0.4b15: PyPI. Gtk.CRITICAL 🪲 F1 help and F5 refresh. GPLv3 instead of MIT. new_version loop.

Author: lkndl

LICENSE.md

@@ -1,8 +1,8 @@
 # AB12PHYLO
 
-![PyPI license](https://img.shields.io/pypi/l/ansicolortags.svg) 
-![github version](https://img.shields.io/static/v1?label=version&message=0.4b013&color=blue&style=flat)
-![Python version](https://img.shields.io/static/v1?label=python&message=3.6&color=orange&style=flat&logo=python)
+![PyPI license](https://img.shields.io/pypi/l/ab12phylo?color=green)
+![github version](https://img.shields.io/static/v1?label=version&message=0.4.15-beta&color=brightgreen&style=flat)
+![PyPI Python version](https://img.shields.io/pypi/pyversions/ab12phylo)
 
 [AB12PHYLO](https://github.com/lkndl/ab12phylo) is an integrated, easy-to-use pipeline for Maximum Likelihood (ML) phylogenetic tree inference from ABI sequencing data. 
 At its core, AB12PHYLO runs parallelized instances of [RAxML-NG](https://github.com/amkozlov/raxml-ng) (Kozlov et al. 2019) and a BLAST search in a reference database. 
@@ -15,11 +15,11 @@ AB12PHYLO was developed to identify plant pathogen populations possibly under ba
 
 ## Installation
 
-First, clone the AB12PHYLO repository:
- 
+The recommended way to install AB12PHYLO is via
 ```shell script
-git clone https://github.com/lkndl/ab12phylo
+pip install ab12phylo
 ```
+
 All [external tools](#external-tools) are in the [Bioconda](https://anaconda.org/bioconda/repo) channel, which can simplify installation. To create a new or activate an existing python3 [conda](https://docs.conda.io/) environment:
 ```shell script
 conda create -n <your_python3_conda_env> python=3
@@ -47,15 +47,18 @@ If you are on Linux and using conda, please check `which python` and `which pip`
 ```
 In the case shown here, `pip` points to a version outside of your conda installation, so use `pip3`. If neither points to your conda, re-start your shell and check your environment. Sometimes there is no `pip` at all, which can be fixed on Linux using your package manager (or `sudo apt-get install python3-pip` on Ubuntu), or in conda via `conda install -c conda-forge pip`.
 
-Now install AB12PHYLO and its python [dependencies](#dependencies) via `pip` or `pip3`:
+Now install AB12PHYLO and its python [dependencies](#dependencies) via `pip` or `pip3` as shown at the top. 
+
+Alternatively, build AB12PHYLO from source:
 
- ```shell script
+```shell script
+git clone https://github.com/lkndl/ab12phylo
 cd ab12phylo
 pip install --upgrade pip
 pip install .
 ```
 
