Tuned eslint config

eslint.config.mjs

@@ -11,36 +11,79 @@ export default tsEslint.config(
       plugins: {
           '@stylistic': stylisticEslint,
       },
-      rules:{
-        'prefer-const': 'off',
+      rules: {
+        // Relax recommended rules
+        'prefer-const': ['error', { 
+          destructuring: 'all', // Allow `let` when at least one destructured element will be changed
+        }],
         '@typescript-eslint/no-explicit-any': 'off',
         '@typescript-eslint/no-inferrable-types': 'off',
         '@typescript-eslint/consistent-indexed-object-style': 'off',
         '@typescript-eslint/no-namespace': 'off',
         '@typescript-eslint/no-unused-vars': 'off',
-        '@typescript-eslint/consistent-type-definitions': 'off',
-        '@typescript-eslint/no-unused-expressions': 'off',
-        '@typescript-eslint/no-empty-object-type': 'off',
 
+        // Additional rules - general
+        'eqeqeq': 'error', // Forbid using `==`, enforce `===`
+        'no-eval': 'error', // Forbid using `eval`
+        'no-new-wrappers': 'error', 
+        'no-restricted-syntax': ['error', {
+          selector: 'ExportDefaultDeclaration',
+          message: 'Default exports are not allowed',
+        }],
+        'no-var': 'error', // Forbid using `var`
+        'no-throw-literal': 'error', // Forbid throwing anything that's not Error, e.g. `throw 'Blabla'`
+        '@typescript-eslint/prefer-namespace-keyword': 'error', // Forbid `module` keyword
+
+        // Additional rules - @stylistic
         '@stylistic/indent': ['error', 4],
-        '@stylistic/quotes': ['error', 'single', {
+        '@stylistic/semi': 'error', // Enforce trailing semicolons, including after type definitions
+        '@stylistic/comma-dangle': ['error', 'always-multiline'], // Enforce comma after last listed item when closing ] or } is on the next line
+        '@stylistic/quotes': ['error', 'single', { // Enforce single quotes: 'hello'
           avoidEscape: true,
           allowTemplateLiterals: true,
         }],
-        '@stylistic/semi': 'off',
-        '@stylistic/type-annotation-spacing': 'error',
-        '@stylistic/brace-style': ['error', '1tbs', {
+        '@stylistic/brace-style': ['error', '1tbs', { // Enforce line break after { and before }
             allowSingleLine: true,
         }],
-        '@stylistic/comma-spacing': 'error',
-        '@stylistic/space-infix-ops': 'error',
+        '@stylistic/member-delimiter-style': ['error', { // Enforce commas in interfaces and types
+          multiline: {
+            delimiter: 'comma',
+            requireLast: true,
+          },
+          singleline: {
+            delimiter: 'comma',
+            requireLast: false,
+          },
+          'multilineDetection': 'brackets',
+        }],
+
+        // Additional rules - @stylistic - spacing
+        '@stylistic/array-bracket-spacing': 'error', // Forbid spaces in array: [_1, 2_]
+        '@stylistic/arrow-spacing': 'error', // Enforce space in lambda function: x_=>_x**2
+        '@stylistic/block-spacing': 'error', // Enforce space in one-line block: () => {_return true;_}
+        '@stylistic/comma-spacing': 'error', // Enforce space after comma: [1,_2,_3]
+        '@stylistic/computed-property-spacing': 'error', // Forbid spaces in indexing: a[_0_]
+        '@stylistic/function-call-spacing': 'error', // Forbid space when calling function: f_(0)
+        '@stylistic/key-spacing': 'error', // Enforce space after colon in object: { a:_1, b:_2 }
+        '@stylistic/keyword-spacing': 'error', // Enforce space after `if`, `try`, etc.: if_(true)
+        '@stylistic/no-multi-spaces': 'error', // Forbid more than one space: x =__5
+        '@stylistic/no-trailing-spaces': 'error', // No spaces at the end of line: foo()_
+        '@stylistic/object-curly-spacing': ['error', 'always'], // Enforce spaces in object: {_a: 1, b: 2_}
+        '@stylistic/semi-spacing': 'error', // Enforce space after semicolon: for (let i = 0;_i < n;_i++)
+        '@stylistic/space-before-blocks': 'error', // Enforce space before block: if (true)_{}
         '@stylistic/space-before-function-paren': ['error', {
-            anonymous: 'always',
-            named: 'never',
-            asyncArrow: 'always',
+          anonymous: 'always', // function_() {}
+          named: 'never', // function foo_() {}
+          asyncArrow: 'always', // async_() {}
+        }],
+        '@stylistic/space-in-parens': 'error', // Forbid spaces in parentheses: (_1, 2_)
+        '@stylistic/space-infix-ops': 'error', // Enforce space around infix operators: 1_+_2
+        '@stylistic/spaced-comment': ['error', 'always', { // Enforce space in comment: /**_Comment_*/ //_comment
+          block: {
+            balanced: true,
+          },
         }],
-        '@stylistic/func-call-spacing': ['error'],
-        '@stylistic/keyword-spacing': ['error'],
+        '@stylistic/type-annotation-spacing': 'error', // Enforce space after type annotation colon: let x:_string;
       },
     },
   );

src/_spec/_utils.ts

@@ -20,7 +20,7 @@ import { setFSModule } from 'molstar/lib/commonjs/mol-util/data-source';
 
 
 export const TESTING_PDBS = ['1hda', '1ad5', '176d', 'AF-Q8W3K0-F1-model_v4'] as const;
-export type TestingPdb = typeof TESTING_PDBS[number]
+export type TestingPdb = typeof TESTING_PDBS[number];
 /** Timeout for long-running tests (in ms) */
 export const LONG_TEST_TIMEOUT = 600_000;
 

src/_spec/api.spec.ts

@@ -68,7 +68,7 @@ describe('api', () => {
     it('getModifiedResidue', async () => {
         expect(await API.getModifiedResidue('1hda')).toEqual([] as PDBeAPIReturn<'getModifiedResidue'>);
         expect(await API.getModifiedResidue('1gkt')).toEqual([
-            { authChainId: 'A', compoundId: 'SUI', compoundName: '(3-AMINO-2,5-DIOXO-1-PYRROLIDINYL)ACETIC ACID', entityId: 1, labelChainId: 'A', residueNumber: 54 }
+            { authChainId: 'A', compoundId: 'SUI', compoundName: '(3-AMINO-2,5-DIOXO-1-PYRROLIDINYL)ACETIC ACID', entityId: 1, labelChainId: 'A', residueNumber: 54 },
         ] as PDBeAPIReturn<'getModifiedResidue'>);
         expect(await API.getModifiedResidue('1l7c')).toEqual([
             { authChainId: 'A', compoundId: 'MSE', compoundName: 'SELENOMETHIONINE', entityId: 1, labelChainId: 'A', residueNumber: 70 },
@@ -166,7 +166,7 @@ describe('api', () => {
                     { chunks: [{ endResidue: 125, startResidue: 1, chainId: 'B', authChainId: 'B', entityId: '2', segment: 1 }], family: 'RF00234', familyName: 'glmS glucosamine-6-phosphate activated ribozyme', id: 'RF00234_1', source: 'Rfam' },
                 ],
             },
-            SCOP: {}
+            SCOP: {},
         } as PDBeAPIReturn<'getSiftsMappings'>);
     });
 

src/_spec/expected-files.spec.ts

@@ -9,7 +9,6 @@ import { checkMissingFiles, getExpectedFiles } from '../expected-files';
 
 
 const API = new PDBeAPI('file://./test_data/api');
-const NO_API = new PDBeAPI('', true);
 
 
 describe('expected-filenames', () => {

src/_spec/image-generator.spec.ts

@@ -14,7 +14,8 @@ import { ImageGenerator } from '../image-generator';
 import { TestingPdb, getTestingHeadlessPlugin } from './_utils';
 
 
-PluginContext; // ensure PluginContext is imported before ImageGenerator
+// Ensure PluginContext is imported before ImageGenerator:
+PluginContext; // eslint-disable-line @typescript-eslint/no-unused-expressions
 
 const TEST_TIMEOUT = 180_000; // ms
 

src/_spec/save.spec.ts

@@ -8,7 +8,7 @@ import fs from 'fs';
 import path from 'path';
 
 import { loadPngToRaw } from '../image/resize';
-import { makeSaveFunction, } from '../save';
+import { makeSaveFunction } from '../save';
 import { getTestingHeadlessPlugin, isBorderBlank, isImageBlank } from './_utils';
 
 

src/api.ts

@@ -309,8 +309,8 @@ export class PDBeAPI {
     }
 }
 
-export type PDBeAPIMethod = 'pdbeStructureQualityReportPrefix' | 'getEntityNames' | 'getEntityTypes' | 'getAssemblies' | 'getPreferredAssemblyId' | 'getModifiedResidue' | 'getSiftsMappings' | 'getExperimentalMethods' | 'getChainCoverages' | 'getChainCoverageRatios'
-export type PDBeAPIReturn<key extends PDBeAPIMethod> = Awaited<ReturnType<PDBeAPI[key]>>
+export type PDBeAPIMethod = 'pdbeStructureQualityReportPrefix' | 'getEntityNames' | 'getEntityTypes' | 'getAssemblies' | 'getPreferredAssemblyId' | 'getModifiedResidue' | 'getSiftsMappings' | 'getExperimentalMethods' | 'getChainCoverages' | 'getChainCoverageRatios';
+export type PDBeAPIReturn<key extends PDBeAPIMethod> = Awaited<ReturnType<PDBeAPI[key]>>;
 
