Releases: etetoolkit/ete
v4.1.0-beta
This pre-release includes a new newick parser and other infrastructure-related changes.
The API changes are mainly these:
convert_to_ultrametric() -> to_ultrametric() (also, new implementation)
topology_only -> topological (argument in several functions)
feature(s), attribute(s), property(ies) -> prop(s) (argument in several functions)
popup_prop_keys -> include_props, exclude_props (in explore() and others)
t & 'A' -> t['A']
tree['A'] (get the node called 'A')
tree[0,1,0] (get the node that comes from the root's 1st child, then its 2nd child, and then its 1st child)
node.id (tuple like [0,1,0])
node.level (number of nodes between node and root)
t.get_tree_root() -> t.root
t.is_root() -> t.is_root
t.is_leaf() -> t.is_leaf
t.get_common_ancestor(n1, n2, n3) -> t.common_ancestor([n1, n2, n3])
t.get_ancestors() -> t.ancestors()
t.get_leaves(), t.iter_leaves() -> t.leaves()
t.get_leaf_names() -> t.leaf_names()
t.get_descendants() , t.iter_descendants() -> t.descendants()
t.get_ascii() -> t.to_str()
t.write(props=[], format=1) -> t.write(props=None, parser=1)
A.get_distance(B) -> t.get_distance(A, B)
Tree(name='Hi', dist=1, support=1) -> Tree({'name': 'Hi', 'dist': 1, 'support': 1})
->
Tree(nw, format=1) -> Tree(nw, parser=1)
nw = t.write(format=f, dist_formatter="%0.1f", name_formatter="TEST-%s", support_formatter="SUP-%0.1f")
->
parser = newick.make_parser(f, dist='%0.1f', name='TEST-%s', support='SUP-%0.1f')
nw = t.write(parser=parser)
props=None (default in some functions) -> write all extended properties
props=[] -> do not write any extended properties
_FaceContainer -> Grid
_HeaderFaceContainer -> AlignedGrid
get_FaceAreas -> make_faces
smartview/b64pickle.py -> parser/ete_format.py
3.1.3
This is a maintenance pre-release that should fix most obvious problems with Qt >= 5.12 due to overflow checking issues.
See https://www.riverbankcomputing.com/static/Docs/PyQt5/incompatibilities.html\#pyqt-v5-12.
Setting PyQt5.sip.enableoverflowchecking(False) had no effect, apparently, so many calls to the Qt drawing directives have been reviewed and changed accordingly. Other may be still present. Please report any other potential incompatibilities founds.
ete4.0.0 beta
4.0.0-beta mute tree style in explore
3.1.2
Main changes:
- Improves Py3 compatibility (Python 3.6 recommended for full compatibility with
ete_toolchainpkg) - Python 2 support dropped (i.e. new fixes and changes are not considering Python 2.7 compatibility)
- Fixes NCBI Taxonomy problems parsing the latest DB versions
- Added function for cophenetic matrix
- Other small bug fixes
Most important commits:
7a1f0c5 Fixes #469 NCBI db update crashes due to nocase duplicate synonyms
7597af3 ncbi_query get_topology does not break when some taxids are not found.
7914155 get_midpoint function does not return None when tree already rooted at midpoint. Returns first child instead
6cad2f7 Merge pull request #452 from etetoolkit/mca_method_issue_398
59dea1b clean up code for Python3
465f56f if the same node is provided as first argument to get_common_ancestor, returns itself. Unittest of get_common_ancestor improved.
98e255f Merge pull request #450 from dengzq1234/instance#436
1324f66 read synonyms table in get_descendant_taxa() if taxid deprecated #436
766f211 Merge pull request #449 from dengzq1234/instance#428
0b84a2a disables python 3.4 travis test
3f20592 Merge pull request #447 from dengzq1234/instance#416
437efd9 Merge pull request #446 from dengzq1234/instance#443
c639381 Merge pull request #355 from linsalrob/master
337647f Merge branch 'master' into master
b524047 Merge pull request #442 from dengzq1234/master
efbc215 Merge pull request #412 from matsen/master
068df09 Merge pull request #405 from davidhwyllie/master
573bb71 updates unitest to check sos_thr and bug #404
b345501 fixes bug when sos_thr > 0 in spoverlap get_my_evol_events . Fixes #404
1752154 Resolve long tree string problem on Windows #258
6f3d59c Merge pull request #400 from fransua/master
3.1.1
- tree: added support for quoted names in Newick strings
- treeview: Solved compatibility problems between Qt4 and Qt5 (both are now accepted)
- treeview: added compatibility for a new webplugin tool (https://github.com/etetoolkit/webplugin)
- ete-build: added preliminary iqtree support
- ete_evol: output file names are now compatible with large trees
- improves python3 compatibility and a number of small fixes.
