jcampconverter 9.0.6 → 9.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (26) hide show
  1. package/lib/convert.d.ts +5 -0
  2. package/lib/convert.d.ts.map +1 -1
  3. package/lib/convert.js +2 -0
  4. package/lib/convert.js.map +1 -1
  5. package/lib/postProcessingNMR.d.ts.map +1 -1
  6. package/lib/postProcessingNMR.js +6 -5
  7. package/lib/postProcessingNMR.js.map +1 -1
  8. package/lib/profiling.d.ts +1 -1
  9. package/lib/profiling.d.ts.map +1 -1
  10. package/lib/profiling.js +2 -1
  11. package/lib/profiling.js.map +1 -1
  12. package/lib-esm/convert.d.ts +5 -0
  13. package/lib-esm/convert.d.ts.map +1 -1
  14. package/lib-esm/convert.js +2 -0
  15. package/lib-esm/convert.js.map +1 -1
  16. package/lib-esm/postProcessingNMR.d.ts.map +1 -1
  17. package/lib-esm/postProcessingNMR.js +6 -5
  18. package/lib-esm/postProcessingNMR.js.map +1 -1
  19. package/lib-esm/profiling.d.ts +1 -1
  20. package/lib-esm/profiling.d.ts.map +1 -1
  21. package/lib-esm/profiling.js +2 -1
  22. package/lib-esm/profiling.js.map +1 -1
  23. package/package.json +15 -13
  24. package/src/convert.js +4 -0
  25. package/src/postProcessingNMR.js +9 -5
  26. package/src/profiling.js +2 -1
package/lib/convert.d.ts CHANGED
@@ -11,6 +11,7 @@
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  * @property {boolean} [noContour=false] - Don't calculate countour in case of 2D.
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  * @property {number} [nbContourLevels=7] - Number of positive / negative contour levels to calculate.
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  * @property {number} [noiseMultiplier=5] - Define for 2D the level as 5 times the median as default.
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+ * @property {import('@types/pino').Logger} [logger] - A logger like 'pino'
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  * @property {boolean} [profiling=false] - Add profiling information.
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  */
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  /**
@@ -113,6 +114,10 @@ export type ConvertOptions = {
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  * - Define for 2D the level as 5 times the median as default.
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  */
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  noiseMultiplier?: number | undefined;
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+ /**
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+ * - A logger like 'pino'
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+ */
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+ logger?: any;
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  /**
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  * - Add profiling information.
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  */
package/lib/convert.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../src/convert.js"],"names":[],"mappings":"AA8BA;;;;;;;;;;;;;;GAcG;AAEH;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;;GASG;AAEH;;;;;;;;;;;;GAYG;AAEH;;;;;;;GAOG;AAEH;;;;;;;GAOG;AAEH,+BALW,MAAM,GAAC,WAAW,GAAC,UAAU,yCAE3B,aAAa,CAmSzB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;uBA1Ua,OAAO,MAAM,EAAE,GAAG,CAAC;;aAanB,QAAQ,EAAE;aACV,OAAO;UACP,MAAM;UACN,MAAM;SACN,MAAM;;;;;;;eAUL,MAAM,EAAE,GAAG,OAAO;UAClB,MAAM,EAAE;aACR,MAAM,EAAE;aACR,KAAK,EAAE"}
1
+ {"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../src/convert.js"],"names":[],"mappings":"AA8BA;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;;GASG;AAEH;;;;;;;;;;;;GAYG;AAEH;;;;;;;GAOG;AAEH;;;;;;;GAOG;AAEH,+BALW,MAAM,GAAC,WAAW,GAAC,UAAU,yCAE3B,aAAa,CAsSzB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;uBA7Ua,OAAO,MAAM,EAAE,GAAG,CAAC;;aAanB,QAAQ,EAAE;aACV,OAAO;UACP,MAAM;UACN,MAAM;SACN,MAAM;;;;;;;eAUL,MAAM,EAAE,GAAG,OAAO;UAClB,MAAM,EAAE;aACR,MAAM,EAAE;aACR,KAAK,EAAE"}
package/lib/convert.js CHANGED
@@ -43,6 +43,7 @@ const defaultOptions = {
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  * @property {boolean} [noContour=false] - Don't calculate countour in case of 2D.
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  * @property {number} [nbContourLevels=7] - Number of positive / negative contour levels to calculate.
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  * @property {number} [noiseMultiplier=5] - Define for 2D the level as 5 times the median as default.
