From f1494f19595191e4968235858f57a3f44767db46 Mon Sep 17 00:00:00 2001
From: Ye11owSub <exactlythatguy@gmail.com>
Date: Sat, 17 Aug 2024 11:02:45 +0100
Subject: [PATCH 1/3] refactoring shortcut.py
---
.github/workflows/build.yml | 15 +-
modules/pymol/cmd.py | 4 +-
modules/pymol/shortcut.py | 351 ++++++++++++++++------------------
pyproject.toml | 3 +-
testing/tests/api/shortcut.py | 6 +-
tests/pymol/test_shortcut.py | 123 ++++++++++++
6 files changed, 307 insertions(+), 195 deletions(-)
create mode 100644 tests/pymol/test_shortcut.py
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index b5462115b..8c4f43e0c 100644
--- a/.github/workflows/build.yml
+++ b/.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
diff --git a/modules/pymol/cmd.py b/modules/pymol/cmd.py
index 09ae92f9e..c2dcb6da8 100644
--- a/modules/pymol/cmd.py
+++ b/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
diff --git a/modules/pymol/shortcut.py b/modules/pymol/shortcut.py
index ed654b79b..1f172a85d 100644
--- a/modules/pymol/shortcut.py
+++ b/modules/pymol/shortcut.py
@@ -1,184 +1,171 @@
-#A* -------------------------------------------------------------------
-#B* This file contains source code for the PyMOL computer program
-#C* Copyright (c) Schrodinger, LLC.
-#D* -------------------------------------------------------------------
-#E* It is unlawful to modify or remove this copyright notice.
-#F* -------------------------------------------------------------------
-#G* Please see the accompanying LICENSE file for further information.
-#H* -------------------------------------------------------------------
-#I* Additional authors of this source file include:
-#-*
-#-*
-#-*
-#Z* -------------------------------------------------------------------
-
-if __name__=='pymol.shortcut':
- from . import parsing
- from .checking import is_string, is_list
-
-if True:
- def mkabbr(a, m=1):
- b = a.split('_')
- b[:-1] = [c[0:m] for c in b[:-1]]
- return '_'.join(b)
-
- class Shortcut:
-
- def __call__(self):
- return self
-
- def __init__(self, keywords=(), filter_leading_underscore=1):
- self.filter_leading_underscore = filter_leading_underscore
- if filter_leading_underscore:
- self.keywords = [x for x in keywords if x[:1]!='_']
- else:
- self.keywords = list(keywords)
- self.shortcut = {}
- self.abbr_dict = {}
- self.rebuild()
-
- def add_one(self,a):
- # optimize symbols
- hash = self.shortcut
- abbr_dict = self.abbr_dict
- for b in range(1,len(a)):
- sub = a[0:b]
- hash[sub] = 0 if sub in hash else a
- if '_' in a:
- for n in (1, 2):
- abbr = mkabbr(a, n)
- if a!=abbr:
- if abbr in abbr_dict:
- if a not in abbr_dict[abbr]:
- abbr_dict[abbr].append(a)
- else:
- abbr_dict[abbr]=[a]
- for b in range(abbr.find('_')+1,len(abbr)):
- sub = abbr[0:b]
- hash[sub] = 0 if sub in hash else a
-
- def rebuild(self, keywords=None):
- if keywords is not None:
- if self.filter_leading_underscore:
- self.keywords = [x for x in keywords if x[:1]!='_']
- else:
- self.keywords = list(keywords)
- # optimize symbols
- self.shortcut = {}
- hash = self.shortcut
- self.abbr_dict = {}
- abbr_dict = self.abbr_dict
- #
- for a in self.keywords:
- for b in range(1,len(a)):
- sub = a[0:b]
- hash[sub] = 0 if sub in hash else a
- if '_' in a:
- for n in (1, 2):
- abbr = mkabbr(a, n)
- if a!=abbr:
- if abbr in abbr_dict:
- abbr_dict[abbr].append(a)
- else:
- abbr_dict[abbr]=[a]
- for b in range(abbr.find('_')+1,len(abbr)):
- sub = abbr[0:b]
- hash[sub] = 0 if sub in hash else a
-
- self._rebuild_finalize()
-
- def _rebuild_finalize(self):
- hash = self.shortcut
- for a, adk in self.abbr_dict.items():
- if len(adk)==1:
- hash[a]=adk[0]
- for a in self.keywords:
- hash[a]=a
-
- def interpret(self,kee, mode=0):
- '''
- Returns None (no hit), str (one hit) or list (multiple hits)
-
- kee = str: query string, setting prefix or shortcut