 
 /** Represents one instance of a modified residue. */
@@ -346,7 +346,7 @@ export type SiftsSource = typeof SIFTS_SOURCES[number];
 /**  */
 export interface DomainRecord {
     id: string,
-    source: string
+    source: string,
     family: string,
     familyName: string,
     chunks: DomainChunkRecord[],
@@ -366,5 +366,5 @@ interface DomainChunkRecord {
     endResidue: number,
     /** No idea what this was supposed to mean in the original process (probably segment number
      * from the API before cutting into smaller segments by removing missing residues) */
-    segment: number
+    segment: number,
 }

src/args.ts

@@ -10,12 +10,12 @@ import { LogLevel } from './helpers/logging';
 /** Modes of operation of PDBImages */
 export const Modes = ['pdb', 'alphafold'] as const;
 /** Modes of operation of PDBImages */
-export type Mode = typeof Modes[number]
+export type Mode = typeof Modes[number];
 
 /** Types of images that can be generated */
 export const ImageTypes = ['entry', 'assembly', 'entity', 'domain', 'ligand', 'modres', 'bfactor', 'validation', 'plddt', 'all'] as const;
 /** Types of images that can be generated */
-export type ImageType = typeof ImageTypes[number]
+export type ImageType = typeof ImageTypes[number];
 
 /** Types of images that can be generated for each mode */
 export const ImageTypesForModes = {
@@ -72,7 +72,7 @@ export interface Args {
     log: LogLevel,
 }
 
-export type OptionalArgs = Omit<Args, 'entry_id' | 'output_dir'>
+export type OptionalArgs = Omit<Args, 'entry_id' | 'output_dir'>;
 
 /** Default values for `Args` */
 export const Defaults = {

src/captions/_spec/captions.spec.ts

@@ -16,11 +16,11 @@ const COMMON_CONTEXT = {
         '1': { description: 'HEMOGLOBIN (DEOXY) (ALPHA CHAIN)', type: 'polymer', chains: [0, 1] as any, index: 0 },
         '2': { description: 'HEMOGLOBIN (DEOXY) (BETA CHAIN)', type: 'polymer', chains: [2, 3] as any, index: 1 },
         '3': { description: 'PROTOPORPHYRIN IX CONTAINING FE', type: 'non-polymer', chains: [4, 5, 6, 7] as any, index: 2 },
-        '4': { description: 'water', type: 'water', chains: [8] as any, index: 3 }
+        '4': { description: 'water', type: 'water', chains: [8] as any, index: 3 },
     } as EntityInfo,
     entityNames: { '1': ['Hemoglobin alpha chain'], '2': ['Hemoglobin beta chain', 'blablabla'], '3': [] },
     nModels: 1,
-    view: undefined
+    view: undefined,
 };
 
 
@@ -116,7 +116,7 @@ describe('captions', () => {
     it('domain', () => {
         expect(Captions.forDomain({
             ...COMMON_CONTEXT, entityId: '2',
-            source: 'CATH', familyId: '1.10.490.10', familyName: 'Globin-like', totalCopies: 2, shownCopies: 1, outOfRangeCopies: 0, chainId: 'B', authChainId: 'B', view: 'front'
+            source: 'CATH', familyId: '1.10.490.10', familyName: 'Globin-like', totalCopies: 2, shownCopies: 1, outOfRangeCopies: 0, chainId: 'B', authChainId: 'B', view: 'front',
         })).toEqual({
             _entry_id: '1hda',
             _extras: undefined,

src/captions/captions.ts

@@ -11,7 +11,7 @@ import { TextBuilder } from './text-builder';
 
 /** Orientation of a 3D view.
  * Use `undefined` when only one view is being rendered, thus it is not necessary to specify orientation. */
-export type ViewType = 'front' | 'side' | 'top' | undefined
+export type ViewType = 'front' | 'side' | 'top' | undefined;
 
