@nfdi4plants/arctrl 3.2.1 → 3.2.3

package/README.md

@@ -41,70 +41,6 @@ pip install arctrl
 
 Documentation can be found [here](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/arctrl/)
 
-## Development
-
-#### Requirements
-
-- [nodejs and npm](https://nodejs.org/en/download)
-    - verify with `node --version` (Tested with v18.16.1)
-    - verify with `npm --version` (Tested with v9.2.0)
-- [.NET SDK](https://dotnet.microsoft.com/en-us/download)
-    - verify with `dotnet --version` (Tested with 7.0.306)
-- [Python](https://www.python.org/downloads/)
-    - verify with `py --version` (Tested with 3.12.2, known to work only for >=3.11)
-
-#### Local Setup
-
-##### Windows
-
-On windows you can use the `setup.cmd` to run the following steps automatically!
-
-1. Setup dotnet tools
-
-   `dotnet tool restore`
-
-
-2. Install NPM dependencies
-
-    `npm install`
-
-3. Setup python environment
-
-    `py -m venv .venv`
-
-4. Install [uv](https://docs.astral.sh/uv/) and dependencies
-
-   1. `.\.venv\Scripts\python.exe -m pip install -U pip setuptools`
-   2. `.\.venv\Scripts\python.exe -m pip install uv`
-   3. `.\.venv\Scripts\python.exe -m uv pip install -r pyproject.toml --group dev`
-
-Verify correct setup with `./build.cmd runtests` ✨
-
-##### Linux / macOS
-
-On unix you can use the `setup.sh` to run the following steps automatically!
-
-1. Setup dotnet tools
-
-   `dotnet tool restore`
-
-
-2. Install NPM dependencies
-
-    `npm install`
-
-3. Setup python environment
-
-    `python -m venv .venv`
-
-4. Install [uv](https://docs.astral.sh/uv/) and dependencies
-
-   1. `.venv/bin/python -m pip install -U pip setuptools`
-   2. `.venv/bin/python -m pip install uv`
-   3. `.venv/bin/python -m uv pip install -r pyproject.toml --group dev`
-
-Verify correct setup with `bash build.sh runtests` ✨
-
 ## Branding
 
 Feel free to reference `ARCtrl` on slides or elsewhere using our logos:

package/dist/ts/node_modules/@fable-org/fable-library-ts/CollectionUtil.js

@@ -130,18 +130,12 @@ function remove(col, item) {
 function clear(col) {
   if (typeof col["System.Collections.Generic.ICollection`1.Clear"] === "function") {
     return col["System.Collections.Generic.ICollection`1.Clear"]();
+  } else if (Array.isArray(col)) {
+    col.length = 0;
+  } else if (ArrayBuffer.isView(col)) {
+  } else if (typeof col.clear === "function") {
+    col.clear();
   } else {
-    if (isArrayLike(col)) {
-      if (ArrayBuffer.isView(col)) {
-      } else {
-        col.splice(0);
-      }
-    } else {
-      if (typeof col.clear === "function") {
-        col.clear();
-      } else {
-      }
-    }
   }
 }
 

package/dist/ts/node_modules/@fable-org/fable-library-ts/Guid.js

@@ -57,7 +57,7 @@ function newGuid() {
   return `${hex.slice(0, 8)}-${hex.slice(8, 12)}-${hex.slice(12, 16)}-${hex.slice(16, 20)}-${hex.slice(20)}`;
 }
 function createVersion7(timestamp) {
-  const ms = timestamp != null ? timestamp.getTime() : Date.now();
+  const ms = timestamp == null ? Date.now() : typeof timestamp === "object" ? timestamp.getTime() : Number(timestamp);
   const msHex = Math.floor(ms).toString(16).padStart(12, "0");
   const bytes = new Uint8Array(10);
   crypto.getRandomValues(bytes);

package/dist/ts/node_modules/@fable-org/fable-library-ts/MutableMap.js

@@ -312,7 +312,11 @@ function Dictionary__Remove_2B595(this$, k) {
   }
   switch (matchResult) {
     case 0: {
-      getItemFromDict(this$.hashMap, matchValue[1]).splice(matchValue[2], 1);
+      const h_1 = matchValue[1] | 0;
+      getItemFromDict(this$.hashMap, h_1).splice(matchValue[2], 1);
+      if (getItemFromDict(this$.hashMap, h_1).length === 0) {
+        this$.hashMap.delete(h_1);
+      }
       return true;
     }
     default:

package/dist/ts/node_modules/@fable-org/fable-library-ts/MutableSet.js

@@ -214,7 +214,11 @@ function HashSet__Remove_2B595(this$, k) {
   }
   switch (matchResult) {
     case 0: {
-      getItemFromDict(this$.hashMap, matchValue[1]).splice(matchValue[2], 1);
+      const h_1 = matchValue[1] | 0;
+      getItemFromDict(this$.hashMap, h_1).splice(matchValue[2], 1);
+      if (getItemFromDict(this$.hashMap, h_1).length === 0) {
+        this$.hashMap.delete(h_1);
+      }
       return true;
     }
     default:

package/dist/ts/node_modules/@fable-org/fable-library-ts/Numeric.js

@@ -23,6 +23,15 @@ function multiply(x, y) {
     return x[symbol]().multiply(y);
   }
 }
+function divide(x, y) {
+  if (typeof x === "number") {
+    return x / y;
+  } else if (typeof x === "bigint") {
+    return Number(x) / y;
+  } else {
+    return x[symbol]().multiply(1 / y);
+  }
+}
 function toFixed(x, dp) {
   if (typeof x === "number") {
     return x.toFixed(dp);
@@ -41,11 +50,32 @@ function toPrecision(x, sd) {
     return x[symbol]().toPrecision(sd);
   }
 }
+function bigintToExponential(x, dp) {
+  const sign = x < 0n ? "-" : "";
+  let digits = (x < 0n ? -x : x).toString();
+  if (x === 0n) {
+    return sign + (dp ? "0." + "0".repeat(dp) : "0") + "e+0";
+  }
+  dp = dp ?? digits.length - 1;
+  let exponent = digits.length - 1;
+  if (digits.length > dp + 1) {
+    const roundUp = digits.charCodeAt(dp + 1) >= 53;
+    digits = (BigInt(digits.slice(0, dp + 1)) + (roundUp ? 1n : 0n)).toString();
+    if (digits.length > dp + 1) {
+      digits = digits.slice(0, dp + 1);
+      exponent += 1;
+    }
+  } else {
+    digits = digits.padEnd(dp + 1, "0");
+  }
+  const mantissa = dp > 0 ? digits[0] + "." + digits.slice(1) : digits[0];
+  return sign + mantissa + "e+" + exponent;
+}
 function toExponential(x, dp) {
   if (typeof x === "number") {
     return x.toExponential(dp);
   } else if (typeof x === "bigint") {
-    return x;
+    return bigintToExponential(x, dp);
   } else {
     return x[symbol]().toExponential(dp);
   }
@@ -60,4 +90,4 @@ function toHex(x) {
   }
 }
 
-export { compare, isIntegral, isNumeric, multiply, symbol, toExponential, toFixed, toHex, toPrecision };
+export { compare, divide, isIntegral, isNumeric, multiply, symbol, toExponential, toFixed, toHex, toPrecision };

package/dist/ts/node_modules/@fable-org/fable-library-ts/String.js

@@ -1,9 +1,16 @@
 import { toString } from './Date.js';
-import { compare as compare$1, isNumeric, multiply, toHex, toExponential, toPrecision, toFixed, isIntegral } from './Numeric.js';
+import { compare as compare$1, isNumeric, multiply, toHex, toExponential, toPrecision, toFixed, divide, isIntegral } from './Numeric.js';
 import { escape } from './RegExp.js';
 import { toString as toString$1 } from './Types.js';
 import { Exception } from './Util.js';
 