- mode = 0/1: if mode=1, do prefix search even if kee has exact match
- '''
- if not len(kee): # empty string matches everything
- return list(self.keywords)
-
- try:
- r = self.shortcut[kee]
- except KeyError:
- return None
- if r and not mode:
- return r
-
- # prefix search
- lst_set = set(a for a in self.keywords if a.startswith(kee))
- for abbr, a_list in self.abbr_dict.items():
- if abbr.startswith(kee):
- lst_set.update(a_list)
-
- # no match
- if not lst_set:
- return None
-
- # single match: str
- lst = list(lst_set)
- if len(lst) == 1:
- return lst[0]
-
- # multiple matches: list
- return lst
-
- def has_key(self,kee):
- return kee in self.shortcut
-
- __contains__ = has_key
-
- def __getitem__(self,kee):
- return self.shortcut.get(kee, None)
-
- def __delitem__(self,kee):
- self.keywords.remove(kee)
- self.rebuild()
-
- def append(self,kee):
- self.keywords.append(kee)
- self.add_one(kee)
- self._rebuild_finalize()
-
- def auto_err(self,kee,descrip=None):
- result = None
- if kee not in self.shortcut:
- if descrip is not None:
- msg = "Error: unknown %s: '%s'." % (descrip, kee)
- lst = self.interpret('')
- if is_list(lst):
- if len(lst)<100:
- lst.sort()
- lst = parsing.list_to_str_list(lst)
- msg += " Choices:\n"
- msg += "\n".join(lst)
- raise parsing.QuietException(msg)
-
- else:
- result = self.interpret(kee)
- if not is_string(result):
- if descrip is not None:
- lst = parsing.list_to_str_list(result)
- msg = "Error: ambiguous %s:\n%s" % (descrip, '\n'.join(lst))
- raise parsing.QuietException(msg)
+# A* -------------------------------------------------------------------
+# B* This file contains source code for the PyMOL computer program
+# C* Copyright (c) Schrodinger, LLC.
+# D* -------------------------------------------------------------------
+# E* It is unlawful to modify or remove this copyright notice.
+# F* -------------------------------------------------------------------
+# G* Please see the accompanying LICENSE file for further information.
+# H* -------------------------------------------------------------------
+# I* Additional authors of this source file include:
+# -*
+# -*
+# -*
+# Z* -------------------------------------------------------------------
+
+from typing import Iterable, Optional
+from collections import defaultdict
+from pymol import parsing
+
+
+class Shortcut:
+ def __init__(
+ self,
+ keywords: Optional[Iterable] = None,
+ filter_leading_underscore: bool = True,
+ ):
+ keywords = list(keywords) if keywords is not None else []
+ self.filter_leading_underscore = filter_leading_underscore
+ self.keywords = (
+ [keyword for keyword in keywords if keyword[:1] != "_"]
+ if filter_leading_underscore
+ else keywords
+ )
+ self.shortcut: dict[str, str | int] = {}
+ self.abbreviation_dict = defaultdict(list)
+
+ for keyword in self.keywords:
+ self.optimize_symbols(keyword)
+
+ self._rebuild_finalize()
+
+ def __contains__(self, keyword: str) -> bool:
+ return keyword in self.shortcut
+
+ def __getitem__(self, keyword: str) -> Optional[int | str]:
+ return self.shortcut.get(keyword)
+
+ def __delitem__(self, keyword: str) -> None:
+ self.keywords.remove(keyword)
+ self.rebuild()
+
+ def make_abbreviation(self, s: str, groups_length: int) -> str:
+ """
+ Example 1:
+ Input: s:'abc_def_ghig', groups_length: 1
+ Output: 'a_d_ghig'
+ Example 2:
+ Input: s:'abc_def', groups_length: 2
+ Output: 'a_def'
+ """
+ groups = s.split("_")
+ groups[:-1] = [c[0:groups_length] for c in groups[:-1]]
+ return "_".join(groups)
+
+ def optimize_symbols(self, keyword: str) -> None:
+ for i in range(1, len(keyword)):
+ substr = keyword[0:i]
+ self.shortcut[substr] = 0 if substr in self.shortcut else keyword
+
+ if "_" not in keyword:
+ return
+
+ for n in (1, 2):
+ abbreviation = self.make_abbreviation(keyword, n)
+
+ if keyword == abbreviation:
+ continue
+
+ self.abbreviation_dict[abbreviation].append(keyword)
