From 310f5b072eab098e340fd6ca0517de37c27308ff Mon Sep 17 00:00:00 2001 From: Martijn Vermaat <martijn@vermaat.name> Date: Fri, 3 Oct 2014 16:37:45 +0200 Subject: [PATCH] Update links to issues in changelog --- CHANGES.rst | 72 +++++++++++++++++++++++++++-------------------------- 1 file changed, 37 insertions(+), 35 deletions(-) diff --git a/CHANGES.rst b/CHANGES.rst index 1c815688..6b6768ee 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -25,7 +25,7 @@ Version 2.0.0 Released on September 26th 2014. This release does not bring many new features, but comes with significant -changes to the technical infrastructure. `Merge request #6 +changes to the technical infrastructure. `GitLab!6 <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/6>`_ tracks most of this. @@ -43,38 +43,39 @@ Some highlights especially users of the webservices should be aware of: Other changes: - Upload a genbank file using the SOAP webservice (`uploadGenBankLocalFile`). -- Do not cleanup the cache during request handling (`#18 +- Do not cleanup the cache during request handling (`GitLab#18 <https://git.lumc.nl/mutalyzer/mutalyzer/issues/18>`_). -- Add GRCh38 (hg38) assembly (`#20 +- Add GRCh38 (hg38) assembly (`GitLab!20 <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/20>`_). -- Move from nose to `pytest <http://pytest.org/>`_ for unit tests (`#23 +- Move from nose to `pytest <http://pytest.org/>`_ for unit tests (`GitLab!23 <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/23>`_). - Fix running Mutalyzer in a `virtual environment <http://virtualenv.readthedocs.org/>`_ and have an up-to-date - ``requirements.txt`` for `pip <http://pip.readthedocs.org/>`_ (`#4 + ``requirements.txt`` for `pip <http://pip.readthedocs.org/>`_ (`GitLab!4 <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/4>`_). -- Switch from TAL to Jinja2 (`#3 +- Switch from TAL to Jinja2 (`GitLab!3 <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/3>`_). -- Refactor user interfaces (`#5 +- Refactor user interfaces (`GitLab!5 <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/5>`_). -- Move from configobj to Python module based config (`#7 +- Move from configobj to Python module based config (`GitLab!7 <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/7>`_). -- Use SQLAlchemy as ORM (`#8 +- Use SQLAlchemy as ORM (`GitLab!8 <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/8>`_). -- Use Redis for stat counters (`#10 +- Use Redis for stat counters (`GitLab!10 <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/10>`_). -- Port website from web.py to Flask (`#11 +- Port website from web.py to Flask (`GitLab!11 <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/11>`_). -- Isolated unit tests using fixtures and an in-memory database (`#12 +- Isolated unit tests using fixtures and an in-memory database (`GitLab!12 <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/12>`_). -- Display announcement on website (`#14 +- Display announcement on website (`GitLab!14 <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/14>`_). -- Database migrations with Alembic (`#15 +- Database migrations with Alembic (`GitLab!15 <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/15>`_). -- Update documentation and use Sphinx (`#16 +- Update documentation and use Sphinx (`GitLab!16 <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/16>`_). - Move to `semantic versioning <http://semver.org/>`_, starting with version - 2.0.0 (`#22 <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/22>`_). + 2.0.0 (`GitLab!22 + <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/22>`_). - Add 404 not found page. - Don't auto remove comma characters in syntax checker. - Add a dash (``-``) as an allowed character in the gene name. @@ -116,7 +117,7 @@ Version 2.0.beta-33 Released on August 19th 2014. - Link to `Upcoming server update - <https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/News/2014-08-19-upcoming-server-update>` + <https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/News/2014-08-19-upcoming-server-update>`_ announcement. @@ -147,7 +148,7 @@ Version 2.0.beta-30 Released on February 18th 2014. - Handle NCBI Entrez response validation errors (fixes, among other things, - `LOVD#29 <https://humgenprojects.lumc.nl/trac/LOVD3/ticket/29>`_). + `LOVD Trac#29 <https://humgenprojects.lumc.nl/trac/LOVD3/ticket/29>`_). - Loosen error severity