[med-svn] [Git][med-team/libucsc][master] 6 commits: New upstream version 0.0+git20230913.7b8e37ad+dfsg
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Sep 14 14:40:01 BST 2023
Andreas Tille pushed to branch master at Debian Med / libucsc
Commits:
e5fb1b5a by Andreas Tille at 2023-09-14T12:53:18+02:00
New upstream version 0.0+git20230913.7b8e37ad+dfsg
- - - - -
9409ec18 by Andreas Tille at 2023-09-14T15:14:11+02:00
New upstream version 0.0+git20230913.7b8e37ad+dfsg
- - - - -
c12f35da by Andreas Tille at 2023-09-14T15:15:45+02:00
Exclude some more files
- - - - -
ac1ee193 by Andreas Tille at 2023-09-14T15:18:00+02:00
New upstream version 0.0+git20230913.7b8e37ad+dfsg
- - - - -
019190c1 by Andreas Tille at 2023-09-14T15:18:06+02:00
Update upstream source from tag 'upstream/0.0+git20230913.7b8e37ad+dfsg'
Update to upstream version '0.0+git20230913.7b8e37ad+dfsg'
with Debian dir 9ac7d97574b64e12f6bfee942e582c5c572e1725
- - - - -
a4a024ec by Andreas Tille at 2023-09-14T15:39:11+02:00
Exclude some non-free parts from build - but probably libssl issues are in the free library
- - - - -
5 changed files:
- − .github/ISSUE_TEMPLATE/bug-report-or-other-feedback.md
- debian/copyright
- debian/rules
- − install-hooks.sh
- − pre-commit-prevent-large-files.sh
Changes:
=====================================
.github/ISSUE_TEMPLATE/bug-report-or-other-feedback.md deleted
=====================================
@@ -1,34 +0,0 @@
----
-name: Bug report or other Feedback
-about: Create a report to help us improve
-title: ''
-labels: ''
-assignees: ''
-
----
-
-Note that we have our own ticket system and we use Github issues only for source code related issues or pull requests. If you have bug reports, contacting us via the public mailing list genome at soe.ucsc.edu may be easier. See also https://genome.ucsc.edu/contacts.html for ways to search the mailing lists or contact us directly (not public) via email.
-
- **Describe the bug**
- A clear and concise description of what the bug is.
-
- **To Reproduce**
- Steps to reproduce the behavior:
- 1. Go to '...'
- 2. Click on '....'
- 3. Scroll down to '....'
- 4. See error
-
- **Expected behavior**
- A concise description of what you expected to happen.
-
- **Screenshots**
- If applicable, add screenshots to help explain your problem.
-
- **Desktop (please complete the following information):**
- - OS: [e.g. Windows]
- - Browser [e.g. firefox, chrome, safari]
- - Version [e.g. 22]
-
- **Additional context**
- Add any other context about the problem here.
=====================================
debian/copyright
=====================================
@@ -8,7 +8,6 @@ Files-Excluded:
confs
java
python
- .gitignore
LICENSE
README
src/a*
@@ -40,6 +39,9 @@ Files-Excluded:
*/mgSixhi6.c
src/htslib
src/blatz
+ .github
+ install-hooks.sh
+ pre-commit-prevent-large-files.sh
Comment: The LICENSE file in the root dir says:
LICENSE files in subdirectories override the text of this LICENSE file.
=====================================
debian/rules
=====================================
@@ -21,8 +21,9 @@ override_dh_auto_build:
make --directory=src/jkOwnLib
make --directory=src/lib
mkdir -p $(DESTDIR)/bin
- make --directory=src/blat
- make --directory=src/isPcr/isPcr
+# FIXME: blat and isPcr are non-free and currently are showing issues with libssl 3.x Deactivating this part of the build for the moment
+# make --directory=src/blat
+# make --directory=src/isPcr/isPcr
#make --directory=src/utils/faToTwoBit
#make --directory=src/utils/twoBitToFa
make --directory=src/utils
=====================================
install-hooks.sh deleted
=====================================
@@ -1,7 +0,0 @@
-#!/bin/bash
-
-# Installs pre-commit hook that ensures attempts to commit files that are
-# larger than $limit to your _local_ repo fail, with a helpful error message.
-cd "$(dirname "$0")" # location of this script
-cd .git/hooks/
-ln -sf ../../pre-commit-prevent-large-files.sh pre-commit
=====================================
pre-commit-prevent-large-files.sh deleted
=====================================
@@ -1,47 +0,0 @@
-#!/bin/bash
-
-# This is a pre-commit hook that ensures attempts to commit files that are
-# larger than $limit to your _local_ repo fail, with a helpful error message.
-
-# Maximum file size limit in bytes
-limit=$(( 2200000 )) # 2,2MB
-limitInMB=$(( $limit / 2**20 ))
-
-# Move to the repo root so git files paths make sense
-repo_root=$( git rev-parse --show-toplevel )
-cd $repo_root
-
-empty_tree=$( git hash-object -t tree /dev/null )
-
-if git rev-parse --verify HEAD > /dev/null 2>&1
-then
- against=HEAD
-else
- against="$empty_tree"
-fi
-
-# Set split so that for loop below can handle spaces in file names by splitting on line breaks
-IFS='
-'
-
-echo "Checking staged file sizes"
-shouldFail=false
-# `--diff-filter=d` -> skip deletions ACMRTUXB (everything but D)
-# syntax since lower case filter only available in git version 2.10, we have 1.8.3.1
-# we do not care if deleted files are large or not, they are allowed.
-for file in $( git diff-index --cached --diff-filter=ACMRTUXB --name-only "$against" ); do
- # Skip for directories (git submodules)
- if [[ -f "$file" ]]; then
- file_size=$( ls -lan $file | awk '{ print $5 }' )
- if [ "$file_size" -gt "$limit" ]; then
- echo File $file is $(( $file_size / 2**20 )) MB, which is larger than our configured limit of $limitInMB MB
- shouldFail=true
- fi
- fi
-done
-
-if $shouldFail
-then
- echo Commit aborted
- exit 1;
-fi
View it on GitLab: https://salsa.debian.org/med-team/libucsc/-/compare/58dc6ab9754febaeb70706e5f7c789a22d92c035...a4a024ec175fe1649bf14d7be0d927689c87beb2
--
View it on GitLab: https://salsa.debian.org/med-team/libucsc/-/compare/58dc6ab9754febaeb70706e5f7c789a22d92c035...a4a024ec175fe1649bf14d7be0d927689c87beb2
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