+
+ for i in range(abbreviation.find("_") + 1, len(abbreviation)):
+ sub = abbreviation[0:i]
+ self.shortcut[sub] = 0 if sub in self.shortcut else keyword
+
+ def rebuild(self, keywords: Optional[Iterable] = None) -> None:
+ keywords = list(keywords) if keywords is not None else []
+ self.keywords = (
+ [keyword for keyword in keywords if keyword[:1] != "_"]
+ if self.filter_leading_underscore
+ else keywords
+ )
+ # optimize symbols
+ self.shortcut = {}
+ self.abbreviation_dict = defaultdict(list)
+ for keyword in self.keywords:
+ self.optimize_symbols(keyword)
+
+ self._rebuild_finalize()
+
+ def _rebuild_finalize(self) -> None:
+ for abbreviation, keywords in self.abbreviation_dict.items():
+ if len(keywords) == 1:
+ self.shortcut[abbreviation] = keywords[0]
+ for keyword in self.keywords:
+ self.shortcut[keyword] = keyword
+
+ def interpret(
+ self, keyword: str, mode: bool = False
+ ) -> Optional[int | str | list[str]]:
+ """
+ Returns None (no hit), str (one hit) or list (multiple hits)
+
+ keyword = str: query string, setting prefix or shortcut
+ mode = True/False: if mode=True, do prefix search even if kee has exact match
+ """
+ if keyword == "":
+ return self.keywords
+
+ result = self.shortcut.get(keyword)
+ if result is None:
+ return
+ if result and not mode:
return result
-if __name__=='__main__':
- sc = Shortcut(['warren','wasteland','electric','well'])
- tv = sc.has_key('a')
- print(tv==0,tv)
- tv = sc.has_key('w')
- print(tv==1,tv)
- tv = sc.has_key('war')
- print(tv==1,tv)
- tv = sc.interpret('w')
- print(sorted(tv)==['warren', 'wasteland', 'well'],tv)
- tv = sc.interpret('e')
- print(isinstance(tv, str), tv)
+ # prefix search
+ unique_keywords = set(
+ word for word in self.keywords if word.startswith(keyword)
+ )
+ for abbreviation, keywords in self.abbreviation_dict.items():
+ if abbreviation.startswith(keyword):
+ unique_keywords.update(keywords)
+ # no match
+ if not unique_keywords:
+ return
+
+ # single match: str
+ # multiple matches: list
+ return (
+ unique_keywords.pop()
+ if len(unique_keywords) == 1
+ else list(unique_keywords)
+ )
+
+ def append(self, keyword) -> None:
+ self.keywords.append(keyword)
+ self.optimize_symbols(keyword)
+ self._rebuild_finalize()
+
+ def auto_err(
+ self, keyword: str, descrip: Optional[str] = None
+ ) -> Optional[int | str | list[str]]:
+ if keyword == "":
+ return
+
+ result = self.interpret(keyword)
+
+ if result is None and descrip is not None:
+ msg = f"Error: unknown {descrip}: '{keyword}'."
+ lst = self.interpret("")
+ if isinstance(lst, list) and len(lst) < 100:
+ lst.sort()
+ lst = parsing.list_to_str_list(lst)
+ msg += " Choices:\n" + "\n".join(lst)
+ raise parsing.QuietException(msg)
+
+ if isinstance(result, list) and descrip is not None:
+ lst = parsing.list_to_str_list(result)
+ options = "\n".join(lst)
+ msg = f"Error: ambiguous {descrip}\\n {options}"
+ raise parsing.QuietException(msg)
+
+ return result
diff --git a/pyproject.toml b/pyproject.toml
index d8629e40a..f1f2dc117 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,7 +26,8 @@ requires = [
]
[project.optional-dependencies]
-test = [
+dev = [
+ "numpy>=1.26.4,<2",
"pillow==10.3.0",
"pytest==8.2.2",
]
diff --git a/testing/tests/api/shortcut.py b/testing/tests/api/shortcut.py
index c8d4103d2..a1830b501 100644
--- a/testing/tests/api/shortcut.py
+++ b/testing/tests/api/shortcut.py
@@ -11,7 +11,7 @@ class TestShortcut(testing.PyMOLTestCase):
def testShortcut(self):
# build shortcut
sc = cmd.Shortcut(words)
-
+
# get all keywords
self.assertItemsEqual(words, sc.interpret(''))
@@ -33,8 +33,8 @@ def testShortcut(self):
self.assertItemsEqual(['foo', 'foo_new'], sc.interpret('f'))
self.assertEqual('foo', sc.interpret('foo'))
self.assertEqual('foo_new', sc.interpret('foo_'))
-
- self.assertEqual(False, sc.has_key(''))
+
