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YaoYinYing/REvoDesign-PyMOL-entry.ui

Last active March 12, 2025 05:37
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REvoDesignManager
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REvoDesign-PyMOL-entry.ui
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>Dialog</class>
<widget class="QDialog" name="Dialog">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>490</width>
<height>547</height>
</rect>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>490</width>
<height>534</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>652</width>
<height>547</height>
</size>
</property>
<property name="windowTitle">
<string>REvoDesign Package Manager</string>
</property>
<property name="toolTipDuration">
<number>2</number>
</property>
<widget class="QGroupBox" name="groupBox">
<property name="geometry">
<rect>
<x>10</x>
<y>70</y>
<width>471</width>
<height>101</height>
</rect>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="title">
<string>Source:</string>
</property>
<widget class="QWidget" name="horizontalLayoutWidget_2">
<property name="geometry">
<rect>
<x>10</x>
<y>30</y>
<width>451</width>
<height>64</height>
</rect>
</property>
<layout class="QHBoxLayout" name="horizontalLayout_2">
<item>
<layout class="QVBoxLayout" name="verticalLayout">
<property name="spacing">
<number>0</number>
</property>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_3">
<item>
<widget class="QRadioButton" name="radioButton_from_repo">
<property name="sizePolicy">
<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>From GitHub repository</string>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Repository</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
<item>
<widget class="QRadioButton" name="radioButton_from_local_clone">
<property name="sizePolicy">
<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>From project directory containing `pyproject.toml`</string>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Local Directory</string>
</property>
</widget>
</item>
<item>
<widget class="QRadioButton" name="radioButton_from_local_file">
<property name="sizePolicy">
<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>From released zip/tarball file</string>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Local file</string>
</property>
</widget>
</item>
</layout>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout">
<item>
<widget class="QLineEdit" name="lineEdit_local">
<property name="enabled">
<bool>false</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Maximum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>File/directory path to read</string>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>/Users/yyy/Documents/protein_design/REvoDesign</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="pushButton_open">
<property name="enabled">
<bool>false</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Maximum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="text">
<string>...</string>
</property>
</widget>
</item>
</layout>
</item>
</layout>
</item>
<item>
<layout class="QVBoxLayout" name="verticalLayout_2">
<item>
<widget class="QPushButton" name="pushButton_install">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>Install REvoDesign</string>
</property>
<property name="text">
<string>Install</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="pushButton_remove">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>Remove REvoDesign</string>
</property>
<property name="text">
<string>Remove</string>
</property>
</widget>
</item>
</layout>
</item>
</layout>
</widget>
</widget>
<widget class="QGroupBox" name="groupBox_2">
<property name="geometry">
<rect>
<x>10</x>
<y>170</y>
<width>471</width>
<height>101</height>
</rect>
</property>
<property name="title">
<string>Options:</string>
</property>
<widget class="QWidget" name="layoutWidget">
<property name="geometry">
<rect>
<x>10</x>
<y>30</y>
<width>451</width>
<height>65</height>
</rect>
</property>
<layout class="QVBoxLayout" name="verticalLayout_4">
<property name="spacing">
<number>0</number>
</property>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_5">
<property name="spacing">
<number>20</number>
</property>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_4">
<property name="spacing">
<number>1</number>
</property>
<item>
<widget class="QCheckBox" name="checkBox_upgrade">
<property name="sizePolicy">
<sizepolicy hsizetype="Maximum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>Upgrade to the latest</string>
</property>
<property name="statusTip">
<string/>
</property>
<property name="text">
<string>Upgrade</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
</layout>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_8">
<item>
<widget class="QLabel" name="label">
<property name="toolTip">
<string>The verbosity level for the installation. Defaults to 0.</string>
</property>
<property name="text">
<string>Verbose:</string>
</property>
</widget>
</item>
<item>
<widget class="QSlider" name="horizontalSlider_Verbose">
<property name="toolTip">
<string>left: quite, middle: default; right: noisy.</string>
</property>
<property name="minimum">
<number>-3</number>
</property>
<property name="maximum">
<number>3</number>
</property>
<property name="value">
<number>0</number>
</property>
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="tickPosition">
<enum>QSlider::TicksBothSides</enum>
</property>
<property name="tickInterval">
<number>1</number>
</property>
</widget>
</item>
</layout>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_7">
<item>
<widget class="QCheckBox" name="checkBox_specified_version">
<property name="sizePolicy">
<sizepolicy hsizetype="Maximum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>Install from a release tag from github</string>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Tag:</string>
</property>
</widget>
</item>
<item>
<widget class="QComboBox" name="comboBox_version">
<property name="enabled">
<bool>false</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Maximum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>Install from a release tag from github</string>
</property>
</widget>
</item>
</layout>
</item>
</layout>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_6">
<item>
<widget class="QCheckBox" name="checkBox_specified_commit">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>Install from a specific commit/branch</string>
</property>
<property name="text">
<string>commit:</string>
</property>
</widget>
</item>
<item>
<widget class="QLineEdit" name="lineEdit_commit">
<property name="enabled">
<bool>false</bool>
</property>
<property name="toolTip">
<string>Install from a specific commit/branch</string>
</property>
</widget>
</item>
</layout>
</item>
</layout>
</widget>
</widget>
<widget class="QLabel" name="label_header">
<property name="geometry">
<rect>
<x>20</x>
<y>20</y>
<width>451</width>
<height>41</height>
</rect>
</property>
<property name="font">
<font>
<pointsize>14</pointsize>
<weight>75</weight>
<italic>true</italic>
<bold>true</bold>
<underline>false</underline>
<strikeout>false</strikeout>
</font>
</property>
<property name="frameShape">
<enum>QFrame::Panel</enum>
</property>
<property name="frameShadow">
<enum>QFrame::Sunken</enum>
</property>
<property name="lineWidth">
<number>2</number>
</property>
<property name="midLineWidth">
<number>0</number>
</property>
<property name="text">
<string>Makes enzyme redesign tasks easier to all.</string>
</property>
<property name="textFormat">
<enum>Qt::RichText</enum>
</property>
<property name="alignment">
<set>Qt::AlignCenter</set>
</property>
<property name="margin">
<number>3</number>
</property>
</widget>
<widget class="QGroupBox" name="groupBox_3">
<property name="geometry">
<rect>
<x>10</x>
<y>270</y>
<width>471</width>
<height>101</height>
</rect>
</property>
<property name="title">
<string>Network:</string>
</property>
<widget class="QWidget" name="verticalLayoutWidget">
<property name="geometry">
<rect>
<x>10</x>
<y>30</y>
<width>451</width>
<height>61</height>
</rect>
</property>
<layout class="QVBoxLayout" name="verticalLayout_5">
<property name="spacing">
<number>0</number>
</property>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_9">
<item>
<widget class="QCheckBox" name="checkBox_use_proxy">
<property name="sizePolicy">
<sizepolicy hsizetype="Maximum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>Enable http/socks proxy</string>
</property>
<property name="text">
<string>proxy:</string>
</property>
</widget>
</item>
<item>
<widget class="QLineEdit" name="lineEdit_proxy_url">
<property name="enabled">
<bool>false</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>HTTP/Socks proxy</string>
</property>
<property name="text">
<string>http://localhost:7890</string>
</property>
</widget>
</item>
</layout>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_10">
<item>
<widget class="QCheckBox" name="checkBox_use_mirror">
<property name="sizePolicy">
<sizepolicy hsizetype="Maximum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>Enable PyPi mirror</string>
</property>
<property name="text">
<string>Mirror:</string>
</property>
</widget>
</item>
<item>
<widget class="QLineEdit" name="lineEdit_mirror_url">
<property name="enabled">
<bool>false</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>Set PyPi mirror URL</string>
</property>
<property name="text">
<string>https://mirrors.bfsu.edu.cn/pypi/web/simple</string>
</property>
</widget>
</item>
</layout>
</item>
</layout>
</widget>
</widget>
<widget class="QGroupBox" name="groupBox_4">
<property name="geometry">
<rect>
<x>10</x>
<y>440</y>
<width>471</width>
<height>71</height>
</rect>
</property>
<property name="title">
<string>Cache:</string>
</property>
<widget class="QWidget" name="horizontalLayoutWidget">
<property name="geometry">
<rect>
<x>10</x>
<y>30</y>
<width>451</width>
<height>33</height>
</rect>
</property>
<layout class="QHBoxLayout" name="horizontalLayout_11">
<item>
<widget class="QCheckBox" name="checkBox_user_cache_dir">
<property name="sizePolicy">
<sizepolicy hsizetype="Maximum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>Use customized cache dir. Uncheck this to let REvoDesign choose one.</string>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Use:</string>
</property>
</widget>
</item>
<item>
<widget class="QLineEdit" name="lineEdit_customized_cache_dir">
<property name="enabled">
<bool>false</bool>
</property>
<property name="toolTip">
<string>Cache file on this dir</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="pushButton_open_cache_dir">
<property name="enabled">
<bool>false</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Maximum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>Open a dir as cache directory.</string>
</property>
<property name="text">
<string>...</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="pushButton_set_cache_dir">
<property name="enabled">
<bool>false</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Maximum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>Apply this directory for cache.</string>
</property>
<property name="text">
<string>Apply</string>
</property>
</widget>
</item>
</layout>
</widget>
</widget>
<widget class="QGroupBox" name="groupBox_5">
<property name="geometry">
<rect>
<x>10</x>
<y>370</y>
<width>471</width>
<height>71</height>
</rect>
</property>
<property name="toolTip">
<string>Extra definitions of dependencies. Select `Customized` to expand the right panel.</string>
</property>
<property name="title">
<string>Extras:</string>
</property>
<widget class="QWidget" name="horizontalLayoutWidget_3">
<property name="geometry">
<rect>
<x>10</x>
<y>30</y>
<width>451</width>
<height>32</height>
</rect>
</property>
<layout class="QHBoxLayout" name="horizontalLayout_13">
<item>
<widget class="QPushButton" name="pushButton_refresh_extras">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>120</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>120</width>
<height>16777215</height>
</size>
</property>
<property name="toolTip">
<string>Refresh REvoDesign table</string>
</property>
<property name="text">
<string>Refresh</string>
</property>
</widget>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout_12">