+const dateTimeFormattableSymbol = Symbol.for("Fable.DateTimeFormattable");
+function isNetDateFormattable(rep) {
+  return rep != null && typeof rep[dateTimeFormattableSymbol] === "function";
+}
+function formatDateLike(rep, format2) {
+  return rep instanceof Date ? toString(rep, format2) : rep[dateTimeFormattableSymbol](format2);
+}
 const fsFormatRegExp = /(^|[^%])%([0+\- ]*)(\*|\d+)?(?:\.(\d+))?(\w)/g;
 const interpolateRegExp = /(?:(^|[^%])%([0+\- ]*)(\d+)?(?:\.(\d+))?(\w))?%P\(\)/g;
 const formatRegExp = /\{(\d+)(,-?\d+)?(?:\:([a-zA-Z])(\d{0,2})|\:(.+?))?\}/g;
@@ -230,8 +237,8 @@ function formatReplacement(rep, flags, padLength, precision, format2) {
         rep = String(rep);
         break;
     }
-  } else if (rep instanceof Date) {
-    rep = toString(rep);
+  } else if (rep instanceof Date || isNetDateFormattable(rep)) {
+    rep = formatDateLike(rep, void 0);
   } else if (format2 === "A" && typeof rep === "string") {
     rep = '"' + rep + '"';
   } else {
@@ -375,9 +382,13 @@ function format(str, ...args) {
           }
           break;
         case "e":
-        case "E":
-          rep = precision != null ? toExponential(rep, precision) : toExponential(rep);
+        case "E": {
+          precision = precision != null ? precision : 6;
+          rep = String(toExponential(rep, precision));
+          const eIdx = rep.indexOf("e");
+          rep = rep.slice(0, eIdx) + format2 + rep[eIdx + 1] + padLeft(rep.slice(eIdx + 2), 3, "0");
           break;
+        }
         case "f":
         case "F":
           precision = precision != null ? precision : 2;
@@ -398,7 +409,7 @@ function format(str, ...args) {
             const paddedExpDigits = expDigits.length < 2 ? "0" + expDigits : expDigits;
             const eChar = format2 === "G" ? "E" : "e";
             rep = mantissa + eChar + expSign + paddedExpDigits;
-          } else {
+          } else if (rep.indexOf(".") >= 0) {
             rep = trimEnd(trimEnd(rep, "0"), ".");
           }
           break;
@@ -445,7 +456,17 @@ function format(str, ...args) {
           }
           if (pattern) {
             let sign = "";
-            rep = pattern.replace(/([0#,]+)(\.[0#]+)?/, (_2, intPart, decimalPart) => {
+            const patternStr = pattern;
+            const percents = (patternStr.match(/%/g) ?? []).length;
+            if (percents > 0) {
+              rep = multiply(rep, Math.pow(100, percents));
+            }
+            rep = patternStr.replace(/([0#,]+)(\.[0#]+)?(,*)/, (_2, intPart, decimalPart) => {
+              const scaleCommas = /,*$/.exec(intPart)[0].length;
+              if (scaleCommas > 0) {
+                intPart = intPart.substring(0, intPart.length - scaleCommas);
+                rep = divide(rep, Math.pow(1e3, scaleCommas));
+              }
               if (isLessThan(rep, 0)) {
                 rep = multiply(rep, -1);
                 sign = "-";
@@ -476,8 +497,8 @@ function format(str, ...args) {
             rep = sign + rep;
           }
       }
-    } else if (rep instanceof Date) {
-      rep = toString(rep, pattern || format2);
+    } else if (rep instanceof Date || isNetDateFormattable(rep)) {
+      rep = formatDateLike(rep, pattern || format2);
     } else {
       rep = toString$1(rep);
     }

package/dist/ts/node_modules/@fable-org/fable-library-ts/System.Text.js

@@ -177,6 +177,13 @@ function StringBuilder__set_Chars_413E0D0A(x, index, value) {
     setItem(x.buf, i, item(i, x.buf).slice(0, pos - 1 + 1) + value + item(i, x.buf).slice(pos + 1, item(i, x.buf).length));
   }
 }
+function StringBuilder__get_Length(x) {
+  let len = 0;
+  for (let i = x.buf.length - 1; i >= 0; i--) {
+    len = len + item(i, x.buf).length | 0;
+  }
+  return len | 0;
+}
 function StringBuilder__Replace_Z766F94C0(x, oldValue, newValue) {
   for (let i = x.buf.length - 1; i >= 0; i--) {
     setItem(x.buf, i, replace(item(i, x.buf), oldValue, newValue));
@@ -187,15 +194,8 @@ function StringBuilder__Replace_Z384F8060(x, oldValue, newValue) {
   const str = replace(x.toString(), oldValue, newValue);
   return StringBuilder__Append_Z721C83C5(StringBuilder__Clear(x), str);
 }
-function StringBuilder__get_Length(x) {
-  let len = 0;
-  for (let i = x.buf.length - 1; i >= 0; i--) {
-    len = len + item(i, x.buf).length | 0;
-  }
-  return len | 0;
-}
-function StringBuilder__ToString_Z37302880(x, firstIndex, length) {
-  return substring(x.toString(), firstIndex, length);
+function StringBuilder__ToString_Z37302880(x, startIndex, length) {
+  return substring(x.toString(), startIndex, length);
 }
 