+ self.assertEqual(False, '' in sc)
# abbreviations
diff --git a/tests/pymol/test_shortcut.py b/tests/pymol/test_shortcut.py
new file mode 100644
index 000000000..d7e86aa51
--- /dev/null
+++ b/tests/pymol/test_shortcut.py
@@ -0,0 +1,123 @@
+import pytest
+
+from pymol.shortcut import Shortcut
+
+
+@pytest.fixture
+def sc() -> Shortcut:
+ return Shortcut(["foo", "bar", "baz", "com", "com_bla", "com_xxx"])
+
+
+@pytest.mark.parametrize(
+ "keyword, expected_result",
+ [
+ ("a", False),
+ ("w", True),
+ ("war", True),
+ ],
+)
+def test_contains(keyword: str, expected_result: bool):
+ shortcut = Shortcut(["warren", "wasteland", "electric", "well"])
+ assert (keyword in shortcut) is expected_result
+
+
+def test_interpret():
+ shortcut = Shortcut(["warren", "wasteland", "electric", "well"])
+ list_result = shortcut.interpret("w")
+ assert list_result is not None
+ assert not isinstance(list_result, int)
+ assert sorted(list_result) == ["warren", "wasteland", "well"]
+
+ string_result = shortcut.interpret("e")
+ assert list_result is not None
+ assert string_result == "electric"
+
+
+def test_all_keywords(sc: Shortcut):
+ assert ["foo", "bar", "baz", "com", "com_bla", "com_xxx"] == sc.interpret("")
+
+
+@pytest.mark.parametrize(
+ "prefixs, expected_result",
+ [
+ (["f", "fo", "foo"], "foo"),
+ (["b", "ba"], ["bar", "baz"]),
+ (["bar"], "bar"),
+ (["c", "co"], ["com", "com_bla", "com_xxx"]),
+ (["com"], "com"),
+ ],
+)
+def test_full_prefix_hits(
+ sc: Shortcut, prefixs: list[str], expected_result: str | list[str]
+):
+ for prefix in prefixs:
+ result = sc.interpret(prefix)
+ result = sorted(result) if isinstance(result, list) else result
+ assert expected_result == result
+
+
+def test_append(sc: Shortcut):
+ sc.append("foo_new")
+
+ assert ["foo", "foo_new"], sc.interpret("f")
+ assert "foo", sc.interpret("foo")
+ assert "foo_new", sc.interpret("foo_")
+
+ assert "" not in sc
+
+
+def test_abbreviations(sc: Shortcut):
+ sc.append("foo_new")
+
+ assert "foo_new" == sc.interpret("f_")
+ assert "foo_new" == sc.interpret("f_new")
+ assert "foo_new" == sc.interpret("fo_")
+ assert "com_xxx" == sc.interpret("c_x")
+ assert "com_xxx" == sc.interpret("c_xxx")
+ assert "com_xxx" == sc.interpret("co_x")
+
+
+def test_missing_key(sc: Shortcut):
+ assert None is sc.interpret("missing_key")
+
+
+def test_auto_error(sc: Shortcut):
+ assert None is sc.auto_err("")
+ assert None is sc.auto_err("missing_key")
+
+ result = sc.auto_err("co")
+ assert isinstance(result, list)
+ assert ["com", "com_bla", "com_xxx"] == sorted(result)
+ assert "com", sc.auto_err("com")
+
+
+def test_interpret_mode_true(sc: Shortcut):
+ assert "foo" == sc.interpret("f", True)
+
+ result = sc.interpret("com", True)
+ assert isinstance(result, list)
+ assert ["com", "com_bla", "com_xxx"] == sorted(result)
+
+ sc.append("foo_new")
+ result = sc.interpret("foo", True)
+ assert isinstance(result, list)
+ assert ["foo", "foo_new"] == sorted(result)
+
+
+def test_rebuild(sc: Shortcut):
+ coms = ["com", "com_bla", "com_xxx"]
+ sc.rebuild(coms)
+
+ assert None is sc.interpret("f")
+ assert None is sc.interpret("foo")
+
+ result = sc.interpret("c")
+ assert isinstance(result, list)
+ assert coms == sorted(result)
+
+ result = sc.interpret("com", True)
+ assert isinstance(result, list)
+ assert coms == sorted(result)
+
+ assert "com" == sc.interpret("com")
+ assert "com_xxx" == sc.interpret("c_x")
From cf243e2ca32b7fba719a2a35141c65fee35691b9 Mon Sep 17 00:00:00 2001
From: ye11owSub <exactlythatguy@gmail.com>
Date: Sat, 17 Aug 2024 16:04:56 +0100
Subject: [PATCH 2/3] fixing imports for class Shortcut
---
modules/pymol/commanding.py | 4 +++-
modules/pymol/completing.py | 30 ++++++++++++++++--------------
modules/pymol/constants.py | 2 +-
modules/pymol/controlling.py | 4 ++--
modules/pymol/creating.py | 3 ++-
modules/pymol/editing.py | 3 ++-
