@ca-plant-list/ca-plant-list 0.3.0 → 0.3.2

package/.vscode/settings.json

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

package/data/exceptions.json

@@ -19,7 +19,7 @@
             "translation": "Castilleja ambigua subsp. ambigua"
         }
     },
-    "Lupinus littoralis var. variicolor": {
+    "Downingia ornatissima var. mirabilis": {
         "inat": {
             "notintaxondata": true
         }
@@ -42,17 +42,40 @@
             "notintaxondata": true
         }
     },
-    "Downingia ornatissima var. mirabilis": {
+    "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": "in CNPS Rare Plant Inventory"
+            "notineflora": true
         }
     },
     "Ravenella exigua": {
+        "comment": "in CNPS Rare Plant Inventory as Ravenella",
         "rpi": {
             "translation": "Campanula exigua"
         }

package/data/synonyms.csv

@@ -25,7 +25,7 @@ Achnatherum lemmonii subsp. lemmonii,Stipa lemmonii var. lemmonii
 Acmispon strigosus var. hirtellus,Acmispon strigosus
 Acroptilon repens,Rhaponticum repens
 Actaea rubra subsp. arguta,Actaea rubra
-Adelinia grande,Adelinia grandis,INAT
+Adelinia grandis,Adelinia grandis,INAT
 Adiantum boreale,Adiantum aleuticum
 Adiantum pedatum subsp. calderi,Adiantum aleuticum
 Adiantum pedatum var. aleuticum,Adiantum aleuticum
@@ -832,6 +832,8 @@ Heracleum lanatum,Heracleum maximum
 Herniaria cinerea,Herniaria hirsuta var. cinerea,INAT
 Herniaria hirsuta subsp. cinerea,Herniaria hirsuta var. cinerea
 Herpestris pilosa,Mimetanthe pilosa
+Hesperocyparis macrocarpa,Hesperocyparis macrocarpa,INAT
+Hesperocyparis sargentii,Hesperocyparis sargentii,INAT
 Hesperomecon filiformis,Hesperomecon linearis
 Hesperoscordum hyacinthinum,Triteleia hyacinthina
 Hesperoscordum lacteum,Triteleia hyacinthina
@@ -1121,6 +1123,7 @@ Medicago polymorpha var. brevispina,Medicago polymorpha
 Medicago sativa subsp. falcata,Medicago sativa
 Medicago sativa subsp. sativa,Medicago sativa
 Mentha arvensis var. canadensis,Mentha canadensis
+Mentha arvensis var. villosa,Mentha canadensis
 Mentha citrata,Mentha aquatica
 Mentzelia dispersa var. compacta,Mentzelia dispersa
 Mentzelia dispersa var. dispersa,Mentzelia dispersa
@@ -1265,7 +1268,6 @@ Myosurus minimus subsp. major,Myosurus minimus
 Myosurus minimus var. filiformis,Myosurus minimus
 Myosurus minimus var. major,Myosurus minimus
 Myosurus minimus var. sessiliflorus,Myosurus sessilis
-Myosurus minimus,Myosurus minimus subsp. minimus,INAT
 Myrica californica,Morella californica
 Myriophyllum brasiliense,Myriophyllum aquaticum
 Myriophyllum exalbescens,Myriophyllum sibiricum

package/data/taxa.csv

@@ -27,7 +27,7 @@ Acmispon parviflorus,least trefoil,N,91717,11299,57048
 Acmispon strigosus,,N,91722,11305,58152
 Acmispon wrangelianus,common trefoil,N,82483,11306,57050
 Actaea rubra,baneberry,N,11894,93,49870
-Adelinia grandis,hound's tongue,N,101954,14544,769151,blue
+Adelinia grandis,hound's tongue,N,101954,14544,1520640,blue
 Adenocaulon bicolor,American trailplant,N,721,94,56854
 Adenostoma fasciculatum,chamise,N,11939,97,47146
 Adiantum aleuticum,five-finger fern,N,11945,100,52667
@@ -201,7 +201,7 @@ Balsamorhiza deltoidea,,N,1634,1047,70383
 Balsamorhiza macrolepis,,N,1639,1051,69665,,,,350,1B.2,,,S2,G2
 Barbarea orthoceras,winter cress,N,15481,1057,52976
 Bassia hyssopifolia,,X,15511,1060,58125
-Bellardia trixago var. trixago,,X,8635,1064,1115038
+Bellardia trixago var. trixago,,X,8635,14706,1115038
 Bellis perennis,English daisy,X,1652,1065,55563
 Berberis aquifolium var. aquifolium,,N,71483,1068,126887
 Berberis aquifolium var. dictyota,,N,76967,1069,775436
@@ -846,8 +846,8 @@ Hesperevax acaulis var. ambusticola,fire evax,N,59934,4108,80930
 Hesperevax caulescens,hogwallow starfish,N,28021,4110,60135,,,,1931,4.2,,,S3,G3
 Hesperevax sparsiflora var. sparsiflora,,N,59937,4113,61172
 Hesperocnide tenella,black haired nettle,N,28033,4118,59036
-Hesperocyparis macrocarpa,Monterey cypress,N,89298,11190,322545,,,,536,1B.2,,,S1,G1
-Hesperocyparis sargentii,Sargent cypress,N,89302,10803,83149
+Hesperocyparis macrocarpa,Monterey cypress,N,89298,11190,77378,,,,536,1B.2,,,S1,G1
+Hesperocyparis sargentii,Sargent cypress,N,89302,10803,77381
 Hesperolinon breweri,Brewer's dwarf flax,N,28038,4121,77385,,,,404,1B.2,,,S2,G2
 Hesperolinon californicum,California dwarf flax,N,28039,4122,77386
 Hesperolinon clevelandii,,N,28040,4123,77387
@@ -1103,8 +1103,9 @@ 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,,,,1065,1B.2,,,S2,G2
 Malacothamnus fremontii,white-coat mallow,N,32524,5312,70397
-Malacothamnus arcuatus var. elmeri,,N,108345,14681,1497404
+Malacothamnus hallii,,N,108345,14681,1497404,,,,1065,1B.2,,,S2,G2
 Malacothrix californica,,N,4059,5325,58026
 Malacothrix clevelandii,Cleveland's malacothrix,N,4060,5326,58841
 Malacothrix coulteri,snake's-head,N,4061,5327,58027
@@ -1145,7 +1146,7 @@ Mentha spicata,spearmint,X,33209,10111,62652
 Mentha suaveolens,pineapple mint,X,33212,5417,77993
 Mentzelia affinis,,N,33219,5418,58194
 Mentzelia dispersa,,N,33236,5423,58196
-Mentzelia laevicaulis var. laevicaulis,blazingstar,N,61864,5431,241687
+Mentzelia laevicaulis var. laevicaulis,blazingstar,N,61864,14741,241687
 Mentzelia lindleyi,,N,33255,5432,53923
 Mentzelia micrantha,,N,33259,5433,58933
 Mentzelia pectinata,,N,33274,5439,58198
@@ -1377,7 +1378,7 @@ Pogogyne douglasii,,N,38936,6704,63943
 Pogogyne serpylloides,,N,38939,6708,57118
 Pogogyne zizyphoroides,,N,78298,6709,60209
 Polemonium carneum,royal sky pilot,N,38971,6712,78665,,,,3345,2B.2,,,S2,G3G4
-Polycarpon tetraphyllum subsp. tetraphyllum,four-leaved allseed,X,80560,11032,81277
+Polycarpon tetraphyllum subsp. tetraphyllum,four-leaved allseed,X,80560,14756,81277
 Polygonum argyrocoleon,persian knotweed,X,39158,6738,78676
 Polygonum aviculare subsp. aviculare,,X,80990,10667,80151
 Polygonum aviculare subsp. depressum,,X,80993,11034,63967
@@ -1761,7 +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
@@ -1825,7 +1826,7 @@ Woodwardia fimbriata,giant chain fern,N,48619,8355,52685
 Wyethia angustifolia,narrowleaf mule-ears,N,5572,8356,56987,yellow
 Wyethia glabra,mules ears,N,5578,8359,56988,yellow
 Wyethia helenioides,woolly mules ears,N,5579,8360,50799,yellow
-Xanthium orientale,cocklebur,N,5618,8367,506262
+Xanthium orientale,cocklebur,N,5618,14779,506262
 Xanthium spinosum,spiny cocklebur,X,5590,8366,58045
 Yabea microcarpa,California hedge parsley,N,48745,8373,56847
 Zannichellia palustris,horned-pondweed,N,48827,8379,79546

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/basepagerenderer.js

@@ -12,7 +12,6 @@ class BasePageRenderer {
         const siteGenerator = new Jekyll( outputDir );
 
         // Copy static files
-        Files.rmDir( outputDir );
         // First copy default Jekyll files from package.
         Files.copyDir( Config.getPackageDir() + "/jekyll", outputDir );
         // Then copy Jekyll files from current dir (which may override default files).

package/lib/commandandtaxaprocessor.js

@@ -1,4 +1,5 @@
 import { CommandProcessor } from "./commandprocessor.js";
+import { Files } from "./files.js";
 import { TaxaProcessor } from "./taxaprocessor.js";
 
 class CommandAndTaxaProcessor extends CommandProcessor {
@@ -14,6 +15,8 @@ class CommandAndTaxaProcessor extends CommandProcessor {
         if ( this.helpShown() ) {
             return;
         }
+        Files.rmDir( this.getOptions().outputdir );
+
         await this.#taxaProcessor.process( commandRunner );
     }
 

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.
@@ -218,39 +231,45 @@ export class Taxa {
     getFlowerColor(name: any): any;
     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 };
@@ -272,10 +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 = {
@@ -75,9 +76,13 @@ class Taxa {
     #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 ) {
@@ -153,18 +158,33 @@ class Taxa {
         return this.#sortedTaxa;
     }
 
+    hasSynonym( formerName ) {
+        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" ];
             const taxon = this.getTaxon( currName );
             if ( !taxon ) {
-                if ( inclusionList === true ) {
-                    // If including all taxa, note the error.
+                if ( inclusionList === true && !syn.Type ) {
+                    // If including all taxa, note the error - the target is not defined, and this is not
+                    // a synonym for a non-Jepson system.
                     console.log( "synonym target not found: " + currName );
                 }
                 continue;
             }
-            taxon.addSynonym( syn[ "Former" ], syn[ "Type" ] );
+            const formerName = syn[ "Former" ];
+            this.#synonyms.add( formerName );
+            taxon.addSynonym( formerName, syn[ "Type" ] );
         }
     }
 

package/lib/taxaprocessor.js

@@ -27,8 +27,8 @@ class TaxaProcessor {
         console.log( "loading data" );
         this.#taxaLoader = new this.#taxaLoaderClass( this.#options );
         await this.#taxaLoader.load();
-        await commandRunner( this );
         this.#taxaLoader.writeErrorLog();
+        await commandRunner( this );
     }
 
 }

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": "0.3.0",
+    "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"
     }
-}
+}