<item>
<widget class="QRadioButton" name="radioButton_extra_none">
<property name="sizePolicy">
<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>Default setting with no extra dependencies.</string>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>None</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
<item>
<widget class="QRadioButton" name="radioButton_extra_customized">
<property name="sizePolicy">
<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>Customized extras picked from right panel.</string>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Customized</string>
</property>
</widget>
</item>
<item>
<widget class="QRadioButton" name="radioButton_extra_everything">
<property name="sizePolicy">
<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="toolTip">
<string>Install with all extras except unit tests</string>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="text">
<string>Everything</string>
</property>
<property name="checked">
<bool>false</bool>
</property>
</widget>
</item>
</layout>
</item>
</layout>
</widget>
</widget>
<widget class="QProgressBar" name="progressBar">
<property name="geometry">
<rect>
<x>10</x>
<y>520</y>
<width>471</width>
<height>16</height>
</rect>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Maximum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>0</width>
<height>0</height>
</size>
</property>
<property name="sizeIncrement">
<size>
<width>0</width>
<height>0</height>
</size>
</property>
<property name="baseSize">
<size>
<width>0</width>
<height>0</height>
</size>
</property>
<property name="font">
<font>
<pointsize>3</pointsize>
</font>
</property>
<property name="value">
<number>0</number>
</property>
<property name="alignment">
<set>Qt::AlignHCenter|Qt::AlignTop</set>
</property>
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="textDirection">
<enum>QProgressBar::TopToBottom</enum>
</property>
</widget>
<widget class="QListView" name="listView_extras">
<property name="geometry">
<rect>
<x>490</x>
<y>90</y>
<width>151</width>
<height>431</height>
</rect>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
</widget>
</widget>
<resources/>
<connections>
<connection>
<sender>radioButton_from_repo</sender>
<signal>toggled(bool)</signal>
<receiver>lineEdit_local</receiver>
<slot>setDisabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>85</x>
<y>118</y>
</hint>
<hint type="destinationlabel">
<x>231</x>
<y>100</y>
</hint>
</hints>
</connection>
<connection>
<sender>radioButton_from_repo</sender>
<signal>toggled(bool)</signal>
<receiver>pushButton_open</receiver>
<slot>setDisabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>85</x>
<y>118</y>
</hint>
<hint type="destinationlabel">
<x>398</x>
<y>101</y>
</hint>
</hints>
</connection>
<connection>
<sender>checkBox_specified_version</sender>
<signal>toggled(bool)</signal>
<receiver>comboBox_version</receiver>
<slot>setEnabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>222</x>
<y>186</y>
</hint>
<hint type="destinationlabel">
<x>345</x>
<y>187</y>
</hint>
</hints>
</connection>
<connection>
<sender>checkBox_specified_commit</sender>
<signal>toggled(bool)</signal>
<receiver>lineEdit_commit</receiver>
<slot>setEnabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>221</x>
<y>227</y>
</hint>
<hint type="destinationlabel">
<x>388</x>
<y>227</y>
</hint>
</hints>
</connection>
<connection>
<sender>radioButton_from_local_clone</sender>
<signal>toggled(bool)</signal>
<receiver>lineEdit_local</receiver>
<slot>setEnabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>223</x>
<y>118</y>
</hint>
<hint type="destinationlabel">
<x>195</x>
<y>160</y>
</hint>
</hints>
</connection>
<connection>
<sender>radioButton_from_local_clone</sender>
<signal>toggled(bool)</signal>
<receiver>pushButton_open</receiver>
<slot>setEnabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>223</x>
<y>118</y>
</hint>
<hint type="destinationlabel">
<x>398</x>
<y>161</y>
</hint>
</hints>
</connection>
<connection>
<sender>radioButton_from_local_file</sender>
<signal>toggled(bool)</signal>
<receiver>lineEdit_local</receiver>
<slot>setEnabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>360</x>
<y>118</y>
</hint>
<hint type="destinationlabel">
<x>195</x>
<y>160</y>
</hint>
</hints>
</connection>
<connection>
<sender>radioButton_from_local_file</sender>
<signal>toggled(bool)</signal>
<receiver>pushButton_open</receiver>
<slot>setEnabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>360</x>
<y>118</y>
</hint>
<hint type="destinationlabel">
<x>398</x>
<y>161</y>
</hint>
</hints>
</connection>
<connection>
<sender>radioButton_from_local_file</sender>
<signal>toggled(bool)</signal>
<receiver>comboBox_version</receiver>
<slot>setDisabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>360</x>
<y>113</y>
</hint>
<hint type="destinationlabel">
<x>347</x>
<y>215</y>
</hint>
</hints>
</connection>
<connection>
<sender>checkBox_use_proxy</sender>
<signal>toggled(bool)</signal>
<receiver>lineEdit_proxy_url</receiver>
<slot>setEnabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>51</x>
<y>344</y>
</hint>
<hint type="destinationlabel">
<x>301</x>
<y>344</y>
</hint>
</hints>
</connection>
<connection>
<sender>checkBox_use_mirror</sender>
<signal>toggled(bool)</signal>
<receiver>lineEdit_mirror_url</receiver>
<slot>setEnabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>52</x>
<y>369</y>
</hint>
<hint type="destinationlabel">
<x>303</x>
<y>369</y>
</hint>
</hints>
</connection>
<connection>
<sender>radioButton_from_local_file</sender>
<signal>toggled(bool)</signal>
<receiver>checkBox_specified_version</receiver>
<slot>setDisabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>360</x>
<y>113</y>
</hint>
<hint type="destinationlabel">
<x>224</x>
<y>214</y>
</hint>
</hints>
</connection>
<connection>
<sender>radioButton_from_local_file</sender>
<signal>toggled(bool)</signal>
<receiver>checkBox_specified_commit</receiver>
<slot>setDisabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>360</x>
<y>113</y>
</hint>
<hint type="destinationlabel">
<x>223</x>
<y>243</y>
</hint>
</hints>
</connection>
<connection>
<sender>radioButton_from_local_file</sender>
<signal>toggled(bool)</signal>
<receiver>lineEdit_commit</receiver>
<slot>setDisabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>360</x>
<y>113</y>
</hint>
<hint type="destinationlabel">
<x>389</x>
<y>243</y>
</hint>
</hints>
</connection>
<connection>
<sender>radioButton_from_local_clone</sender>
<signal>toggled(bool)</signal>
<receiver>comboBox_version</receiver>
<slot>setDisabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>223</x>
<y>113</y>
</hint>
<hint type="destinationlabel">
<x>347</x>
<y>215</y>
</hint>
</hints>
</connection>
<connection>
<sender>radioButton_from_local_clone</sender>
<signal>toggled(bool)</signal>
<receiver>checkBox_specified_version</receiver>
<slot>setDisabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>223</x>
<y>113</y>
</hint>
<hint type="destinationlabel">
<x>224</x>
<y>214</y>
</hint>
</hints>
</connection>
<connection>
<sender>radioButton_from_local_clone</sender>
<signal>toggled(bool)</signal>
<receiver>checkBox_specified_commit</receiver>
<slot>setDisabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>223</x>
<y>113</y>
</hint>
<hint type="destinationlabel">
<x>223</x>
<y>243</y>
</hint>
</hints>
</connection>
<connection>
<sender>radioButton_from_local_clone</sender>
<signal>toggled(bool)</signal>
<receiver>lineEdit_commit</receiver>
<slot>setDisabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>223</x>
<y>113</y>
</hint>
<hint type="destinationlabel">
<x>389</x>
<y>243</y>
</hint>
</hints>
</connection>
<connection>
<sender>checkBox_user_cache_dir</sender>
<signal>toggled(bool)</signal>
<receiver>lineEdit_customized_cache_dir</receiver>
<slot>setEnabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>46</x>
<y>418</y>
</hint>
<hint type="destinationlabel">
<x>243</x>
<y>418</y>
</hint>
</hints>
</connection>
<connection>
<sender>checkBox_user_cache_dir</sender>
<signal>toggled(bool)</signal>
<receiver>pushButton_open_cache_dir</receiver>
<slot>setEnabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>46</x>
<y>418</y>
</hint>
<hint type="destinationlabel">
<x>443</x>
<y>419</y>
</hint>
</hints>
</connection>
<connection>
<sender>checkBox_user_cache_dir</sender>
<signal>toggled(bool)</signal>
<receiver>pushButton_set_cache_dir</receiver>
<slot>setEnabled(bool)</slot>
<hints>
<hint type="sourcelabel">
<x>46</x>
<y>418</y>
</hint>
<hint type="destinationlabel">
<x>432</x>
<y>419</y>
</hint>
</hints>
</connection>
</connections>
</ui>
Raw
REvoDesign_PyMOL.py
# pylint: disable=too-many-lines
# pylint: disable=import-outside-toplevel
# pylint: disable=unused-argument
import difflib
import importlib
import importlib.util
import json
import math
import os
import platform
import re
import shutil
import socket
import subprocess
import sys
import time
import urllib.request
import warnings
from contextlib import contextmanager
from dataclasses import dataclass
from functools import partial
from typing import (TYPE_CHECKING, Any, Callable, Dict, Iterable, List,
Mapping, NoReturn, Optional, Tuple, Type, TypeVar, Union,
overload)
from urllib.error import HTTPError, URLError
from pymol import cmd, get_version_message
from pymol.plugins import addmenuitemqt
from pymol.Qt.utils import loadUi
LOGGER_LEVEL = 0
if TYPE_CHECKING:
# type checking branch
from PyQt5 import QtCore, QtGui, QtWidgets
else:
# runtime branch
from pymol.Qt import QtCore, QtGui, QtWidgets
if not __file__.endswith('package_manager.py'):
# PyMOL plugin branch, set docstring to describe the plugin
__doc__ = """Described at GitHub:
https://github.com/YaoYinYing/REvoDesign
Authors : Yinying Yao
Program : REvoDesign
Date : Sept 2023
REvoDesign -- Makes enzyme redesign tasks easier to all."""
# use a mocked logger to handle logging from pymol's concole instead,
# only if it runs as the role ofpackagemanager as a plugin from PyMOL
class MockLogger:
def debug(self, msg: str, *args, **kwargs):
print(f'[DEBUG]: {msg}') if LOGGER_LEVEL < 10 else None
def info(self, msg: str, *args, **kwargs):
print(f'[INFO]: {msg}') if LOGGER_LEVEL < 20 else None
def warning(self, msg: str, *args, **kwargs):
print(f'[WARNING]: {msg}') if LOGGER_LEVEL < 30 else None
def error(self, msg: str, *args, **kwargs):
print(f'[ERROR]: {msg}') if LOGGER_LEVEL < 40 else None
def critical(self, msg: str, *args, **kwargs):
print(f'[CRITICAL]: {msg}') if LOGGER_LEVEL < 50 else None
logging = MockLogger()
logging.info(f'Package manager is running via PyMOL: {__file__}.')
else:
# REvoDesign runtime branch, set docstring to describe the module
__doc__ = '''
Module that contains key functions of constructing the REvoDesign Package Manager
This module also serves as standalone REvoDesign Package Manager,
meaning that any tools existed here is part of the manager.
To make any of them importable in certain modules, import them from here
and add to the `__all__` attributes so that they can be discoverable.
'''
# enable logger from REvoDesign if it is a submodule not a script
from REvoDesign.logger import ROOT_LOGGER
logging = ROOT_LOGGER.getChild(__name__)
logging.info('Package manager is running via REvoDesign.')
REPO_URL: str = "https://github.com/YaoYinYing/REvoDesign"
GIST_BASE_URL: str = 'https://gist.githubusercontent.com/YaoYinYing/c1e8bfe0fc0b9c60bf49ea04a550a044/raw'
# uploaded with `make upload-gists`
UI_FILE_URL = f'{GIST_BASE_URL}/REvoDesign-PyMOL-entry.ui'
# refer to THIS file, an installable package manager via pymol's plugin manager.
THIS_FILE_URL = f'{GIST_BASE_URL}/REvoDesign_PyMOL.py'
# Define the URL of the JSON file
EXTRAS_TABLE_JSON = f'{GIST_BASE_URL}/REvoDesignExtrasTable.json'
DEPTS_TABLE_JSON = f'{GIST_BASE_URL}/REvoDesignDeptsTable.json'
# Define the proxy protocols allowed
ALLOWED_PROXY_PROTOCOLS = ["http", "https", 'socks5', 'socks5h']
HAS_CUDA = shutil.which('nvidia-smi')
HAS_MPS = platform.system() == 'Darwin' and platform.mac_ver()[-1] == 'arm64'
def fetch_gist_file(ui_file_url: str, save_to_file: str) -> None:
"""
Fetch the UI file from the given URL, save it to a temporary file, and yield its absolute path.
Parameters:
ui_file_url (str): The URL of the UI file to be fetched.
save_to_file (str): The name of the temporary file to save the fetched UI file to.
