hook is passed a version (currently 2) and last update token -# formatted as a string and outputs to stdout a new update token and -# all files that have been modified since the update token. Paths must -# be relative to the root of the working tree and separated by a single NUL. -# -# To enable this hook, rename this file to "query-watchman" and set -# 'git config core.fsmonitor .git/hooks/query-watchman' -# -my ($version, $last_update_token) = @ARGV; - -# Uncomment for debugging -# print STDERR "$0 $version $last_update_token\n"; - -# Check the hook interface version -if ($version ne 2) { - die "Unsupported query-fsmonitor hook version '$version'.\n" . - "Falling back to scanning...\n"; -} - -my $git_work_tree = get_working_dir(); - -my $retry = 1; - -my $json_pkg; -eval { - require JSON::XS; - $json_pkg = "JSON::XS"; - 1; -} or do { - require JSON::PP; - $json_pkg = "JSON::PP"; -}; - -launch_watchman(); - -sub launch_watchman { - my $o = watchman_query(); - if (is_work_tree_watched($o)) { - output_result($o->{clock}, @{$o->{files}}); - } -} - -sub output_result { - my ($clockid, @files) = @_; - - # Uncomment for debugging watchman output - # open (my $fh, ">", ".git/watchman-output.out"); - # binmode $fh, ":utf8"; - # print $fh "$clockid\n@files\n"; - # close $fh; - - binmode STDOUT, ":utf8"; - print $clockid; - print "\0"; - local $, = "\0"; - print @files; -} - -sub watchman_clock { - my $response = qx/watchman clock "$git_work_tree"/; - die "Failed to get clock id on '$git_work_tree'.\n" . - "Falling back to scanning...\n" if $? != 0; - - return $json_pkg->new->utf8->decode($response); -} - -sub watchman_query { - 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 $last_update_token but not from the .git folder. - # - # 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. Then we're using the "expression" term to - # further constrain the results. - my $last_update_line = ""; - if (substr($last_update_token, 0, 1) eq "c") { - $last_update_token = "\"$last_update_token\""; - $last_update_line = qq[\n"since": $last_update_token,]; - } - my $query = <<" END"; - ["query", "$git_work_tree", {$last_update_line - "fields": ["name"], - "expression": ["not", ["dirname", ".git"]] - }] - END - - # Uncomment for debugging the watchman query - # open (my $fh, ">", ".git/watchman-query.json"); - # print $fh $query; - # close $fh; - - print CHLD_IN $query; - close CHLD_IN; - my $response = do {local $/; <CHLD_OUT>}; - - # Uncomment for debugging the watch response - # open ($fh, ">", ".git/watchman-response.json"); - # print $fh $response; - # close $fh; - - 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 =~ /^\{/; - - return $json_pkg->new->utf8->decode($response); -} - -sub is_work_tree_watched { - my ($output) = @_; - my $error = $output->{error}; - if ($retry > 0 and $error and $error =~ m/unable to resolve root .* directory (.*) is not watched/) { - $retry--; - my $response = qx/watchman watch "$git_work_tree"/; - die "Failed to make watchman watch '$git_work_tree'.\n" . - "Falling back to scanning...\n" if $? != 0; - $output = $json_pkg->new->utf8->decode($response); - $error = $output->{error}; - die "Watchman: $error.\n" . - "Falling back to scanning...\n" if $error; - - # Uncomment for debugging watchman output - # open (my $fh, ">", ".git/watchman-output.out"); - # close $fh; - - # 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. - my $o = watchman_clock(); - $error = $output->{error}; - - die "Watchman: $error.\n" . - "Falling back to scanning...\n" if $error; - - output_result($o->{clock}, ("/")); - $last_update_token = $o->{clock}; - - eval { launch_watchman() }; - return 0; - } - - die "Watchman: $error.\n" . - "Falling back to scanning...\n" if $error; - - return 1; -} - -sub get_working_dir { - my $working_dir; - if ($^O =~ 'msys' || $^O =~ 'cygwin') { - $working_dir = Win32::GetCwd(); - $working_dir =~ tr/\\/\//; - } else { - require Cwd; - $working_dir = Cwd::cwd(); - } - - return $working_dir; -}
