# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
packageData.py -- data about modules and packages, for PackageDependency.py
@author: Eric M, Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
# NFRs for packageDependency.py: @@@
# unrecognized modules should be classified as alone in a package,
# so they are very visible in the graph
# and so the arcs you see help you classify them properly.
# classification can be "layer|topic", e.g. "model|GAMESS",
# with options to use either or both parts (before/after the '|') as part of the package name;
# if no "|" then assume it's just the layer;
# the layers are what we have now (ui, model, etc)
# but note that in the current table [bruce 071217 2pm] I've also used ui/whatever in the layer
# in an experimental way re finer layer divisions.
#
# layer = general type of code;
# topic = topic of feature re user point of view (ie "which plugin it would be part of")
#
# interaction with colors: just use the layer in the color table, i think.
# (at least do that if the whole thing, layer|topic, is not listed there;
# might fall back to topic for color lookup if necessary)
#
# interaction with good/bad arcs (packageLevel): ideally we have a separate table of levels
# for layer and topic, and each one is a partial order or specific DAG.
# But for now, numerical scheme only makes sense for layer, not for topic, so just use layer for this.
# lower priority: warnings based on the "disallowed" tables below
"""
# disallowed names
# NIM: warn or enforce the non-use of the following names (case-insensitively?)
# We don't list every possible disallowed name,
# just the ones that we might be tempted to use otherwise.
#
# Note: on Mac, python import seems to be case-sensitive even though you can't
# have two filesystem-directory entries differing only by case.
#
# If we can rely
# on this, we can change the rules which use the names below to permit a package
# named opengl, even though OpenGL is an extension module.
# Unfortunately, we'd still have
# to rule out a toplevel package named Build, since build is a reserved
# directory name -- import might not be confused, but the code which wants
# to locally create and use the "build" subdirectory would be.
# Package names we can't use at the top level:
disallowedToplevelPackageNames = {
"build" : "temporary directory for compiling some .pyx files", # can this be renamed? (see setup*.py or extensions.py)
"ui" : "name of subdirectory for icons/images", # should be renamed, but hard to do
"main" : "reserved for main.py",
}
# Package names we can't use at any level:
disallowedPackageNames = {
"globals" : "python built-in function",
"global" : "python keyword",
"CVS" : "name of CVS control directory",
"scratch" : "our convention for a scratch-file directory",
"outtakes" : "our convention for an outtakes directory",
"experimental" : "our convention for an experimental-code directory",
"sim" : "import sim is reserved for sim.so/dll, even if it's missing",
"OpenGL" : "extension module",
"Numeric" : "extension module",
"Image" : "extension module",
"math" : "Python library module",
}
# Module names we can't use at the top level:
disallowedToplevelModuleNames = {
}
# Module names we can't use at any level:
# NOTE: It turns out we also can't use any toplevel package name
# as a module name. [bruce 080202]
disallowedModuleNames = {
"globals" : "python built-in function",
"global" : "python keyword",
"sim" : "import sim is reserved for sim.so/dll, even if it's missing",
"OpenGL" : "extension module",
"Numeric" : "extension module",
"Image" : "extension module",
"math" : "Python library module",
}
# ===
# status of packageMapping as of 071210:
# virtual packages named below but not yet listed above:
# "?" - unclassified [maybe none at present]
# "operation" - tentative, for ops on model, could be model or controller
# "tools"
# names of existing Python packages (in theory all should appear above)
# - appearing above: exprs, PM, utilities, model
# - not yet appearing above: startup, dna_model, dna_updater, gui
# modules listed below but no longer output at toplevel by AllPyFiles.sh:
# assembly - now in model/
# whatsthis - now in gui/
# plans for specific classifications:
# ne1 package, for overall layout of ne1, as opposed some other app made from same pieces incl ui pieces
# (eg a small app for testing or script-running)
# simulation or analysis package, subdirs for GROMACS, GAMESS, ND-1(?), general? runsim too. some io code not separated.
# replaces some "operations" classifications; essentially a type of ops and io combined.
# levels: sim over ops over model, but we expect arcs in all directions in there, for now.
# update, 071217 2pm:
# the layer|topic is only used in a few entries; the others are "layer" with topic mentioned in the comment.
# look for @@@ to see a few things to review, and the place i got to in my overall scan.
# when done i need to review all at once the "simulation", *mode*, "ui", and *dialog entries.
packageColors = { # needs geometry, platform, and whatever new classifications we add below
"ui" : "#8050ff",
"PM" : "#8070ff",
"graphics" : "#80a0ff",
"geometry" : "#8040ff",
"model" : "#80ff50",
"foundation" : "#80ff70",
"exprs" : "#80ffa0",
"commands" : "#80ff20",
"io" : "#ffff80",
"utilities" : "#ffa080",
"platform" : "#ffc080",
"prototype" : "#ffffff",
## "examples" : "#ff3030",
## "test" : "#ff3060",
"top_level" : "#ff3090",
"root" : "#ff3090",
"startup" : "#ff3090",
"top" : "#ff3090",
}
# ==
packageLevels = {
# plan: for each entry, review it, revise subclassifications. @@@
# put in basic topics like dna...
"top_level" : 7, # files that need to stay at top level for technical reasons (we'll put them at top of import graph)
"top" : 7, # files that need to stay at top level for technical reasons (we'll put them at top of import graph)
"root" : 7, # other files that belong at top of import graph (but that might be moved into subdirs)
"startup" : 7, # other files that belong at top of import graph (but that might be moved into subdirs)
## "test" : 7, ### none left!
## "examples" : 7, ### DEPRECATED as a layer, revise it (could be a topic but not sure if we have any yet) @@@
"ui" : 6, # has 137 instances - half the modules. (not counting new ones like command, unsplit_mode, simulation)
"commands" : 6,
"PM" : 6,
"io" : 5, #? hmm, so high?