-If starting AB12PHYLO via `ab12phylo` fails with something like `ValueError: Namespace Gtk not available` or `ModuleNotFoundError: No module named 'gi'`, the conda python cannot see GTK3. This can be fixed by installing GTK3 to `<env>` via:
+If starting AB12PHYLO via `ab12phylo` fails with something like `ValueError: Namespace Gtk not available` or `ModuleNotFoundError: No module named 'gi'`, you're missing PyGObject, the bindings for GTK3. You can find instructions for a system installation [here](https://pygobject.readthedocs.io/en/latest/getting_started.html), or install it to your conda `<env>` via:
 
 ```shell script
 conda install -c conda-forge pygobject gtk3  

README.md

@@ -0,0 +1,8 @@
+# 2021 Leo Kaindl
+
+__author__ = 'Leo Kaindl'
+__email__ = '[email protected]'
+__version__ = '0.4.15-beta'
+__date__ = '14 February 2021'
+__license__ = 'gpl-3.0'
+__status__ = 'Beta'

ab12phylo/__init__.py

@@ -1341,6 +1341,32 @@
       </packing>
     </child>
   </object>
+  <object class="GtkHeaderBar" id="tbar">
+    <property name="name">tbar</property>
+    <property name="visible">True</property>
+    <property name="can-focus">False</property>
+    <property name="title" translatable="yes">AB12PHYLO</property>
+    <property name="has-subtitle">False</property>
+    <property name="spacing">0</property>
+    <property name="show-close-button">True</property>
+    <property name="decoration-layout">menu:minimize,maximize,close</property>
+    <child>
+      <object class="GtkMenuButton">
+        <property name="visible">True</property>
+        <property name="can-focus">True</property>
+        <property name="focus-on-click">False</property>
+        <property name="receives-default">True</property>
+        <property name="direction">none</property>
+        <property name="popover">pop_menu</property>
+        <child>
+          <placeholder/>
+        </child>
+      </object>
+      <packing>
+        <property name="pack-type">end</property>
+      </packing>
+    </child>
+  </object>
   <object class="GtkAdjustment" id="qal_scroll_adj">
     <property name="upper">100</property>
     <property name="step-increment">1</property>
@@ -2644,6 +2670,7 @@ Alternatively, a color legend would nicely fit here.</property>
                         <child>
                           <object class="GtkScrolledWindow" id="parallel_qal">
                             <property name="name">parallel_qal</property>
+                            <property name="height-request">1</property>
                             <property name="visible">True</property>
                             <property name="can-focus">True</property>
                             <property name="hexpand">True</property>
@@ -7193,7 +7220,6 @@ Please define your dataset of ABI trace files or sequence data in &lt;i&gt;.fast
                 <child>
                   <placeholder/>
                 </child>
-                <accelerator key="F1" signal="close"/>
               </object>
               <packing>
                 <property name="left-attach">0</property>
@@ -7271,7 +7297,6 @@ Please define your dataset of ABI trace files or sequence data in &lt;i&gt;.fast
                             <property name="icon-name">window-close-symbolic</property>
                           </object>
                         </child>
-                        <accelerator key="a" signal="clicked" modifiers="GDK_LOCK_MASK"/>
                         <style>
                           <class name="image-button"/>
                         </style>
@@ -7348,31 +7373,4 @@ Please define your dataset of ABI trace files or sequence data in &lt;i&gt;.fast
     <property name="hexpand">False</property>
     <property name="stack">ml_stack</property>
   </object>
-  <object class="GtkHeaderBar" id="tbar">
-    <property name="name">tbar</property>
-    <property name="visible">True</property>
-    <property name="can-focus">False</property>
-    <property name="title" translatable="yes">AB12PHYLO</property>
-    <property name="has-subtitle">False</property>
-    <property name="spacing">0</property>
-    <property name="show-close-button">True</property>
-    <property name="decoration-layout">menu:minimize,maximize,close</property>
-    <child>
-      <object class="GtkMenuButton">
-        <property name="visible">True</property>
-        <property name="can-focus">True</property>
-        <property name="focus-on-click">False</property>
-        <property name="receives-default">True</property>
-        <property name="align-widget">win</property>
-        <property name="direction">none</property>
-        <property name="popover">pop_menu</property>
-        <child>
-          <placeholder/>
-        </child>
-      </object>
-      <packing>
