refactoring shortcut.py script

.github/workflows/build.yml

@@ -28,8 +28,6 @@ jobs:
         python3-dev
         python3-setuptools
         python3-numpy
-        python3-pil
-        python3-pytest
         python3-pip
 
     - name: Install collada2gltf
@@ -45,13 +43,14 @@ jobs:
     - name: Build
       run: |
         pip install --upgrade pip
-        pip install -v --config-settings testing=True .
+        pip install -v --config-settings testing=True '.[dev]'
       env:
         DEBUG: 1
 
     - name: Test
       run: |
         pymol -ckqy testing/testing.py --run all
+        python -m pytest tests -vv
 
   build-Windows:
 
@@ -74,7 +73,7 @@ jobs:
       shell: cmd
       run: |-
         CALL %CONDA_ROOT%\\Scripts\\activate.bat
-        conda install -y -c conda-forge -c schrodinger python cmake libpng freetype pyside6 glew libxml2 numpy=1.26.4 catch2=2.13.3 glm libnetcdf collada2gltf biopython pillow msgpack-python pytest pip python-build
+        conda install -y -c conda-forge -c schrodinger python cmake libpng freetype pyside6 glew libxml2 numpy=1.26.4 catch2=2.13.3 glm libnetcdf collada2gltf biopython msgpack-python pip python-build
 
     - name: Conda info
       shell: cmd
@@ -94,13 +93,14 @@ jobs:
       shell: cmd
       run: |
         CALL %CONDA_ROOT%\\Scripts\\activate.bat
-        pip install -v --config-settings testing=True .
+        pip install -v --config-settings testing=True .[dev]
 
     - name: Test
       shell: cmd
       run: |
         CALL %CONDA_ROOT%\\Scripts\\activate.bat
         pymol -ckqy testing\\testing.py --run all
+        python -m pytest tests -vv
 
   build-MacOS:
 
@@ -117,7 +117,7 @@ jobs:
         bash $CONDA_ROOT.sh -b -p $CONDA_ROOT
         export PATH="$CONDA_ROOT/bin:$PATH"
         conda config --set quiet yes
-        conda install -y -c conda-forge -c schrodinger python cmake libpng freetype pyside6 glew libxml2 numpy=1.26.4 catch2=2.13.3 glm libnetcdf collada2gltf biopython pillow msgpack-python pytest pip python-build
+        conda install -y -c conda-forge -c schrodinger python cmake libpng freetype pyside6 glew libxml2 numpy=1.26.4 catch2=2.13.3 glm libnetcdf collada2gltf biopython msgpack-python pip python-build
         conda info
 
     - name: Get additional sources
@@ -131,9 +131,10 @@ jobs:
       run: |-
         export MACOSX_DEPLOYMENT_TARGET=12.0
         export PATH="$CONDA_ROOT/bin:$PATH"
-        pip install -v --config-settings testing=True .
+        pip install -v --config-settings testing=True '.[dev]'
 
     - name: Test
       run: |-
         export PATH="$CONDA_ROOT/bin:$PATH"
         pymol -ckqy testing/testing.py --run all
+        python -m pytest tests -vv

modules/pymol/cmd.py

@@ -33,6 +33,7 @@
 #
 # In rare cases, certain nonserious error or warning output should
 # also be suppressed.  Set "quiet" to 2 for this behavior.
+from pymol.shortcut import Shortcut
 
 def _deferred_init_pymol_internals(_pymol):
     # set up some global session tasks
@@ -54,7 +55,7 @@ def _deferred_init_pymol_internals(_pymol):
 
     # take care of some deferred initialization
 
-    _pymol._view_dict_sc = Shortcut({})
+    _pymol._view_dict_sc = Shortcut()
 
     #
 if True:
@@ -78,7 +79,6 @@ def _deferred_init_pymol_internals(_pymol):
 
         _pymol = pymol
 
-        from .shortcut import Shortcut
 
         from chempy import io
 

modules/pymol/commanding.py

@@ -12,6 +12,8 @@
 #-*
 #Z* -------------------------------------------------------------------
 
+from pymol.shortcut import Shortcut
+
 if True:
 
     import sys
@@ -39,7 +41,7 @@
     cmd = sys.modules["pymol.cmd"]
     import pymol
 
-    from .cmd import _cmd, Shortcut, QuietException, \
+    from .cmd import _cmd, QuietException, \
           fb_module, fb_mask, is_list, \
           DEFAULT_ERROR, DEFAULT_SUCCESS, is_ok, is_error, is_string
 

modules/pymol/completing.py

@@ -1,14 +1,16 @@
+from pymol.shortcut import Shortcut
+
 cmd = __import__("sys").modules["pymol.cmd"]
 