"model" : 4, #k wants subdivision? not urgent...
"graphics" : 4,
"foundation" : 3,
"exprs" : 3,
"geometry" : 3,
"utilities" : 2,
"platform" : 1,
}
_levels_highest_first = [ # TODO: finish, then use this to compute the above; in future make it a general DAG (not urgent)
["top_level",
"root",
## "test",
## "examples",
],
["ui",
"PM",
],
["io",
],
# ... more
]
# ==
###doc these; anything with '?' is unfinalized; anything with '!' indicates an error in input
layer_aliases = {
# standardize to plural form
"graphics_behavior" : "graphics_behaviors",
"graphics_drawable" : "graphics_drawables",
"graphics_mode" : "graphics_modes",
"graphics_view" : "graphics_views", # should rename right here to graphics_display_styles
"graphics_widget" : "graphics_widgets",
"operation" : "operations",
"temporary_command" : "temporary_commands",
"widget" : "widgets",
}
topic_mapping = {
# default topics for layers
"graphics_behaviors": "graphics/behaviors",
"graphics_drawables": "graphics/drawables",
"graphics_drawing" : "graphics/drawing",
"graphics_images" : "graphics/images",
"graphics_io" : "graphics/io!", # deprecated, all to be refiled
"graphics_modes" : "graphics/modes!", # deprecated
"graphics_views" : "graphics/display_styles", ###
"graphics_widgets" : "graphics/widgets",
"ui/menu" : "ne1_ui/menus",
"ui/toolbar" : "ne1_ui/toolbars",
# layers which are deprecated when used directly for topics
"graphics" : "graphics!", # all have been refiled (I think)
"io" : "io!", # all have been refiled (I think)
"ui" : "ui!", # all have been refiled (I think)
"unsplit_mode" : "unsplit_mode!", # all have been refiled (I think)
# expand topic abbrevs into actual pathnames
"ESP" : "analysis/ESP", # refactoring: maybe io part (if more general) would be processes/NanoHive
"GAMESS" : "analysis/GAMESS",
"GROMACS" : "simulation/GROMACS",
"DnaSequenceEditor" : "dna/DnaSequenceEditor",
# add notes to certain topics -- for that see subdir_notes below
}
# ==
packageMapping_for_packages = {
# existing packages (in each case so far, all files now in them have the same fate)
# (in two cases, gui and startup, they should first just be renamed, then new files moved into them)
"dna_model" : "model|dna/model",
"dna_updater" : "model_updater|dna/updater", ###?? be consistent with what we do for other model_updater code
"exprs" : "exprs", # (someday will be refactored and split)
"gui" : "ui|ne1_ui", # along with other files (or into a whatsthis subpackage?)
"model" : "model", # along with other files
"PM" : "widgets|PM",
"startup" : "root|ne1_startup",
"utilities" : "utilities",
}
packageMapping_for_files = {
# files presently at toplevel (except for a few that are already moved)
# Note: of these modules, platform.py is in the way of proposed new package names,
# so it needs to be renamed, but it is listed here in the usual way.
# We also want to rename main.py -> ne1_main.py, but that's not urgent.
# For all other module renamings, we can wait a bit; see a wiki page about them.
"assembly" : "model", # (some foundation, but knows part.py which knows lots of ops & model constructors)
# (also: knows about selection, undo state, change counting, open file)
"Assembly_API" : "model_api|foundation", # since not legit to be used below foundation
"AtomGenerator" : "command|commands/BuildAtom",
"AtomGeneratorPropertyManager" : "ui/propmgr|commands/BuildAtom",
"atomtypes" : "model", # or chemistry?
"bonds" : "model", # Bond
"bonds_from_atoms" : "operation",
"bond_chains" : "operation",
"bond_constants" : "model",
"bond_drawer" : "graphics_drawing",
"bond_updater" : "model_updater",
"bond_utils" : "operation", # maybe also some ui
"BoundingBox" : "geometry", # mostly geometry, some graphics, some hardcoded distance constants from model
"BreakStrands_Command" : "command|dna/commands/BreakStrands", # plural BreakStrands to match featurename as of 080104
"BreakStrands_PropertyManager" : "ui/propmgr|dna/commands/BreakStrands",
"BuildAtomsPropertyManager" : "ui/propmgr|commands/BuildAtoms",
"BuildAtoms_Command" : "command|commands/BuildAtoms",
"BuildAtoms_GraphicsMode" : "graphics_mode|commands/BuildAtoms",
"BuildDna_EditCommand" : "command|dna/commands/BuildDna",
"BuildDna_GraphicsMode" : "graphics_mode|dna/commands/BuildDna",
"BuildDna_PropertyManager" : "ui/propmgr|dna/commands/BuildDna",
"build_utils" : "operation|commands/BuildAtoms", # AtomDepositionTool
"builtin_command_loaders" : "operations|commandSequencer",
"changedicts" : "foundation",
"changes" : "foundation",
"chem" : "model",
"chem_patterns" : "operation",
"chunk" : "model",
"ChunkProp" : "ui|commands/ChunkProperties?", #?? guess, probably wrong featurename
"ChunkPropDialog" : "ui|commands/ChunkProperties?",
"CommandToolbar_Constants" : "widget|commandToolbar", # see module docstring for why
"Command" : "command|command_support",
"CommandToolbar" : "widget|commandToolbar", # controls the main hierarchical toolbar
"CommandSequencer" : "operations|commandSequencer",
"Comment" : "model",
"CommentProp" : "ui/dialog|commands/CommentProperties?",
"CommentPropDialog" : "ui/dialog|commands/CommentProperties?",
"confirmation_corner" : "graphics_behavior",#? a MouseEventHandler; like a GraphicsMode or DragHandler; graphics_what?