Returns:
None
"""
# Validate and sanitize the URL
if not ui_file_url.startswith('https'):
raise ValueError("URL must start with 'https'")
try:
# Fetch the file content and write it to the temporary file
with urllib.request.urlopen(ui_file_url) as response, open(save_to_file, 'w') as ui_handle:
ui_data = response.read().decode('utf-8')
ui_handle.write(ui_data)
except (URLError, HTTPError) as e:
raise URLError(f"Failed to download file: {e}") from e
except ValueError as e:
raise ValueError(f"Invalid URL: {e}") from e
# Fetch and validate JSON data
def fetch_gist_json(url: str) -> Dict[str, str]:
"""
Fetches JSON data from the specified URL and validates its structure.
Parameters:
url (str): The URL from which to fetch the JSON data.
Returns:
Dict[str, str]: The fetched and validated JSON data, or an empty dictionary if an error occurs.
"""
try:
with urllib.request.urlopen(url, timeout=10) as response: # Set a timeout for safety
data = response.read().decode('utf-8')
json_data = json.loads(data)
logging.debug('Extras table is fetched and parsed: \n'
f'{json_data}')
# Validate the structure of the fetched data
if not isinstance(json_data, dict):
raise ValueError("Fetched data is not a dictionary.")
for key, value in json_data.items():
if not isinstance(key, str) or not (isinstance(value, str) or value is None):
raise ValueError("Invalid key-value format in JSON data.")
return json_data
except Exception as e:
logging.error(f"Error fetching or validating the JSON data: {e}: ")
return {}
# Define a generic type variable for the return type of worker_function
R = TypeVar("R")
class UnsupportedWidgetValueTypeError(TypeError):
"""
Exception raised when an unsupported value type is assigned to a Widget.
This exception class inherits from TypeError and is used to indicate that the value type
assigned to a Widget instance is not supported.
"""
def run_command(
cmd: Union[Tuple[str], List[str]],
verbose: bool = False,
env: Optional[Mapping[str, str]] = None,
) -> subprocess.CompletedProcess:
"""
Execute a specified command in the shell.
Parameters:
- cmd: A tuple or string representing the command to be executed. If it's a tuple, it represents the command
and its parameters.
- verbose: A boolean indicating whether to print detailed execution information.
- env: A mapping object containing environment variables for the command.
Returns:
- The CompletedProcess object returned by subprocess.run(), containing the command execution information.
Raises:
- When the command execution fails (return code is not 0) and verbose is True, a RuntimeError is raised.
"""
# Optionally print the command for debugging
if verbose:
logging.info(f'launching command: {" ".join(cmd)}')
# Execute the command using subprocess.run()
result = subprocess.run(
cmd,
capture_output=True,
encoding="utf-8",
env=env if env else None,
text=True,
check=False,
)
# Optionally print the command output for debugging
if verbose and (res_text := result.stdout):
logging.info(res_text)
# If the command execution fails and verbose is True, raise an exception
if result.returncode != 0 and verbose:
raise RuntimeError(f"--> Command failed: \n{'-'*79}\n{result.stderr}\n{'-'*79}")
# Return the execution result
return result
# Additional widget for extra selection
class CheckableListView(QtWidgets.QWidget):
"""
Checkable list view widget, allowing users to check items in the list.
Attributes:
list_view: The QListView instance this widget operates on.
model: The data model instance used by the list view.
"""
def __init__(self, list_view, items: Dict[str, str] = {}, parent=None):
"""
Initializes the CheckableListView instance.
Parameters:
listView: The QListView instance to use.
items: Optional list of item texts to add to the list.
separators: Optional list of separator texts, used to categorize items.
parent: The parent widget, defaults to None.
"""
super().__init__(parent)
# Use the existing list view
self.list_view = list_view
# Set up the model (use existing one if set, otherwise create a new one)
if self.list_view.model() is None:
self.model = QtGui.QStandardItemModel(self.list_view)
self.list_view.setModel(self.model)
else:
self.model = self.list_view.model()
# Clear the model before adding new items
self.model.clear()
# Add items to the model with optional separators
if not items:
return
self.items = items
for k, v in items.items():
if not v:
# Add as a separator
separator_item = QtGui.QStandardItem(k)
separator_item.setEnabled(False) # Non-interactive
separator_item.setSelectable(False) # Non-selectable
separator_item.setCheckable(False) # Non-checkable
separator_item.setForeground(QtGui.QBrush(QtCore.Qt.yellow))
separator_item.setBackground(QtGui.QBrush(QtCore.Qt.blue)) # Different background
separator_item.setFont(QtGui.QFont("Arial", weight=QtGui.QFont.Bold)) # Bold text
self.model.appendRow(separator_item)
else:
# Add as a regular checkable item
item = QtGui.QStandardItem(k)
item.setCheckable(True)
item.setCheckState(QtCore.Qt.Unchecked) # Default unchecked
self.model.appendRow(item)
def _get_items_by_check_state(self, check_state):
"""
Helper function to get items based on their check state.
Args:
check_state (int): The check state to filter items by (e.g., QtCore.Qt.Checked).
Returns:
A list of strings representing the texts of items with the specified check state.
"""
items = []
for row in range(self.model.rowCount()):
item = self.model.item(row)
if item.isCheckable() and item.checkState() == check_state:
items.append(self.items.get(item.text(), None))
return items
def get_checked_items(self):
"""
Returns a list of all checked items' text.
Returns:
A list of strings representing the texts of all checked items.
"""
checked_items = self._get_items_by_check_state(QtCore.Qt.Checked)
logging.debug(f'Checked: {checked_items}')
return checked_items
def get_unchecked_items(self):
"""
Returns a list of all unchecked items' text.
Returns:
A list of strings representing the texts of all unchecked items.
"""
return self._get_items_by_check_state(QtCore.Qt.Unchecked)
def check_all(self):
"""
Check all items in the list, excluding separators.
"""
for row in range(self.model.rowCount()):
item = self.model.item(row)
if item.isCheckable() and item.text() != 'Test':
item.setCheckState(QtCore.Qt.Checked)
def uncheck_all(self):
"""
Uncheck all items in the list, excluding separators.
"""
for row in range(self.model.rowCount()):
item = self.model.item(row)
if item.isCheckable():
item.setCheckState(QtCore.Qt.Unchecked)
@dataclass
class GitSolver:
"""
A class that checks for the presence of Git, Conda, and Winget on the system and can install Git if necessary.
"""
has_git: Optional[str] = None
has_conda: Optional[str] = None
has_mamba: Optional[str] = None
has_winget: Optional[str] = None
has_brew: Optional[str] = None
has_choco: Optional[str] = None
def __post_init__(self):
"""
Initializes instance attributes to check if git, conda, and winget are installed.
This method is automatically called after the object initialization.
It sets the object's properties based on whether these tools are available in the system path.
This ensures that the object can determine if it can perform related operations before doing so.
"""
# subprocess.run on Windows treat conda as a excutable file and will check its existence
# however conda is AKA a alias in shell and does not exist as a file.
# shutil.which will return the real path of conda script
for cmd_tool in ["git", "conda", "mamba", "winget", "brew", 'choco']:
setattr(self, f"has_{cmd_tool}", shutil.which(cmd_tool))
logging.debug(f"Command tool check: {cmd_tool}: {getattr(self, f'has_{cmd_tool}')}")
@property
def where_to_install(self) -> Optional[List[str]]:
if self.has_winget:
return [
self.has_winget,
"install",
"--id",
"Git.Git",
"-e",
"--source",
"winget",
"--accept-package-agreements",
"--accept-source-agreements",
]
# Determine the installation command based on Conda's presence or the system type (Windows with Winget)
if self.has_mamba:
return [self.has_mamba, "install", "-y", "git"]
if self.has_conda:
return [self.has_conda, "install", "-y", "git"]
if self.has_brew:
return [self.has_brew, "install", "git"]
if self.has_choco:
return [self.has_choco, "install", "git"]
return None
def fetch_git(self, git_fetch_command: List[str], env: Optional[Mapping[str, str]] = None) -> Tuple[bool, str]:
"""
Installs Git if it is not present on the system.
This method attempts to install Git based on the available installers (Conda, Winget) or the system type.
If the installation is successful, it returns True. Otherwise, it provides error information and returns False.
Parameters:
env (Optional[Mapping[str, str]]): Environment variables for the installation process.
"""
# Check if Git is already installed
if self.has_git:
return True, ''
# Execute the Git installation command in a worker thread and monitor progress
git_install_std: subprocess.CompletedProcess = run_command(
cmd=git_fetch_command,
verbose=True,
env=env,
)
# Check if the Git installation was successful
if (git_install_std and git_install_std.returncode == 0) or shutil.which('git'):
self.has_git = shutil.which('git')
return True, ''
# If installation failed, show error information and return False
with open((file_path := os.path.abspath("error.log")), "w", encoding="utf-8") as f:
f.write(f"STDOUT:\n{git_install_std.stdout}\n\n\n\nSTDERR:\n{git_install_std.stderr}")
return False, file_path
@dataclass
class PIPInstaller:
"""
A class for installing, uninstalling, and ensuring the installation of packages using pip.
Attributes:
python_exe (str): The path to the Python executable.
env (Optional[Mapping[str, str]]): Optional environment variables for running commands.
verbose_level (int): The verbosity level for running commands.
-3~-1: Maximum - Minimum silent
0: Default
1~3: Minimum - Maximum noisy
"""
python_exe: str = ''
# run_command args
env: Optional[Mapping[str, str]] = None
verbose_level: int = 0
def ensurepip(self):
"""
Run the ensurepip command to ensure pip is installed in the current Python environment.
If ensurepip fails, raise a RuntimeError with the command output.
"""
# run installation via pip
ensurepip = run_command([self.python_exe, "-m", "ensurepip"], verbose=self.verbose_level > -1, env=self.env)
if ensurepip.returncode:
notify_box(
f"ensurepip failed.",
RuntimeError,
details=f'\nSTDOUT:\n{ensurepip.stdout}\n\nSTDERR:\n{ensurepip.stderr}')
def __post_init__(self):
"""
Post-initialization method to set the real path of the Python executable and run ensurepip.
"""
self.python_exe = os.path.realpath(sys.executable)
self.ensurepip()
def install(self,
package_name: str = 'REvoDesign',
source: Optional[str] = None,
upgrade: bool = False,
extras: Optional[str] = None,
mirror: Optional[str] = "",
verbose_level: int = 0,
env: Optional[Mapping[str, str]] = None,
):
"""
Install a package in the current Python environment.
Args:
package_name (str): The name of the package to install. Defaults to 'REvoDesign'.
source (Optional[str]): The source URL for the package. Required if package_name is 'REvoDesign'.
upgrade (bool): If True, upgrade the package if it is already installed. Defaults to False.
extras (Optional[str]): Additional requirements to install. Defaults to None.
mirror (Optional[str]): The URL of the package mirror to use. Defaults to None.
verbose_level (int): The verbosity level for the installation. Defaults to 1.
env (Optional[Mapping[str, str]]): Optional environment variables for running the pip command.
Returns:
The result of running the pip install command.
"""
logging.info("Installation is started. This may take a while.")
if package_name != 'pip':
logging.info('Upgrading pip to the latest version...')
self.install('pip', upgrade=True, verbose_level=verbose_level, env=self.env)
def get_source_and_tag(source: str):
"""
Parse the source URL and tag.
Args:
source (str): The source URL of the REvoDesign, or name of a package.
Returns:
Returns a tuple containing the git directory and git tag.