 export { StringBuilder, StringBuilder_$ctor, StringBuilder_$ctor_Z18115A39, StringBuilder_$ctor_Z524259A4, StringBuilder_$ctor_Z721C83C5, StringBuilder_$reflection, StringBuilder__AppendFormat_10D165E0, StringBuilder__AppendFormat_26802C9E, StringBuilder__AppendFormat_433E080, StringBuilder__AppendFormat_6C2E3E6E, StringBuilder__AppendFormat_Z17053F5, StringBuilder__AppendFormat_Z3B30EC65, StringBuilder__AppendFormat_Z471ADCBB, StringBuilder__AppendFormat_Z696D8D1B, StringBuilder__AppendLine, StringBuilder__AppendLine_Z721C83C5, StringBuilder__Append_244C7CD6, StringBuilder__Append_244D3E44, StringBuilder__Append_43A65C09, StringBuilder__Append_487EF8FB, StringBuilder__Append_4E60E31B, StringBuilder__Append_5E38073B, StringBuilder__Append_61B1CA, StringBuilder__Append_Z1FBCCD16, StringBuilder__Append_Z372E4D23, StringBuilder__Append_Z510FF069, StringBuilder__Append_Z524259A4, StringBuilder__Append_Z524259C1, StringBuilder__Append_Z524259E6, StringBuilder__Append_Z6EF827B6, StringBuilder__Append_Z6EF827D7, StringBuilder__Append_Z6EF82811, StringBuilder__Append_Z7138B98C, StringBuilder__Append_Z721C83C5, StringBuilder__Clear, StringBuilder__Replace_Z384F8060, StringBuilder__Replace_Z766F94C0, StringBuilder__ToString_Z37302880, StringBuilder__get_Chars_Z524259A4, StringBuilder__get_Length, StringBuilder__set_Chars_413E0D0A };

package/dist/ts/node_modules/@fable-org/fable-library-ts/Util.js

@@ -518,10 +518,16 @@ function count(col) {
   }
 }
 function clear(col) {
-  if (isArrayLike(col)) {
-    col.splice(0);
-  } else {
+  if (Array.isArray(col)) {
+    col.length = 0;
+  } else if (ArrayBuffer.isView(col)) {
+  } else if (typeof col.clear === "function") {
     col.clear();
+  } else if (typeof col["System.Collections.Generic.ICollection`1.Clear"] === "function") {
+    col["System.Collections.Generic.ICollection`1.Clear"]();
+  } else if (typeof col["System.Collections.IList.Clear"] === "function") {
+    col["System.Collections.IList.Clear"]();
+  } else {
   }
 }
 const curried = /* @__PURE__ */ new WeakMap();

package/dist/ts/node_modules/@fable-org/fable-library-ts/lib/big.js

@@ -267,6 +267,11 @@ function round(x, sd, rm, more) {
 }
 
 
+function hasNonzeroDigit(x) {
+  return x.c.some(d => d !== 0);
+}
+
+
 /*
  * Return a string representing the value of Big x in normal or exponential notation.
  * Handles P.toExponential, P.toFixed, P.toJSON, P.toPrecision, P.toString and P.valueOf.
@@ -932,7 +937,7 @@ P.times = P.mul = function (y) {
  */
 P.toExponential = function (dp, rm) {
   var x = this,
-    n = x.c[0];
+    n = hasNonzeroDigit(x);
 
   if (dp !== UNDEFINED) {
     if (dp !== ~~dp || dp < 0 || dp > MAX_DP) {
@@ -942,7 +947,7 @@ P.toExponential = function (dp, rm) {
     for (; x.c.length < dp;) x.c.push(0);
   }
 
-  return stringify(x, true, !!n);
+  return stringify(x, true, n);
 };
 
 
@@ -953,24 +958,24 @@ P.toExponential = function (dp, rm) {
  * dp? {number} Decimal places: integer, 0 to MAX_DP inclusive.
  * rm? {number} Rounding mode: 0 (down), 1 (half-up), 2 (half-even) or 3 (up).
  *
- * (-0).toFixed(0) is '0', but (-0.1).toFixed(0) is '-0'.
- * (-0).toFixed(1) is '0.0', but (-0.01).toFixed(1) is '-0.0'.
+ * Unlike JavaScript, the sign is omitted when the rounded result is zero:
+ * (-0.1).toFixed(0) is '0' and (-0.01).toFixed(1) is '0.0', matching .NET.
  */
 P.toFixed = function (dp, rm) {
-  var x = this,
-    n = x.c[0];
+  var x = this;
 
   if (dp !== UNDEFINED) {
     if (dp !== ~~dp || dp < 0 || dp > MAX_DP) {
       throw Error(INVALID_DP);
     }
-    x = round(new x.constructor(x), dp + x.e + 1, rm);
+    x = new x.constructor(x);
+    x = round(x, dp + x.e + 1, rm);
 