-class ExprShortcut(cmd.Shortcut):
+class ExprShortcut(Shortcut):
     '''
     Expression shortcut for iterate/alter/label with "s." prefix
     setting autocompletion.
     '''
-    def interpret(self, kee, mode=0):
-        if not kee.startswith('s.'):
-            return cmd.Shortcut.interpret(self, kee, mode)
-        v = cmd.setting.setting_sc.interpret(kee[2:])
+    def interpret(self, keyword, mode=False):
+        if not keyword.startswith('s.'):
+            return super().interpret(keyword, mode)
+        v = cmd.setting.setting_sc.interpret(keyword[2:])
         if isinstance(v, str):
             return 's.' + v
         if isinstance(v, list):
@@ -32,17 +34,17 @@ def interpret(self, kee, mode=0):
 def fragments_sc():
     import os
     import chempy
-    return cmd.Shortcut([
+    return Shortcut([
         f[:-4] for f in os.listdir(chempy.path + 'fragments')
         if f.endswith('.pkl')
     ])
 
 
 def vol_ramp_sc():
     from . import colorramping
-    return cmd.Shortcut(colorramping.namedramps)
+    return Shortcut(colorramping.namedramps)
 
-names_sc = lambda: cmd.Shortcut(cmd.get_names('public'))
+names_sc = lambda: Shortcut(cmd.get_names('public'))
 
 aa_nam_e = [ names_sc                   , 'name'            , ''   ]
 aa_nam_s = [ names_sc                   , 'name'            , ' '  ]
@@ -58,24 +60,24 @@ def vol_ramp_sc():
 aa_rep_c = [ cmd.repres_sc              , 'representation'  , ', ' ]
 aa_rem_c = [ cmd.repmasks_sc            , 'representation'  , ', ' ]
 aa_v_r_c = [ vol_ramp_sc                , 'volume ramp'     , ', ' ]
-aa_ali_e = [ cmd.Shortcut(['align', 'super', 'cealign']), 'alignment method', '']
+aa_ali_e = [ Shortcut(['align', 'super', 'cealign']), 'alignment method', '']
 
 def wizard_sc():
     import os, pymol.wizard
     names_glob = [name[:-3] for p in pymol.wizard.__path__
             for name in os.listdir(p) if name.endswith('.py')]
-    return cmd.Shortcut(names_glob)
+    return Shortcut(names_glob)
 
 def get_auto_arg_list(self_cmd=cmd):
     self_cmd = self_cmd._weakrefproxy
 
     aa_vol_c = [ lambda:
-            cmd.Shortcut(self_cmd.get_names_of_type('object:volume')),
+            Shortcut(self_cmd.get_names_of_type('object:volume')),
             'volume', '' ]
     aa_ramp_c = [ lambda:
-            cmd.Shortcut(self_cmd.get_names_of_type('object:ramp')),
+            Shortcut(self_cmd.get_names_of_type('object:ramp')),
             'ramp', '' ]
-    aa_scene_e = [lambda: cmd.Shortcut(cmd.get_scene_list()), 'scene', '']
+    aa_scene_e = [lambda: Shortcut(cmd.get_scene_list()), 'scene', '']
 
     return [
 # 1st
@@ -168,7 +170,7 @@ def get_auto_arg_list(self_cmd=cmd):
         'sculpt_iterate' : aa_obj_c,
         'set'            : aa_set_c,
         'set_bond'       : aa_set_c,
-        'set_key'        : [ lambda: cmd.Shortcut(cmd.key_mappings), 'key'       , ', ' ],
+        'set_key'        : [ lambda: Shortcut(cmd.key_mappings), 'key'       , ', ' ],
         'set_name'       : aa_nam_c,
         'set_title'      : aa_obj_c,
         'show'           : aa_rem_c,

modules/pymol/constants.py

@@ -1,8 +1,8 @@
 
 # constant objects
 
+from pymol.shortcut import Shortcut
 from .parsing import QuietException
-from .shortcut import Shortcut
 from .constants_palette import palette_dict
 import re
 

modules/pymol/controlling.py

@@ -12,18 +12,18 @@
 #-*
 #Z* -------------------------------------------------------------------
 
+from pymol.shortcut import Shortcut
+
 if True:
     try:
         from . import selector, internal
-        from .shortcut import Shortcut
         cmd = __import__("sys").modules["pymol.cmd"]
         from .cmd import _cmd, QuietException, is_string, \
              boolean_dict, boolean_sc, \
              DEFAULT_ERROR, DEFAULT_SUCCESS, is_ok, is_error, \
              location_code, location_sc
         import pymol
     except:
-        from shortcut import Shortcut
         cmd = None
 
 

modules/pymol/creating.py

@@ -12,6 +12,7 @@
 #-*
 #Z* -------------------------------------------------------------------
 
+from pymol.shortcut import Shortcut
 from .constants import CURRENT_STATE, ALL_STATES
 
 if True:
@@ -23,7 +24,7 @@
     import re
     import gzip
     import os
-    from .cmd import _cmd, Shortcut, is_list, is_string, \
+    from .cmd import _cmd, is_list, is_string, \
           safe_list_eval, safe_alpha_list_eval, \
           DEFAULT_ERROR, DEFAULT_SUCCESS, is_ok, is_error, \
           is_tuple

modules/pymol/editing.py

@@ -13,6 +13,7 @@
 #Z* -------------------------------------------------------------------
 
 import pymol
+from pymol.shortcut import Shortcut
 from .constants import CURRENT_STATE, ALL_STATES
 
 
@@ -67,7 +68,7 @@ def _iterate_prepare_args(expression, space, _self):
     import math
     from . import selector
     cmd = __import__("sys").modules["pymol.cmd"]
-    from .cmd import _cmd,lock,unlock,Shortcut,is_string, \
+    from .cmd import _cmd,lock,unlock,is_string, \
           boolean_sc,boolean_dict,safe_list_eval, is_sequence, \
           DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error
     from chempy import cpv

modules/pymol/experimenting.py

@@ -15,7 +15,7 @@
 if True:
 
     from . import selector
-    from .cmd import _cmd,lock,unlock,Shortcut,QuietException, \
+    from .cmd import _cmd,lock,unlock,QuietException, \
           DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error
     cmd = __import__("sys").modules["pymol.cmd"]
     import threading

modules/pymol/exporting.py

@@ -12,6 +12,7 @@
 #-*
 #Z* -------------------------------------------------------------------
 
+from pymol.shortcut import Shortcut
 from . import colorprinting
 
 if True:
@@ -24,7 +25,7 @@
 
     import pymol
     cmd = sys.modules["pymol.cmd"]
-    from .cmd import _cmd,Shortcut,QuietException
+    from .cmd import _cmd,QuietException
     from chempy import io
     from chempy.pkl import cPickle
     from .cmd import _feedback,fb_module,fb_mask, \

modules/pymol/externing.py

@@ -23,7 +23,7 @@
     import traceback
 
     from glob import glob
-    from .cmd import _cmd,lock,unlock,Shortcut,QuietException, \
+    from .cmd import _cmd,lock,unlock,QuietException, \
           _feedback,fb_module,fb_mask, exp_path, \
           DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error
 

modules/pymol/feedingback.py

@@ -1,6 +1,7 @@
 import sys
+from pymol.shortcut import Shortcut
 cmd = __import__("sys").modules["pymol.cmd"]
-from .cmd import Shortcut, is_string, QuietException
+from .cmd import is_string, QuietException
 from .cmd import fb_module, fb_mask, fb_action,_raising
 import copy
 

modules/pymol/fitting.py

@@ -20,7 +20,7 @@
         import os
         import pymol
 
-        from .cmd import _cmd,lock,unlock,Shortcut, \
+        from .cmd import _cmd,lock,unlock, \
             DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error
 
 

modules/pymol/internal.py

@@ -1,6 +1,7 @@
 import os
 import sys
 cmd = sys.modules["pymol.cmd"]
+from pymol.shortcut import Shortcut
 from pymol import _cmd
 import threading
 import traceback
@@ -14,7 +15,7 @@
 
 import chempy.io
 
-from .cmd import DEFAULT_ERROR, DEFAULT_SUCCESS, loadable, _load2str, Shortcut, \
+from .cmd import DEFAULT_ERROR, DEFAULT_SUCCESS, loadable, _load2str, \
    is_string, is_ok
 
 # cache management:

modules/pymol/movie.py

@@ -21,6 +21,7 @@
 import threading
 import time
 from . import colorprinting
+from pymol.shortcut import Shortcut
 
 def get_movie_fps(_self):
     r = _self.get_setting_float('movie_fps')
@@ -817,7 +818,7 @@ def _encode(filename,first,last,preserve,
     'ray'     : 2,
     }
 
-produce_mode_sc = cmd.Shortcut(produce_mode_dict.keys())
+produce_mode_sc = Shortcut(produce_mode_dict.keys())
 
 
 def find_exe(exe):

modules/pymol/moving.py

@@ -11,6 +11,7 @@
 #-*
 #-*
 #Z* -------------------------------------------------------------------
+from pymol.shortcut import Shortcut
 
 if True:
 
@@ -21,7 +22,7 @@
     import pymol
     import re
     cmd = sys.modules["pymol.cmd"]
-    from .cmd import _cmd,Shortcut, \
+    from .cmd import _cmd, \
           toggle_dict,toggle_sc, \
           DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error
 

modules/pymol/plugins/__init__.py

@@ -11,6 +11,7 @@
 import pymol
 from pymol import cmd
 from pymol import colorprinting
+from pymol.shortcut import Shortcut
 from .legacysupport import *
 
 # variables
@@ -434,6 +435,6 @@ def initialize(pmgapp=-1):
 cmd.extend('plugin_pref_save', pref_save)
 
 # autocompletion
-cmd.auto_arg[0]['plugin_load'] = [ lambda: cmd.Shortcut(plugins), 'plugin', ''  ]
+cmd.auto_arg[0]['plugin_load'] = [ lambda: Shortcut(plugins), 'plugin', ''  ]
 
 # vi:expandtab:smarttab:sw=4

modules/pymol/querying.py

@@ -20,7 +20,7 @@
     from . import selector
     import pymol
     cmd = __import__("sys").modules["pymol.cmd"]
-    from .cmd import _cmd,lock,unlock,Shortcut, \
+    from .cmd import _cmd,lock,unlock, \
           _feedback,fb_module,fb_mask,is_list, \
           DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error