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+ * @property {import('@types/pino').Logger} [logger] - A logger like 'pino'
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  * @property {boolean} [profiling=false] - Add profiling information.
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  */
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  /**
@@ -103,6 +104,7 @@ const defaultOptions = {
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  function convert(jcamp, options = {}) {
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  jcamp = (0, ensure_string_1.ensureString)(jcamp);
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  options = { ...defaultOptions, ...options };
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+ options.logger?.debug('Starting jcamp conversion');
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  options.wantXY = !options.withoutXY;
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  options.start = Date.now();
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  let entriesFlat = [];
package/lib/convert.js.map CHANGED
@@ -1 +1 @@
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package/lib/postProcessingNMR.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"postProcessingNMR.d.ts","sourceRoot":"","sources":["../src/postProcessingNMR.js"],"names":[],"mappings":"AAEA,kEA4FC"}
1
+ {"version":3,"file":"postProcessingNMR.d.ts","sourceRoot":"","sources":["../src/postProcessingNMR.js"],"names":[],"mappings":"AAEA,kEAgGC"}
package/lib/postProcessingNMR.js CHANGED
@@ -44,23 +44,24 @@ function postProcessingNMR(entriesFlat) {
44
44
  for (let i = 0; i < entry.ntuples.nucleus.length; i++) {
45
45
  let symbol = entry.ntuples.symbol[i];
46
46
  let nucleus = entry.ntuples.nucleus[i];
47
- if (symbol.startsWith('F') && !nucleus) {
48
- if (symbol === 'F1') {
47
+ if (symbol.match(/^[F|T]/) && !nucleus) {
48
+ if (symbol.match(/[F|T]1/)) {
49
49
  // if F1 is defined we will use F2
50
50
  if (entry.tmp.$NUC2) {
51
51
  entry.ntuples.nucleus[i] = entry.tmp.$NUC2;
52
52
  }
53
53
  else {
54
- let f2index = entry.ntuples.symbol.indexOf('F2');
54
+ let f2index = entry.ntuples.symbol.indexOf(symbol.replace(/^([F|T]).*/, '$12'));
55
55
  if (f2index && entry.ntuples.nucleus[f2index]) {
56
56
  entry.ntuples.nucleus[i] = entry.ntuples.nucleus[f2index];
57
57
  }
58
58
  }
59
59
  }
60
- if (symbol === 'F2')
60
+ if (symbol.match(/[F|T]2/)) {
61
61
  entry.ntuples.nucleus[i] = entry.tmp.$NUC1;
62
+ }
62
63
  }
63
- if (symbol === 'F2') {
64
+ if (symbol.match(/[F|T]2/)) {
64
65
  entry.yType = entry.ntuples.nucleus[0];
65
66
  }
66
67
  }
package/lib/postProcessingNMR.js.map CHANGED
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package/lib/profiling.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- export default function profiling(result: any, action: any, options: any): void;
1
+ export default function profiling(result: any, action: any, options?: {}): void;
2
2
  //# sourceMappingURL=profiling.d.ts.map
package/lib/profiling.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"profiling.d.ts","sourceRoot":"","sources":["../src/profiling.js"],"names":[],"mappings":"AAAA,gFAOC"}
1
+ {"version":3,"file":"profiling.d.ts","sourceRoot":"","sources":["../src/profiling.js"],"names":[],"mappings":"AAAA,gFAQC"}
package/lib/profiling.js CHANGED
@@ -1,6 +1,7 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- function profiling(result, action, options) {
3
+ function profiling(result, action, options = {}) {
4
+ options.logger?.trace(action);
4
5
  if (result.profiling) {
5
6
  result.profiling.push({
6
7
  action,
package/lib/profiling.js.map CHANGED
@@ -1 +1 @@
1
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+ {"version":3,"file":"profiling.js","sourceRoot":"","sources":["../src/profiling.js"],"names":[],"mappings":";;AAAA,SAAwB,SAAS,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,GAAG,EAAE;IAC5D,OAAO,CAAC,MAAM,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC;IAC9B,IAAI,MAAM,CAAC,SAAS,EAAE;QACpB,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC;YACpB,MAAM;YACN,IAAI,EAAE,IAAI,CAAC,GAAG,EAAE,GAAG,OAAO,CAAC,KAAK;SACjC,CAAC,CAAC;KACJ;AACH,CAAC;AARD,4BAQC"}
package/lib-esm/convert.d.ts CHANGED
@@ -11,6 +11,7 @@
11
11
  * @property {boolean} [noContour=false] - Don't calculate countour in case of 2D.