"constants" : "utilities",
"CoNTubGenerator" : "command|commands/InsertHeterojunction",###?? @@@
"BuildCrystal_PropertyManager" : "ui|commands/BuildCrystal",
"BuildCrystal_Command" : "unsplit_mode|commands/BuildCrystal",
"BuildCrystal_PropertyManager" : "ui/propmgr|commands/BuildCrystal",
"CrystalShape" : "command|commands/BuildCrystal", # see docstring for reasons and caveats
"crossovers" : "operation|dna/operations",
"cursors" : "ui|ne1_ui",
"CylinderChunks" : "graphics_view", # a ChunkDisplayMode
"debug" : "utilities",
"DebugMenuMixin" : "ui|widgets", # standard debug menu, used by multiple widgets
"debug_prefs" : "utilities",
"depositMode" : "unsplit_mode|commands/BuildAtoms", # Build Atoms Command and GraphicsMode
"dimensions" : "graphics_drawing", # graphics output, not opengl-specific in principle
"DirectionArrow" : "graphics_drawable", # a kind of DragHandler (drawable with behavior)
"displaymodes" : "graphics_view", # ChunkDisplayMode
"DnaCylinderChunks" : "graphics_view", # a ChunkDisplayMode
"DnaDuplex" : "operation|dna/commands/BuildDuplex", # class to help construct model objects defined elsewhere
"DnaDuplex_EditCommand" : "command|dna/commands/BuildDuplex",
"DnaDuplexPropertyManager" : "ui/propmgr|dna/commands/BuildDuplex",
"DnaGenerator" : "command|dna/commands/BuildDuplex_old",
"DnaGeneratorPropertyManager" : "ui/propmgr|dna/commands/BuildDuplex_old",
"DnaGenHelper" : "operation|dna/commands/BuildDuplex_old",
"DnaLineMode" : "temporary_command|dna/temporary_commands", #?
"DnaSegment_EditCommand" : "command|dna/commands/DnaSegment",
"DnaSegment_GraphicsMode" : "graphics_mode|dna/commands/DnaSegment",
"DnaSegment_PropertyManager" : "ui/propmgr|dna/commands/DnaSegment",
"DnaSegment_ResizeHandle" : "graphics_drawable|dna/commands/DnaSegment", # [bruce 080207 reclassified to stay with command]
"DnaSequenceEditor" : "widget|DnaSequenceEditor", # a major ui component, and maybe a widget (guess, didn't look at code)
"DnaStrand_EditCommand" : "command|dna/commands/DnaStrand",
"DnaStrand_GraphicsMode" : "graphics_mode|dna/commands/DnaStrand",
"DnaStrand_PropertyManager" : "ui/propmgr|dna/commands/DnaStrand",
"DnaStrand_ResizeHandle" : "graphics_drawable|dna/commands/DnaStrand",
"Dna_Constants" : "model|dna/model", # (since used by lots of files in several dna-related commands)
"DragHandler" : "graphics_drawable",
"drawNanotubeLadder" : "graphics_drawing",
"drawDnaRibbons" : "graphics_drawing",
"drawDnaLadder" : "graphics_drawing",
"drawing_globals" : "graphics_drawing",
"glprefs" : "graphics_drawing",
"setup_draw" : "graphics_drawing",
"shape_vertices" : "graphics_drawing",
"ColorSorter" : "graphics_drawing",
"CS_workers" : "graphics_drawing",
"CS_ShapeList" : "graphics_drawing",
"CS_draw_primitives" : "graphics_drawing",
"drawers" : "graphics_drawing",
"draw_bond_vanes" : "graphics_drawing",
"draw_grid_lines" : "graphics_drawing",
"DynamicTip" : "graphics_widgets", # but some should be refactored into GraphicsMode
"EditCommand" : "command|command_support",
"EditCommand_PM" : "ui/propmgr|command_support",
"Elem" : "model", # chemistry?
"elementColors" : "ui/dialog|commands/ElementColors?",
"ElementColorsDialog" : "ui/dialog|commands/ElementColors?",
"elements" : "model", # class PeriodicTable, and our specific one??
"elementSelector" : "ui/dialog|commands/ElementSelector?",
"ElementSelectorDialog" : "ui/dialog|commands/ElementSelector?",
"elements_data" : "model", # model_data? like some constants?