 
 /** Data needed to save an image, related captions, and metadata. */
@@ -24,7 +24,7 @@ export interface ImageSpec {
     description: string,
     /** Image caption, plain-text */
     clean_description: string,
-    /** PDB or AlphaFoldDB identifier*/
+    /** PDB or AlphaFoldDB identifier */
     _entry_id: string,
     /** View orientation */
     _view: ViewType,
@@ -172,7 +172,7 @@ export namespace Captions {
         shownCopies: number,
         /** Number of domain instances in the shown chain which are completely out of the observed residue range (therefore not visible) */
         outOfRangeCopies: number,
-        view: ViewType
+        view: ViewType,
     }): ImageSpec {
         const { entryId, source, familyId, familyName, entityId, chainId, authChainId, totalCopies, shownCopies, outOfRangeCopies, view } = context;
         const name = entityName(context, entityId);

src/expected-files.ts

@@ -77,7 +77,7 @@ async function getExpectedFilenameStemsForPdbMode(entryId: string, types: Set<Im
     if (types.has('entity')) {
         const entities = await promises.entities.result();
         for (const entityId in entities) {
-            const { type, compId } = entities[entityId];
+            const { type } = entities[entityId];
             if (type !== 'water') {
                 if (view === 'front') {
                     result.push(

src/helpers/_spec/camera.spec.ts

@@ -93,7 +93,7 @@ describe('camera', () => {
         const plugin = await getTestingPlugin();
         try {
             const oldSnapshot = plugin.canvas3d?.camera.getSnapshot();
-            adjustCamera(plugin, s => ({ ...Camera.createDefaultSnapshot(), position: Vec3.create(11, 1, 1) }));
+            adjustCamera(plugin, () => ({ ...Camera.createDefaultSnapshot(), position: Vec3.create(11, 1, 1) }));
             const newSnapshot = plugin.canvas3d?.camera.getSnapshot();
             expect(newSnapshot).not.toEqual(oldSnapshot);
         } finally {

src/helpers/_spec/helpers.spec.ts

@@ -57,7 +57,7 @@ describe('helpers', () => {
                     label: undefined,
                     sets: { 'X': [123] },
                 },
-            }
+            },
         });
 
         expect(getModifiedResidueInfo([
@@ -85,7 +85,7 @@ describe('helpers', () => {
                     label: undefined,
                     sets: { 'Z': [999] },
                 },
-            }
+            },
         });
     });
 

src/helpers/_spec/structure-info.spec.ts

@@ -35,7 +35,7 @@ describe('structure-info', () => {
                 description: 'water',
                 index: 3,
                 type: 'water',
-            }
+            },
         });
     });
 
@@ -65,7 +65,7 @@ describe('structure-info', () => {
         expect(countChainResidues(model)).toEqual({
             A: 141, B: 145, C: 141, D: 145, // proteins
             E: 1, F: 1, G: 1, H: 1, // hems
-            I: 19, J: 8, K: 10, L: 5 // waters
+            I: 19, J: 8, K: 10, L: 5, // waters
         });
     });
 

src/helpers/helpers.ts

@@ -16,7 +16,7 @@ import { SubstructureDef } from './substructure-def';
 
 
 /** Like `Partial<T>` but recursive (i.e. values themselves can be partial). */
-export type PPartial<T> = T extends {} ? { [P in keyof T]?: PPartial<T[P]> } | undefined : T
+export type PPartial<T> = T extends object ? { [P in keyof T]?: PPartial<T[P]> } | undefined : T;
 
 /** Create a new object with values from `first`, optionally overridden by values from `second`, recursively.
  * (I know there is `mergeDeep` in `immutable` but this implementation also gives type hints). */
@@ -151,7 +151,7 @@ export function safePromise<T>(asyncFunction: () => Promise<T>): SafePromise<T>
             } else {
                 throw theReason;
             }
-        }
+        },
     };
 }
 

src/helpers/logging.ts

@@ -11,7 +11,7 @@ import util from 'util';
 
 /** Available levels for logging */
 export const LogLevels = ['ALL', 'TRACE', 'DEBUG', 'INFO', 'WARN', 'ERROR', 'FATAL', 'MARK', 'OFF'] as const;
-export type LogLevel = typeof LogLevels[number]
+export type LogLevel = typeof LogLevels[number];
 
 const ROOT_DIRS = ['src', 'lib', 'build'];
 

src/helpers/structure-info.ts

@@ -13,10 +13,17 @@ import { getLogger } from './logging';
 const logger = getLogger(module);
 
 /** Entity type (i.e. value of _entity.type in mmCIF): polymer, non-polymer, water... */
-type EntityType = ReturnType<Entities['data']['type']['value']>
+type EntityType = ReturnType<Entities['data']['type']['value']>;
 
 /** Basic info about several entities, mapped by entityId */
-export type EntityInfo = { [entityId: string]: { description: string, type: EntityType, chains: ChainIndex[], index: number } }
+export interface EntityInfo {
+    [entityId: string]: {
+        description: string,
+        type: EntityType,
+        chains: ChainIndex[],
+        index: number,
+    },
+}
 
 /** Return basic info about entities in the structure, mapped by entityId */
 export function getEntityInfo(structure: Structure) {