"""
git_dir = source.split("@")[0]
if "@" in source:
git_tag = source.split("@")[1]
else:
git_tag = ""
return git_dir, git_tag
if package_name != 'REvoDesign':
# use package_name as package_string for other packages then 'REvoDesign'
package_string = package_name
else:
if source is None or source == '':
raise ValueError("Source must be specified for REvoDesign")
git_url, git_tag = get_source_and_tag(source=source)
package_string = solve_installation_config(
source=source,
git_url=git_url,
git_tag=git_tag,
extras=extras,
package_name=package_name
)
pip_cmd = [
self.python_exe,
"-m",
"pip",
"install",
f"{package_string}",
]
if upgrade:
pip_cmd.append("-U")
if mirror:
logging.info(f"using mirror from {mirror}")
pip_cmd.extend(["-i", mirror])
if verbose_level < 0:
pip_cmd.append(f"-{'q'*-verbose_level}")
elif verbose_level > 0:
pip_cmd.append(f"-{'v'*verbose_level}")
logging.debug(f'Using verbose level {verbose_level}')
result: subprocess.CompletedProcess = run_command(
pip_cmd, verbose=self.verbose_level > -1, env=env or self.env)
return result
def uninstall(self, package_name: str = 'REvoDesign'):
"""
Uninstall a package from the current Python environment.
Args:
package_name (str): The name of the package to uninstall. Defaults to 'REvoDesign'.
Returns:
The result of running the pip uninstall command.
"""
pip_cmd = [
self.python_exe,
"-m",
"pip",
"uninstall",
"-y",
package_name,
]
result: subprocess.CompletedProcess = run_command(pip_cmd, verbose=self.verbose_level > -1, env=self.env)
return result
def ensure_package(self, package_string: str,
env: Optional[Mapping[str, str]] = None, mirror: Optional[str] = None):
"""
Ensure a package is installed in the current Python environment.
If the package is not installed or needs to be upgraded, run the pip install command.
Args:
package_string (str): The name of the package to ensure.
env (Optional[Mapping[str, str]]): Optional environment variables for running the pip command.
mirror (Optional[str]): The URL of the package mirror to use. Defaults to None.
"""
# Execute the pip installation command
result = self.install(package_string, upgrade=True, env=env, mirror=mirror)
# If the pip downgrade command fails, notify the user to manually execute the command
if result.returncode:
notify_box(
f"Failed to ensure {package_string}. Please upgrade/downgrade manually.\n"
f'Run this command in your shell - `{" ".join(result.args)}`',
details=f"STDOUT:\n{result.stdout}\n\nSTDERR:\n{result.stderr}"
)
@dataclass(frozen=True)
class MenuItem:
"""
A data class representing a menu item.
This class is used to define the properties of a menu item, including its name, associated function, and optional arguments.
The use of the @dataclass decorator automatically generates special methods such as __init__(), __repr__(), and __eq__().
The frozen parameter ensures that instances of the class are immutable, enhancing thread safety and consistency.
Attributes:
name (str): The name of the menu item, used for display and identification.
func (Callable): The function associated with the menu item, which is executed when the item is selected.
kwargs (Optional[Mapping]): Optional arguments passed to the associated function when it is executed. Defaults to None.
"""
name: str
func: Optional[Callable] = None
kwargs: Optional[Mapping] = None
@dataclass
class REvoDesignPackageManager:
"""
Class to manage the installation of the REvoDesign plugin.
This class firstly performs a self-bootstrap including the following:
1. fetch UI file and load it
2. fetch extras table
3. fetch repo release tags if possible
4. add menu items
Then it register widget signals and get all things ready.
Attributes:
dialog (QWidget): The main dialog window for the plugin GUI.
extra_checkbox (CheckableListView): A checkbox list for selecting extra components.
"""
dialog: Any = None
installer_ui: Any = None
extra_checkbox: CheckableListView = None
pip_installer: PIPInstaller = None
def ensure_ui_file(self, upgrade: bool = False):
ui_file = os.path.abspath(
os.path.join(
os.path.dirname(__file__),
'REvoDesign-manager',
'UI',
'REvoDesign_installer.ui'))
os.makedirs(os.path.dirname(ui_file), exist_ok=True)
# if not exists, preform the first fetch
if not os.path.isfile(ui_file):
fetch_gist_file(ui_file_url=UI_FILE_URL, save_to_file=ui_file)
logging.info(f"Fetched UI file for manager: {ui_file}")
return ui_file
# otherwise, if the user not requires an upgrade, return
if not upgrade:
logging.debug(f'pre-downloaded UI file found: {ui_file}')
return ui_file
# otherwise, preform the upgrade
new_ui_file = f'{ui_file}.swp'
fetch_gist_file(ui_file_url=UI_FILE_URL, save_to_file=new_ui_file)
self.upgrade_check(
original_file=ui_file,
new_file=new_ui_file,
title='REvoDesign Manager UI file'
)
return ui_file
@staticmethod
def upgrade_check(original_file: str, new_file: str, title: str):
"""
Check and apply an upgrade if necessary.
This function compares the original file with a new fetched file, generates a diff file if there are differences,
and prompts the user to confirm whether to apply the upgrade. If the user confirms, the new file replaces the original file.
Parameters:
- original_file (str): The path to the original file.
- new_file (str): The path to the new fetched file.
- title (str): The title used in notifications.
Returns:
- None
"""
diff_file = f'{original_file}.diff'
# Open the original, new fetched, and diff files
with open(original_file) as original, open(new_file) as new_fetched:
diffs = tuple(
difflib.context_diff(
original.readlines(),
new_fetched.readlines(),
fromfile=original_file,
tofile=new_file
)
)
if not diffs:
return notify_box(f'{title} is already up to date.')
num_added_lines = len([l for l in diffs if l.startswith('+ ')])
num_chged_lines = len([l for l in diffs if l.startswith('! ')])
num_deled_lines = len([l for l in diffs if l.startswith('- ')])
with open(diff_file, 'w') as diff:
diff.writelines(diffs)
# Prompt the user to confirm the upgrade
accept_upgraded = decide(
title='Upgrade', description='Do you REALLY want to apply the upgrade?<p><p>'
'<a style="background-color:yellow;color:blue;">:::::Upgrade Summary:::::</a><p>'
'<table>'
'<tr><th><b>Event</b></th><th>-</th><th><b>Affected Lines<b></th></tr>'
f'<tr><td><a style="background-color:green;color:white">Added </a></td><td>:</td><td><a style="background-color:white;color:green;">{num_added_lines}</a></td></tr>'
f'<tr><td><a style="background-color:blue; color:white">Changed</a></td><td>:</td><td><a style="background-color:white;color:blue ;">{num_chged_lines}</a></td></tr>'
f'<tr><td><a style="background-color:red; color:white">Deleted</a></td><td>:</td><td><a style="background-color:white;color:red ;">{num_deled_lines}</a></td></tr>'
'</table>'
'You must check out these changes carefully.<p>'
f"See all changes in this <a href=file://{diff_file}>diff file of {title}</a>.", rich=True, details='\n'.join(diffs))
# Clean up the diff file
if os.path.isfile(diff_file):
os.remove(diff_file)
# Handle user response
if not accept_upgraded:
os.remove(new_file)
return notify_box('Upgrade cancelled.')
shutil.move(new_file, original_file)
return notify_box(
f'{title} has been upgraded successfully, please restart PyMOL to take effects.'
)
def self_upgrade(self):
confirmed = decide(
title='Upgrade REvoDesign',
description='[WARNING]\n'
'Do you want to upgrade REvoDesign Manager to the latest version?'
)
if not confirmed:
return notify_box('Upgrade cancelled.')
new_py_file = f'{__file__}.swp'
fetch_gist_file(THIS_FILE_URL, new_py_file)
self.upgrade_check(
original_file=__file__,
new_file=new_py_file,
title='REvoDesign Manager'
)
def run_plugin_gui(self):
"""
Runs the plugin GUI.
This method initializes and displays the plugin's graphical user interface. It also sets up
the extra components checkbox list and connects the radio button signals to the appropriate
methods for checking or unchecking all items.
Steps:
- Initialize the dialog window if it hasn't been created yet.
- Display the dialog window.
- Create and position the extra components checkbox list.
- Connect the 'None' radio button to uncheck all items in the checkbox list.
- Connect the 'Everything' radio button to check all items in the checkbox list.
- Run a worker thread to fetch tags with a progress bar.
"""
if self.dialog is None:
self.dialog = self.make_window()
self.dialog.show()
self.refresh_extras_table()
self.pip_installer = run_worker_thread_with_progress(PIPInstaller)
self.extra_checkbox.setGeometry(QtCore.QRect(540, 90, 141, 431))
# Connect the 'None' radio button to uncheck all items
self.installer_ui.radioButton_extra_none.toggled["bool"].connect(
self.extra_checkbox.uncheck_all,
)
# Connect the 'Everything' radio button to check all items
self.installer_ui.radioButton_extra_everything.toggled["bool"].connect(
self.extra_checkbox.check_all,
)
self.installer_ui.pushButton_refresh_extras.clicked.connect(self.refresh_extras_table)
# Run a worker thread to fetch tags with a progress bar
self.fetch_tags()
def proxy_in_env(self, proxy: Optional[str] = None, mirror: Optional[str] = None) -> Dict[str, str]:
"""
Generates an environment mapping based on the provided proxy string.
Args:
proxy (str): The proxy string to use for creating the environment variables.
Returns:
Dict[str, str]: A dictionary containing the proxy settings for environment variables.
If `proxy` is empty, returns an empty dictionary.
"""
if not proxy:
return {}
if not any(proxy.startswith(prefix) for prefix in ALLOWED_PROXY_PROTOCOLS):
notify_box(f'Unsupported proxy type: {proxy}\nPlease use one of the following protocols: \n'
+ "\n".join(f"{p}://..." for p in ALLOWED_PROXY_PROTOCOLS), ValueError)
if proxy.startswith('socks5'):
logging.info('Ensuring pysocks is installed...')
run_worker_thread_with_progress(
worker_function=self.pip_installer.ensure_package,
package_string='pysocks',
mirror=mirror,
env={},
progress_bar=self.installer_ui.progressBar)
logging.info(f"using proxy: {proxy}")
proxy_env = {
"http_proxy": proxy,
"https_proxy": proxy,
"all_proxy": proxy,
}
return proxy_env
def refresh_extras_table(self):
"""
Refreshes the list of available extras by fetching data from a JSON source.
This method uses a worker thread to fetch extras data with a progress bar indication.
If fetching fails, it shows an error notification and sets up an empty extras list.
"""
# Run a worker thread to fetch extras with a progress bar
AVAILABLE_EXTRAS = run_worker_thread_with_progress(
worker_function=fetch_gist_json,
url=EXTRAS_TABLE_JSON,
progress_bar=self.installer_ui.progressBar)
# Handle the case where no extras are fetched
if not AVAILABLE_EXTRAS:
AVAILABLE_EXTRAS = {"No Extras is Fetched": ''}
notify_box("Error fetching or validating the JSON data. \n"
"Please reconfigure your network and press <Refresh> to try again "
"if you wish to continue installation with extra packages")
# remove device specific extras if not available
if not HAS_CUDA or not HAS_MPS:
AVAILABLE_EXTRAS = {
k: v for k, v in AVAILABLE_EXTRAS.items()
if ('CUDA' not in k or HAS_CUDA) and ('MPS' not in k or HAS_MPS)
}
# Create and position the extra components checkbox list
self.extra_checkbox = CheckableListView(
self.installer_ui.listView_extras, AVAILABLE_EXTRAS
)
def collect_diagnostic_data(self, collect_dummy: bool = False, drop_sensitives=True):
"""
Collects diagnostic data and copies it to the clipboard.
This function clears the clipboard, collects diagnostic data by starting a worker thread,
and then copies the collected data in JSON format to the clipboard. It finally notifies the user
to paste the diagnostic information when creating a new issue on GitHub.
Parameters:
collect_dummy (bool): A flag indicating whether to collect dummy data. Default is False.
drop_sensitives (bool): A flag indicating whether to drop sensitive data. Default is True.
