ete3 - 4.4.0

The main change is the use of a high-performance multithreaded http server for the backend (cheroot wsgi server, instead of our old wsgiref.simple_server). This allows the use of ete to serve efficiently many users at the same time.

Some fixes: - order of headers in aligned panels work the same and well in all browsers - multiple headers will not overlap now (not even a little), and their underlines have the exact size (do not extend to infinity) - faces zoom correctly in aligned panels - t.render_sm() (render with smartview) draws the full tree expanded by default - updated and fixed examples in the examples directory - minor corrections in closest_leaf() and related functions

Some additions: - SeqFace accepts marking some positions - t.distance_matrix() (faster and supersedes t.cophenetic_matrix()) - examples of extending the server api - net_relatedness_index() and nearest_taxon_index()

Full Changelog since previous release: https://github.com/etetoolkit/ete/compare/4.3.0...4.4.0

Also available in PyPI: https://pypi.org/project/ete4/

The updated documentation can be found at https://etetoolkit.github.io/ete/

- Python
Published by jordibc 6 months ago

ete3 - 4.3.0

Also available in PyPI: https://pypi.org/project/ete4/

The updated documentation can be found at https://etetoolkit.github.io/ete/

Full Changelog since previous release: https://github.com/etetoolkit/ete/compare/4.1.1...4.3.0

- Python
Published by jordibc 10 months ago

ete3 - 4.1.1

This release takes ete4 out of beta and makes it available in PyPI too.

The updated documentation can be found at https://etetoolkit.github.io/ete/

Changes with respect to ete3 can be found at https://github.com/etetoolkit/ete/wiki/3to4

- Python
Published by jordibc 11 months ago

ete3 - https://github.com/etetoolkit/ete/releases/tag/4.0.0

- Python
Published by github-actions[bot] 11 months ago

ete3 - 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

- Python
Published by jordibc over 2 years ago

ete3 - 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.

closes #684 #667 #617 #635

- Python
Published by jhcepas almost 3 years ago

ete3 - ete4.0.0 beta

- Python
Published by jhcepas about 4 years ago

ete3 -

Main changes: - Improves Py3 compatibility (Python 3.6 recommended for full compatibility with ete_toolchain pkg)
- 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:

7a1f0c596cc5cf2eb709da2ed991cbeb1d79250f Fixes #469 NCBI db update crashes due to nocase duplicate synonyms 7597af36a2d9f36e8a041bda618bae86dd0776d9 ncbiquery gettopology does not break when some taxids are not found. 791415518f60c9ff329383266978102685105d11 getmidpoint function does not return None when tree already rooted at midpoint. Returns first child instead 6cad2f71c0a1f9331bb6ee8a3619f91b22b24e95 Merge pull request #452 from etetoolkit/mcamethodissue398 59dea1b7218829757f32c58934e292d6158a9948 clean up code for Python3 465f56f6aa24bb815cf859fd6273529e114e4410 if the same node is provided as first argument to getcommonancestor, returns itself. Unittest of getcommonancestor improved. 98e255f4fc80ab4d8b7c4eabe4262bdb5946ced6 Merge pull request #450 from dengzq1234/instance#436 1324f6656928f2810ca1de51fb9c3bb47e5f54ce read synonyms table in getdescendanttaxa() if taxid deprecated #436 766f211b55e9086a1df9ba970b931693ebe73c55 Merge pull request #449 from dengzq1234/instance#428 0b84a2aba603d743612cf06ebbcd1cff917e03a4 disables python 3.4 travis test 3f205928054d3e071ec5927cc128a707cc096521 Merge pull request #447 from dengzq1234/instance#416 437efd95290716248d9a1dc2c39a630cd4120b14 Merge pull request #446 from dengzq1234/instance#443 c639381ba06234c3607ec5f814b7f619107c93ec Merge pull request #355 from linsalrob/master 337647f09ffb14a15c82907cce91f84ffc653ec4 Merge branch 'master' into master b524047837726d2a70fbba3552f290fffa3eaa86 Merge pull request #442 from dengzq1234/master efbc215a2df298dce3ae3cff5d70e9c27be41a0c Merge pull request #412 from matsen/master 068df09f891122a3cfdbbbd415b658da8ffde2bb Merge pull request #405 from davidhwyllie/master 573bb717fa96daa486f71c088654158c109cf1d6 updates unitest to check sosthr and bug #404 b3455019bf690d11ce1be620ad43adbb154876fc fixes bug when sosthr > 0 in spoverlap getmyevol_events . Fixes #404 1752154f361f57144ce4b09f3993f6b8374b2993 Resolve long tree string problem on Windows #258 6f3d59c7341fb5c2efb326f28d04d0a472a4ccbb Merge pull request #400 from fransua/master

- Python
Published by jhcepas over 5 years ago

ete3 -

• 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

- Python
Published by jhcepas over 8 years ago

ete3 -

- Python
Published by jhcepas over 8 years ago