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Merge pull request #766 from etetoolkit/faster
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Get the new drawing code from the branch "faster"
jordibc authored Dec 29, 2024
2 parents bf32525 + fa97548 commit 94daa41
Showing 205 changed files with 9,751 additions and 60,439 deletions.
20 changes: 4 additions & 16 deletions CONTRIBUTING.md
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@@ -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.
2 changes: 1 addition & 1 deletion VERSION
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@@ -1 +1 @@
4.0.0-beta2
4.0.0-beta3
2 changes: 1 addition & 1 deletion doc/conf.py
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@@ -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()

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1 change: 0 additions & 1 deletion doc/reference/index.rst
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@@ -8,7 +8,6 @@ Reference Guide
reference_operations
reference_parsers
reference_phylo
reference_clustering
reference_seqgroup
reference_taxonomy
reference_smartview
8 changes: 0 additions & 8 deletions doc/reference/reference_clustering.rst

This file was deleted.

168 changes: 16 additions & 152 deletions doc/reference/reference_smartview.rst
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@@ -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
3 changes: 0 additions & 3 deletions doc/reference/reference_treeview.rst
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@@ -61,9 +61,6 @@ Faces
.. autoclass:: PieChartFace
:members:

.. autoclass:: ProfileFace
:members:

.. autoclass:: TreeFace
:members:

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