Thanks to all contributors!
Most important commits:
Nov 2 2017 a36adb1 Add support for Qt5
Sep 25 2017 1bb716b test all branches with travis
Sep 25 2017 a040b0c more informative ete3 version command
Aug 8 2017 f66f996 fixes rounding problemin StackedBarFace. Fixes #298
Aug 8 2017 20d4be5 temporary fix problem reusing profileFaces. Recycling pixmap faces is not allowed. Should it be?
Aug 8 2017 398c71c fix tests for get_cached_content
Aug 7 2017 f6d041f changes behaviour of get_cached_content(leaves_only=False), so content does not include node itself unless tip
Aug 7 2017 6f60503 fixes bug in get_cached_content(leaves_only=False)
Jul 26 2017 c368b3f Fix logical typo in NCBI database update
Jul 25 2017 6f56ba5 Add is_taxadb_up_to_date to exports
Jul 25 2017 15361d9 ncbiquery: Add is_taxadb_up_to_date(dbfile=...)
Jun 12 2017 0a89664 Merge pull request #286 from chrstphrchvz/patch-1
May 1 2017 b6f9cee tree.py: typo fixes, spelling/grammar improvements
Apr 25 2017 e20712a export sorted features when using tree.write(features=[]). Fixes #267
Apr 24 2017 6b4045f moves DiamondFace for correct inheritance of StatictItemFace
Apr 24 2017 db33616 Merge pull request #251 from mortonjt/diamond
Apr 24 2017 7feb004 add iqtree to the tests
Apr 24 2017 22d5905 Solves problem calculating dimension of TextFaces hacing newline chars. Fixes #241
Apr 24 2017 2b2a96e removes length restrictions in scale bar. Fixes #266
Apr 24 2017 b362cb7 fixes #278
Apr 21 2017 55b6e60 really fixes problem exporting quoted names in newick format
Mar 21 2017 c75cfc7 fixes ncbiquery test regarding Bacteria synonym
Mar 20 2017 2323e3f BUG Fix python3 compatibility with Popen
Jan 10 2017 4f08992 clean whitespaces
Jan 3 2017 a339100 ete build: add iqtree support (experimental)
Apr 28 2016 fa8a6be really fixes wrong file name in setup script
Apr 19 2016 a945e9d ete-build: add missing workflow names
Feb 14 2016 70d3a45 allows CODON models through iqtree
Feb 14 2016 6a7d43e more iqtree confs and fix: clearall deletes workflow directories!
Jan 3 2017 8169cf7 fixes problem of plotting alignments using lowercase
Jan 2 2017 8c6bf06 added SVGFace. Related to #238
Jan 2 2017 bf9988b Merge pull request #211 from etetoolkit/feature/quotednames
Jul 29 2016 90c7e63 allows single node trees with quoted names;
Jun 29 2016 85fa70b changed flag name to "leaves_only", put flag before "_store", added lines in the unittest to cover functionality
Jan 10 2017 4c55ce9 ENH: Adding diamond face as an optional face
Oct 6 2016 cfcb619 BUG FIX: EvolTree run_model kwargs defining non-default parameters were overridden
Sep 10 2016 3a2f631 ete_evol: hash for naming output folders now includes the newick of the tree
Sep 10 2016 07f996b evol tree: updated documentation in order to explain that M1 and M2 model are refering to M1a and M2a models in PAML user guide.
Sep 10 2016 d696df3 ete_evol: Fixed problem with big trees generating long output folder names
Aug 23 2016 aa5a488 fixes #236
Aug 12 2016 993d53c thread safe web img rendering
Jun 15 2016 3e1464a allow db file from local taxdump file + add create db option
Aug 2 2016 c60e172 %%return option generates img_map (needed for new webplugin)
May 13 2016 15bc8ad Store testdb in tmp_test for travis caching
May 13 2016 dbdea7e Use the git tag for the ete3 version if available
Jun 15 2016 1e1e3d0 do not ignore dfile argument
May 19 2016 b7e56d2 Workaround FTP proxy issues by downloading NCBI taxonomy via HTTP
Apr 27 2016 5b3dc6b Multiple automatic fixes from quantifiedcode.com
Mar 17 2016 c524b2c Python3 compat fix for _ph.py
Mar 10 2016 6592638 Minor change to get_topology method
Mar 10 2016 3ec463d solves test fail due to unsolved dependency in new conda/scikit-bio installation
Mar 10 2016 3b8e335 fixes newick dialog in GUI. Solves #185
Mar 9 2016 efa0816 ete_evol tool: fixed small bug in summary statitistcs displayed for site models with only one site
Feb 12 2016 2b49a1a improves get_topology by resolving taxid synonyms