-        <property name="pack-type">end</property>
-      </packing>
-    </child>
-  </object>
 </interface>

ab12phylo/files/gui.glade

@@ -17,10 +17,13 @@
 from ab12phylo.gtk_tree import tree_page
 
 gi.require_version('Gtk', '3.0')
-
 LOG = logging.getLogger(__name__)
 
 
+# debug via G_DEBUG="fatal_warnings" gdb --args python /home/quirin/PYTHON/AB12PHYLO/ab12phylo/gtk_app.py
+# python3 -m build
+# twine upload dist/*
+
 # set the icon theme
 # Gtk.Settings.get_default().set_property('gtk-icon-theme-name', 'Papirus-Dark-Maia')
 # Gtk.Settings.get_default().set_property('gtk-theme-name', 'Matcha-dark-sea')
@@ -183,6 +186,7 @@ def delete_and_ignore_rows(self, *args):
             elif page == 4:
                 self.iface.view_gbl.grab_focus()
                 self.drop_seqs()
+        return True
 
 
 def main():

ab12phylo/gtk_app.py

@@ -1,28 +1,32 @@
 # 2021 Leo Kaindl
 
 import ast
+import hashlib
 import logging
 import mmap
 import pickle
 import shutil
-import sys
-import hashlib
 import threading
-import warnings, zipfile
+import warnings
+import zipfile
 from argparse import Namespace
 from pathlib import Path
 from time import sleep
 
 import gi
-import matplotlib.pyplot as plt
+import matplotlib
 import pandas as pd
+import sys
 from matplotlib.colorbar import ColorbarBase
 from matplotlib.colors import ListedColormap
 
-from ab12phylo_cmd import msa
 from ab12phylo import repo
-from ab12phylo_cmd.__init__ import __version__, __author__, __email__
+from ab12phylo.__init__ import __version__, __author__, __email__
 from ab12phylo.gtk_proj import project_dataset
+from ab12phylo_cmd import msa
+
+matplotlib.use('agg')
+import matplotlib.pyplot as plt
 
 gi.require_version('Gtk', '3.0')
 from gi.repository import Gtk, Gdk, Gio, GLib, GObject, GdkPixbuf
@@ -67,11 +71,13 @@ def do_startup(self):
             self.set_accels_for_action(detailed_action_name='app.%s' % act,
                                        accels=['<Control>%s' % acc])
         self.set_accels_for_action(detailed_action_name='app.help',
-                                   accels=['<Control>F1', '<Control>h'])
+                                   accels=['F1', '<Control>h'])
         # self.add_accelerator(accelerator='<Control>h', action_name='app.help', parameter=None)
 
     def do_command_line(self, cmd):
         options = cmd.get_options_dict().end().unpack()
+        if 'version' in options:
+            sys.exit('ab12phylo: %s' % __version__)
         if 'open' in options:
             self.load(options['open'])
         if 'proceed' in options:
@@ -87,8 +93,9 @@ def __init__(self):
                              'to open a project from the commandline. '
                              'A .proj file next to a directory of data.')
         self.add_main_option('proceed', ord('p'), GLib.OptionFlags.IN_MAIN,
-                             GLib.OptionArg.NONE, 'try to proceed',
-                             'to go to the next analysis stage.')
+                             GLib.OptionArg.NONE, 'try to proceed')
+        self.add_main_option('version', ord('v'), GLib.OptionFlags.IN_MAIN,
+                             GLib.OptionArg.NONE, 'print version')
         # fetch all named objects from the .glade XML
         iface = dict()
         for widget in Gtk.Builder().new_from_file(str(ab12phylo_app_base.TEMPLATE)).get_objects():
@@ -129,7 +136,7 @@ def __init__(self):
         mod = b'lighter', b'darker'
         mod2 = 200  # per default, make TreeView text color darker
         theme = Gtk.Settings.get_default().get_property('gtk-theme-name')
-        if 'dark' in theme:
+        if 'dark' in theme.lower():
             mod = mod[::-1]
             mod2 = 255
 
@@ -148,7 +155,7 @@ def __init__(self):
         button:active { background-color: #17f }
         notebook header { background-color: transparent; }
         '''
-        if 'atcha' in theme:
+        if 'matcha' in theme.lower():
             css += b'''
             .codeview text { background-color: %s(@bg_color); color: %s(@fg_color); }
             window { background-color: mix(@bg_color, rgba(127,127,127,0), 0.05) }
@@ -187,10 +194,12 @@ def __init__(self):
         # connect buttons
         iface.next.connect('clicked', self.proceed)
         self.bind_accelerator(self.accelerators, iface.next, '<Alt>Right')
+        iface.next.grab_focus()
         iface.back.connect('clicked', self.step_back)
         self.bind_accelerator(self.accelerators, iface.back, '<Alt>Left')
         iface.refresh.connect('clicked', self.re_run)
         self.bind_accelerator(self.accelerators, iface.refresh, 'Return')
+        self.bind_accelerator(self.accelerators, iface.refresh, 'F5')
         iface.reset.connect('clicked', self.reset)
         # any page change
         iface.notebook.connect_after('switch-page', self.refresh)