modules/pymol/experimenting.py | 2 +-
modules/pymol/exporting.py | 3 ++-
modules/pymol/externing.py | 2 +-
modules/pymol/feedingback.py | 3 ++-
modules/pymol/fitting.py | 2 +-
modules/pymol/internal.py | 3 ++-
modules/pymol/movie.py | 3 ++-
modules/pymol/moving.py | 3 ++-
modules/pymol/plugins/__init__.py | 3 ++-
modules/pymol/querying.py | 2 +-
modules/pymol/selecting.py | 3 ++-
modules/pymol/setting.py | 4 +++-
modules/pymol/viewing.py | 3 ++-
modules/pymol/wizarding.py | 2 +-
20 files changed, 50 insertions(+), 34 deletions(-)
diff --git a/modules/pymol/commanding.py b/modules/pymol/commanding.py
index 470994f33..27d724e05 100644
--- a/modules/pymol/commanding.py
+++ b/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
diff --git a/modules/pymol/completing.py b/modules/pymol/completing.py
index e9280582c..a9d525220 100644
--- a/modules/pymol/completing.py
+++ b/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):
@@ -32,7 +34,7 @@ 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')
])
@@ -40,9 +42,9 @@ def fragments_sc():
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,
diff --git a/modules/pymol/constants.py b/modules/pymol/constants.py
index dc19cdebc..caa70aab4 100644
--- a/modules/pymol/constants.py
+++ b/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
diff --git a/modules/pymol/controlling.py b/modules/pymol/controlling.py
index 74929e149..9de1de7ca 100644
--- a/modules/pymol/controlling.py
+++ b/modules/pymol/controlling.py
@@ -12,10 +12,11 @@
#-*
#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, \
@@ -23,7 +24,6 @@
location_code, location_sc
import pymol
except:
- from shortcut import Shortcut
cmd = None
diff --git a/modules/pymol/creating.py b/modules/pymol/creating.py
index ac9c7fbc9..6ea15cc45 100644
--- a/modules/pymol/creating.py
+++ b/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
diff --git a/modules/pymol/editing.py b/modules/pymol/editing.py
index 4f288b237..420073fa6 100644
--- a/modules/pymol/editing.py
+++ b/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
diff --git a/modules/pymol/experimenting.py b/modules/pymol/experimenting.py
index 5dda05c17..e91c1abed 100644
--- a/modules/pymol/experimenting.py
+++ b/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
diff --git a/modules/pymol/exporting.py b/modules/pymol/exporting.py
index 132a8407a..e6cd9f18c 100644
--- a/modules/pymol/exporting.py
+++ b/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, \
diff --git a/modules/pymol/externing.py b/modules/pymol/externing.py
index 7f43cf792..20a6169bf 100644
--- a/modules/pymol/externing.py
+++ b/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
diff --git a/modules/pymol/feedingback.py b/modules/pymol/feedingback.py
index 3e4d0bcb8..56e6b8266 100644
--- a/modules/pymol/feedingback.py
+++ b/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
diff --git a/modules/pymol/fitting.py b/modules/pymol/fitting.py
index 7097b2080..213b15d42 100644
--- a/modules/pymol/fitting.py
+++ b/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
diff --git a/modules/pymol/internal.py b/modules/pymol/internal.py
index 087ed03fa..0e5c5fb79 100644
--- a/modules/pymol/internal.py
+++ b/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:
diff --git a/modules/pymol/movie.py b/modules/pymol/movie.py
index 1c9bdf43b..3bde747fd 100644
--- a/modules/pymol/movie.py
+++ b/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):
diff --git a/modules/pymol/moving.py b/modules/pymol/moving.py
index 8c489c9e3..67c03eec2 100644
--- a/modules/pymol/moving.py
+++ b/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
diff --git a/modules/pymol/plugins/__init__.py b/modules/pymol/plugins/__init__.py
index 91772d764..23c236431 100644
--- a/modules/pymol/plugins/__init__.py
+++ b/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
diff --git a/modules/pymol/querying.py b/modules/pymol/querying.py
