Merge pull request #766 from etetoolkit/faster

Get the new drawing code from the branch "faster"

Author: jordibc

CONTRIBUTING.md

@@ -32,21 +32,9 @@ To run the tests, after you have a local installation (see
 [README.md](README.md) for details), you can:
 
 ```sh
-python -m unittest tests.test_arraytable
-python -m unittest tests.test_clustertree
-python -m unittest tests.test_gtdbquery
-python -m unittest tests.test_interop
-python -m unittest tests.test_phylotree
-python -m unittest tests.test_seqgroup
-python -m unittest tests.test_tree
-python -m unittest tests.test_treediff
-python -m unittest tests.test_orthologs_group_delineation
-python -m unittest tests.test_ncbiquery
-python -m unittest tests.test_nexus
+./run_tests.py
 ```
 
-Eventually we will fix the remaining tests, and then we expect to run them all with:
-
-```sh
-python -m unittest tests.test_all
-```
+which will run the subset of the tests that should be working. You can
+use the `--list` argument to see the tests, or `--help` to see all the
+options.

VERSION

@@ -1 +1 @@
-4.0.0-beta2
+4.0.0-beta3

doc/conf.py

@@ -13,7 +13,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = 'ETE Toolkit'
-copyright = '2008 - 2023, The ETE Toolkit Team'
+copyright = '2008 - 2024, The ETE Toolkit Team'
 author = 'Jaime Huerta-Cepas et al.'
 release = open('../VERSION').readline().strip()
 

doc/images/collapsed.png

@@ -8,7 +8,6 @@ Reference Guide
    reference_operations
    reference_parsers
    reference_phylo
-   reference_clustering
    reference_seqgroup
    reference_taxonomy
    reference_smartview

doc/images/combined.png

@@ -4,187 +4,51 @@ Smartview (web graphics)
 .. contents::
 
 
-Server
-------
-
-.. automodule:: ete4.smartview.gui.server
-   :members:
-   :undoc-members:
-   :special-members: __init__
-
-
-Renderer
+Explorer
 --------
 
-Drawer
-~~~~~~
-
-.. automodule:: ete4.smartview.renderer.drawer
+.. automodule:: ete4.smartview.explorer
    :members:
    :undoc-members:
    :special-members: __init__
 
 
-Draw helpers
-~~~~~~~~~~~~
+Layout
+------
 
-.. automodule:: ete4.smartview.renderer.draw_helpers
+.. automodule:: ete4.smartview.layout
    :members:
    :undoc-members:
    :special-members: __init__
 
 
 Faces
-~~~~~
-
-.. automodule:: ete4.smartview.renderer.faces
-   :members:
-   :undoc-members:
-   :special-members: __init__
-
-
-Face positions
-~~~~~~~~~~~~~~
-
-.. automodule:: ete4.smartview.renderer.face_positions
-   :members:
-   :undoc-members:
-   :special-members: __init__
-
-
-NodeStyle
-~~~~~~~~~
+-----
 
-.. automodule:: ete4.smartview.renderer.nodestyle
+.. automodule:: ete4.smartview.faces
    :members:
    :undoc-members:
    :special-members: __init__
 
 
-TreeLayout
-~~~~~~~~~~
-
-.. automodule:: ete4.smartview.renderer.treelayout
-   :members:
-   :undoc-members:
-   :special-members: __init__
-
-
-TreeStyle
-~~~~~~~~~
-
-.. automodule:: ete4.smartview.renderer.treestyle
-   :members:
-   :undoc-members:
-   :special-members: __init__
-
-
-Layouts
-~~~~~~~
-
-context
-^^^^^^^
-
-.. automodule:: ete4.smartview.renderer.layouts.context_layouts
-   :members:
-   :undoc-members:
-   :special-members: __init__
-
-
-default
-^^^^^^^
-
-.. automodule:: ete4.smartview.renderer.layouts.default_layouts
-   :members:
-   :undoc-members:
-   :special-members: __init__
-
-
-domain
-^^^^^^
-
-.. automodule:: ete4.smartview.renderer.layouts.domain_layouts
-   :members:
-   :undoc-members:
-   :special-members: __init__
-
-
-eggnog6
-^^^^^^^
-
-.. automodule:: ete4.smartview.renderer.layouts.eggnog6_layouts
-   :members:
-   :undoc-members:
-   :special-members: __init__
-
-
-etecompare
-^^^^^^^^^^
-
-.. automodule:: ete4.smartview.renderer.layouts.etecompare_layouts
-   :members:
-   :undoc-members:
-   :special-members: __init__
-
-
-evocell
-^^^^^^^
-
-.. automodule:: ete4.smartview.renderer.layouts.evocell_layouts
-   :members:
-   :undoc-members:
-   :special-members: __init__
-
-
-evol_events
-^^^^^^^^^^^
-
-.. automodule:: ete4.smartview.renderer.layouts.evol_events_layouts
-   :members:
-   :undoc-members:
-   :special-members: __init__
-
-
-ncbi_taxonomy
-^^^^^^^^^^^^^
-
-.. automodule:: ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts
-   :members:
-   :undoc-members:
-   :special-members: __init__
-
-
-phylocloud_egg5
-^^^^^^^^^^^^^^^
-
-.. automodule:: ete4.smartview.renderer.layouts.phylocloud_egg5_layouts
-   :members:
-   :undoc-members:
-   :special-members: __init__
-
-
-seq
-^^^
+Graphics
+--------
 
-.. automodule:: ete4.smartview.renderer.layouts.seq_layouts
+.. automodule:: ete4.smartview.graphics
    :members:
    :undoc-members:
    :special-members: __init__
 
 
-spongilla
-^^^^^^^^^
+Coordinates
+-----------
 
-.. automodule:: ete4.smartview.renderer.layouts.spongilla_layouts
+.. automodule:: ete4.smartview.coordinates
    :members:
    :undoc-members:
    :special-members: __init__
 
 
-staple
-^^^^^^
-
-.. automodule:: ete4.smartview.renderer.layouts.staple_layouts
-   :members:
-   :undoc-members:
-   :special-members: __init__
+.. TODO: Maybe recreate and add old layouts: context, default, domain,
+   eggnog6, compare, evocell, evol_events, ncbi_taxonomy,
+   phylocloud_egg5, seq, spongilla, staple

doc/images/context_menu.png

@@ -61,9 +61,6 @@ Faces
 .. autoclass:: PieChartFace
    :members:
 
-.. autoclass:: ProfileFace
-   :members:
-
 .. autoclass:: TreeFace
    :members: