@ca-plant-list/ca-plant-list 0.3.1 → 0.3.2

package/.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "editor.formatOnSave": true
+}

package/data/exceptions.json

@@ -1,88 +1,96 @@
 {
-  "Campanula exigua": {
-    "rpi": {
-      "translation-to-rpi": "Ravenella exigua"
-    }
-  },
-  "Campanula sharsmithiae": {
-    "rpi": {
-      "translation-to-rpi": "Ravenella sharsmithiae"
-    }
-  },
-  "Castilleja ambigua subsp. ambigua": {
-    "rpi": {
-      "translation-to-rpi": "Castilleja ambigua var. ambigua"
-    }
-  },
-  "Castilleja ambigua var. ambigua": {
-    "rpi": {
-      "translation": "Castilleja ambigua subsp. ambigua"
-    }
-  },
-  "Downingia ornatissima var. mirabilis": {
-    "inat": {
-      "notintaxondata": true
-    }
-  },
-  "Erysimum capitatum var. angustatum": {
-    "calflora": {
-      "badjepsonid": true
+    "Campanula exigua": {
+        "rpi": {
+            "translation-to-rpi": "Ravenella exigua"
+        }
     },
-    "jepson": {
-      "allowsynonym": true
-    }
-  },
-  "Heterotheca oregona var. rudis": {
-    "inat": {
-      "notintaxondata": true
-    }
-  },
-  "Horkelia californica var. frondosa": {
-    "inat": {
-      "notintaxondata": true
-    }
-  },
-  "Lupinus littoralis var. variicolor": {
-    "inat": {
-      "notintaxondata": true
-    }
-  },
-  "Malacothamnus hallii": {
-    "comment": "in CNPS Rare Plant Inventory",
-    "calflora": {
-      "notintaxondata": true
+    "Campanula sharsmithiae": {
+        "rpi": {
+            "translation-to-rpi": "Ravenella sharsmithiae"
+        }
     },
-    "jepson": {
-      "allowsynonym": true
-    }
-  },
-  "Malacothamnus arcuatus var. elmeri": {
-    "calflora": {
-      "badjepsonid": true
-    }
-  },
-  "Myosurus minimus subsp. apus": {
-    "comment": "in CNPS Rare Plant Inventory",
-    "jepson": {
-      "notineflora": true
-    }
-  },
-  "Ravenella exigua": {
-    "rpi": {
-      "translation": "Campanula exigua"
-    }
-  },
-  "Ravenella sharsmithiae": {
-    "rpi": {
-      "translation": "Campanula sharsmithiae"
-    }
-  },
-  "Streptanthus albidus subsp. peramoenus": {
-    "calflora": {
-      "notintaxondata": true
+    "Castilleja ambigua subsp. ambigua": {
+        "rpi": {
+            "translation-to-rpi": "Castilleja ambigua var. ambigua"
+        }
+    },
+    "Castilleja ambigua var. ambigua": {
+        "rpi": {
+            "translation": "Castilleja ambigua subsp. ambigua"
+        }
+    },
+    "Downingia ornatissima var. mirabilis": {
+        "inat": {
+            "notintaxondata": true
+        }
+    },
+    "Erysimum capitatum var. angustatum": {
+        "calflora": {
+            "badjepsonid": true
+        },
+        "jepson": {
+            "allowsynonym": true
+        }
+    },
+    "Heterotheca oregona var. rudis": {
+        "inat": {
+            "notintaxondata": true
+        }
+    },
+    "Horkelia californica var. frondosa": {
+        "inat": {
+            "notintaxondata": true
+        }
+    },
+    "Lupinus littoralis var. variicolor": {
+        "inat": {
+            "notintaxondata": true
+        }
+    },
+    "Malacothamnus hallii": {
+        "comment": "in CNPS Rare Plant Inventory",
+        "calflora": {
+            "notintaxondata": true
+        },
+        "jepson": {
+            "allowsynonym": true
+        },
+        "rpi": {
+            "translation": "Malacothamnus arcuatus var. elmeri"
+        }
+    },
+    "Malacothamnus arcuatus var. elmeri": {
+        "comment": "in CNPS Rare Plant Inventory as Malacothamnus hallii",
+        "calflora": {
+            "badjepsonid": true
+        },
+        "rpi": {
+            "translation-to-rpi": "Malacothamnus hallii"
+        }
+    },
+    "Myosurus minimus subsp. apus": {
+        "comment": "in CNPS Rare Plant Inventory",
+        "jepson": {
+            "notineflora": true
+        }
+    },
+    "Ravenella exigua": {
+        "comment": "in CNPS Rare Plant Inventory as Ravenella",
+        "rpi": {
+            "translation": "Campanula exigua"
+        }
+    },
+    "Ravenella sharsmithiae": {
+        "rpi": {
+            "translation": "Campanula sharsmithiae"
+        }
     },
-    "jepson": {
-      "allowsynonym": true
+    "Streptanthus albidus subsp. peramoenus": {
+        "calflora": {
+            "notintaxondata": true
+        },
+        "jepson": {
+            "allowsynonym": true
+        }
     }
-  }
-}
+}