index 6750eaaf0..bf8b3eae2 100644
--- a/modules/pymol/querying.py
+++ b/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
diff --git a/modules/pymol/selecting.py b/modules/pymol/selecting.py
index 3be7b5f93..c8552aa69 100644
--- a/modules/pymol/selecting.py
+++ b/modules/pymol/selecting.py
@@ -11,6 +11,7 @@
#-*
#-*
#Z* -------------------------------------------------------------------
+from pymol.shortcut import Shortcut
if True:
@@ -18,7 +19,7 @@
cmd = __import__("sys").modules["pymol.cmd"]
- from .cmd import _cmd,Shortcut, \
+ from .cmd import _cmd, \
DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error
import pymol
diff --git a/modules/pymol/setting.py b/modules/pymol/setting.py
index 21ebba646..f6c36cc61 100644
--- a/modules/pymol/setting.py
+++ b/modules/pymol/setting.py
@@ -13,6 +13,9 @@
#Z* -------------------------------------------------------------------
# must match layer1/Setting.h
+from pymol.shortcut import Shortcut
+
+
cSetting_tuple = -1
cSetting_blank = 0
cSetting_boolean = 1
@@ -26,7 +29,6 @@
import traceback
from . import selector
- from .shortcut import Shortcut
cmd = __import__("sys").modules["pymol.cmd"]
from .cmd import _cmd,lock,lock_attempt,unlock,QuietException, \
is_string, \
diff --git a/modules/pymol/viewing.py b/modules/pymol/viewing.py
index a65970949..ba2f7dbc2 100644
--- a/modules/pymol/viewing.py
+++ b/modules/pymol/viewing.py
@@ -12,6 +12,7 @@
#-*
#Z* -------------------------------------------------------------------
+from pymol.shortcut import Shortcut
from . import colorprinting
if True:
@@ -25,7 +26,7 @@
import re
cmd = sys.modules["pymol.cmd"]
- from .cmd import _cmd, Shortcut, \
+ from .cmd import _cmd, \
_feedback,fb_module,fb_mask, \
repres,repres_sc, is_string, is_list, \
repmasks,repmasks_sc, \
diff --git a/modules/pymol/wizarding.py b/modules/pymol/wizarding.py
index bf707d48c..48512575e 100644
--- a/modules/pymol/wizarding.py
+++ b/modules/pymol/wizarding.py
@@ -17,7 +17,7 @@
import pymol
import sys
cmd = __import__("sys").modules["pymol.cmd"]
- from .cmd import _cmd,lock,unlock,Shortcut,QuietException,_raising, \
+ from .cmd import _cmd,lock,unlock,QuietException,_raising, \
_feedback,fb_module,fb_mask, \
DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error
From 5c63bea80319aedb145edfb8235cc18ea7165c64 Mon Sep 17 00:00:00 2001
From: ye11owSub <exactlythatguy@gmail.com>
Date: Sun, 5 Jan 2025 18:02:46 +0000
Subject: [PATCH 3/3] fixes after review
---
.github/workflows/build.yml | 3 -
modules/pymol/completing.py | 13 +--
modules/pymol/shortcut.py | 50 +++++++++---
pyproject.toml | 1 -
testing/tests/api/shortcut.py | 80 -------------------
.../tests/api}/test_shortcut.py | 0
6 files changed, 49 insertions(+), 98 deletions(-)
delete mode 100644 testing/tests/api/shortcut.py
rename {tests/pymol => testing/tests/api}/test_shortcut.py (100%)
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 8c4f43e0c..2abbf922b 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -50,7 +50,6 @@ jobs:
- name: Test
run: |
pymol -ckqy testing/testing.py --run all
- python -m pytest tests -vv
build-Windows:
@@ -100,7 +99,6 @@ jobs:
run: |
CALL %CONDA_ROOT%\\Scripts\\activate.bat
pymol -ckqy testing\\testing.py --run all
- python -m pytest tests -vv
build-MacOS:
@@ -137,4 +135,3 @@ jobs:
run: |-
export PATH="$CONDA_ROOT/bin:$PATH"
pymol -ckqy testing/testing.py --run all
- python -m pytest tests -vv
diff --git a/modules/pymol/completing.py b/modules/pymol/completing.py
index a9d525220..169006032 100644
--- a/modules/pymol/completing.py
+++ b/modules/pymol/completing.py
@@ -1,3 +1,5 @@
+from typing import Optional
+
from pymol.shortcut import Shortcut
cmd = __import__("sys").modules["pymol.cmd"]
@@ -7,14 +9,15 @@ class ExprShortcut(Shortcut):
Expression shortcut for iterate/alter/label with "s." prefix
setting autocompletion.