--- a/oldgit/hooks/post-update.sample Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -#!/bin/sh -# -# An example hook script to prepare a packed repository for use over -# dumb transports. -# -# To enable this hook, rename this file to "post-update". - -exec git update-server-info
--- a/oldgit/hooks/pre-applypatch.sample Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -#!/bin/sh -# -# An example hook script to verify what is about to be committed -# by applypatch from an e-mail message. -# -# The hook should exit with non-zero status after issuing an -# appropriate message if it wants to stop the commit. -# -# To enable this hook, rename this file to "pre-applypatch". - -. git-sh-setup -precommit="$(git rev-parse --git-path hooks/pre-commit)" -test -x "$precommit" && exec "$precommit" ${1+"$@"} -:
--- a/oldgit/hooks/pre-commit.sample Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,49 +0,0 @@ -#!/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 --type=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 $against --
--- a/oldgit/hooks/pre-merge-commit.sample Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#!/bin/sh -# -# An example hook script to verify what is about to be committed. -# Called by "git merge" with no arguments. The hook should -# exit with non-zero status after issuing an appropriate message to -# stderr if it wants to stop the merge commit. -# -# To enable this hook, rename this file to "pre-merge-commit". - -. git-sh-setup -test -x "$GIT_DIR/hooks/pre-commit" && - exec "$GIT_DIR/hooks/pre-commit" -:
--- a/oldgit/hooks/pre-push.sample Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ -#!/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 oid> <remote ref> <remote oid> -# -# This sample shows how to prevent push of commits where the log message starts -# with "WIP" (work in progress). - -remote="$1" -url="$2" - -zero=$(git hash-object --stdin </dev/null | tr '[0-9a-f]' '0') - -while read local_ref local_oid remote_ref remote_oid -do - if test "$local_oid" = "$zero" - then - # Handle delete - : - else - if test "$remote_oid" = "$zero" - then - # New branch, examine all commits - range="$local_oid" - else - # Update to existing branch, examine new commits - range="$remote_oid..$local_oid" - fi - - # Check for WIP commit - commit=$(git rev-list -n 1 --grep '^WIP' "$range") - if test -n "$commit" - then - echo >&2 "Found WIP commit in $local_ref, not pushing" - exit 1 - fi - fi -done - -exit 0
--- a/oldgit/hooks/pre-rebase.sample Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,169 +0,0 @@ -#!/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
--- a/oldgit/hooks/pre-receive.sample Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -#!/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
--- a/oldgit/hooks/prepare-commit-msg.sample Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ -#!/bin/sh -# -# An example hook script to prepare the commit log message. -# Called by "git commit" with the name of the file that has the -# commit message, followed by the description of the commit -# message's source. The hook's purpose is to edit the commit -# message file. If the hook fails with a non-zero status, -# the commit is aborted. -# -# To enable this hook, rename this file to "prepare-commit-msg". - -# This hook includes three examples. The first one removes the -# "# Please enter the commit message..." help message. -# -# The second includes the output of "git diff --name-status -r" -# into the message, just before the "git status" output. It is -# commented because it doesn't cope with --amend or with squashed -# commits. -# -# The third example adds a Signed-off-by line to the message, that