Changeset 3144

Timestamp:

Dec 18, 2013, 9:18:48 AM (10 years ago)

Author:

Peter

Message:

merge patch release 0.11.1 into trunk

Location:

trunk

Files:

• . (modified) (1 prop)
• NEWS (modified) (1 diff)
• README.developer (modified) (1 diff)
• m4/version.m4 (modified) (1 diff)
• test/Makefile.am (modified) (1 diff)
• test/bam_header2.cc (copied) (copied from branches/0.11-stable/test/bam_header2.cc)
• yat/omic/BamHeader.cc (modified) (1 diff)

trunk/NEWS

@@ -9 +9 @@
 
 yat 0.11.x series from http://dev.thep.lu.se/yat/svn/branches/0.11-stable
+
+version 0.11.1 (released 18 December 2013)
+  - Fixed bug in BamHeader::tid(const std::string&) (see bug #776)
+
+  A complete list of closed tickets can be found here [[br]]
+  http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.11.1
 
 version 0.11 (released 18 November 2013)

trunk/README.developer

@@ -142 +142 @@
 http://www.gnu.org/software/libtool/manual/libtool.html#Debugging-executables
 
+
+= Release Procedure =
+
+These instructions cover how to release minor and patch releases in a
+project that uses trac/subversion for revision control and project
+management. How to release major releases is not covered yet since we
+have not done that (with the exception of the first release). Release
+numbering follows the normal convention of major.minor.patch and the
+APR (see http://apr.apache.org/versioning.html) guidelines for
+releases are used.
+
+The main development is performed in the trunk branch of the
+repository. A new release branch is created for each minor release
+from the trunk and patch releases are snapshots of the minor release
+branch. This implies that patch work is performed in the minor release
+branch, and changes made release branch is transferred to the trunk
+every time a new patch release is made. Remember, patch work should be
+limited to bug fixes and important fixes only leaving development of
+new features and designs to the trunk branch.
+
+Releases should only be performed by an appointed member of the team,
+the Release Manager.
+
+
+=== Creating a release branch ===
+
+Once people agree that a new release branch should be made, the
+Release Manager creates it with the following procedure
+(substitute A.B with the version you are preparing, e.g. 0.3)
+
+ 1. Check that 'YAT_LT_VERSION_INFO' is set correcly
+    otherwise update following line in 'm4/version.m4'
+
+8<----
+    m4_define([YAT_LT_VERSION_INFO], [c:r:a])
+8<----
+
+ 2. Add a line in NEWS
+8<----
+     See the end for copyrights and conditions.
+
+    +yat A.B.x series from http://dev.thep.lu.se/yat/svn/branches/A.B-stable
+    +
+     Version A.B (released NOT YET)
+8<----
+
+ 3. Commit the changes with
+
+    #> svn ci -m "Prepare A.B-stable branch"
+
+ 4. For this step svncopyright is needed, http://dev.thep.lu.se/svndigest.
+    Update copyright statements with command:
+
+    #> make copyright
+
+    Examine the updates and commit changes with
+
+    #> svn ci -m "updating copyright statements"`.
+
+ 5. Create a new stable branch with
+
+    #> make svn-stable-branch
+
+ 6. Prepare the trunk for the next minor release
+
+   a) Update version number in 'm4/version.m4'. Locate and change the
+      below lines
+
+8<----
+      MY_VERSION_early([A], [B+1], [0], [true])
+      m4_define([YAT_LT_VERSION_INFO], [c+1:0:0])
+8<----
+
+   b) Add an entry in `NEWS`
+
+8<----
+      version A.[B+1] (released NOT YET)
+8<----
+
+      The date is set when version A.[B+1] is released. [[br]][[br]]
+
+   c) Commit changes to the repository:
+
+    #> svn ci -m "Bumping VERSION to A.[B+1]pre"
+
+ 7. When someone with access to documentation site has time available,
+    they will upgrade to the new branch. This person is usually not the
+    release manager, so please send a reminder.
+
+=== Rolling a minor release ===
+
+    These instructions describe how to make a release. Replace A.B.C
+    with current VERSION (A.B if this is not a patch release).
+
+ 1. Update version number in 'm4/version.m4'. Locate and change the
+    below line
+
+8<----
+      MY_VERSION_early([A], [B], [C], [false])