package/data/taxa.csv

@@ -1103,7 +1103,7 @@ Madia radiata,showy madia,N,4053,5296,77924,,,,1054,1B.1,,,S3,G3
 Madia sativa,coast tarweed,N,4055,5298,53143,yellow
 Maianthemum racemosum,false Solomon's seal,N,32495,10096,51062
 Maianthemum stellatum,,N,32497,9629,53268
-Malacothamnus arcuatus var. elmeri,,N,108345,14681,1497404
+Malacothamnus arcuatus var. elmeri,,N,108345,14681,1497404,,,,1065,1B.2,,,S2,G2
 Malacothamnus fremontii,white-coat mallow,N,32524,5312,70397
 Malacothamnus hallii,,N,108345,14681,1497404,,,,1065,1B.2,,,S2,G2
 Malacothrix californica,,N,4059,5325,58026
@@ -1762,7 +1762,7 @@ Triglochin concinna var. concinna,slender arrow-grass,N,74018,8112,81439
 Triglochin maritima,seaside arrow-grass,N,47197,8114,60264
 Triglochin scilloides,flowering quillwort,N,91083,12117,79437
 Triglochin striata,,N,47201,8116,79438
-Trillium chloropetalum,giant trillium,N,47218,8119,50823
+Trillium chloropetalum,giant trillium,N,47218,8119,50823,"yellow,pink,purple,white",4,5
 Trillium ovatum subsp. ovatum,white trillium,N,53276,8122,63972
 Triodanis biflora,Venus' looking-glass,N,47267,8126,79440
 Triphysaria eriantha subsp. eriantha,butter-and-eggs,N,53279,8129,59332

package/data/text/Trillium-chloropetalum.md

@@ -1 +1 @@
-Tissue between anther sacs purple. Ovaries purple.
+Tissue between anther sacs purple, ovaries purple. In _T. albidum_, both ovaries and tissue between anther sacs are usually greenish.

package/lib/csv.js

@@ -39,6 +39,12 @@ class CSV {
         return options;
     }
 
+    /**
+     * @param {string} dir 
+     * @param {string} fileName 
+     * @param {boolean|undefined} [columns] 
+     * @param {string|undefined} [delimiter] 
+     */
     static parseFile( dir, fileName, columns = true, delimiter ) {
         const content = fs.readFileSync( dir + "/" + fileName );
 
@@ -46,6 +52,13 @@ class CSV {
         return parseSync( content, options );
     }
 
+    /**
+     * @param {string} dir 
+     * @param {string} fileName 
+     * @param {boolean|undefined} columns 
+     * @param {string|undefined} delimiter 
+     * @param {*} callback 
+     */
     static async parseStream( dir, fileName, columns = true, delimiter, callback ) {
         const options = this.#getOptions( fileName, columns, delimiter );
         const processFile = async () => {

package/lib/exceptions.js

@@ -18,6 +18,8 @@ class Exceptions {
         const localExceptions = readConfig( dir + "/exceptions.json" );
         for ( const [ k, v ] of Object.entries( localExceptions ) ) {
             this.#exceptions[ k ] = v;
+            // Tag as a local exception so we can distinguish between global and local.
+            v.local = true;
         }
 
     }

package/lib/html.js

@@ -52,8 +52,8 @@ export class HTML {
      * Generate HTML for an <a> element.
      * @param {string|undefined} href 
      * @param {string} linkText 
-     * @param {Object} attributes 
-     * @param {boolean} openInNewWindow true if the link should open in a new window.
+     * @param {Object} [attributes] 
+     * @param {boolean} [openInNewWindow] true if the link should open in a new window.
      * @returns {string} an HTML <a> element.
      */
     static getLink( href, linkText, attributes = {}, openInNewWindow ) {