can -# still be edited. This is rarely a good idea. - -COMMIT_MSG_FILE=$1 -COMMIT_SOURCE=$2 -SHA1=$3 - -/usr/bin/perl -i.bak -ne 'print unless(m/^. Please enter the commit message/..m/^#$/)' "$COMMIT_MSG_FILE" - -# case "$COMMIT_SOURCE,$SHA1" in -# ,|template,) -# /usr/bin/perl -i.bak -pe ' -# print "\n" . `git diff --cached --name-status -r` -# if /^#/ && $first++ == 0' "$COMMIT_MSG_FILE" ;; -# *) ;; -# esac - -# SOB=$(git var GIT_COMMITTER_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p') -# git interpret-trailers --in-place --trailer "$SOB" "$COMMIT_MSG_FILE" -# if test -z "$COMMIT_SOURCE" -# then -# /usr/bin/perl -i.bak -pe 'print "\n" if !$first_line++' "$COMMIT_MSG_FILE" -# fi
--- a/oldgit/hooks/push-to-checkout.sample Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,78 +0,0 @@ -#!/bin/sh - -# An example hook script to update a checked-out tree on a git push. -# -# This hook is invoked by git-receive-pack(1) when it reacts to git -# push and updates reference(s) in its repository, and when the push -# tries to update the branch that is currently checked out and the -# receive.denyCurrentBranch configuration variable is set to -# updateInstead. -# -# By default, such a push is refused if the working tree and the index -# of the remote repository has any difference from the currently -# checked out commit; when both the working tree and the index match -# the current commit, they are updated to match the newly pushed tip -# of the branch. This hook is to be used to override the default -# behaviour; however the code below reimplements the default behaviour -# as a starting point for convenient modification. -# -# The hook receives the commit with which the tip of the current -# branch is going to be updated: -commit=$1 - -# It can exit with a non-zero status to refuse the push (when it does -# so, it must not modify the index or the working tree). -die () { - echo >&2 "$*" - exit 1 -} - -# Or it can make any necessary changes to the working tree and to the -# index to bring them to the desired state when the tip of the current -# branch is updated to the new commit, and exit with a zero status. -# -# For example, the hook can simply run git read-tree -u -m HEAD "$1" -# in order to emulate git fetch that is run in the reverse direction -# with git push, as the two-tree form of git read-tree -u -m is -# essentially the same as git switch or git checkout that switches -# branches while keeping the local changes in the working tree that do -# not interfere with the difference between the branches. - -# The below is a more-or-less exact translation to shell of the C code -# for the default behaviour for git's push-to-checkout hook defined in -# the push_to_deploy() function in builtin/receive-pack.c. -# -# Note that the hook will be executed from the repository directory, -# not from the working tree, so if you want to perform operations on -# the working tree, you will have to adapt your code accordingly, e.g. -# by adding "cd .." or using relative paths. - -if ! git update-index -q --ignore-submodules --refresh -then - die "Up-to-date check failed" -fi - -if ! git diff-files --quiet --ignore-submodules -- -then - die "Working directory has unstaged changes" -fi - -# This is a rough translation of: -# -# head_has_history() ? "HEAD" : EMPTY_TREE_SHA1_HEX -if git cat-file -e HEAD 2>/dev/null -then - head=HEAD -else - head=$(git hash-object -t tree --stdin </dev/null) -fi - -if ! git diff-index --quiet --cached --ignore-submodules $head -- -then - die "Working directory has staged changes" -fi - -if ! git read-tree -u -m "$commit" -then - die "Could not update working tree to new HEAD" -fi