12
12
  * @property {number} [nbContourLevels=7] - Number of positive / negative contour levels to calculate.
13
13
  * @property {number} [noiseMultiplier=5] - Define for 2D the level as 5 times the median as default.
14
+ * @property {import('@types/pino').Logger} [logger] - A logger like 'pino'
14
15
  * @property {boolean} [profiling=false] - Add profiling information.
15
16
  */
16
17
  /**
@@ -113,6 +114,10 @@ export type ConvertOptions = {
113
114
  * - Define for 2D the level as 5 times the median as default.
114
115
  */
115
116
  noiseMultiplier?: number | undefined;
117
+ /**
118
+ * - A logger like 'pino'
119
+ */
120
+ logger?: any;
116
121
  /**
117
122
  * - Add profiling information.
118
123
  */
package/lib-esm/convert.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../src/convert.js"],"names":[],"mappings":"AA8BA;;;;;;;;;;;;;;GAcG;AAEH;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;;GASG;AAEH;;;;;;;;;;;;GAYG;AAEH;;;;;;;GAOG;AAEH;;;;;;;GAOG;AAEH,+BALW,MAAM,GAAC,WAAW,GAAC,UAAU,yCAE3B,aAAa,CAmSzB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;uBA1Ua,OAAO,MAAM,EAAE,GAAG,CAAC;;aAanB,QAAQ,EAAE;aACV,OAAO;UACP,MAAM;UACN,MAAM;SACN,MAAM;;;;;;;eAUL,MAAM,EAAE,GAAG,OAAO;UAClB,MAAM,EAAE;aACR,MAAM,EAAE;aACR,KAAK,EAAE"}
1
+ {"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../src/convert.js"],"names":[],"mappings":"AA8BA;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;;GASG;AAEH;;;;;;;;;;;;GAYG;AAEH;;;;;;;GAOG;AAEH;;;;;;;GAOG;AAEH,+BALW,MAAM,GAAC,WAAW,GAAC,UAAU,yCAE3B,aAAa,CAsSzB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;uBA7Ua,OAAO,MAAM,EAAE,GAAG,CAAC;;aAanB,QAAQ,EAAE;aACV,OAAO;UACP,MAAM;UACN,MAAM;SACN,MAAM;;;;;;;eAUL,MAAM,EAAE,GAAG,OAAO;UAClB,MAAM,EAAE;aACR,MAAM,EAAE;aACR,KAAK,EAAE"}
package/lib-esm/convert.js CHANGED
@@ -37,6 +37,7 @@ const defaultOptions = {
37
37
  * @property {boolean} [noContour=false] - Don't calculate countour in case of 2D.
38
38
  * @property {number} [nbContourLevels=7] - Number of positive / negative contour levels to calculate.
39
39
  * @property {number} [noiseMultiplier=5] - Define for 2D the level as 5 times the median as default.
40
+ * @property {import('@types/pino').Logger} [logger] - A logger like 'pino'
40
41
  * @property {boolean} [profiling=false] - Add profiling information.