@@ -412,9 +421,10 @@ def _import(self, *args):
             self.iface.notebook.set_current_page(7)
         dialog.destroy()
 
-    def help(self, show=False, *args):
+    def help(self, *args, **kwargs):
         bar = self.iface.infobar
-        bar.set_revealed(not bar.get_revealed() or show)
+        bar.set_revealed(not bar.get_revealed() or 'show' in kwargs)
+        return True
 
     def test(self, *args):
         if self.wd != Path('untitled'):
@@ -453,12 +463,13 @@ def on_quit(self, *args):
 
     def about(self, *args):
         Gtk.AboutDialog(transient_for=self.win, modal=True, title='About AB12PHYLO',
-                        authors=['%s<%s>' % (__author__, __email__), 'Dr Remco Stam', 'Corinn Small'],
+                        authors=['%s<%s>' % (__author__, __email__),
+                                 'Remco Stam<[email protected]>', 'Corinn Small'],
                         comments='An integrated pipeline for Maximum Likelihood (ML) '
                                  'phylogenetic tree inference from ABI sequencing data',
                         program_name='AB12PHYLO', version=__version__,
                         website='https://github.com/lkndl/ab12phylo',
-                        website_label='Github Repo', license_type=Gtk.License.MIT_X11,
+                        website_label='Github Repo', license_type=Gtk.License.GPL_3_0,
                         logo=GdkPixbuf.Pixbuf.new_from_file(str(ab12phylo_app_base.ICON))).present()
 
     def _init_log(self, **kwargs):
@@ -1042,10 +1053,9 @@ def edit_numerical_entry_up_down(self, widget, event):
         key = Gdk.keyval_name(event.keyval)
         if key == 'Up':
             widget.set_text(str(1 + int(widget.get_text())))
-            return True
         elif key == 'Down':
             widget.set_text(str(max(0, -1 + int(widget.get_text()))))
-            return True
+        return True
 
     def edit_numerical_entry(self, widget):
         # filter for numbers only

ab12phylo/gtk_base.py

@@ -42,9 +42,9 @@ def __init__(self):
 
         # connect buttons
         iface.msa_build.connect('clicked', self.start_align)
-        self.bind_accelerator(self.accelerators, iface.msa_build, '<Enter>')
+        self.bind_accelerator(self.accelerators, iface.msa_build, 'Return')
         iface.remote_build.connect('clicked', self.start_align, True)
-        self.bind_accelerator(self.accelerators, iface.remote_build, '<Enter>')
+        self.bind_accelerator(self.accelerators, iface.remote_build, 'Return')
 
         data.msa.stack_child_name = iface.align_stack.get_visible_child_name()
 

ab12phylo/gtk_msa.py

@@ -41,7 +41,7 @@ def __init__(self):
                                              bool)  # low quality
         self.search_rev = False
         self.rgx = Namespace()
-        self.qal = Namespace(gene_roll='all', accept_rev=False, accept_nophred=True,
+        self.qal = Namespace(gene_roll='all', accept_rev=True, accept_nophred=True,
                              min_phred=30, trim_out=8, trim_of=10, bad_stretch=5)
         self.msa = Namespace(cmd=dict(), remote_cmd=dict(), last_cmd='')
         self.gbl = Namespace(ignore_ids=set())

ab12phylo/gtk_proj.py

@@ -148,10 +148,11 @@ def inc_priv_timestamp():
            'www.ncbi.nlm.nih.gov/nuccore/AF347033.1?report=fasta">AF347033.1</a>. '
            'If wellsplates are used in conjunction with sequence data for multiple '
            'genes, please make sure the plate layouts are identical.',
-        1: 'Parse sample IDs / well coordinates, gene, orientation and wellsplate ID '
-           'from the respective file name or sequence ID using <a href="https://regex101'
-           '.com/r/Yulwlf/8" title="pre-publication/development stage examples">Regular '
-           'Expressions</a> with capturing groups. Fields may be manually corrected.',
+        1: 'Parse sample ID / well coordinates, gene, orientation and wellsplate ID '
+           'from the file name using <a href="https://regex101.com/r/Yulwlf/8" title='
+           '"development stage examples">Regular Expressions</a> with capturing groups. '
+           'For <i>.fasta</i> files with multiple records, the sequence ID is used. '
+           'Fields can be edited manually.',
         2: 'ABI trace files can be trimmed to remove low-quality regions here, based '
            'on phred quality scores. The maximum score is 60, indicating the probability '
            'of an incorrect base call is 1:10^6. Equivalently, 30 indicates 1:1000.',

ab12phylo/repo.py

@@ -2,7 +2,7 @@
 
 __author__ = 'Leo Kaindl'
 __email__ = '[email protected]'
-__version__ = '0.4b13'
-__date__ = '12 February 2021'
-__license__ = 'MIT'
+__version__ = '0.4.15-beta'
+__date__ = '14 February 2021'
+__license__ = 'gpl-3.0'
 __status__ = 'Beta'