"elements_data_PAM3" : "model|dna/model",
"elements_data_PAM5" : "model|dna/model",
"EndUser" : "utilities",
"env" : "foundation", # not utilities - only meant to be used from foundation or above
"ESPImage" : "model|ESP", # (but all ESPImage code should be refactored for more general images)
"ESPImageProp" : "ui/dialog|ESP", # question: is this a property manager? are ui/dialog and ui/propmgr the same?
"ESPImagePropDialog" : "ui/dialog|ESP",
"example_expr_command" : "command|prototype",
"ExecSubDir" : "top_level",
"extrudeMode" : "unsplit_mode|commands/Extrude",
"ExtrudePropertyManager" : "ui/propmgr|commands/Extrude",
"fileIO" : "graphics_io|graphics/rendering", # should be split into files_mdl and files_povray
"files_gms" : "io|GAMESS",
"files_mmp" : "io|files/mmp", # along with a sibling doc file, files_mmp_format_version.txt
"files_mmp_registration" : "foundation|files/mmp",
"files_mmp_writing" : "io|files/mmp",
"files_nh" : "io|ESP",
"files_pdb" : "io|files/pdb",
"Font3D" : "graphics_drawing",
"FuseChunks_Command" : "command|commands/Fuse",
"FuseChunks_GraphicsMode" : "graphics_mode|commands/Fuse",
"fusechunksMode" : "unsplit_mode|commands/Fuse",
"FusePropertyManager" : "ui/propmgr|commands/Fuse",
"GamessJob" : "operations|GAMESS", # contains operations and io
"GamessProp" : "ui|GAMESS",
"GamessPropDialog" : "ui|GAMESS",
"GeneratorBaseClass" : "ui/propmgr|command_support",
# or as itself, so import implications are clearer in package import graph?
# todo in code: split subclasses so this can be superceded by EditCommand and EditCommand_PM
"GeneratorController" : "ui/propmgr|command_support", # code type is a guess, but doesn't matter for now
"generator_button_images" : "ui/dialog|command_support",
"geometry" : "geometry",
"GlobalPreferences" : "utilities", #? - imports debug_prefs & prefs_constants, dubious for utilities; or constants??
"global_model_changedicts" : "model",
"GLPane" : "graphics_widgets",
"GLPane_minimal" : "graphics_widgets",
"glselect_name_dict" : "graphics_drawing", #bruce 080223; really an "OpenGL drawing utility"
"gpl_only" : "platform",
"GrapheneGenerator" : "command|commands/InsertGraphene",
"GrapheneGeneratorPropertyManager" : "ui/propmgr|commands/InsertGraphene",
"GraphicsMode" : "graphics_mode|command_support",
"GraphicsMode_API" : "ui_api|command_support", # not legit to be needed by anything below ui, i think
"GridPlaneProp" : "ui/dialog|commands/GridPlaneProperties?",
"GridPlanePropDialog" : "ui/dialog|commands/GridPlaneProperties?",
"GROMACS" : "io|GROMACS", #? - old demo code. runs a GROMACS process. contains io.
"Group" : "foundation", # some model code?
"GroupButtonMixin" : "PM", # (deprecated, and its only callers should use things from PM instead)
"GroupProp" : "ui/dialog|commands/GroupProperties?",
"GroupPropDialog" : "ui/dialog|commands/GroupProperties?",
"Guides" : "graphics_drawing", # drawing code for rulers
"handles" : "graphics_drawable", # graphical handles (for Extrude, but could be general)
"help" : "ui/dialog|ne1_ui/help",
"HelpDialog" : "ui/dialog|ne1_ui/help",
"HistoryWidget" : "ui|history", # the history subsystem (should be split into several files)
"icon_utilities" : "io|utilities", #? - could be considered utilities, io, or platform, or maybe images
"ImageUtils" : "graphics_images", # graphics_images? images? graphics? graphics_io? (only use of graphics_images)
"_import_roots" : "top_level",
"Initialize" : "utilities",
"inval" : "foundation",
"jigmakers_Mixin" : "operations", # tells Part how to create & edit various Jigs (some ui?)
"JigProp" : "ui/propmgr|command_support", # used directly for simple jigs, but clearest if treated as class
"JigPropDialog" : "ui/propmgr|command_support", # (and pkg name/loc should not look like a command name)
"jigs" : "model", # class Jig, and a few subclasses
"jigs_measurements" : "model",
"jigs_motors" : "model",
"jigs_planes" : "model",
"jig_Gamess" : "model|GAMESS",
"JobManager" : "ui|GAMESS", # ui/operations/io; scratch; needs refactoring; job_manager package?
# note: this is in GAMESS only due to an import cycle issue. It should be in processes or in its own toplevel package.
"JobManagerDialog" : "ui|GAMESS", # same package as JobManager (wrong now, see its note for why)
"JoinStrands_Command" : "command|dna/commands/JoinStrands",
"JoinStrands_PropertyManager" : "ui/propmgr|dna/commands/JoinStrands",
"Line" : "model",
"LinearMotor_EditCommand" : "command|commands/LinearMotorProperties?",
"LinearMotorPropertyManager" : "ui/propmgr|commands/LinearMotorProperties?",
"Line_Command" : "temporary_command", #?? a temporary command and gm... apparently can be used directly?