Returns:
None
"""
if not drop_sensitives:
confirmed = decide(
title='Agree to collect SENSITIVE data?',
description='[!!!CAUSION!!!]Do you REALLY want to collect diagnostic information INCLUDING ALL SENSITIVE data?\n'
'Please DO NOT share this information with anyone else or post it to public channels.',
)
if not confirmed:
return notify_box('Diagnostic information collection cancelled.')
# Clear the clipboard to ensure no old data is mixed in
cb = QtWidgets.QApplication.clipboard()
cb.clear(mode=cb.Clipboard)
# Collect diagnostic data using a worker thread
diagnostic_data = run_worker_thread_with_progress(
worker_function=issue_collection,
collect_dummy=collect_dummy,
drop_sensitives=drop_sensitives,
progress_bar=self.installer_ui.progressBar
)
diagnostic_data_json = json.dumps(diagnostic_data, indent=2)
# Copy the collected diagnostic data to the clipboard in JSON format
cb.setText(diagnostic_data_json, mode=cb.Clipboard)
# Notify the user that the diagnostic data has been copied and instruct them on what to do next
notify_box(
"Issue collection copied to clipboard. "
"Please paste it in a new issue in the REvoDesign repository on GitHub.",
details=diagnostic_data_json,
)
def add_right_click_menu(self, items: List[MenuItem]):
"""
Adds a right-click context menu to the installer UI.
Args:
items (List[MenuItem]): A list of menu items to be added to the right-click menu.
This method creates a right-click menu with actions defined by the `items` parameter.
Each item in the list is converted into a QAction, which is then added to the menu.
"""
# Create the right-click menu
self.menu = QtWidgets.QMenu(self.installer_ui)
for item in items:
if item.func is not None: # active item
# Add the item as active
upgrade_action = QtWidgets.QAction(item.name, self.installer_ui)
upgrade_action.triggered.connect(partial(item.func, **item.kwargs if item.kwargs else {}))
upgrade_action.setEnabled(True)
self.menu.addAction(upgrade_action)
else: # menu section
self.menu.addSection(item.name)
# Set the context menu policy to show the menu on right-click
self.installer_ui.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
self.installer_ui.customContextMenuRequested.connect(self.show_menu)
def show_menu(self, pos):
"""
Shows the context menu at the position of the mouse cursor.
Args:
pos (QPoint): The position where the menu should be shown, in widget coordinates.
"""
# Show the menu at the position of the mouse cursor
global_pos = self.installer_ui.mapToGlobal(pos)
self.menu.exec_(global_pos)
def make_window(self) -> QtWidgets.QDialog:
"""
Creates and configures the application window.
This method initializes a QDialog object and sets up its UI elements using the `Ui_Dialog` class.
It also connects various buttons to their respective methods for handling user interactions.
Returns:
QtWidgets.QDialog: The configured dialog window.
"""
# Create a new dialog window
dialog = QtWidgets.QDialog()
ui_file = run_worker_thread_with_progress(
worker_function=self.ensure_ui_file
)
# Set up the UI for the dialog
try:
self.installer_ui = loadUi(ui_file, dialog)
except Exception as e:
decided = decide(
'UI Error',
f'Error Occurs while loading UI file, this UI may out-of-dated.\nCleanup and fetch the latest?',
details=str(e),)
if decided:
os.remove(ui_file)
return self.make_window()
else:
raise RuntimeError(f"Error occurs while loading UI file: {e}.")
# add right-click menu on `self.installer_ui.label_header`,
# add a item `Upgrade UI` and connect `partial(self.ensure_ui_file, upgrade=True)`
menuitems = [
MenuItem('Upgrades'),
MenuItem("Upgrade UI", self.ensure_ui_file, kwargs={"upgrade": True}),
MenuItem("Upgrade this manager", self.self_upgrade),
MenuItem('Fetch remote data'),
MenuItem('Refresh GitHub Release tags', self.fetch_tags),
MenuItem('Diagnostics'),
MenuItem(
'Collect diagnostic data (reduced)',
self.collect_diagnostic_data,
kwargs={'collect_dummy': False}
),
MenuItem(
'Collect diagnostic data (full, non-sensitive)',
self.collect_diagnostic_data,
kwargs={'collect_dummy': True}
),
MenuItem(
'Collect diagnostic data (full, with sensitive)',
self.collect_diagnostic_data,
kwargs={'collect_dummy': True, 'drop_sensitives': False}
),
MenuItem('Configuration Force Reset'),
MenuItem(
'Reset REvoDesign\'s Configuration',
self.reinitialize_config,
)
]
self.add_right_click_menu(menuitems)
# Connect the open files button to the open_files method
self.installer_ui.pushButton_open.clicked.connect(self.open_files)
# Connect the open cache directory button to the open_cache_dir method
self.installer_ui.pushButton_open_cache_dir.clicked.connect(self.open_cache_dir)
# Connect the set cache directory button to the setup_cache_dir method
self.installer_ui.pushButton_set_cache_dir.clicked.connect(self.setup_cache_dir)
# Connect the install button to the install method
self.installer_ui.pushButton_install.clicked.connect(self.install)
# Connect the remove button to the uninstall method
self.installer_ui.pushButton_remove.clicked.connect(self.uninstall)
# Connect the radio button for customized extra options to the resize_extra_widget method with expand=True
self.installer_ui.radioButton_extra_customized.toggled["bool"].connect(
partial(
self.resize_extra_widget,
expand=True,
)
)
# Connect the radio button for no extra options to the resize_extra_widget method with expand=False
self.installer_ui.radioButton_extra_none.toggled["bool"].connect(
partial(
self.resize_extra_widget,
expand=False,
)
)
# Connect the radio button for all extra options to the resize_extra_widget method with expand=False
self.installer_ui.radioButton_extra_everything.toggled["bool"].connect(
partial(
self.resize_extra_widget,
expand=False,
)
)
# Return the configured dialog window
return dialog
@staticmethod
def animate_to_size(widget, target_size, duration=300):
"""
Animates the given widget to the target size over a specified duration.
:param widget: The widget to animate.
:param target_size: A tuple (width, height) representing the target size.
:param duration: The duration of the animation in milliseconds.
"""
animation = QtCore.QPropertyAnimation(widget, b"size")
animation.setDuration(duration)
animation.setStartValue(widget.size())
animation.setEndValue(QtCore.QSize(*target_size))
animation.setEasingCurve(QtCore.QEasingCurve.OutQuad)
animation.start()
# Prevent animation from being garbage collected
widget.anim = animation
def resize_extra_widget(self, expand: bool = False):
"""
Resize the extra widget based on the expand parameter.
Parameters:
- expand (bool): If True, expands the widget to a larger size; if False, shrinks it to a smaller size.
This function animates the resizing of `self.dialog` and `self.ui.label_header` to the specified dimensions.
"""
if expand:
# Expand the dialog and label to larger sizes
self.animate_to_size(self.dialog, (652, 534))
self.animate_to_size(self.installer_ui.label_header, (611, 41))
else:
# Shrink the dialog and label to smaller sizes
self.animate_to_size(self.dialog, (490, 534))
self.animate_to_size(self.installer_ui.label_header, (451, 41))
def fetch_tags(self):
"""
Retrieves the tags of a GitHub repository and sets them as the value of the version combo box.
This method calls the `get_github_repo_tags` function to obtain the tags information of the
specified GitHub repository,
and then sets the result as the value of the `comboBox_version` combo box in the UI.
"""
# Run a worker thread to fetch tags with a progress bar
tags = run_worker_thread_with_progress(
worker_function=get_github_repo_tags,
repo_url=REPO_URL,
progress_bar=self.installer_ui.progressBar)
if tags and isinstance(tags, list):
return set_widget_value(self.installer_ui.comboBox_version, tags)
return notify_box(f'Failed to fetch version tags from GitHub repo: \n{REPO_URL}')
# a copy from `REvoDesign/tools/customized_widgets.py`
def get_existing_directory(self):
"""
Opens a dialog for the user to select an existing directory.
Parameters:
- self: The instance of the class this method is called on.
Returns:
- str: The path of the selected directory.
"""
return QtWidgets.QFileDialog.getExistingDirectory(
None,
"Open Directory",
os.path.expanduser("~"),
QtWidgets.QFileDialog.DontResolveSymlinks,
)
# a copy from `REvoDesign/tools/customized_widgets.py`
# an open file version of pymol.Qt.utils.getSaveFileNameWithExt ;-)
def get_open_file_name_with_ext(self, *args, **kwargs):
"""
Return a file name, append extension from filter if no extension provided.
"""
fname, ext_filter = QtWidgets.QFileDialog.getOpenFileName(*args, **kwargs)
if not fname:
return ""
if "." not in os.path.split(fname)[-1]:
ext_match = re.search(r"\*(\.[\w\.]+)", ext_filter)
if ext_match:
# append first extension from filter
fname += ext_match.group(1)
return fname
def open_cache_dir(self):
"""
Opens the cache directory.
This method retrieves an existing directory path and sets it as the value of a line edit widget.
If the directory exists, it updates the UI with the directory path.
Returns:
The method returns the result of `set_widget_value` function, which is typically None or a
status indicating success.
"""
# Retrieve the existing directory path
cache_dir = self.get_existing_directory()
# Check if the directory exists and update the UI
if cache_dir and os.path.exists(cache_dir):
return set_widget_value(self.installer_ui.lineEdit_customized_cache_dir, cache_dir)
def open_files(self):
"""
Opens files or directories based on user selection from the UI.
This function checks which radio button is selected (local clone or local file) and then opens
the corresponding directory or file.
Returns:
None: The function updates the UI with the selected directory or file path.
"""
# Check if the 'from local clone' radio button is selected
from_local_clone = self.installer_ui.radioButton_from_local_clone.isChecked()
# Check if the 'from local file' radio button is selected
from_local_file = self.installer_ui.radioButton_from_local_file.isChecked()
if from_local_clone:
# Get the existing directory path from the user
opened_dir = self.get_existing_directory()
# If a valid directory is selected, update the UI with the directory path
if opened_dir and os.path.exists(opened_dir):
return set_widget_value(self.installer_ui.lineEdit_local, opened_dir)
if from_local_file:
# Define supported file extensions and their descriptions
ext = {"zip": "ZIP archive", "tar.gz": "Tarball (TAR.GZ)"}
# Open a file dialog to select a file with the specified extensions
file = self.get_open_file_name_with_ext(
self.dialog,
"Open",
filter=";;".join([f"{ext_description} ( *.{ext_} )" for ext_, ext_description in ext.items()]),
)
# If a valid file is selected, update the UI with the file path
if file and os.path.exists(file):
return set_widget_value(self.installer_ui.lineEdit_local, file)
def uninstall(self):
"""
Uninstall the REvoDesign package.
This function checks if REvoDesign is installed. If it is installed, it initiates the uninstallation process
through a separate thread, displaying the progress on the UI progress bar. After uninstallation is complete,
it provides feedback on the operation's success or failure.
"""
# Check if REvoDesign is installed
installed = importlib.util.find_spec("REvoDesign") is not None
# If REvoDesign is not installed, notify the user and exit the function
if not installed:
notify_box(message="REvoDesign is not installed.")
return
# During the uninstallation process, hold down the remove button on the UI to prevent multiple triggers
with hold_trigger_button(self.installer_ui.pushButton_remove):
# Run the uninstallation process in a separate thread and monitor its progress
ret: Optional[subprocess.CompletedProcess] = run_worker_thread_with_progress(
worker_function=self.pip_installer.uninstall,
package_name='REvoDesign',
progress_bar=self.installer_ui.progressBar,
)
if ret is None or ret.returncode:
# If the uninstallation fails, notify the user of the failure and raise an error
return notify_box(message="Failed to remove REvoDesign.", error_type=RuntimeError, details=ret.stdout)
remove_deps = decide(
'Clean up warning', 'Do you want to remove all the dependencies?')
if remove_deps:
run_worker_thread_with_progress(
self.remove_depts,
progress_bar=self.installer_ui.progressBar
)
# If the uninstallation is successful, notify the user
return notify_box(
message="REvoDesign is removed successfully. Bye-bye.",
)
def remove_depts(self):
"""
Removes selected dependencies.