+8<----
+
+
+ 2. Update the interface version number in 'm4/version.m4'. Locate and
+    set the version in the below line
+
+8<----
+      m4_define([YAT_LT_VERSION_INFO], [c:r:a])
+8<----
+
+    appropriately. Refer to file 'm4/version.m4' for details on how to
+    decide triplet 'c:r:a'.
+
+
+ 3. Set the date for the new release in 'NEWS'.
+
+8<----
+      version A.B.C (released 26 June 2007)
+8<----
+
+
+ 4. Make sure that the items in 'NEWS' cover the new features of the
+    release.
+
+
+ 5. Commit changes to the repository:
+
+    #> svn ci -m "Preparing release A.B.C"
+
+
+ 6. For this step svncopyright is needed, http://dev.thep.lu.se/svndigest.
+    Update copyright statements with command:
+
+    #> make copyright
+
+    Examine the updates and commit changes with
+
+    #> svn ci -m "updating copyright statements"
+
+
+ 7. Now it's time to create a tarball, an svn tag, and upload the
+    tarball to sourceforge. For this to work you need to hold write
+    permissions at libyat project page at sourceforge. If your sf user
+    id is different from the one defined in 'Makefile.am', you can
+    override the default with 'sf_user=<your id>'. Issue the
+    convenience target:
+
+    #> make release-tag-upload
+
+    This will run some sanity checks, run maintainer-check and
+    distcheck, create an svn tag, and upload the newly created tarball
+    to sourceforge. The last step requires that you provide your SF password.
+
+
+ 8. On WikiStart update links
+    '[source:tags/A.B.C/NEWS NEWS]' and
+    '[source:branches/A.B-stable/README README]'
+
+ 9. Update SubversionCheckout
+
+   a) In section 'yat latest release' update command to
+      'svn checkout http://dev.thep.lu.se/yat/svn/tags/A.B.C yat-A.B.C
+      and link to
+      '[source:tags/A.B.C/NEWS NEWS]'
+      If this is a patch release jump to point 10).
+
+   b) In section 'yat stable' update command to
+      'svn checkout http://dev.thep.lu.se/yat/svn/branches/A.B-stable yat-A.B.x
+      and link to
+      '[source:branches/A.B-stable/NEWS NEWS]'
+
+
+ 10. Close the milestone associated with this release.
+
+
+ 11. Update the version list in Trac using the trac-admin tool.
+
+
+ 12. Use file 'announcement.txt' as template and send email to
+    libyat-users@lists.sourceforge.net
+
+
+ 13. Merge the release into the trunk.
+
+    a) Go to a pristine trunk WC:
+
+       #> cd /path/to/yat-trunk/
+       #> make check-svn-diff
+
+    b) Merge changes into trunk:
+
+       #> svn merge ^/branches/A.B-stable
+
+    c) Resolve potential conflicts. Run tests and perform all other
+       appropriate tests to make sure that the merge does not create
+       havoc. Typically changes in `m4/version.m4` are problematic so
+       check this file extra carefully.
+
+    d) Commit changes to the trunk branch.
+
+       #> svn commit -m "Merged release A.B.C into trunk."
+
+
+ 14. Prepare the stable branch for the next patch release.
+
+    a) Update version number in 'm4/version.m4'. Locate and change the
+       below line
+
+8<---
+       MY_VERSION_early([A], [B], [C+1], [true])
+8<---
+
+       Run 'make all' and while waiting finalize item b) below
+
+    b) Add an entry in 'NEWS'
+
+8<----
+       version A.B.[C+1] (released NOT YET)
+8<----
+
+       The date is set when version A.B.[C+1] is released.
+
+
+ 15. Commit changes to the repository:
+
+    #> svn ci -m "Bumping VERSION to A.B.[C+1]pre"
+
+
 = Versioning =
 

trunk/m4/version.m4

@@ -74 +74 @@
 # yat-0.10.3 7:3:0
 # yat-0.11   8:0:0
+# yat-0.11.1 8:1:0
 #
 # *Accidently, the libtool number was not updated for yat 0.5

trunk/test/Makefile.am

@@ -45 +45 @@
   test/bam_region_iterator.test \
   test/bam_header.test \
+  test/bam_header2.test \
   test/codon.test test/commandline.test \
   test/concept.test \

trunk/yat/omic/BamHeader.cc

@@ -75 +75 @@
       // hash get populated.
       int tid, b, e;
-      bam_parse_region(header_, target_name(0), &tid, &b, &e);
+      bam_parse_region(header_, name.c_str(), &tid, &b, &e);
       assert(header_->hash);
       assert(tid == bam_get_tid(header_, name.c_str()));