"main" : "top_level", # someday to be renamed to ne1_main
"master_model_updater" : "model_updater",
"mdldata" : "graphics_io|graphics/rendering/mdl",
"menu_helpers" : "widgets",
"MinimizeEnergyProp" : "ui/dialog|commands/MinimizeEnergy",
"MinimizeEnergyPropDialog" : "ui/dialog|commands/MinimizeEnergy",
"ModelTree" : "model|modelTree", # a model which implems the api class for modelTreeGui (rename modelTree.py to modelTree/ModelTree.py)
"modelTreeGui" : "widget|modelTree", # a widget with view & maybe some control code
"modes" : "unsplit_mode|command_support",
"MotorPropertyManager" : "ui/propmgr|command_support", # and rename to EditMotor_PM.py? but we don't have EditMotor.py ...
"Move_Command" : "command|commands/Move",
"Move_GraphicsMode" : "graphics_mode|commands/Move",
"MovePropertyManager" : "ui/propmgr|commands/Move",
"movie" : "simulation", #? hold simparams, or open moviefile - internal model, some ui/control/ops/io
"moviefile" : "io|files/dpb_trajectory",
"movieMode" : "unsplit_mode|commands/PlayMovie",
"MoviePropertyManager" : "ui/propmgr|commands/PlayMovie",
"MWsemantics" : "ui|ne1_ui",
"NamedView" : "model", # was Csys
"NanoHive" : "ui|ESP", # ui/control/ops for running ESP (etc?) calcs using NanoHive. ui for now.
"NanoHiveDialog" : "ui|ESP",
"NanoHiveUtils" : "?|ESP", # Mostly control & io code. Some model & ui code (via assy arg & assy.w).
"NanoHive_SimParameters" : "model|ESP",
"NE1ToolBar" : "widget", # Variant of QToolBar
"NE1_QToolBar" : "widget", # New main toolbar class for the NE1 main window.
"Node_as_MT_DND_Target" : "controller|modelTree",
"node_indices" : "foundation",
"NodeWithAtomContents" : "foundation",
"objectBrowse" : "utilities", # debug
"ops_atoms" : "operations",
"ops_connected" : "operations",
"ops_copy" : "operations", # parts may be foundation
"ops_files" : "operations", # also has some io
"ops_motion" : "operations",
"ops_rechunk" : "operations",
"ops_select" : "operations", # for a selection package??
"ops_view" : "operations", # for a view package???
"ops_display" : "operations",
"ops_modify" : "operations",
"op_select_doubly" : "operations",
"PanMode" : "temporary_command",
"ParameterDialog" : "widget|command_support", #?
"parse_utils" : "utilities",
"part" : "model", #? - foundation (if clipboard is), but knows lots of model & operations too
"PartLibPropertyManager" : "ui/propmgr|commands/PartLibrary",
"PartLibrary_Command" : "command|commands/PartLibrary",
"PartProp" : "ui/dialog|commands/PartProperties?",
"PartPropDialog" : "ui/dialog|commands/PartProperties?",
"pastables" : "operations", # supports pasting operations
"PasteFromClipboard_Command" : "command|commands/Paste",
"PastePropertyManager" : "ui/propmgr|commands/Paste",
"pi_bond_sp_chain" : "model",
"Plane" : "model",
"Plane_EditCommand" : "command|commands/PlaneProperties?",
"PlanePropertyManager" : "ui/propmgr|commands/PlaneProperties?",
"PlatformDependent" : "platform", # ok, but really it's a mix of platform, utilities, io.
"PlotTool" : "ui/dialog|commands/Plot?",
"PlotToolDialog" : "ui/dialog|commands/Plot?",
"Plugins" : "ui|processes", # ui, operations or utility, and io;
# relates to "external processes" - we might add a classification for that
"povheader" : "graphics_io|graphics/rendering/povray",
"povray" : "graphics_io|graphics/rendering/povray", # also has ui code
"PovrayScene" : "model", # for povray package, maybe
"PovraySceneProp" : "ui/dialog|commands/PovraySceneProperties?", # for povray package, maybe
"PovrayScenePropDialog" : "ui/dialog|commands/PovraySceneProperties?", # for povray package, maybe
"preferences" : "foundation", # see module docstring for explanation
"prefsTree" : "model", # see docstring for caveats
"prefs_constants" : "utilities", # or constants? see module docstring for explanation
"prefs_widgets" : "widgets", #? - might not work -- ### needs splitting, some goes in foundation
"Process" : "io|processes",
"ProteinChunks" : "graphics_view",
"PyrexSimulator" : "io|simulation",
"qt4transition" : "utilities",
"qutemol" : "graphics_io|graphics/rendering/qutemol",
"QuteMolPropertyManager" : "ui/propmgr|commands/QuteMol?", # commandname? (or, for a qutemol package??)
# it's a single-file Command, View->QuteMol, with a launch (external renderer) button and maybe some options...
# but what is the VerbNoun form? Does it have a featurename now? Wiki & whatsthis say Feature:QuteMol, so I went with that.
"ReferenceGeometry" : "model",
"reposition_baggage" : "operations",
"ResizeHandle" : "graphics_drawable", # (a DragHandler)
"RotaryMotor_EditCommand" : "command|commands/RotaryMotorProperties?", ###?? to fit VerbNoun, and not conflict with model class @@@
"RotaryMotorPropertyManager" : "ui/propmgr|commands/RotaryMotorProperties?",
"RotateMode" : "temporary_command",
"RotationHandle" : "graphics_drawable",#? needs reclassification?