41
42
  */
42
43
  /**
@@ -97,6 +98,7 @@ const defaultOptions = {
97
98
  export function convert(jcamp, options = {}) {
98
99
  jcamp = ensureString(jcamp);
99
100
  options = { ...defaultOptions, ...options };
101
+ options.logger?.debug('Starting jcamp conversion');
100
102
  options.wantXY = !options.withoutXY;
101
103
  options.start = Date.now();
102
104
  let entriesFlat = [];
package/lib-esm/convert.js.map CHANGED
@@ -1 +1 @@
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package/lib-esm/postProcessingNMR.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"postProcessingNMR.d.ts","sourceRoot":"","sources":["../src/postProcessingNMR.js"],"names":[],"mappings":"AAEA,kEA4FC"}
1
+ {"version":3,"file":"postProcessingNMR.d.ts","sourceRoot":"","sources":["../src/postProcessingNMR.js"],"names":[],"mappings":"AAEA,kEAgGC"}
package/lib-esm/postProcessingNMR.js CHANGED
@@ -42,23 +42,24 @@ export default function postProcessingNMR(entriesFlat) {
42
42
  for (let i = 0; i < entry.ntuples.nucleus.length; i++) {
43
43
  let symbol = entry.ntuples.symbol[i];
44
44
  let nucleus = entry.ntuples.nucleus[i];
45
- if (symbol.startsWith('F') && !nucleus) {
46
- if (symbol === 'F1') {
45
+ if (symbol.match(/^[F|T]/) && !nucleus) {
46
+ if (symbol.match(/[F|T]1/)) {
47
47
  // if F1 is defined we will use F2
48
48
  if (entry.tmp.$NUC2) {
49
49
  entry.ntuples.nucleus[i] = entry.tmp.$NUC2;
50
50
  }
51
51
  else {
52
- let f2index = entry.ntuples.symbol.indexOf('F2');
52
+ let f2index = entry.ntuples.symbol.indexOf(symbol.replace(/^([F|T]).*/, '$12'));
53
53
  if (f2index && entry.ntuples.nucleus[f2index]) {
54
54
  entry.ntuples.nucleus[i] = entry.ntuples.nucleus[f2index];
55
55
  }
56
56
  }
57
57
  }
58
- if (symbol === 'F2')
58
+ if (symbol.match(/[F|T]2/)) {
59
59
  entry.ntuples.nucleus[i] = entry.tmp.$NUC1;
60
+ }
60
61
  }
61
- if (symbol === 'F2') {
62
+ if (symbol.match(/[F|T]2/)) {
62
63
  entry.yType = entry.ntuples.nucleus[0];
63
64
  }
64
65
  }
package/lib-esm/postProcessingNMR.js.map CHANGED
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1
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package/lib-esm/profiling.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- export default function profiling(result: any, action: any, options: any): void;
1
+ export default function profiling(result: any, action: any, options?: {}): void;
2
2
  //# sourceMappingURL=profiling.d.ts.map
package/lib-esm/profiling.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"profiling.d.ts","sourceRoot":"","sources":["../src/profiling.js"],"names":[],"mappings":"AAAA,gFAOC"}
1
+ {"version":3,"file":"profiling.d.ts","sourceRoot":"","sources":["../src/profiling.js"],"names":[],"mappings":"AAAA,gFAQC"}
package/lib-esm/profiling.js CHANGED
@@ -1,4 +1,5 @@
1
- export default function profiling(result, action, options) {
1
+ export default function profiling(result, action, options = {}) {
2
+ options.logger?.trace(action);
2
3
  if (result.profiling) {
3
4
  result.profiling.push({
4
5
  action,
package/lib-esm/profiling.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"profiling.js","sourceRoot":"","sources":["../src/profiling.js"],"names":[],"mappings":"AAAA,MAAM,CAAC,OAAO,UAAU,SAAS,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO;IACvD,IAAI,MAAM,CAAC,SAAS,EAAE;QACpB,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC;YACpB,MAAM;YACN,IAAI,EAAE,IAAI,CAAC,GAAG,EAAE,GAAG,OAAO,CAAC,KAAK;SACjC,CAAC,CAAC;KACJ;AACH,CAAC"}
1
+ {"version":3,"file":"profiling.js","sourceRoot":"","sources":["../src/profiling.js"],"names":[],"mappings":"AAAA,MAAM,CAAC,OAAO,UAAU,SAAS,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,GAAG,EAAE;IAC5D,OAAO,CAAC,MAAM,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC;IAC9B,IAAI,MAAM,CAAC,SAAS,EAAE;QACpB,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC;YACpB,MAAM;YACN,IAAI,EAAE,IAAI,CAAC,GAAG,EAAE,GAAG,OAAO,CAAC,KAAK;SACjC,CAAC,CAAC;KACJ;AACH,CAAC"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "jcampconverter",
3
- "version": "9.0.6",
3
+ "version": "9.1.0",
4
4
  "description": "Parse and convert JCAMP data",
5
5
  "main": "lib/index.js",
6
6
  "module": "lib-esm/index.js",
@@ -44,26 +44,28 @@
44
44
  },
45
45
  "homepage": "https://github.com/cheminfo/jcampconverter#readme",
46
46
  "devDependencies": {
47
- "@types/jest": "^29.1.1",
48
- "@vitest/coverage-c8": "^0.23.4",
47
+ "@types/jest": "^29.4.4",
48
+ "@types/pino": "^7.0.5",
49
+ "@vitest/coverage-c8": "^0.29.3",
49
50
  "benchmark": "^2.1.4",
50
- "c8": "^7.12.0",
51
- "cheminfo-build": "^1.1.11",
52
- "eslint": "^8.24.0",
53
- "eslint-config-cheminfo-typescript": "^11.1.0",
51
+ "c8": "^7.13.0",
52
+ "cheminfo-build": "^1.2.0",
53
+ "eslint": "^8.36.0",
54
+ "eslint-config-cheminfo-typescript": "^11.3.0",
54
55
  "esm": "^3.2.25",
56
+ "fifo-logger": "^0.6.0",
55
57
  "jest-matcher-deep-close-to": "^3.0.2",
56
- "jscpd": "^3.5.0",
57
- "prettier": "^2.7.1",
58
- "rimraf": "^3.0.2",
59
- "typescript": "^4.8.4",
60
- "vitest": "^0.23.4"
58
+ "jscpd": "^3.5.3",
59
+ "prettier": "^2.8.4",
60
+ "rimraf": "^4.4.0",
61
+ "typescript": "^4.9.5",
62
+ "vitest": "^0.29.3"
61
63
  },
62
64
  "dependencies": {
63
65
  "dynamic-typing": "^1.0.0",
64
66
  "ensure-string": "^1.2.0",
65
67
  "gyromagnetic-ratio": "^1.0.0",
66
68
  "ml-array-median": "^1.1.6",
67
- "ml-spectra-processing": "^11.12.0"
69
+ "ml-spectra-processing": "^12.0.0"
68
70
  }
69
71
  }
package/src/convert.js CHANGED
@@ -41,6 +41,7 @@ const defaultOptions = {
41
41
  * @property {boolean} [noContour=false] - Don't calculate countour in case of 2D.
42
42
  * @property {number} [nbContourLevels=7] - Number of positive / negative contour levels to calculate.
43
43
  * @property {number} [noiseMultiplier=5] - Define for 2D the level as 5 times the median as default.
44
+ * @property {import('@types/pino').Logger} [logger] - A logger like 'pino'
44
45
  * @property {boolean} [profiling=false] - Add profiling information.
45
46
  */
46
47
 
@@ -107,6 +108,9 @@ const defaultOptions = {
107
108
  export function convert(jcamp, options = {}) {
108
109
  jcamp = ensureString(jcamp);
109
110
  options = { ...defaultOptions, ...options };
111
+
112
+ options.logger?.debug('Starting jcamp conversion');
113
+
110
114
  options.wantXY = !options.withoutXY;
111
115
  options.start = Date.now();
112
116
 
package/src/postProcessingNMR.js CHANGED
@@ -45,21 +45,25 @@ export default function postProcessingNMR(entriesFlat) {
45
45
  for (let i = 0; i < entry.ntuples.nucleus.length; i++) {
46
46
  let symbol = entry.ntuples.symbol[i];
47
47
  let nucleus = entry.ntuples.nucleus[i];
48
- if (symbol.startsWith('F') && !nucleus) {
49
- if (symbol === 'F1') {
48
+ if (symbol.match(/^[F|T]/) && !nucleus) {
49
+ if (symbol.match(/[F|T]1/)) {
50
50
  // if F1 is defined we will use F2
51
51
  if (entry.tmp.$NUC2) {
52
52
  entry.ntuples.nucleus[i] = entry.tmp.$NUC2;
53
53
  } else {
54
- let f2index = entry.ntuples.symbol.indexOf('F2');
54
+ let f2index = entry.ntuples.symbol.indexOf(
55
+ symbol.replace(/^([F|T]).*/, '$12'),
56
+ );
55
57
  if (f2index && entry.ntuples.nucleus[f2index]) {
56
58
  entry.ntuples.nucleus[i] = entry.ntuples.nucleus[f2index];
57
59
  }
58
60
  }
59
61
  }
60
- if (symbol === 'F2') entry.ntuples.nucleus[i] = entry.tmp.$NUC1;
62
+ if (symbol.match(/[F|T]2/)) {
63
+ entry.ntuples.nucleus[i] = entry.tmp.$NUC1;
64
+ }
61
65
  }
62
- if (symbol === 'F2') {
66
+ if (symbol.match(/[F|T]2/)) {
63
67
  entry.yType = entry.ntuples.nucleus[0];
64
68
  }
65
69
  }
package/src/profiling.js CHANGED
@@ -1,4 +1,5 @@
1
- export default function profiling(result, action, options) {
1
+ export default function profiling(result, action, options = {}) {
2
+ options.logger?.trace(action);
2
3
  if (result.profiling) {
3
4
  result.profiling.push({
4
5
  action,