'''
- def interpret(self, keyword, mode=False):
+ def interpret(self, keyword: str, mode: bool = 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
+ v: Optional[int | str | list[str]] = cmd.setting.setting_sc.interpret(keyword[2:])
+
+ if isinstance(v, str) or isinstance(v, int):
+ return f"s.{v}"
if isinstance(v, list):
- return ['s.' + v for v in v]
+ return [f"s.{v}" for v in v]
return None
expr_sc = ExprShortcut([
diff --git a/modules/pymol/shortcut.py b/modules/pymol/shortcut.py
index 1f172a85d..f97e3272f 100644
--- a/modules/pymol/shortcut.py
+++ b/modules/pymol/shortcut.py
@@ -34,7 +34,7 @@ def __init__(
self.abbreviation_dict = defaultdict(list)
for keyword in self.keywords:
- self.optimize_symbols(keyword)
+ self._optimize_symbols(keyword)
self._rebuild_finalize()
@@ -48,20 +48,30 @@ def __delitem__(self, keyword: str) -> None:
self.keywords.remove(keyword)
self.rebuild()
- def make_abbreviation(self, s: str, groups_length: int) -> str:
+ def _make_abbreviation(self, s: str, groups_length: int) -> str:
"""
+ Creates an abbreviation for a string by shortening its components.
+ The abbreviation takes the first `groups_length`
+ characters of each part before the last component.
+
Example 1:
Input: s:'abc_def_ghig', groups_length: 1
Output: 'a_d_ghig'
+
Example 2:
Input: s:'abc_def', groups_length: 2
- Output: 'a_def'
+ Output: 'ab_def'
"""
groups = s.split("_")
groups[:-1] = [c[0:groups_length] for c in groups[:-1]]
return "_".join(groups)
- def optimize_symbols(self, keyword: str) -> None:
+ def _optimize_symbols(self, keyword: str) -> None:
+ """
+ Optimizes the given keyword by adding abbreviations and shortening
+ components. This method also builds a shortcut dictionary
+ for the keyword and its abbreviated forms.
+ """
for i in range(1, len(keyword)):
substr = keyword[0:i]
self.shortcut[substr] = 0 if substr in self.shortcut else keyword
@@ -70,7 +80,7 @@ def optimize_symbols(self, keyword: str) -> None:
return
for n in (1, 2):
- abbreviation = self.make_abbreviation(keyword, n)
+ abbreviation = self._make_abbreviation(keyword, n)
if keyword == abbreviation:
continue
@@ -81,7 +91,13 @@ def optimize_symbols(self, keyword: str) -> None:
sub = abbreviation[0:i]
self.shortcut[sub] = 0 if sub in self.shortcut else keyword
- def rebuild(self, keywords: Optional[Iterable] = None) -> None:
+ def rebuild(self, keywords: Optional[Iterable[str]] = None) -> None:
+ """
+ Rebuilds the shortcuts and abbreviation dictionaries
+ based on the provided list of keywords.
+ This method clears the existing shortcuts and optimizes symbols
+ for the new list of keywords.
+ """
keywords = list(keywords) if keywords is not None else []
self.keywords = (
[keyword for keyword in keywords if keyword[:1] != "_"]
@@ -92,11 +108,18 @@ def rebuild(self, keywords: Optional[Iterable] = None) -> None:
self.shortcut = {}
self.abbreviation_dict = defaultdict(list)
for keyword in self.keywords:
- self.optimize_symbols(keyword)
+ self._optimize_symbols(keyword)
self._rebuild_finalize()
def _rebuild_finalize(self) -> None:
+ """
+ Finalizes the rebuild process
+ by setting shortcuts for abbreviations and keywords.
+
+ This method ensures that each abbreviation points to a single keyword and that
+ each keyword has a shortcut.
+ """
for abbreviation, keywords in self.abbreviation_dict.items():
if len(keywords) == 1:
self.shortcut[abbreviation] = keywords[0]
@@ -140,14 +163,23 @@ def interpret(
else list(unique_keywords)
)
- def append(self, keyword) -> None:
+ def append(self, keyword: str) -> None:
+ """Adds a new keyword to the list and rebuilds the shortcuts."""