"runSim" : "simulation", # includes perhaps ui, controller, io
"SelectAtoms_Command" : "command|commands/SelectAtoms", # even though only used as a superclass now
"SelectAtoms_GraphicsMode" : "graphics_mode|commands/SelectAtoms",
"SelectChunks_Command" : "command|commands/SelectChunks", # used directly, as well as as a superclass
"SelectChunks_GraphicsMode" : "graphics_mode|commands/SelectChunks",
"SelectChunks_GraphicsMode" : "unsplit_mode|commands/SelectChunks",
"Select_Command" : "command|commands/Select",
"Select_GraphicsMode" : "graphics_mode|commands/Select",
"Select_GraphicsMode_DrawMethod_preMixin" : "graphics_mode|commands/Select",
"Select_GraphicsMode_MouseHelpers_preMixin" : "graphics_mode|commands/Select",
"selectMode" : "unsplit_mode|commands/Select",
"Selobj" : "graphics_drawable", #bruce 080116/080202 revised this (would be _api if we had that)
"ServerManager" : "ui|processes", #? specific to GAMESS? maybe, but shouldn't. persistent db/UI for servers list
"ServerManagerDialog" : "ui|processes",
"shape" : "graphics_behavior", # tentative, maybe risky; see docstring
"Slab" : "geometry",
"SimJob" : "model|simulation", #? only subclass is GamessJob; unclear whether specific to GAMESS; io too
"SimServer" : "model|simulation", # hold attrs for a sim server (unclear whether specific to GAMESS); io too
"SimSetup" : "ui|simulation",
"SimSetupDialog" : "ui|simulation",
"Sponsors" : "ui|sponsors", # the Sponsors subsystem (lots of kinds of code; exports widgets)
"state_constants" : "foundation",
"state_utils" : "foundation", # note: utilities/Comparison.py and samevals.c might go with this too
"StatProp" : "ui/dialog|commands/ThermostatProperties?",
"StatPropDialog" : "ui/dialog|commands/ThermostatProperties?",
"StatusBar" : "widget", # used as a specific part of the NE1 main window, but general-purpose code
"SurfaceChunks" : "graphics_view",
"TemporaryCommand" : "temporary_commands", # or command_support??
"testdraw" : "graphics_mode|exprs", # (mostly prototype, but also has some exprs framework code)
"testmode" : "unsplit_mode|exprs", # (ditto)
"test_commands" : "command|prototype",
"test_commands_init" : "command|prototype",
"test_command_PMs" : "ui/propmgr|prototype",
"test_connectWithState" : "command|prototype",
"test_connectWithState_constants" : "command|prototype",
"test_connectWithState_PM" : "ui/propmgr|prototype",
"texture_fonts" : "graphics_drawing",
"texture_helpers" : "graphics_drawing", #? also graphics_io - split it?
"ThermoProp" : "ui/dialog|commands/ThermometerProperties?",
"ThermoPropDialog" : "ui/dialog|commands/ThermometerProperties?",
"ThumbView" : "graphics_widgets",
"Trackball" : "graphics_behavior",
"TranslateChunks_Command" : "command|commands/Translate",
"TranslateChunks_GraphicsMode" : "graphics_mode|commands/Translate",
"RotateChunks_Command" : "command|commands/Rotate",
"RotateChunks_GraphicsMode" : "graphics_mode|commands/Rotate",
# Note: many of the following (and of the other modules slated for ne1_ui)
# ought to get refactored, with some parts not remaining in ne1_ui.
# Also, some of them might be best off in specific subpackages of ne1_ui,
# but I'm not yet trying to classify anything in ne1_ui that finely,
# partly since some of them need too much refactoring for that
# to make sense just yet, and partly since I don't know them well,
# and Mark is presently doing some refactoring within them.
# The only exception is ne1_ui/help, which may not be complete,
# but seems obvious enough and worth doing.
# [bruce 080101]
"Ui_BuildAtomsPropertyManager" : "ui/propmgr|commands/BuildAtoms",
"Ui_BuildStructuresMenu" : "ui/menu",
"Ui_BuildStructuresToolBar" : "ui/toolbar",
"Ui_BuildToolsMenu" : "ui/menu",
"Ui_BuildToolsToolBar" : "ui/toolbar",
"Ui_CommandToolbar" : "ui/toolbar|ne1_ui/toolbars", # UI and content/layout for Command Toolbar
"Ui_BuildCrystal_PropertyManager" : "ui/propmgr|commands/BuildCrystal",
"Ui_DimensionsMenu" : "ui/menu",#?
"Ui_DisplayStylesToolBar" : "ui/toolbar|ne1_ui/toolbars",
"Ui_NanotubeFlyout" : "ui/toolbar|ne1_ui/toolbars", # I'm guessing this has to be in ne1_ui, not dna
"Ui_DnaFlyout" : "ui/toolbar|ne1_ui/toolbars", # I'm guessing this has to be in ne1_ui, not dna
"Ui_EditMenu" : "ui/menu",
"Ui_ExtrudePropertyManager" : "ui/propmgr|commands/Extrude",
"Ui_FileMenu" : "ui/menu",
"Ui_HelpMenu" : "ui/menu|ne1_ui/help", #??? ne1_ui/menus?