when CDS cannot be translated. - Mutalyzer development migrated from Subversion to Git for version control. @@ -183,7 +184,7 @@ Version 2.0.beta-26 Released on April 9th 2013. - Added mm10 (Mouse) transcript mappings to position converter. -- LRG parser updated to LRG 1.7 schema (`#127 +- LRG parser updated to LRG 1.7 schema (`Trac#127 <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/127>`_). @@ -196,7 +197,7 @@ Released on March 25th 2013. - Move documentation to Trac. - Exon table is included in `runMutalyzer` webservice results. - Temporarily disable frameshift detection in experimental description - extractor (`#124 + extractor (`Trac#124 <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/124>`_). - Allow selectors on transcript references in position converter. - Syntax checker now supports protein level variant descriptions. @@ -207,7 +208,7 @@ Version 2.0.beta-24 Released on December 10th 2012. -- Rename some warning codes (webservice API) (`#98 +- Rename some warning codes (webservice API) (`Trac#98 <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/98>`_). - Variants on mtDNA in position converter. @@ -225,17 +226,17 @@ Version 2.0.beta-22 Released on November 2nd 2012. -- Submitting batch jobs via the web services (`#115 +- Submitting batch jobs via the web services (`Trac#115 <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/115>`_). -- Allow for leading whitespace in batch job input (`#107 +- Allow for leading whitespace in batch job input (`Trac#107 <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/107>`_). - New `descriptionExtract` webservice function. - Name checker now includes description extractor output as an experimental service. - Slice chromosome by gene name in reference file loader is now case - insensitive (`#118 + insensitive (`Trac#118 <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/118>`_). -- Warn on missing positioning scheme (`#114 +- Warn on missing positioning scheme (`Trac#114 <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/114>`_). @@ -245,10 +246,11 @@ Version 2.0.beta-21 Released on July 23rd 2012. - Support compound variants in position converter. -- Support non-coding transcripts in position converter (`#102 +- Support non-coding transcripts in position converter (`Trac#102 <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/102>`_). - Move to new RPC library version, causing slight change in HTTP/RPC+JSON - webservice output (more wrappers around output), but fixes #104. + webservice output (more wrappers around output), but fixes `Trac#104 + <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/104>`_. - Fix position converter for delins with explicit deleted sequence. - Fix description update from Version 2.0.beta-20 to use- notation instead of counting. @@ -268,7 +270,7 @@ Version 2.0.beta-19 Released on June 21st 2012. -- Fix crash on inversions (`#99 +- Fix crash on inversions (`Trac#99 <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/99>`_). @@ -277,19 +279,19 @@ Version 2.0.beta-18 Released on June 7th 2012. -- Moved from soaplib to rpclib for webservices (`#66 +- Moved from soaplib to rpclib for webservices (`Trac#66 <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/66>`_). -- Added HTTP/RPC+JSON webservice (`#18 +- Added HTTP/RPC+JSON webservice (`Trac#18 <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/18>`_). -- Fixed name checker errors in some adjacent variants (`#83 +- Fixed name checker errors in some adjacent variants (`Trac#83 <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/83>`_). - Name checker form now uses GET requests to support easier linking to result pages. -- You can now specify chromosomes by name in the reference file loader (`#92 - <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/92>`_). -- Made batch daemon not crash on MySQL restarts (`#91 +- You can now specify chromosomes by name in the reference file loader + (`Trac#92 <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/92>`_). +- Made batch daemon not crash on MySQL restarts (`Trac#91 <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/91>`_). -- Position converter now detects incorrect order in position ranges (`#95 +- Position converter now detects incorrect order in position ranges (`Trac#95 <https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/95>`_). - Added NBIC logo to 'about' page. -- GitLab