jssm 5.44.0 → 5.46.0

package/src/ts/jssm_types.ts

@@ -1,346 +0,0 @@
-
-type StateType = string;
-
-
-
-
-
-type JssmSuccess        = { success: true };
-type JssmFailure        = { success: false, error: any };
-type JssmIncomplete     = { success: 'incomplete' };
-type JssmResult         = JssmSuccess | JssmFailure | JssmIncomplete;
-
-type JssmColor          = string;  // TODO FIXME constrain to #RRGGBBAA later // whargarbl
-
-
-
-type JssmPermitted      = 'required' | 'disallowed';
-type JssmPermittedOpt   = 'required' | 'disallowed' | 'optional';
-
-type JssmArrow          = '->' | '<-' | '<->' | '<=->' | '<~->'
-                        | '=>' | '<=' | '<=>' | '<-=>' | '<~=>'
-                        | '~>' | '<~' | '<~>' | '<-~>' | '<=~>';
-                        // | '⇒'  | '⇐'  | '⇔'  | '⇐→' | '↚→'
-                        // | '→'  | '←'  | '↔'  | '←⇒' | '↚⇒'
-                        // | '↛'  | '↚'  | '↮'  | '←↛' | '⇐↛';
-
-// TODO finish the arrow types - unicode *and* mixed
-
-type JssmShape          = "box" | "polygon" | "ellipse" | "oval" | "circle" | "point" | "egg" | "triangle"
-                        | "plaintext" | "plain" | "diamond" | "trapezium" | "parallelogram" | "house" | "pentagon"
-                        | "hexagon" | "septagon" | "octagon" | "doublecircle" | "doubleoctagon" | "tripleoctagon"
-                        | "invtriangle" | "invtrapezium" | "invhouse" | "Mdiamond" | "Msquare" | "Mcircle" | "rect"
-                        | "rectangle" | "square" | "star" | "none" | "underline" | "cylinder" | "note" | "tab"
-                        | "folder" | "box3d" | "component" | "promoter" | "cds" | "terminator" | "utr" | "primersite"
-                        | "restrictionsite" | "fivepoverhang" | "threepoverhang" | "noverhang" | "assembly"
-                        | "signature" | "insulator" | "ribosite" | "rnastab" | "proteasesite" | "proteinstab"
-                        | "rpromoter" | "rarrow" | "larrow" | "lpromoter" | "record";
-
-type JssmArrowDirection = 'left' | 'right' | 'both';
-type JssmArrowKind      = 'none' | 'legal' | 'main' | 'forced';
-
-type JssmLayout         = 'dot' | 'circo' | 'twopi' | 'fdp';  // todo add the rest
-
-type JssmCorner         = 'regular' | 'rounded' | 'lined';
-type JssmLineStyle      = 'solid' | 'dashed' | 'dotted';
-
-
-
-
-
-type FslDirection       = 'up' | 'right' | 'down' | 'left';
-type FslTheme           = 'default' | 'ocean' | 'modern' | 'none';
-
-
-
-
-
-type State = string;
-
-
-
-
-
-type JssmTransitionPermitter<DataType> =
-  (OldState: StateType, NewState: StateType, OldData: DataType, NewData: DataType) => boolean;
-
-type JssmTransitionPermitterMaybeArray<DataType> =
-    JssmTransitionPermitter<DataType>
-  | Array< JssmTransitionPermitter<DataType> >;
-
-
-
-
-
-type JssmTransition<DataType> = {
-
-  from         : StateType,
-  to           : StateType,
-  name?        : string,
-  action?      : StateType,
-  check?       : JssmTransitionPermitterMaybeArray<DataType>,  // validate this edge's transition; usually about data
-  probability? : number,                                       // for stoch modelling, would like to constrain to [0..1], dunno how // TODO FIXME
-  kind         : JssmArrowKind,
-  forced_only  : boolean,
-  main_path    : boolean
-
-};
-
-type JssmTransitions<DataType> =
-  Array< JssmTransition<DataType> >;
-
-type JssmTransitionList = {
-  entrances : Array<StateType>,
-  exits     : Array<StateType>
-};
-
-type JssmTransitionCycle = {
-  key   : 'cycle',
-  value : StateType
-};
-
-type JssmTransitionRule =
-  StateType
-| JssmTransitionCycle;
-
-
-
-
-
-type JssmGenericState = {
-
-  from     : Array< StateType > ,
-  name     :        StateType   ,
-  to       : Array< StateType > ,
-  complete : boolean
-
-};
-
-
-
-
-
-type JssmMachineInternalState<DataType> = {
-
-  internal_state_impl_version : 1,
-
-  state                       : StateType,
-  states                      : Map< StateType, JssmGenericState >,
-  named_transitions           : Map< StateType, number >,
-  edge_map                    : Map< StateType, Map<StateType, number> >,
-  actions                     : Map< StateType, Map<StateType, number> >,
-  reverse_actions             : Map< StateType, Map<StateType, number> >,
-  edges                       : Array< JssmTransition<DataType> >
-
-};
-
-
-
-
-
-type JssmStatePermitter<DataType> =
-  (OldState: StateType, NewState: StateType, OldData: DataType, NewData: DataType) => boolean;
-
-type JssmStatePermitterMaybeArray<DataType> =
-  JssmStatePermitter<DataType> | Array< JssmStatePermitter<DataType> >;
-
-type JssmGenericMachine<DataType> = {
-
-  name?            : string,
-  state            : StateType,
-  data?            : DataType,
-  nodes?           : Array<StateType>,
-  transitions      : JssmTransitions<DataType>,
-  check?           : JssmStatePermitterMaybeArray<DataType>,
-
-  min_transitions? : number,
-  max_transitions? : number,
-
-  allow_empty?     : boolean,
-  allow_islands?   : boolean,
-  allow_force?     : boolean,
-
-  keep_history?    : boolean | number
-
-};
-
-
-
-
-
-type JssmStateDeclarationRule = {
-  key   : string,
-  value : any  // TODO FIXME COMEBACK enumerate types against concrete keys
-};
-
-type JssmStateDeclaration = {
-
-  declarations     : Array<JssmStateDeclarationRule>,
-
-  shape?           : JssmShape,
-  color?           : JssmColor,
-  corners?         : JssmCorner,
-  linestyle?       : JssmLineStyle,
-
-  textColor?       : JssmColor,
-  backgroundColor? : JssmColor,
-  borderColor?     : JssmColor,
-
-  state            : StateType
-
-};
-
-
-
-
-
-type JssmGenericConfig<DataType> = {
-
-  graph_layout?              : JssmLayout,
-
-  complete?                  : Array<StateType>,
-  transitions                : JssmTransitions<DataType>,
-
-  theme?                     : FslTheme,
-  flow?                      : FslDirection,
-
-  name?                      : string,
-  data?                      : DataType,
-  nodes?                     : Array<StateType>,  // uncommon
-  check?                     : JssmStatePermitterMaybeArray<DataType>,
-
-//locked?                    : bool = true,
-  min_exits?                 : number,
-  max_exits?                 : number,
-  allow_islands?             : false,
-  allow_force?               : false,
-  actions?                   : JssmPermittedOpt,
-
-  simplify_bidi?             : boolean,
-
-  dot_preamble?              : string,
-
-  start_states               : Array<StateType>,
-  end_states?                : Array<StateType>,
-
-  state_declaration?         : Array<Object>,
-
-  arrange_declaration?       : Array<Array<StateType>>,
-  arrange_start_declaration? : Array<Array<StateType>>,
-  arrange_end_declaration?   : Array<Array<StateType>>,
-
-  machine_author?            : string | Array<string>,
-  machine_comment?           : string,
-  machine_contributor?       : string | Array<string>,
-  machine_definition?        : string,
-  machine_language?          : string,   // TODO FIXME COMEBACK
-  machine_license?           : string,   // TODO FIXME COMEBACK
-  machine_name?              : string,
-  machine_version?           : string,   // TODO FIXME COMEBACK
-
-  fsl_version?               : string,   // TODO FIXME COMEBACK
-
-  auto_api?                  : boolean | string  // TODO FIXME COMEBACK // boolean false means don't; boolean true means do; string means do-with-this-prefix
-
-};
-
-
-
-
-
-type JssmCompileRule = {
-
-  agg_as : string,
-  val    : any      // TODO COMEBACK FIXME
-
-};
-
-
-
-
-
-type JssmCompileSe = {
-
-  to            : StateType,
-  se            : JssmCompileSe,
-  kind          : JssmArrow,
-  l_action?     : StateType,
-  r_action?     : StateType,
-  l_probability : number,
-  r_probability : number
-
-};
-
-
-
-
-
-type JssmCompileSeStart<DataType> = {
-
-  from   : DataType,
-  se     : JssmCompileSe,
-  key    : string,
-  value? : string | number,
-  name?  : string
-
-};
-
-
-
-
-
-type JssmParseTree =
-
-  Array< JssmCompileSeStart<StateType> >;
-
-
-
-
-
-type JssmParseFunctionType =
-
-  (string) => JssmParseTree;
-
-
-
-
-
-export {
-
-  JssmColor,
-
-  JssmTransition,
-    JssmTransitions,
-    JssmTransitionList,
-    JssmTransitionRule,
-
-  JssmArrow,
-    JssmArrowKind,
-    JssmArrowDirection,
-
-  JssmGenericConfig,
-    JssmGenericState,
-    JssmGenericMachine,
-
-  JssmParseTree,
-    JssmCompileSe,
-    JssmCompileSeStart,
-    JssmCompileRule,
-
-  JssmPermitted,
-    JssmPermittedOpt,
-    JssmResult,
-
-  JssmStateDeclaration,
-    JssmStateDeclarationRule,
-
-  JssmLayout,
-
-  JssmParseFunctionType,
-
-  JssmMachineInternalState,
-
-  FslDirection,
-    FslTheme
-
-};