This function removes the packages corresponding to the dependencies checked by the user.
It first fetches the dependency mapping table, filters out the dependencies that need to be removed,
and then calls the uninstall method of pip_installer to remove each package.
Parameters:
- self: The instance of the class containing this method.
Returns:
- None
"""
# Fetch the dependency package mapping table
deps_table: Dict[str, str] = fetch_gist_json(DEPTS_TABLE_JSON)
# Filter out dependencies whose package ID is empty
deps_table = {k: v for k, v in deps_table.items() if v != ''}
# Get the list of dependencies checked by the user for uninstallation
checked_depts_to_uninstall = self.extra_checkbox.get_checked_items()
# Iterate over the dependency table
for pkg_name, pkg_id in deps_table.items():
if pkg_name not in checked_depts_to_uninstall:
logging.debug(f'Skip unchecked item: {pkg_name}')
continue
# Uninstall each package associated with the checked dependency
for _p in pkg_id.split(';'):
logging.info(f"Removing {_p}...")
self.pip_installer.uninstall(_p)
def install(self):
"""
Handles the installation process based on user-selected options.
This function determines the installation source and method based on the user's choices,
validates the input, and performs the installation process. It also manages network settings,
such as proxies and mirrors, and provides feedback on the installation result.
"""
# sources
from_repo = self.installer_ui.radioButton_from_repo.isChecked()
from_local_clone = self.installer_ui.radioButton_from_local_clone.isChecked()
from_local_file = self.installer_ui.radioButton_from_local_file.isChecked()
local_source: str = self.installer_ui.lineEdit_local.text()
# Determine additional components to install
extras = ",".join(self.extra_checkbox.get_checked_items())
upgrade = self.installer_ui.checkBox_upgrade.isChecked()
verbose_level = self.installer_ui.horizontalSlider_Verbose.value()
# version tags
use_version = self.installer_ui.checkBox_specified_version.isChecked()
target_version = self.installer_ui.comboBox_version.currentText()
# git commits
use_commit = self.installer_ui.checkBox_specified_commit.isChecked()
target_commit = self.installer_ui.lineEdit_commit.text()
# networking
use_proxy = self.installer_ui.checkBox_use_proxy.isChecked()
proxy_url = self.installer_ui.lineEdit_proxy_url.text()
use_mirror = self.installer_ui.checkBox_use_mirror.isChecked()
mirror_url = self.installer_ui.lineEdit_mirror_url.text()
# Determine the installation source based on user selection
if from_repo:
install_source = REPO_URL
if use_version and target_version:
install_source += f"@{target_version}"
elif use_commit and target_commit:
install_source += f"@{target_commit}"
elif from_local_clone:
install_source = local_source
# Validate the local directory
if not local_source:
notify_box(f"Empty local dir: {local_source}", ValueError)
if not os.path.exists(local_source):
notify_box(f"dir not exists: {local_source}", ValueError)
if not os.path.isdir(local_source):
notify_box(f"{local_source} not a directory", FileNotFoundError)
if use_version and target_version:
install_source = f"file://{install_source}@{target_version}"
elif use_commit and target_commit:
install_source = f"file://{install_source}@{target_commit}"
elif from_local_file:
install_source = local_source
# Validate the local file
if not os.path.exists(local_source):
notify_box(f"{local_source} is not found.", FileNotFoundError)
if not os.path.isfile(local_source):
notify_box(f"{local_source} is not a file.", ValueError)
if not (local_source.endswith(".zip") or local_source.endswith(".tar.gz")):
notify_box(
f"{local_source} must be a .zip or .tar.gz file!",
ValueError,
)
if use_version or use_commit or target_version or target_commit:
logging.warning("installation from zip/tar file cannot use specified version/commit.")
install_source = local_source
else:
notify_box("Installation configuration is failed. Aborded. ", ValueError)
env: Dict[str, str] = {}
# Update environment variables based on proxy settings
env.update(self.proxy_in_env(
proxy=proxy_url if (use_proxy and proxy_url) else None,
mirror=mirror_url if (use_mirror and mirror_url) else None))
# pass env to installer
self.pip_installer.env = env
# Perform the installation process
with hold_trigger_button(self.installer_ui.pushButton_install):
git_solver = GitSolver()
if not git_solver.has_git:
git_fetch_command = git_solver.where_to_install
if not git_fetch_command:
# If none of package managers is present, prompt the user to install Git manually
notify_box(
message="Failed on resolving Git with package managers [winget/conda/brew]. \n"
"Git is required to install REvoDesign. Please install Git first.\n"
"See https://git-scm.com/downloads",
)
return
git_solver_res = run_worker_thread_with_progress(
worker_function=git_solver.fetch_git,
git_fetch_command=git_fetch_command,
env=env,
progress_bar=self.installer_ui.progressBar,
)
if not git_solver.has_git:
notify_box(
message=f"Git not installed. \n{git_solver_res[-1] if git_solver_res else ''}"
)
return
# If successful, show a notification and return True
notify_box(message="Git installed successfully.")
installed: Union[subprocess.CompletedProcess, None] = run_worker_thread_with_progress(
worker_function=self.pip_installer.install,
source=install_source,
upgrade=upgrade,
extras=extras,
verbose_level=verbose_level,
mirror=mirror_url if (use_mirror and mirror_url) else '',
progress_bar=self.installer_ui.progressBar,
)
# Provide feedback on the installation result
if isinstance(installed, subprocess.CompletedProcess) and installed.returncode == 0:
notify_box(
message="Installation succeeded. \nIf this is an upgrade, "
"please restart PyMOL for it to take effect.",
details=f'STDOUT:\n{installed.stdout}\n\nSTDERR:\n{installed.stderr}' if installed else None)
return
notify_box(
message=f"Installation failed from: {install_source} \n",
error_type=RuntimeError,
details=f'STDOUT: \n{installed.stderr}\n\nSTDERR: \n{installed.stderr}' if installed else None,
)
def setup_cache_dir(self):
"""
Set up the custom cache directory.
This function attempts to import `ConfigBus` and `save_configuration` from the REvoDesign library
to update the cache directory settings.
If the specified cache directory is valid, it updates the configuration and saves it.
Returns:
None
"""
try:
# Import necessary components from REvoDesign
from REvoDesign import ConfigBus, save_configuration
bus = ConfigBus()
# Get the new cache directory from the UI input
new_cache_dir = self.installer_ui.lineEdit_customized_cache_dir.text()
# Check if the new cache directory is valid
if new_cache_dir and os.path.isdir(new_cache_dir):
# Update the cache directory settings
bus.cfg.cache_dir.under_home_dir = False
bus.cfg.cache_dir.customized = new_cache_dir
# Save the updated configuration
save_configuration(new_cfg=bus.cfg)
# Notify the user that the cache directory has been updated
notify_box(f"The customized cache directory has been updated: \n{new_cache_dir}")
else:
# Notify the user that the cache directory is invalid
notify_box(f"The cache directory is not valid. Please check the path: \n{new_cache_dir}", UserWarning)
# Reset the ConfigBus instance
ConfigBus.reset_instance()
except ImportError:
# Notify the user that REvoDesign is not installed
notify_box(
message="REvoDesign is not installed. \nPlease install it first.",
error_type=RuntimeError,
)
def reinitialize_config(self):
comfirmed = decide(
"Reinitialize REvoDesign configuration?",
'[WARNING] This will delete your current configuration files.')
if not comfirmed:
return
from REvoDesign.bootstrap.set_config import set_REvoDesign_config_file
set_REvoDesign_config_file(delete_user_config_tree=True)
class WorkerThread(QtCore.QThread):
"""
Custom worker thread for executing a function in a separate thread.
Attributes:
- result_signal (QtCore.pyqtSignal): Signal emitted when the result is available.
- finished_signal (QtCore.pyqtSignal): Signal emitted when the thread finishes its execution.
- interrupt_signal (QtCore.pyqtSignal): Signal to interrupt the thread.
Methods:
- __init__: Initializes the WorkerThread object.
- run: Executes the specified function with arguments and emits the result through signals.
- handle_result: Returns the result obtained after the thread execution.
- interrupt: Interrupts the execution of the thread.
Example Usage:
```python
def some_function(x, y):
return x + y
worker = WorkerThread(func=some_function, args=(10, 20))
worker.result_signal.connect(handle_result_function)
worker.finished_signal.connect(handle_finished_function)
worker.interrupt_signal.connect(handle_interrupt_function)
worker.start()
# To interrupt the execution:
# worker.interrupt()
```
"""
result_signal = QtCore.pyqtSignal(list)
finished_signal = QtCore.pyqtSignal()
interrupt_signal = QtCore.pyqtSignal()
def __init__(self, func, args=None, kwargs=None):
super().__init__()
self.func = func
self.args = args or ()
self.kwargs = kwargs or {}
self.results = None # Define the results attribute
def run(self):
"""
Executes the task and handles the results.
This function checks if an interruption has been requested. If not, it runs the specified function with
given arguments and keyword arguments.
The result is then emitted through a signal if available, and a completion signal is emitted at the end.
Parameters:
- self: The instance of the class containing this method. It should have the following attributes:
- func: The function to be executed.
- args: A tuple of positional arguments for the function.
- kwargs: A dictionary of keyword arguments for the function.
- result_signal: A signal to emit the results.
- finished_signal: A signal to indicate the task has finished.
- isInterruptionRequested: A method that returns True if an interruption has been requested,
otherwise False.
"""
# Check if an interruption has been requested
if not self.isInterruptionRequested():
# Execute the function with provided arguments and store the result
self.results = [self.func(*self.args, **self.kwargs)]
# Emit the result if it exists
if self.results:
self.result_signal.emit(self.results)
# Emit the finished signal
self.finished_signal.emit()
def handle_result(self):
"""
Retrieves the results from the current instance.
This method returns the 'results' attribute of the current instance.
It is used to obtain the result data within other methods of the class.
"""
return self.results
def interrupt(self):
"""
Emit an interrupt signal.
This function triggers an interrupt signal.
"""
self.interrupt_signal.emit()
@overload
def run_worker_thread_with_progress(
worker_function: Callable[..., R], *args, progress_bar: Optional[Any] = None, **kwargs
) -> R: ...
def run_worker_thread_with_progress(
worker_function: Callable[..., Optional[R]], *args, progress_bar: Optional[Any] = None, **kwargs
) -> Optional[R]:
"""
Runs a worker function in a separate thread and optionally updates a progress bar.
This function is designed to execute a given task (worker_function) in a separate thread,
allowing the main thread to remain responsive, such as updating a progress bar.
After the task is completed, it restores the progress bar's state and returns the result of the task.
Parameters:
- worker_function: The function to execute in a separate thread.
- progress_bar: An optional progress bar object to update during the execution of the worker function.
- *args, **kwargs: Additional arguments and keyword arguments to pass to the worker function.
Returns:
- The result of the worker function or None if no result is available.
"""
# If a progress bar is provided, store its current state and set it to indeterminate progress
if progress_bar:
# store the progress bar state
_min = progress_bar.minimum()
_max = progress_bar.maximum()
_val = progress_bar.value()
progress_bar.setRange(0, 0)
# Create and start a worker thread with the given function and parameters
work_thread = WorkerThread(worker_function, args=args, kwargs=kwargs)
work_thread.start()
# Keep the main thread running until the worker thread finishes
while not work_thread.isFinished():
refresh_window()
time.sleep(0.01)
# If a progress bar was used, restore its state after the task is completed
if progress_bar:
# restore the progressbar state
progress_bar.setRange(_min, _max)
progress_bar.setValue(_val)
# Obtain and return the result of the worker function
result = work_thread.handle_result()
return result[0] if result else None
def get_github_repo_tags(repo_url) -> list[str]:
"""
Retrieve all released tags of a GitHub repository using urllib.
