diff --git a/CGAT/version.py b/CGAT/version.py index 493f7415..260c070a 100644 --- a/CGAT/version.py +++ b/CGAT/version.py @@ -1 +1 @@ -__version__ = "0.3.0" +__version__ = "0.3.1" diff --git a/doc/CGATRelease.rst b/doc/CGATRelease.rst index bfcdbfa3..c5010130 100644 --- a/doc/CGATRelease.rst +++ b/doc/CGATRelease.rst @@ -7,6 +7,31 @@ latest code can always be found in the code repository. Nevertheless, we occasionally prepare releases. Notes on each release are below. +Release 0.3.1 +============= + +* bugfix cgat CLI +* added scripts to help find R and Python dependencies: scripts/cgat_deps_R.sh, scripts/cgat_deps_python.sh +* modified install script to use conda environment files instead of conda meta-packages; https://github.com/CGATOxford/cgat/pull/343 +* update test_style.py to reflect new repository structure; https://github.com/CGATOxford/cgat/pull/345 +* update test_import.py to reflect new repository structure; https://github.com/CGATOxford/cgat/commit/decc5ec0e93b4d2c05b6fa3793b5a73caf1fa8b9 +* added script to perform Gene Set Enrichment Analysis; https://github.com/CGATOxford/cgat/pull/344 +* updated scripts to work with Python 3.6; https://github.com/CGATOxford/cgat/pull/346 +* bugfix bed2bed script; https://github.com/CGATOxford/cgat/pull/349; https://github.com/CGATOxford/cgat/issues/347 +* bugfix GTF.py module file; https://github.com/CGATOxford/cgat/issues/350 +* various bugfixes for Python 3 problems when running pipeline_annotations in python 3, plus a modification of the new "assembly report" section to allow genomes without a standard assembly report (e.g. yeast) to be processed; https://github.com/CGATOxford/cgat/pull/348 +* refactor CGAT/PipelineGWAS.py to CGAT/GWAS.py; https://github.com/CGATOxford/cgat/pull/354 +* removed unused imports with autoflakes; https://github.com/CGATOxford/cgat/pull/355 +* removed basestr, use str instead in Python 3; https://github.com/CGATOxford/cgat/pull/359 +* added test for csv2db; https://github.com/CGATOxford/cgat/pull/360 +* fixed rename_transcripts test for gtf2gtf.py; https://github.com/CGATOxford/cgat/pull/361 +* updated installation; https://github.com/CGATOxford/cgat/pull/364 ; https://github.com/CGATOxford/cgat/pull/373 +* updated documentation; https://github.com/CGATOxford/cgat/pull/365 ; https://github.com/CGATOxford/cgat/pull/367 +* replaced bx.bbi.bigwig_file with pyBigWig ; https://github.com/CGATOxford/cgat/pull/369 +* updated Expression.py to iterate over pandas dataframe; https://github.com/CGATOxford/cgat/pull/370 +* updated Expression.py to work with DESeq2 > 1.16 ; https://github.com/CGATOxford/cgat/pull/371 +* moved bed_vs_bed.py to obsolete ; https://github.com/CGATOxford/cgat/pull/372 + Release 0.3.0 ============= @@ -101,6 +126,14 @@ The following people have contributed to the CGAT Code collection: * Ian Sudbery * Hu Xiaoming * Lesheng Kong +* Michael Morgan +* Thomas Smith +* Katherine Brown +* Charlotte George +* Adam Cribbs +* Hania Pavlou +* Reshma Nibhani +* Sebastian Luna-Valero 3rd party code ============== diff --git a/doc/release.rst b/doc/release.rst index 8b94aca1..c5010130 100644 --- a/doc/release.rst +++ b/doc/release.rst @@ -1,34 +1,193 @@ ============= -Release notes +Release Notes ============= -The full CGAT code collection is unreleased. Please use -the latest version from the repository. +The code collection is under continuous improvement and the +latest code can always be found in the code repository. +Nevertheless, we occasionally prepare releases. Notes on +each release are below. -Contributions +Release 0.3.1 ============= -We included publicly and freely available code into the tool -collection for convenience. +* bugfix cgat CLI +* added scripts to help find R and Python dependencies: scripts/cgat_deps_R.sh, scripts/cgat_deps_python.sh +* modified install script to use conda environment files instead of conda meta-packages; https://github.com/CGATOxford/cgat/pull/343 +* update test_style.py to reflect new repository structure; https://github.com/CGATOxford/cgat/pull/345 +* update test_import.py to reflect new repository structure; https://github.com/CGATOxford/cgat/commit/decc5ec0e93b4d2c05b6fa3793b5a73caf1fa8b9 +* added script to perform Gene Set Enrichment Analysis; https://github.com/CGATOxford/cgat/pull/344 +* updated scripts to work with Python 3.6; https://github.com/CGATOxford/cgat/pull/346 +* bugfix bed2bed script; https://github.com/CGATOxford/cgat/pull/349; https://github.com/CGATOxford/cgat/issues/347 +* bugfix GTF.py module file; https://github.com/CGATOxford/cgat/issues/350 +* various bugfixes for Python 3 problems when running pipeline_annotations in python 3, plus a modification of the new "assembly report" section to allow genomes without a standard assembly report (e.g. yeast) to be processed; https://github.com/CGATOxford/cgat/pull/348 +* refactor CGAT/PipelineGWAS.py to CGAT/GWAS.py; https://github.com/CGATOxford/cgat/pull/354 +* removed unused imports with autoflakes; https://github.com/CGATOxford/cgat/pull/355 +* removed basestr, use str instead in Python 3; https://github.com/CGATOxford/cgat/pull/359 +* added test for csv2db; https://github.com/CGATOxford/cgat/pull/360 +* fixed rename_transcripts test for gtf2gtf.py; https://github.com/CGATOxford/cgat/pull/361 +* updated installation; https://github.com/CGATOxford/cgat/pull/364 ; https://github.com/CGATOxford/cgat/pull/373 +* updated documentation; https://github.com/CGATOxford/cgat/pull/365 ; https://github.com/CGATOxford/cgat/pull/367 +* replaced bx.bbi.bigwig_file with pyBigWig ; https://github.com/CGATOxford/cgat/pull/369 +* updated Expression.py to iterate over pandas dataframe; https://github.com/CGATOxford/cgat/pull/370 +* updated Expression.py to work with DESeq2 > 1.16 ; https://github.com/CGATOxford/cgat/pull/371 +* moved bed_vs_bed.py to obsolete ; https://github.com/CGATOxford/cgat/pull/372 -* IGV.py was written by Brent Pedersen. -* SVGdraw.py was written by ... -* The NCL module draws from code written by ... -* list_overlap.py -* Iterators.py +Release 0.3.0 +============= + +First release of the code working in Python 3 only. + +Release 0.2.7 +============= + +This release is compatible with pysam-0.11.1 and is the last +version of the code compatible with Python 2.7. Next releases +will be in Python 3 only. + +Release 0.2.6 +============= + +This release is compatible with pysam-0.10.0 and it is also half +way through the upgrade to Python 3 compatible code. + +Release 0.2.5 +============= + +Minor bugfix release to ensure compatibility with pysam >= 0.8.4 + +Release 0.2.4 +============= + +Minor bugfix release to ensure compatibility with pysam 0.8.4 + +Release 0.2.3 +============= + +Minor release to ensure compatibility with pysam-0.8.1 + +Release 0.2.2 +============= + +We have reviewed the command line options in all of the CGAT +scripts and have changed them to make them more consistent +between tools and more informative on the command line. This +means that existing scripts that call CGAT tools need to be +updated. A table with all options used in scripts and how +they have or have not changed +`here `_. + +There is a script called `cgat_refactor.py +`_ +to facilicate refactoring the repository. Instructions on how to use +the script are given at the command line help. + +There are also several bugfixes and new features. + +Release 0.2.1 +============= + +Bugfix release + +* Fixed a variety of bugs +* Increased test coverage +* Updated documentation +* Added paired read counting to gtf2table + +Release 0.2 +=========== + +* release for CGAT manuscript - fixed various installation issues + +Release 0.1.9 +============= + +* alignlib incompatibility fixed +* various bugfixes + +Release 0.1.8 +============= + +* OS X compatibility release +* various bugfixes Contributors ------------- - -Andreas Heger -Antonio Berlanga-Taylor -Martin Dienstbier -Nicholas Ilott -Jethro Johnson -Katherine Fawcett -Stephen Sansom -David Sims -Ian Sudbery -Hu Xiaoming +============ + +The following people have contributed to the CGAT Code collection: + +* Andreas Heger +* Antonio Berlanga-Taylor +* Martin Dienstbier +* Nicholas Ilott +* Jethro Johnson +* Katherine Fawcett +* Stephen Sansom +* David Sims +* Ian Sudbery +* Hu Xiaoming +* Lesheng Kong +* Michael Morgan +* Thomas Smith +* Katherine Brown +* Charlotte George +* Adam Cribbs +* Hania Pavlou +* Reshma Nibhani +* Sebastian Luna-Valero + +3rd party code +============== + +The CGAT code collection has been made possible by the many developers +in the bioinformatics and python community that have made their code +available for sharing. The code collection includes some snippets of +code taken from elsewhere for convenience, most notably: + +1. IGV.py from Brent Petersen + https://github.com/brentp/bio-playground/blob/master/igv/igv.py + +2. Nested containment list from the Pygr project + http://code.google.com/p/pygr/ + +3. SVGdraw.py was written by Fedor Baart & Hans de Wit + +4. list_overlap.py from Brent Petersen + https://github.com/brentp/bio-playground/blob/master/utils/list_overlap_p.py + +5. Iterators.py from an unknown source. + +Licence +======= + +The CGAT code is released under the new BSD licence:: + + Copyright (c) 2013, Andreas Heger, MRC CGAT + + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are + met: + + Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the + distribution. Neither the name of the Medical Research Council nor the + names of its contributors may be used to endorse or promote + products derived from this software without specific prior written + permission. + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.