package/lib/index.d.ts

@@ -36,8 +36,21 @@ export class CSV {
     static "__#8@#getOptions"(fileName: any, columns: any, delimiter: any): {
         relax_column_count_less: boolean;
     };
-    static parseFile(dir: any, fileName: any, columns: boolean, delimiter: any): any;
-    static parseStream(dir: any, fileName: any, columns: boolean, delimiter: any, callback: any): Promise<void>;
+    /**
+     * @param {string} dir
+     * @param {string} fileName
+     * @param {boolean|undefined} [columns]
+     * @param {string|undefined} [delimiter]
+     */
+    static parseFile(dir: string, fileName: string, columns?: boolean | undefined, delimiter?: string | undefined): any;
+    /**
+     * @param {string} dir
+     * @param {string} fileName
+     * @param {boolean|undefined} columns
+     * @param {string|undefined} delimiter
+     * @param {*} callback
+     */
+    static parseStream(dir: string, fileName: string, columns: boolean | undefined, delimiter: string | undefined, callback: any): Promise<void>;
 }
 export class DateUtils {
     static getMonthName(monthNum: any): string;
@@ -118,8 +131,8 @@ export class GenericTaxaLoader {
 }
 import { ErrorLog } from "./errorlog.js";
 export namespace HTML_OPTIONS {
-    const OPEN_NEW: number;
-    const NO_ESCAPE: number;
+    let OPEN_NEW: number;
+    let NO_ESCAPE: number;
 }
 /** HTML utility functions. */
 export class HTML {
@@ -135,11 +148,11 @@ export class HTML {
      * Generate HTML for an &lt;a> element.
      * @param {string|undefined} href
      * @param {string} linkText
-     * @param {Object} attributes
-     * @param {boolean} openInNewWindow true if the link should open in a new window.
+     * @param {Object} [attributes]
+     * @param {boolean} [openInNewWindow] true if the link should open in a new window.
      * @returns {string} an HTML &lt;a> element.
      */
-    static getLink(href: string | undefined, linkText: string, attributes: any, openInNewWindow: boolean): string;
+    static getLink(href: string | undefined, linkText: string, attributes?: any, openInNewWindow?: boolean): string;
     /**
      * Get a Bootstrap formatted tooltip element.
      * @param {string} text - The text or HTML that should trigger the tooltip on hover.
@@ -219,39 +232,44 @@ export class Taxa {
     getTaxon(name: any): any;
     getTaxonList(): any[];
     hasSynonym(formerName: any): boolean;
+    /**
+     * true if an inclusion list was supplied when reading the taxa.
+     * @returns {boolean}
+     */
+    isSubset(): boolean;
     #private;
 }
 export namespace TAXA_LIST_COLS {
     namespace CESA {
-        const title: string;
+        let title: string;
         function data(t: any): any;
     }
     namespace COMMON_NAME {
-        const title_1: string;
+        let title_1: string;
         export { title_1 as title };
         export function data_1(t: any): any;
         export { data_1 as data };
     }
     namespace CNPS_RANK {
-        const title_2: string;
+        let title_2: string;
         export { title_2 as title };
         export function data_2(t: any): string;
         export { data_2 as data };
     }
     namespace FESA {
-        const title_3: string;
+        let title_3: string;
         export { title_3 as title };
         export function data_3(t: any): any;
         export { data_3 as data };
     }
     namespace SPECIES {
-        const title_4: string;
+        let title_4: string;
         export { title_4 as title };
         export function data_4(t: any): any;
         export { data_4 as data };
     }
     namespace SPECIES_BARE {
-        const title_5: string;
+        let title_5: string;
         export { title_5 as title };
         export function data_5(t: any): any;
         export { data_5 as data };
@@ -273,10 +291,10 @@ export class TaxaProcessor {
 }
 import { TaxaLoader } from "./taxaloader.js";
 export namespace TAXA_COLNAMES {
-    const BLOOM_START: string;
-    const BLOOM_END: string;
-    const COMMON_NAME: string;
-    const FLOWER_COLOR: string;
+    let BLOOM_START: string;
+    let BLOOM_END: string;
+    let COMMON_NAME: string;
+    let FLOWER_COLOR: string;
 }
 export class Taxon {
     constructor(data: any);

package/lib/taxa.js

@@ -11,6 +11,7 @@ const FLOWER_COLORS = [
     { name: "orange", color: "orange" },
     { name: "yellow", color: "yellow" },
     { name: "blue", color: "blue" },
+    { name: "purple", color: "purple" },
 ];
 
 const TAXA_LIST_COLS = {
@@ -76,9 +77,12 @@ class Taxa {
     #flower_colors = {};
     #sortedTaxa;
     #synonyms = new Set();
+    #isSubset;
 
     constructor( inclusionList, errorLog, showFlowerErrors, taxaMeta = {}, taxonClass = Taxon, extraTaxa = [], extraSynonyms = [] ) {
 
+        this.#isSubset = ( inclusionList !== true );
+
         this.#errorLog = errorLog;
 
         for ( const color of FLOWER_COLORS ) {
@@ -158,6 +162,14 @@ class Taxa {
         return this.#synonyms.has( formerName );
     }
 
+    /**
+     * true if an inclusion list was supplied when reading the taxa.
+     * @returns {boolean}
+     */
+    isSubset() {
+        return this.#isSubset;
+    }
+
     #loadSyns( synCSV, inclusionList ) {
         for ( const syn of synCSV ) {
             const currName = syn[ "Current" ];

package/lib/web/pagetaxon.js

@@ -1,9 +1,9 @@
-import { HTML } from "@ca-plant-list/ca-plant-list";
 import { Jepson } from "../jepson.js";
 import { RarePlants } from "../rareplants.js";
 import { GenericPage } from "../genericpage.js";
 import { ExternalSites } from "../externalsites.js";
 import { DateUtils } from "../dateutils.js";
+import { HTML } from "../html.js";
 
 class PageTaxon extends GenericPage {
 

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.3.1",
+    "version": "0.3.2",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {
@@ -36,6 +36,6 @@
     "devDependencies": {
         "@types/node": "^18.11.9",
         "eslint": "^8.26.0",
-        "typescript": "^4.9.3"
+        "typescript": "^5.3.3"
     }
-}
+}