"Ui_InsertMenu" : "ui/menu",
"Ui_MainWindow" : "ui|ne1_ui",
"Ui_MainWindowWidgets" : "ui|ne1_ui",
"Ui_MainWindowWidgetConnections" : "ui|ne1_ui",
"Ui_MovePropertyManager" : "ui/propmgr|commands/Move",
"Ui_MoviePropertyManager" : "ui/propmgr|commands/PlayMovie",
"Ui_PartWindow" : "widget|ne1_ui", #?
"Ui_RenderingMenu" : "ui/menu",
"Ui_RenderingToolBar" : "ui/toolbar",
"Ui_ReportsDockWidget" : "widget|ne1_ui",
"Ui_SelectMenu" : "ui/menu",
"Ui_SelectToolBar" : "ui/toolbar",
"Ui_DnaSequenceEditor" : "widget|DnaSequenceEditor", # in dna/ ??
"Ui_SimulationMenu" : "ui/menu",
"Ui_SimulationToolBar" : "ui/toolbar",
"Ui_StandardToolBar" : "ui/toolbar",
"Ui_StandardViewsToolBar" : "ui/toolbar",
"Ui_ToolsMenu" : "ui/menu",
"Ui_ViewMenu" : "ui/menu",
"Ui_ViewOrientation" : "ui|ne1_ui",
"Ui_ViewToolBar" : "ui/toolbar",
"undo_internals" : "foundation",
"undo_archive" : "foundation",
"undo_manager" : "foundation",
"undo_UI" : "operations", # or operations/undo?
"UserPrefs" : "ui|ne1_ui",
"UserPrefsDialog" : "ui|ne1_ui",
"Utility" : "foundation", # some model code?
"version" : "utilities", # or constants? see docstring for caveats
"ViewOrientationWindow" : "widget|ne1_ui",
"VQT" : "geometry",
"whatsthis_utilities" : "foundation", #? or utilities?
# (imports of this file are foundation or above)
# this file imports env (for win; could be refactored to not do so, eg use an arg), nothing else high up.
"widget_helpers" : "widgets", # soon to be renamed to this from widgets.py
"widget_controllers" : "widgets",
"wiki_help" : "ui|foundation", # mostly ui, some io.
# conclusion, bruce 080101: if we have a help module outside ne1_ui, put it there;
# if we don't, it probably belongs in something like foundation.
# (Note: if we want a toplevel help package, we'd need to rename help.py first.
# Guess: for now just put this into foundation; probably "help" makes more sense
# as a subpackage of foundation than as something independent and toplevel, anyway.)
"ZoomToAreaMode" : "temporary_command",
"ZoomInOutMode" : "temporary_command",
}
# ==
# now combine those into one dict for use by current code in packageDependency.py
for package_name in packageMapping_for_packages.keys():
assert not packageMapping_for_files.has_key( package_name)
packageMapping = dict( packageMapping_for_files)
packageMapping.update( packageMapping_for_packages)