+
self.keywords.append(keyword)
- self.optimize_symbols(keyword)
+ self._optimize_symbols(keyword)
self._rebuild_finalize()
def auto_err(
self, keyword: str, descrip: Optional[str] = None
) -> Optional[int | str | list[str]]:
+ """
+ Automatically raises an error if a keyword is unknown or ambiguous.
+
+ This method checks if a keyword is valid, and if not,
+ raises a descriptive error with suggestions for possible matches.
+ """
+
if keyword == "":
return
diff --git a/pyproject.toml b/pyproject.toml
index f1f2dc117..fc0cfab43 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,7 +27,6 @@ requires = [
[project.optional-dependencies]
dev = [
- "numpy>=1.26.4,<2",
"pillow==10.3.0",
"pytest==8.2.2",
]
diff --git a/testing/tests/api/shortcut.py b/testing/tests/api/shortcut.py
deleted file mode 100644
index a1830b501..000000000
--- a/testing/tests/api/shortcut.py
+++ /dev/null
@@ -1,80 +0,0 @@
-import pymol
-from pymol import cmd, testing, stored
-
-foos = ['foo']
-ba_s = ['bar', 'baz']
-coms = ['com', 'com_bla', 'com_xxx']
-words = foos + ba_s + coms
-
-class TestShortcut(testing.PyMOLTestCase):
-
- def testShortcut(self):
- # build shortcut
- sc = cmd.Shortcut(words)
-
- # get all keywords
- self.assertItemsEqual(words, sc.interpret(''))
-
- # full/prefix hits
- self.assertEqual('foo', sc.interpret('f'))
- self.assertEqual('foo', sc.interpret('fo'))
- self.assertEqual('foo', sc.interpret('foo'))
-
- self.assertItemsEqual(ba_s, sc.interpret('b'))
- self.assertItemsEqual(ba_s, sc.interpret('ba'))
- self.assertEqual('bar', sc.interpret('bar'))
-
- self.assertItemsEqual(coms, sc.interpret('c'))
- self.assertItemsEqual(coms, sc.interpret('co'))
- self.assertEqual('com', sc.interpret('com'))
-
- # add one
- sc.append('foo_new')
- self.assertItemsEqual(['foo', 'foo_new'], sc.interpret('f'))
- self.assertEqual('foo', sc.interpret('foo'))
- self.assertEqual('foo_new', sc.interpret('foo_'))
-
- self.assertEqual(False, '' in sc)
-
-
- # abbreviations
- self.assertEqual('foo_new', sc.interpret('f_'))
- self.assertEqual('foo_new', sc.interpret('f_new'))
- self.assertEqual('foo_new', sc.interpret('fo_'))
- self.assertEqual('com_xxx', sc.interpret('c_x'))
- self.assertEqual('com_xxx', sc.interpret('c_xxx'))
- self.assertEqual('com_xxx', sc.interpret('co_x'))
-
- # missing key
- self.assertEqual(None, sc.interpret('missing_key'))
-
- # auto error
- self.assertEqual(None, sc.auto_err(''))
- self.assertEqual(None, sc.auto_err('missing_key'))
- self.assertItemsEqual(coms, sc.auto_err('co'))
- self.assertEqual('com', sc.auto_err('com'))
-
- def testShortcutMode1(self):
- # build shortcut
- sc = cmd.Shortcut(words)
-
- # full/prefix hits
- self.assertEqual('foo', sc.interpret('f', 1))
- self.assertItemsEqual(coms, sc.interpret('com', 1))
-
- # add one
- sc.append('foo_new')
- self.assertItemsEqual(['foo', 'foo_new'], sc.interpret('foo', 1))
-
- def testShortcutRebuild(self):
- sc = cmd.Shortcut(words)
- sc.rebuild(coms)
-
- self.assertEqual(None, sc.interpret('f'))
- self.assertEqual(None, sc.interpret('foo'))
-
- self.assertItemsEqual(coms, sc.interpret('c'))
- self.assertItemsEqual(coms, sc.interpret('com', 1))
- self.assertEqual('com', sc.interpret('com'))
- self.assertEqual('com_xxx', sc.interpret('c_x'))
-
diff --git a/tests/pymol/test_shortcut.py b/testing/tests/api/test_shortcut.py
similarity index 100%
rename from tests/pymol/test_shortcut.py
rename to testing/tests/api/test_shortcut.py