     // x.e may have changed if the value is rounded up.
     for (dp = dp + x.e + 1; x.c.length < dp;) x.c.push(0);
   }
 
-  return stringify(x, false, !!n);
+  return stringify(x, false, hasNonzeroDigit(x));
 };
 
 
@@ -983,7 +988,7 @@ P.toFixed = function (dp, rm) {
 P.toJSON = P.toString = function () {
   var x = this,
     Big = x.constructor;
-  return stringify(x, x.e <= Big.NE || x.e >= Big.PE, !!x.c[0]);
+  return stringify(x, x.e <= Big.NE || x.e >= Big.PE, hasNonzeroDigit(x));
 };
 
 
@@ -1011,7 +1016,7 @@ P.toNumber = function () {
 P.toPrecision = function (sd, rm) {
   var x = this,
     Big = x.constructor,
-    n = x.c[0];
+    n = hasNonzeroDigit(x);
 
   if (sd !== UNDEFINED) {
     if (sd !== ~~sd || sd < 1 || sd > MAX_DP) {
@@ -1021,7 +1026,7 @@ P.toPrecision = function (sd, rm) {
     for (; x.c.length < sd;) x.c.push(0);
   }
 
-  return stringify(x, sd <= x.e || x.e <= Big.NE || x.e >= Big.PE, !!n);
+  return stringify(x, sd <= x.e || x.e <= Big.NE || x.e >= Big.PE, n);
 };
 
 

package/dist/ts/ts/ARC.d.ts

@@ -1,7 +1,7 @@
 import { FileSystem } from './FileSystem/FileSystem.ts';
 import { Option } from '@fable-org/fable-library-ts/Option.ts';
 import { License } from './License.ts';
-import { ArcStudy, ArcWorkflow, ArcRun, ArcAssay, ArcInvestigation } from './Core/ArcTypes.ts';
+import { ArcRun, ArcWorkflow, ArcStudy, ArcAssay, ArcInvestigation } from './Core/ArcTypes.ts';
 import { MutableArray } from '@fable-org/fable-library-ts/Util.ts';
 import { Contract } from './Contract/Contract.ts';
 import { FSharpResult$2_$union } from '@fable-org/fable-library-ts/Result.ts';
@@ -29,7 +29,7 @@ export declare class ARC extends ArcInvestigation {
     get License(): License | undefined;
     set License(license: Option<License>);
     static fromArcInvestigation(isa: ArcInvestigation, fs?: FileSystem, license?: License): ARC;
-    TryWriteAsync(arcPath: string, forceOverwrite?: boolean): Promise<FSharpResult$2_$union<MutableArray<Contract>, MutableArray<string>>>;
+    TryWriteAsync(arcPath: string, forceOverwrite?: boolean, additionalContracts?: MutableArray<Contract>): Promise<FSharpResult$2_$union<MutableArray<Contract>, MutableArray<string>>>;
     TryUpdateAsync(arcPath: string, forceOverwrite?: boolean): Promise<FSharpResult$2_$union<MutableArray<Contract>, MutableArray<string>>>;
     SetLicenseFulltext(fulltext: string, path?: string): void;
     static tryLoadAsync(arcPath: string): Promise<FSharpResult$2_$union<ARC, MutableArray<string>>>;
@@ -53,7 +53,7 @@ export declare class ARC extends ArcInvestigation {
     TryRemoveStudyAsync(arcPath: string, studyIdentifier: string): Promise<FSharpResult$2_$union<MutableArray<Contract>, MutableArray<string>>>;
     GetStudyRenameContracts(oldStudyIdentifier: string, newStudyIdentifier: string): MutableArray<Contract>;
     TryRenameStudyAsync(arcPath: string, oldStudyIdentifier: string, newStudyIdentifier: string): Promise<FSharpResult$2_$union<MutableArray<Contract>, MutableArray<string>>>;
-    WriteAsync(arcPath: string): Promise<void>;
+    WriteAsync(arcPath: string, additionalContracts?: MutableArray<Contract>): Promise<void>;
     UpdateAsync(arcPath: string): Promise<void>;
     RemoveAssayAsync(arcPath: string, assayIdentifier: string): Promise<void>;
     RenameAssayAsync(arcPath: string, oldAssayIdentifier: string, newAssayIdentifier: string): Promise<void>;

package/dist/ts/ts/ARC.d.ts.map

@@ -1 +1 @@
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