packageGroupMapping = {
"analysis.ESP" : "model",
"analysis.GAMESS" : "model",
"cnt.commands.BuildNanotube" : "commands",
"cnt.commands.NanotubeSegment" : "commands",
"cnt.commands.InsertNanotube" : "commands",
"cnt.model" : "model",
"cnt.temporary_commands" : "commands",
"cnt.updater" : "model",
"commands.BuildAtom" : "commands",
"commands.BuildAtoms" : "commands",
"commands.BuildCrystal" : "commands",
"commands.ChunkProperties" : "commands",
"commands.CommentProperties" : "commands",
"commands.ElementColors" : "commands",
"commands.ElementSelector" : "commands",
"commandSequencer" : "commands",
"commands.Extrude" : "commands",
"commands.Fuse" : "commands",
"commands.GridPlaneProperties" : "commands",
"commands.GroupProperties" : "commands",
"commands.InsertGraphene" : "commands",
"commands.InsertHeterojunction" : "commands",
"commands.InsertNanotube" : "commands",
"commands.InsertPeptide" : "commands",
"commands.LinearMotorProperties" : "commands",
"commands.MinimizeEnergy" : "commands",
"commands.Move" : "commands",
"commands.PartLibrary" : "commands",
"commands.PartProperties" : "commands",
"commands.Paste" : "commands",
"commands.PlaneProperties" : "commands",
"commands.PlayMovie" : "commands",
"commands.Plot" : "commands",
"commands.PovraySceneProperties" : "commands",
"commands.QuteMol" : "commands",
"commands.RotaryMotorProperties" : "commands",
"commands.Rotate" : "commands",
"commands.SelectAtoms" : "commands",
"commands.SelectChunks" : "commands",
"commands.Select" : "commands",
"commands.ThermometerProperties" : "commands",
"commands.ThermostatProperties" : "commands",
"commands.Translate" : "commands",
"command_support" : "commands",
"commandToolbar" : "commands",
"dna.commands.BreakStrands" : "commands",
"dna.commands.BuildDna" : "commands",
"dna.commands.BuildDuplex" : "commands",
"dna.commands.BuildDuplex_old" : "commands",
"dna.commands.DnaSegment" : "commands",
"dna.commands.DnaStrand" : "commands",
"dna.commands.JoinStrands" : "commands",
"dna.DnaSequenceEditor" : "ui",
"dna.model" : "model",
"dna.operations" : "model",
"dna.temporary_commands" : "commands",
"dna.updater" : "model",
"exprs" : "exprs",
"files.dpb_trajectory" : "io",
"files.mmp" : "io",
"files.pdb" : "io",
"foundation" : "foundation",
"geometry" : "geometry",
"graphics.behaviors" : "graphics",
"graphics.display_styles" : "graphics",
"graphics.drawables" : "graphics",
"graphics.drawing" : "graphics",
"graphics.images" : "graphics",
"graphics.rendering" : "graphics",
"graphics.rendering.mdl" : "graphics",
"graphics.rendering.povray" : "graphics",
"graphics.rendering.qutemol" : "graphics",
"graphics.widgets" : "graphics",
"history" : "utilities",
"modelTree" : "ui",
"model_updater" : "model",
"ne1_startup" : "startup",
"ne1_ui.help" : "ui",
"ne1_ui.menus" : "ui",
"ne1_ui" : "ui",
"ne1_ui.toolbars" : "ui",
"operations" : "model",
"platform" : "platform",
"PM" : "ui",
"processes" : "ui",
"simulation.GROMACS" : "io",
"simulation" : "io",
"sponsors" : "ui",
"temporary_commands" : "commands",
"widgets" : "ui",
}
# ==
# these definitions are to make the listing done by packageData_checker more informative.
# lists of highly desirable renamings and/or refactorings, needed for understandability of classification
needs_renaming_for_clarity = { # just suggestions, not yet discussed/decided
"bond_utils" : "bond_menu_helpers",
"cursors" : "load_custom_cursors?",
"fileIO" : "povray/files_povray and mdl/files_mdl (split it)", # also needs_refactoring
"GROMACS" : "GROMACS_demo?", # temporary demo of atomic-level-DNA GROMACS simulation (maybe for outtakes?)
"help" : "Ne1HelpDialog or HelpDialog",
"HelpDialog" : "Ui_HelpDialog",
"Line" : "ReferenceLine?", # Line should be reserved for pure geometry
"main" : "ne1_main (hard, not urgent)",
"movie" : "what?", # it's an object for a set of sim params, and optionally the results file made by using them
"moviefile" : "files_dpb?",
"Plane" : "ReferencePlane?", # Plane should be reserved for pure geometry
"platform" : "debug_flags",
"Selobj" : "Selobj_API for now", # not urgent; not the correct new name
"shape" : "what?", # also needs_refactoring
"StatProp" : "ThermostatProperties?", # disambiguate Thermometer and Thermostat
"ThermoProp" : "ThermometerProperties?", # disambiguate Thermometer and Thermostat
"Utility" : "Node",
"qutemol" : "qutemol_io?",
# deprecated files
"GroupButtonMixin" : "GroupButtonMixin_deprecated?",
## # kluge: use fake renamings to add notes for the listing
## "JobManager" : "(should be processes or own package -- import cycle issue)",
## "JobManagerDialog" : "(should stay with JobManager)",
}
needs_refactoring = [
"fileIO", # needs splitting in two, each part renamed; exports writepovfile, writemdlfile
"GLPane", # needs splitting into several classes, some for general use and some for "main graphics area"
# (also needs to not be the same object as the CommandSequencer)
"HistoryWidget", # needs split into a few cooperating objects (archive, widget, io, storage ops)
"JobManager", # import cycle issue - GamessJob used in two places: value in jobType, constructor in __createJobs
"PlatformDependent", # needs split
"prefs_widgets", # needs connectWithState stuff (and more?) split out into foundation
"shape", # needs splitting
"version", # split/register: ne1_ui part to supply data, foundation part for access
]
# listing order for toplevel packages, outer to inner
# (will be related to permitted import order, when that's implemented, but not equal to it, e.g. "less important later")
# (a string here matches itself, or itself + " " + anything, to permit added notes in topic_mapping)
# (nfr: permit inserted note strings to be printed before sets of toplevel dirs?)
listing_order = [ ### should be complete, but not yet properly ordered
"ne1_startup",
"ne1_ui",
# commands
"command_support",
"commands",
"temporary_commands",
# major subsystems (order?)
"history",
"modelTree",
"commandSequencer",
"commandToolbar",
"sponsors",
# functional areas
"dna",
"simulation",
"analysis",
# kinds of operations
"model_updater",
"operations",
# other kinds of code (order?)
"model",
"graphics",
"widgets",
"processes",
"files",
"PM",
"exprs",
"foundation",
"geometry",
"platform",
"utilities",
# special kinds
"top_level",
"prototype",
]
# notes for specific subdirs, to include in the listing (with word-wrapping)
subdir_notes = {
"analysis/GAMESS" : "JobManager doesn't belong here, but is here for now "\
"to work around an import cycle issue. Probably easy to fix "\
"when it matters.",
"commands" : "command package names ending with '?' need discussion",
"files" : "should we de-abbreviate file extensions used in directory names, "\
"e.g. ProteinDataBank, MolecularMachinePart, DifferentialPositionBytes? [-- EricM]",
"graphics/rendering" : "(this is only about rendering by external programs; rename it?)",
"ne1_ui" : "could define more (or fewer, or different) subpackages if desired",
"ne1_ui/help" : "(not sure about Ui_HelpMenu being in here)",
"PM" : "should PM be renamed to PropertyManager? [-- EricM]",
"top_level" : "(these files can't presently be moved into subdirectories, for technical reasons)",
}
# ==
# some topics above:
# todo: review:
# - processes
# - io
# eg povray
# - simulation
# - exprs/prototype
# - prototype
# end