package/src/ts/jssm_util.ts

@@ -1,100 +0,0 @@
-
-function arr_uniq_p<T>(el: T, i: number, source: T[]): boolean {
-  return source.indexOf(el) === i;
-}
-
-
-
-
-
-const array_box_if_string = n =>
-  typeof n === 'string'? [n] : n;
-
-
-
-
-
-// this is explicitly about other peoples' data, so it has to be weakly typed
-/* eslint-disable flowtype/no-weak-types */
-const weighted_rand_select: Function = (options: Array<any>, probability_property: string = 'probability'): any => {
-
-  if (!Array.isArray(options)) {
-    throw new TypeError('options must be a non-empty array of objects');
-  }
-
-  if (!(typeof options[0] === 'object')) {
-    throw new TypeError('options must be a non-empty array of objects');
-  }
-
-  const frand      : Function = (cap): number => Math.random() * cap,
-        or_one     : Function = (item): any   => item === undefined? 1 : item,
-        prob_sum   : number   = options.reduce( (acc, val:any): number => acc + or_one(val[probability_property]), 0 ),
-        rnd        : number   = frand(prob_sum);
-
-  let   cursor     : number   = 0,
-        cursor_sum : number   = 0;
-
-  while ((cursor_sum += or_one(options[cursor++][probability_property])) <= rnd) { } // eslint-disable-line no-empty,fp/no-loops
-  return options[cursor-1];
-
-};
-/* eslint-enable flowtype/no-weak-types */
-
-
-
-
-
-const seq: Function = (n: number): Array<number> =>
-
-    (new Array(n)).fill(true)
-                  .map( (_, i): number => i );
-
-
-
-
-
-const histograph: Function = (ar : Array<any>): Map<any, number> => // eslint-disable-line flowtype/no-weak-types
-
-    ar.sort()
-      .reduce(
-        (m,v): Map<any, any> =>    // TODO FIXME eslint-disable-line flowtype/no-weak-types,no-sequences
-          ( m.set(v, (m.has(v)? m.get(v)+1 : 1)) , m),
-          new Map()
-      );
-
-
-
-
-
-const weighted_sample_select: Function = (n: number, options: Array<any>, probability_property: string): Array<any> => // TODO FIXME no any // eslint-disable-line flowtype/no-weak-types
-
-    seq(n)
-      .map( (_i): any =>   // TODO FIXME eslint-disable-line flowtype/no-weak-types
-        weighted_rand_select(options, probability_property)
-      );
-
-
-
-
-
-const weighted_histo_key: Function = (n: number, opts: Array<any>, prob_prop: string, extract: string): Array<any> => // TODO FIXME no any // eslint-disable-line flowtype/no-weak-types
-
-    histograph(
-      weighted_sample_select(n, opts, prob_prop)
-        .map(
-          (s): any => s[extract]     // TODO FIXME eslint-disable-line flowtype/no-weak-types
-        )
-    );
-
-
-
-
-
-export {
-  seq,
-  arr_uniq_p,
-  histograph, weighted_histo_key,
-  weighted_rand_select, weighted_sample_select,
-  array_box_if_string
-};
-

package/src/ts/tests/actions.spec.ts

@@ -1,167 +0,0 @@
-
-/* eslint-disable max-len */
-
-import * as jssm from '../jssm';
-
-
-
-
-
-describe('Reports on actions', () => {
-
-  const roa_machine = new jssm.Machine({
-    start_states : ['off'],
-    transitions  : [
-      { name: 'turn_on', action: 'power_on', from: 'off', to: 'red', kind: 'legal', forced_only: false, main_path: false }
-    ]
-  });
-
-  const roa_la = roa_machine.list_actions();  // todo comeback
-
-  test('Actions that it has', () =>
-    expect( typeof roa_machine.current_action_for('power_on') )
-      .toBe('number') );
-
-  test('Actions that it doesn\'t have', () =>
-    expect( typeof roa_machine.current_action_for('power_left') )
-      .toBe('undefined') );
-
-  test('Correct list type', () =>
-    expect( Array.isArray(roa_la) )
-      .toBe(true) );
-
-  test('Correct list size', () =>
-    expect( roa_la.length )
-      .toBe(1) );
-
-});
-
-
-
-
-
-describe('Actions', () => {
-
-  const act_machine = new jssm.Machine({
-    start_states : ['off'],
-    transitions  : [
-      { from: 'off', to: 'red', action: 'on',  kind: 'legal', forced_only: false, main_path: false },
-      { from: 'red', to: 'off', action: 'off', kind: 'legal', forced_only: false, main_path: false }
-    ]
-  });
-
-  test('Red has actions().length 1', () =>
-    expect( act_machine.actions().length )
-      .toBe(1) );
-
-  test('Red has actions()[0] "on"', () =>
-    expect( act_machine.actions()[0] )
-      .toBe('on') );
-
-  test('Red has actions().length 1 again', () =>
-    expect( act_machine.actions('off').length )
-      .toBe(1) );
-
-  test('Red has actions()[0] "on" again', () =>
-    expect( act_machine.actions('off')[0] )
-      .toBe('on') );
-
-  test('Red has actions().length 1 re-again', () =>
-    expect( act_machine.actions('red').length )
-      .toBe(1) );
-
-  test('Red has actions()[0] "off" re-again', () =>
-    expect( act_machine.actions('red')[0] )
-      .toBe('off') );
-
-});
-
-
-
-
-
-describe('States having actions', () => {
-
-  const sha_machine = new jssm.Machine({
-    start_states : ['off'],
-    transitions  : [
-      { from: 'off', to: 'red', action: 'on',  kind: 'legal', forced_only: false, main_path: false },
-      { from: 'red', to: 'off', action: 'off', kind: 'legal', forced_only: false, main_path: false }
-    ]
-  });
-
-  test('One action has "on"', () =>
-    expect( sha_machine.list_states_having_action('on').length )
-      .toBe(1) );
-
-  test('"on" is had by "off"', () =>
-    expect( sha_machine.list_states_having_action('on')[0] )
-      .toBe('off') );
-
-});
-
-
-
-
-
-describe('List exit actions', () => {
-
-  const lea_machine = new jssm.Machine({
-    start_states : ['off'],
-    transitions  : [
-      { from: 'off', to: 'red', action: 'on',  kind: 'legal', forced_only: false, main_path: false },
-      { from: 'red', to: 'off', action: 'off', kind: 'legal', forced_only: false, main_path: false }
-    ]
-  });
-
-  test('List exit actions, shows "on" from off as default', () =>
-    expect( lea_machine.list_exit_actions()[0] )
-      .toBe('on')  );
-
-  test('List exit actions, shows "on" from off', () =>
-    expect( lea_machine.list_exit_actions('off')[0] )
-      .toBe('on') );
-
-  test('List exit actions, shows "off" from red', () =>
-    expect( lea_machine.list_exit_actions('red')[0] )
-      .toBe('off') );
-
-});
-
-
-
-
-
-describe('Reports on action edges', () => {
-
-  const roae_machine = new jssm.Machine({
-    start_states : ['off'],
-    transitions  : [
-      { name:'turn_on', action:'power_on', from:'off', to:'red', kind: 'legal', forced_only: false, main_path: false }
-    ]
-  });
-
-  test('Reports on action edges, that it has', () =>
-    expect( typeof roae_machine.current_action_edge_for('power_on') )
-      .toBe('object') );
-
-  test('Reports on action edges, that it doesn\'t have', () =>
-    expect( () => roae_machine.current_action_edge_for('power_west') )
-      .toThrow() );
-
-});
-
-
-
-
-
-describe('Two nodes should be able to have matching edges with differing action labels', () => {
-
-  // const machine = sm`a 'first' -> a; a 'second' -> a;`;
-
-  // test('that it has',           () => expect( typeof machine.current_action_edge_for('power_on')  ).toBe('object') );
-  // test('that it doesn\'t have', () => expect( () => machine.current_action_edge_for('power_west') ).toThrow()      );
-
-  test.todo('todo - uncomment when #531 is resolved');
-
-});