--- a/oldgit/hooks/sendemail-validate.sample Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,77 +0,0 @@ -#!/bin/sh - -# An example hook script to validate a patch (and/or patch series) before -# sending it via email. -# -# The hook should exit with non-zero status after issuing an appropriate -# message if it wants to prevent the email(s) from being sent. -# -# To enable this hook, rename this file to "sendemail-validate". -# -# By default, it will only check that the patch(es) can be applied on top of -# the default upstream branch without conflicts in a secondary worktree. After -# validation (successful or not) of the last patch of a series, the worktree -# will be deleted. -# -# The following config variables can be set to change the default remote and -# remote ref that are used to apply the patches against: -# -# sendemail.validateRemote (default: origin) -# sendemail.validateRemoteRef (default: HEAD) -# -# Replace the TODO placeholders with appropriate checks according to your -# needs. - -validate_cover_letter () { - file="$1" - # TODO: Replace with appropriate checks (e.g. spell checking). - true -} - -validate_patch () { - file="$1" - # Ensure that the patch applies without conflicts. - git am -3 "$file" || return - # TODO: Replace with appropriate checks for this patch - # (e.g. checkpatch.pl). - true -} - -validate_series () { - # TODO: Replace with appropriate checks for the whole series - # (e.g. quick build, coding style checks, etc.). - true -} - -# main ------------------------------------------------------------------------- - -if test "$GIT_SENDEMAIL_FILE_COUNTER" = 1 -then - remote=$(git config --default origin --get sendemail.validateRemote) && - ref=$(git config --default HEAD --get sendemail.validateRemoteRef) && - worktree=$(mktemp --tmpdir -d sendemail-validate.XXXXXXX) && - git worktree add -fd --checkout "$worktree" "refs/remotes/$remote/$ref" && - git config --replace-all sendemail.validateWorktree "$worktree" -else - worktree=$(git config --get sendemail.validateWorktree) -fi || { - echo "sendemail-validate: error: failed to prepare worktree" >&2 - exit 1 -} - -unset GIT_DIR GIT_WORK_TREE -cd "$worktree" && - -if grep -q "^diff --git " "$1" -then - validate_patch "$1" -else - validate_cover_letter "$1" -fi && - -if test "$GIT_SENDEMAIL_FILE_COUNTER" = "$GIT_SENDEMAIL_FILE_TOTAL" -then - git config --unset-all sendemail.validateWorktree && - trap 'git worktree remove -ff "$worktree"' EXIT && - validate_series -fi
--- a/oldgit/hooks/update.sample Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,128 +0,0 @@ -#!/bin/sh -# -# An example hook script to block unannotated tags from entering. -# Called by "git receive-pack" with arguments: refname sha1-old sha1-new -# -# To enable this hook, rename this file to "update". -# -# Config -# ------ -# hooks.allowunannotated -# This boolean sets whether unannotated tags will be allowed into the -# repository. By default they won't be. -# hooks.allowdeletetag -# This boolean sets whether deleting tags will be allowed in the -# repository. By default they won't be. -# hooks.allowmodifytag -# This boolean sets whether a tag may be modified after creation. By default -# it won't be. -# hooks.allowdeletebranch -# This boolean sets whether deleting branches will be allowed in the -# repository. By default they won't be. -# hooks.denycreatebranch -# This boolean sets whether remotely creating branches will be denied -# in the repository. By default this is allowed. -# - -# --- Command line -refname="$1" -oldrev="$2" -newrev="$3" - -# --- Safety check -if [ -z "$GIT_DIR" ]; then - echo "Don't run this script from the command line." >&2 - echo " (if you want, you could supply GIT_DIR then run" >&2 - echo " $0 <ref> <oldrev> <newrev>)" >&2 - exit 1 -fi - -if [ -z "$refname" -o -z "$oldrev" -o -z "$newrev" ]; then - echo "usage: $0 <ref> <oldrev> <newrev>" >&2 - exit 1 -fi - -# --- Config -allowunannotated=$(git config --type=bool hooks.allowunannotated) -allowdeletebranch=$(git config --type=bool hooks.allowdeletebranch) -denycreatebranch=$(git config --type=bool hooks.denycreatebranch) -allowdeletetag=$(git config --type=bool hooks.allowdeletetag) -allowmodifytag=$(git config --type=bool hooks.allowmodifytag) - -# check for no description -projectdesc=$(sed -e '1q' "$GIT_DIR/description") -case "$projectdesc" in -"Unnamed repository"* | "") - echo "*** Project description file hasn't been set" >&2 - exit 1 - ;; -esac - -# --- Check types -# if $newrev is 0000...0000, it's a commit to delete a ref. -zero=$(git hash-object --stdin </dev/null | tr '[0-9a-f]' '0') -if [ "$newrev" = "$zero" ]; then - newrev_type=delete -else - newrev_type=$(git cat-file -t $newrev) -fi - -case "$refname","$newrev_type" in - refs/tags/*,commit) - # un-annotated tag - short_refname=${refname##refs/tags/} - if [ "$allowunannotated" != "true" ]; then - echo "*** The un-annotated tag, $short_refname, is not allowed in this repository" >&2 - echo "*** Use 'git tag [ -a | -s ]' for tags you want to propagate." >&2 - exit 1 - fi - ;; - refs/tags/*,delete) - # delete tag - if [ "$allowdeletetag" != "true" ]; then - echo "*** Deleting a tag is not allowed in this repository" >&2 - exit 1 - fi - ;; - refs/tags/*,tag) - # annotated tag - if [ "$allowmodifytag" != "true" ] && git rev-parse $refname > /dev/null 2>&1 - then - echo "*** Tag '$refname' already exists." >&2 - echo "*** Modifying a tag is not allowed in this repository." >&2 - exit 1 - fi - ;; - refs/heads/*,commit) - # branch - if [ "$oldrev" = "$zero" -a "$denycreatebranch" = "true" ]; then - echo "*** Creating a branch is not allowed in this repository" >&2 - exit 1 - fi - ;; - refs/heads/*,delete) - # delete branch - if [ "$allowdeletebranch" != "true" ]; then - echo "*** Deleting a branch is not allowed in this repository" >&2 - exit 1 - fi - ;; - refs/remotes/*,commit) - # tracking branch - ;; - refs/remotes/*,delete) - # delete tracking branch - if [ "$allowdeletebranch" != "true" ]; then - echo "*** Deleting a tracking branch is not allowed in this repository" >&2 - exit 1 - fi - ;; - *) - # Anything else (is there anything else?) - echo "*** Update hook: unknown type of update to ref $refname of type $newrev_type" >&2 - exit 1 - ;; -esac - -# --- Finished -exit 0
--- a/oldgit/info/exclude Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -# git ls-files --others --exclude-from=.git/info/exclude -# Lines that start with '#' are comments. -# For a project mostly in C, the following would be a good set of -# exclude patterns (uncomment them if you want to use them): -# *.[oa] -# *~
--- a/oldgit/logs/HEAD Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -0000000000000000000000000000000000000000 8173d01b08d9a91c9ec5f6cb50af346edc8020c4 fubar2 <ross.lazarus@gmail.com> 1722655773 +1000 clone: from https://github.com/ncbi/egapx.git -8173d01b08d9a91c9ec5f6cb50af346edc8020c4 375ac3ad6c77bc7efad8b0c8c3375c7157e29651 fubar2 <ross.lazarus@gmail.com> 1722728096 +1000 commit: update help
--- a/oldgit/logs/refs/heads/main Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -0000000000000000000000000000000000000000 8173d01b08d9a91c9ec5f6cb50af346edc8020c4 fubar2 <ross.lazarus@gmail.com> 1722655773 +1000 clone: from https://github.com/ncbi/egapx.git -8173d01b08d9a91c9ec5f6cb50af346edc8020c4 375ac3ad6c77bc7efad8b0c8c3375c7157e29651 fubar2 <ross.lazarus@gmail.com> 1722728096 +1000 commit: update help
--- a/oldgit/packed-refs Sun Aug 04 00:06:43 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -# pack-refs with: peeled fully-peeled sorted -203afce5dc30d03a6aab0d27a5a60d26276f3413 refs/tags/v0.1.0-alpha -4c01189ce1d1e3970fc7d8b9326083cc006c3d28 refs/tags/v0.1.1-alpha -^2380370cc0c522742619ba6c463a5b7f7a79507c -5a916d370a13cd49d70cad71cd7589f01fdea573 refs/tags/v0.1.2-alpha -314cbbc4ff1480f8f470c0ccef8979ef302a15cd refs/tags/v0.2-alpha