Usage:
tags = get_github_repo_tags("https://github.com/BradyAJohnston/MolecularNodes")
print(tags)
Args:
repo_url (str): The URL of the GitHub repository.
Returns:
list: A list of tag names for the repository.
"""
# Extract the owner and repo name from the URL
parts = repo_url.split("/")
owner = parts[-2]
repo = parts[-1]
# GitHub API URL for listing tags
api_url = f"https://api.github.com/repos/{owner}/{repo}/tags"
try:
# Send a GET request to the GitHub API
with urllib.request.urlopen(api_url) as response:
# Read the response and decode from bytes to string
response_data = response.read().decode()
# Parse JSON response data
tags = json.loads(response_data)
# Extract the name of each tag
tag_names = [tag["name"] for tag in tags]
return tag_names
except HTTPError as e:
# Handle HTTP errors (e.g., repository not found, rate limit exceeded)
logging.warning(f"GitHub API returned status code {e.code}")
return []
except URLError as e:
# Handle URL errors (e.g., network issues)
logging.error(f"Failed to reach the server. Reason: {e.reason}")
return []
# a minimum copy from `REvoDesign/tools/customized_widgets.py`
def set_widget_value(widget, value):
"""
Sets the value of a PyQt5 widget based on the provided value.
****************************************************************
A minimum version for installer.
****************************************************************
Args:
- widget: The PyQt5 widget whose value needs to be set.
- value: The value to be set on the widget.
Supported Widgets and Value Types:
- QComboBox: Supports str, list, tuple, dict.
- QLineEdit: Supports str.
- QProgressBar: Supports int, list or tuple (for setting range).
- QCheckBox: Supports bool.
"""
# Preprocess values according to types
if callable(value):
value = value() # Call the function to get the value if value is callable
if isinstance(value, Iterable) and not isinstance(value, (str, list, tuple, dict)):
value = list(value) # Convert iterable (excluding strings, lists, tuples, dicts) to list
# Setting values
if isinstance(widget, QtWidgets.QComboBox):
if isinstance(value, (list, tuple)):
widget.clear()
widget.addItems(map(str, value))
return
if isinstance(value, dict):
widget.clear()
for k, v in value.items():
widget.addItem(v, k)
return
widget.setCurrentText(str(value))
return
if isinstance(widget, QtWidgets.QLineEdit):
widget.setText(str(value))
return
if isinstance(widget, QtWidgets.QProgressBar):
if isinstance(value, int):
widget.setValue(value)
return
if isinstance(value, (list, tuple)) and len(value) == 2:
widget.setRange(*value)
return
raise ValueError(
f"Invalid value {value} for QProgressBar. Value must be an integer or a list/tuple of two integers."
)
if isinstance(widget, QtWidgets.QCheckBox):
widget.setChecked(bool(value))
return
raise UnsupportedWidgetValueTypeError(
f"FIX ME: Value {value} is not currently supported on widget {type(widget).__name__}"
)
def refresh_window():
"""
Refresh the application window by processing all pending events.
This function is copied from `REvoDesign/tools/customized_widgets.py`.
No parameters are required for this function.
Returns:
None
"""
QtWidgets.QApplication.processEvents()
# Overload #1: None or Warning => returns bool
@overload
def notify_box(
message: str = "",
error_type: Union[None, Type[Warning]] = None,
details: Optional[str] = None
) -> None:
...
# Overload #2: Exception => NoReturn
@overload
def notify_box(
message: str,
error_type: Type[Exception],
details: Optional[str] = None
) -> NoReturn:
...
def notify_box(
message: str = "",
error_type: Optional[Type[Exception]] = None,
details: Optional[str] = None
) -> Union[None, NoReturn]:
"""
Display a notification message box.
Parameters:
- message: str, the content of the message box.
- error_type: Optional[Union[Exception, Warning]], the type of error or warning, can be None.
If `error_type` is None or a Warning, returns bool.
If `error_type` is an Exception (and not a Warning), raises => NoReturn.
"""
refresh_window()
# Create an information message box
msg = QtWidgets.QMessageBox()
if error_type is None:
msg.setIcon(QtWidgets.QMessageBox.Information)
elif issubclass(error_type, Warning):
msg.setIcon(QtWidgets.QMessageBox.Warning)
elif issubclass(error_type, Exception):
msg.setIcon(QtWidgets.QMessageBox.Critical)
msg.setText(message)
if details is not None:
msg.setDetailedText(details)
msg.setStandardButtons(QtWidgets.QMessageBox.Ok)
# Display the message box
msg.exec_()
# If error_type is None, end the function execution
if error_type is None:
return
# error_type is a Warning => also bool
if issubclass(error_type, Warning):
warnings.warn(error_type(message))
return
# Otherwise, raise => NoReturn
raise_error(error_type, message)
def raise_error(error_type: Type[Exception], message: str) -> NoReturn:
"""
Raises an error of the specified type with the given message.
Args:
- error_type: Type[Exception], the type of error to raise.
- message: str, the error message.
"""
raise error_type(message)
def decide(title="", description="", rich: bool = False, details: Optional[str] = None):
"""
Function: decide
Usage: result = decide(title='', description='', rich=True)
This function displays a confirmation message box with a title and description,
allowing the user to proceed or cancel.
Args:
- title (str): Title of the confirmation box (default is empty)
- description (str): Description displayed in the confirmation box (default is empty)
- rich (bool): Whether to proceed with rich text or not (default is False)
Returns:
- bool: True if 'Yes' is selected, False otherwise
"""
refresh_window()
# A confirmation message.
msg = QtWidgets.QMessageBox()
msg.setIcon(QtWidgets.QMessageBox.Question)
msg.setWindowTitle(title)
msg.setText(description)
if details is not None:
msg.setDetailedText(details)
if rich:
msg.setTextFormat(QtCore.Qt.RichText)
msg.setStandardButtons(QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No)
result = msg.exec_()
return result == QtWidgets.QMessageBox.Yes
def is_package_installed(package):
"""
Function: is_package_installed
Usage: is_installed = is_package_installed(package)
This function checks if a specified package is installed in the current Python environment.
Args:
- package (str): Name of the package to check
Returns:
- bool: True if the package is installed, False otherwise
"""
package_loader = importlib.util.find_spec(package)
return package_loader is not None
def filter_sensitive_data(env):
"""
Filters out sensitive data keys from the provided environment dictionary.
Args:
env (dict): The dictionary to filter.
Returns:
dict: A new dictionary with sensitive keys removed.
"""
# Define the regex pattern to match sensitive keys
sensitive_pattern = re.compile(
r"(token|passwd|password|pass|session|_id|secret|access|auth|api_key|apikey|"
r"access_key|accesskey|secret_key|secretkey|auth_token|authtoken|"
r"session_id|session_token|private_key|ssh_key|key|login|cred|"
r"credential|authenticator|certificate|cert|identity|oauth|jwt|bearer|csrf)",
re.IGNORECASE
)
# Filter out sensitive keys
filtered_env = {
key: value for key, value in env.items() if not sensitive_pattern.search(key)
}
return filtered_env
def issue_collection(
collect_dummy: bool = False,
network: bool = True,
drop_sensitives: bool = True,
) -> Dict[str, Any]:
"""
Collects system and environment information and returns it as a dictionary.
Parameters:
- collect_dummy: A boolean indicating whether to collect additional 'dummy' information for debugging purposes.
- network: A boolean indicating whether to collect network information.
- drop_sensitives: A boolean indicating whether to drop sensitive information like passwords, tokens, etc.
Returns:
- A dictionary containing detailed information about the system, environment, and installed software.
"""
issue_dict = {}
# Collect platform information
platform_info = platform.uname()
# Platform
issue_dict.update({'Platform::Platform': sys.platform})
issue_dict.update({'Platform::Architecture': platform.architecture()[0]})
issue_dict.update({'Platform::OS': platform_info.system})
if platform_info.system == 'Darwin':
issue_dict.update({'Platform::MacOS::Version': platform.mac_ver()[0]})
elif platform_info.system == 'Windows':
issue_dict.update({'Platform::Windows::Version': platform.win32_ver()})
issue_dict.update({'Platform::Windows::Edition': platform.win32_edition()})
issue_dict.update({'Platform::Windows::IsIotDevice': platform.win32_is_iot()})
elif platform_info.system == 'Linux':
issue_dict.update({'Platform::Linux::Version': platform.freedesktop_os_release()
if hasattr(platform, 'freedesktop_os_release') else None})
issue_dict.update({'Platform::Release': platform_info.release})
issue_dict.update({'Platform::Version': platform_info.version})
if platform_info.system == 'Windows':
issue_dict.update({'Platform::CPU': platform_info.processor})
elif platform_info.system == 'Linux':
cpuinfo = run_command(['cat', '/proc/cpuinfo']).stdout.strip()
cpu_model = re.search(r'model name\s+:\s+(.+)', cpuinfo)
issue_dict.update({'Platform::CPU': cpu_model.group(1) if cpu_model else 'Unknown'})
elif platform_info.system == 'Darwin':
issue_dict.update({'Platform::CPU': run_command(['sysctl', '-n', 'machdep.cpu.brand_string']).stdout.strip()})
else:
issue_dict.update({'Platform::CPU': 'Unknown'})
issue_dict.update({'Platform::CPU::Num': os.cpu_count()})
issue_dict.update({'Platform::Machine': platform_info.machine})
issue_dict.update({'Platform::Hostname': platform_info.node})
is_rosetta_mac = "ARM64" in platform_info.version and platform_info.machine == "x86_64" if platform_info.system == "Darwin" else False
issue_dict.update({'Platform::IsRosettaTranlated': is_rosetta_mac})
which_chcp = shutil.which("chcp")
if which_chcp:
try:
issue_dict.update({'Platform::Windows::Chcp': run_command(['chcp']).stdout.strip()})
except Exception as e:
issue_dict.update({'Platform::Windows::Chcp': f"Error: {e}"})
# Shell
issue_dict.update({'Shell::Name': os.getenv('SHELL')})
issue_dict.update({'Shell::Encoding': sys.stdout.encoding})
issue_dict.update({'Shell::IsCygwin': 'CYGWIN' in os.environ.get('MSYSTEM', '')})
# Python
issue_dict.update({'Python::Version': sys.version})
issue_dict.update({'Python::PythonPath': sys.executable})
issue_dict.update({'Python::PIP': run_command([sys.executable, '-m', 'pip', '--version']).stdout.strip()})
issue_dict.update({'Python::Compiler': platform.python_compiler()})
issue_dict.update({'Python::Implementation': platform.python_implementation()})
# PyQt
issue_dict.update({'PyQt::Version': QtCore.PYQT_VERSION_STR})
issue_dict.update({'PyQt::QtPath': QtCore.__file__})
# Tools
git_solver = GitSolver()
try:
conda_version = run_command([git_solver.has_conda, '--version']