package/src/ts/tests/arrange.spec.ts

@@ -1,72 +0,0 @@
-
-import { sm } from '../jssm';
-
-
-
-
-
-describe('Arrange', () => {
-
-
-
-  test('Single arrange', () => {
-
-    expect( () => { const _foo = sm`arrange [a b]; a -> b;`; })
-      .not.toThrow();
-
-    expect(
-      sm`arrange [a b]; a -> b;`._arrange_declaration
-    ).toEqual(
-      [['a','b']]
-    );
-
-  });
-
-
-
-  test('Multiple arrange', () => {
-
-    expect( () => { const _foo = sm`arrange [a b]; a -> b; c -> d; arrange [c d];`; })
-      .not.toThrow();
-
-    expect(
-      sm`arrange [a b]; a -> b; c -> d; arrange [c d];`._arrange_declaration
-    ).toEqual(
-      [['a','b'],['c','d']]
-    );
-
-  });
-
-
-
-  test('start', () => {
-
-    expect( () => { const _foo = sm`arrange-start [a c]; a -> b -> c -> d;`; })
-      .not.toThrow();
-
-    expect(
-      sm`arrange-start [a c]; a -> b -> c -> d;`._arrange_start_declaration
-    ).toEqual(
-      [['a','c']]
-    );
-
-  });
-
-
-
-  test('end', () => {
-
-    expect( () => { const _foo = sm`arrange-end [a c]; a -> b -> c -> d;`; })
-      .not.toThrow();
-
-    expect(
-      sm`arrange-end [b d]; a -> b -> c -> d;`._arrange_end_declaration
-    ).toEqual(
-      [['b','d']]
-    );
-
-  });
-
-
-
-});

package/src/ts/tests/arrange.stoch.ts

@@ -1,4 +0,0 @@
-
-// import { sm } from '../jssm';
-
-test('TODO placeholder', () => { expect(1).toBe(1); });