).stdout.strip() if git_solver.has_conda else 'Not Found'
except Exception:
conda_version = 'Not Found'
issue_dict.update({'Tools::Conda': conda_version})
try:
mamba_version = run_command([git_solver.has_mamba, '--version']
).stdout.strip() if git_solver.has_mamba else 'Not Found'
except Exception:
mamba_version = 'Not Found'
issue_dict.update({'Tools::Mamba': mamba_version})
issue_dict.update({'Tools::Git': git_solver.has_git})
issue_dict.update({'Tools::Git::Version': run_command(
[git_solver.has_git, '--version']).stdout.strip() if git_solver.has_git else 'Not Found'})
issue_dict.update({'Tools::Homebrew': git_solver.has_brew})
issue_dict.update({'Tools::Homebrew::Version': run_command(
[git_solver.has_brew, '--version']).stdout.strip() if git_solver.has_brew else 'Not Found'})
issue_dict.update({'Tools::Win-Get': git_solver.has_winget})
issue_dict.update({'Tools::Win-Get::Version': run_command(
[git_solver.has_winget, '--version']).stdout.strip() if git_solver.has_winget else 'Not Found'})
# Env Vars
issue_dict.update({'Env::CondaPath::0': os.getenv('CONDA_PREFIX')})
issue_dict.update({'Env::CondaPath::1': os.getenv('CONDA_PREFIX_1')})
issue_dict.update({'Env::CondaPath::2': os.getenv('CONDA_PREFIX_2')})
issue_dict.update({'Env::CondaEnvName': os.getenv('CONDA_DEFAULT_ENV')})
issue_dict.update({'Env::CondaPython': os.getenv('CONDA_PYTHON_EXE')})
issue_dict.update({'User::HomeDir': os.getenv('HOME')})
try:
issue_dict.update({'User::Username': os.getlogin()})
except OSError:
issue_dict.update({'User::Username': 'Unknown'})
# Network
try:
ip = socket.gethostbyname_ex(socket.gethostname())[2]
except Exception as e:
ip = f'Failed to fetch client ip: {e}'
issue_dict.update({'Network::IP': ip})
if network:
ip_location = fetch_gist_json('https://ipinfo.io')
if ip_location:
issue_dict.update({'Network::Location': ip_location})
else:
issue_dict.update({'Network::Location': 'Failed to fetch client location'})
# PyMOL
issue_dict.update({'PyMOL::Version': cmd.get_version()[0]})
issue_dict.update({'PyMOL::Build': get_version_message()})
# REvoDesign
issue_dict.update({'REvoDesign::Installer': __file__})
if is_package_installed('REvoDesign'):
import REvoDesign
from REvoDesign.driver.ui_driver import ConfigBus
from REvoDesign.magician import ALL_DESIGNER_CLASSES
from REvoDesign.sidechain.sidechain_solver import ALL_RUNNER_CLASSES
issue_dict.update({'REvoDesign::Version': REvoDesign.__version__})
issue_dict.update({'REvoDesign::Config': REvoDesign.REVODESIGN_CONFIG_FILE})
issue_dict.update({'REvoDesign::UI::Language': ConfigBus(
).cfg.language if ConfigBus._instance is not None else 'N/A'})
logfile_in_cfg = ConfigBus().cfg.log.handlers.file.filename if ConfigBus._instance is not None else 'N/A'
if logfile_in_cfg == 'AUTO':
from platformdirs import user_log_path
logdir = user_log_path("REvoDesign")
logfile = os.path.join(logdir, "REvoDesign.runtime.log")
else:
logfile = logfile_in_cfg
issue_dict.update({'REvoDesign::Logger::File': logfile})
issue_dict.update({'REvoDesign::Extras::SidechainSolver': [
runner.name for runner in ALL_RUNNER_CLASSES if runner.installed]})
issue_dict.update({'REvoDesign::Extras::Designers': [
designer.name for designer in ALL_DESIGNER_CLASSES if designer.installed]})
issue_dict.update({'REvoDesign::Extras::TestSuite': is_package_installed('pytest')})
else:
issue_dict.update({'REvoDesign::Version': 'Not Installed'})
# Dummy
if collect_dummy:
if drop_sensitives:
env_dict = filter_sensitive_data(os.environ)
logging.info('Sensitive data are removed.')
else:
env_dict = dict(os.environ)
logging.warning('Sensitive data may be kept.')
issue_dict.update({'Dummy::Environ': env_dict})
pip_list_stdout: List[str] = run_command(['pip', 'list']).stdout.split('\n')
pip_list_stdout_body: List[List[str]] = [l.split(' ') for l in pip_list_stdout[2:]]
issue_dict.update({'Dummy::Pip::List': {
line[0]: line[-1]
for line in pip_list_stdout_body
if line[0]
}})
if is_package_installed('REvoDesign'):
import REvoDesign
from REvoDesign.bootstrap.set_config import ConfigConverter
from REvoDesign.driver.ui_driver import ConfigBus
issue_dict.update({'Dummy::REvoDesign::Configurations': ConfigConverter().convert(
ConfigBus().cfg) if ConfigBus._instance is not None else 'N/A'})
return issue_dict
@contextmanager
def hold_trigger_button(
buttons: Union[tuple[QtWidgets.QPushButton, ...], QtWidgets.QPushButton],
animation_duration: int = 1000 # Duration of the breathing cycle (in milliseconds)
):
"""
A context manager for holding and releasing trigger buttons with a breathing effect
using the system's accent color.
Args:
buttons: One or more QPushButton objects.
animation_duration: Duration of the breathing animation cycle (in milliseconds).
"""
if not isinstance(buttons, (tuple, list, set)):
buttons = (buttons,)
timers = []
def get_accent_color():
color = QtGui.QColor(76, 217, 100)
return color
def start_breathing_animation(button: QtWidgets.QPushButton):
accent_color = get_accent_color()
base_color = accent_color.lighter(150) # Start with a lighter shade
darker_color = accent_color.darker(150) # Use a darker shade for the trough
timer = QtCore.QTimer(button)
timer.setInterval(30) # Update every 30 milliseconds
elapsed = 0
def update_stylesheet():
nonlocal elapsed
elapsed += timer.interval()
t = (elapsed % animation_duration) / animation_duration # Normalized time [0, 1]
# Calculate intermediate intensity using sine wave
factor = (1 + math.sin(2 * math.pi * t)) / 2 # Normalized to [0, 1]
r = int(base_color.red() * factor + darker_color.red() * (1 - factor))
g = int(base_color.green() * factor + darker_color.green() * (1 - factor))
b = int(base_color.blue() * factor + darker_color.blue() * (1 - factor))
button.setStyleSheet(f"background-color: rgb({r}, {g}, {b});")
timer.timeout.connect(update_stylesheet)
timer.start()
timers.append(timer)
def stop_breathing_animation(button: QtWidgets.QPushButton):
# Stop all timers associated with this button
for timer in timers:
if timer.parent() == button:
timer.stop()
timers.remove(timer)
button.setStyleSheet("") # Reset the button's style
try:
for b in buttons:
b.setEnabled(False)
b.setProperty("held", True) # Mark the button as held
b.setProperty("original_style", b.styleSheet() if b.styleSheet() else "")
start_breathing_animation(b)
logging.debug(f"Held button: {b.text()}: ({b.objectName()})")
yield
finally:
for b in buttons:
b.setProperty("held", False) # Remove the held mark
stop_breathing_animation(b)
b.setStyleSheet(b.property("original_style") if b.property("original_style") else "")
b.setEnabled(True) # Re-enable the button
logging.debug(f"Released button: {b.text()}: ({b.objectName()})")
def solve_installation_config(
source: str,
git_url: str,
git_tag: str,
extras: Optional[str],
package_name: str = 'REvoDesign',
):
"""
Solves the installation configuration based on the provided parameters.
Parameters:
- source (str): The source of the package to install. Can be a URL, a file path, or a directory.
- git_url (str): The Git URL of the repository.
- git_tag (str): The Git tag or branch to use for installation.
- extras (str): Additional extras to include in the installation.
Returns:
- str: The formatted package string for installation.
"""
extra_string = f'[{extras}]' if extras else ''
package_string = f"{package_name}{extra_string}"
logging.info(f"Installing as {package_string}...")
# Handle installation from a GitHub URL with a tag
if source and source.startswith("https://"):
package_string += f' @ git+{git_url}{f"@{git_tag}" if git_tag else ""}'
return package_string
# Handle installation from a local directory
if os.path.isdir(source):
# preprocess
if source.endswith("/"):
source = source[:-1]
# # a local Git repository? # TODO: not fully implemented yet
# if os.path.isdir(os.path.join(source, ".git")):
# package_string += f' @ git+file://{source}{f"@{git_tag}" if git_tag else ""}'
# return package_string
# or just an unzipped code directory?
if os.path.exists(os.path.join(source, "pyproject.toml")):
if git_tag:
notify_box("Ignore unzipped code directory tag!")
package_string = f"{source}{extra_string}"
return package_string
notify_box(f"{source} should atleast be a Git repository or a code directory!", ValueError)
# Handle installation from a zipped code file
if os.path.isfile(source):
if git_tag:
notify_box("Ignore zipped file tag!")
if source.endswith(".zip") or source.endswith(".tar.gz"):
package_string = f"{source}{extra_string}"
return package_string
notify_box(
f"{source} is neither a zipped file nor a tar.gz file!",
FileNotFoundError,
)
notify_box(f"Unknown installation source {source}({package_name})!", ValueError)
# entrypoint of PyMOL plugin
def __init_plugin__(app=None):
"""
Add an entry to the PyMOL "Plugin" menu
"""
logging.info(f"REvoDesign entrypoint is located at {os.path.dirname(__file__)}")
plugin = REvoDesignPackageManager()
addmenuitemqt("REvoDesign Package Manager", plugin.run_plugin_gui)
if is_package_installed('REvoDesign'):
from REvoDesign import REvoDesignPlugin
plugin = REvoDesignPlugin()
addmenuitemqt("REvoDesign", plugin.run_plugin_gui)
else:
logging.critical("REvoDesign is not available.")
Raw
REvoDesignDeptsTable.json
{
"Sidechain Solvers": "",
"dlpacker": "DLPacker",
"pippack": "PIPPack",
"Designers": "",
"colabdesign": "colabdesign",
"Predictors": "",
"thermompnn": "thermompnn",
"Protein Models": "",
"esm2": "fair-esm2",
"esme": "esm-efficient;flash-attn",
"Molecular Dynamics": "",
"openmm": "openmm;asgiref;pdbfixer;openmm-setup",
"Backbone Sampler": "",
"rfdiffusion_cuda": "rfdiffusion;nvtx;se3-transformer",
"rfdiffusion_mps": "rfdiffusion;nvtx;se3-transformer;nvtx-mock",
"rfdiffusion_cpu": "rfdiffusion;nvtx;se3-transformer;nvtx-mock",
"Developer Tool": "",
"test": "bandit;black;check-manifest;flake8-bugbear;flake8-docstrings;flake8-formatter_junit_xml;flake8;flake8-pyproject;pylint;pylint_junit;pytest;pytest-qt;pytest-cov;pytest-mock;pytest-runner;pytest;pytest-order;pytest-emoji;pytest-github-actions-annotate-failures;shellcheck-py;pre-commit;virtualenv;pooch;coverage"
}
Raw
REvoDesignExtrasTable.json
{
"Sidechain Solvers": "",
"DLPacker": "dlpacker",
"PIPPack": "pippack",
"Designers": "",
"ColabDesign": "colabdesign",
"Predictors": "",
"ThermoMPNN": "thermompnn",
"Protein Models": "",
"ESM1/2": "esm2",
"ESM-Efficient(CUDA)": "esme",
"Molecular Dynamics": "",
"OpenMM": "openmm",
"Backbone Sampler": "",
"RFdiffusion(CUDA)": "rfdiffusion_cuda",
"RFdiffusion(MacOS, Apple Silicon)": "rfdiffusion_mps",
"RFdiffusion(CPU)": "rfdiffusion_cpu",
"Developer Tool": "",
"Test": "test"
}
@YaoYinYing
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permalink guide: https://gist.github.com/atenni/5604615

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