@ca-plant-list/ca-plant-list 0.4.17 → 0.4.18

package/data/taxa.csv

@@ -227,10 +227,10 @@ Bolboschoenus maritimus subsp. paludosus,saltmarsh bulrush,N,49436,10796,79646,P
 Bolboschoenus robustus,seacoast bulrush,N,77450,10798,75840,Big Bulrush
 Bowlesia incana,,N,15999,1133,56822,Hoary Bowlesia
 Brachypodium distachyon,false-brome,X,16042,1137,57158
-Brassica juncea,India mustard,X,16072,1142,64241
-Brassica nigra,black mustard,X,16079,1144,1555489,,,yellow
-Brassica oleracea,cabbage,X,16080,9040,54516
-Brassica rapa,field mustard,X,16081,1145,53271,,,yellow
+Brassica juncea,India mustard,X,16072,1142,64241,,"annual,perennial",yellow,5,9
+Brassica nigra,black mustard,X,16079,1144,1555489,,annual,yellow,4,9
+Brassica oleracea,cabbage,X,16080,9040,54516,,"biennial,perennial",yellow,5,8
+Brassica rapa,field mustard,X,16081,1145,53271,,"annual,biennial",yellow,1,5
 Brickellia californica,California brickelbush,N,1794,1152,58803,Brickell Bush
 Briza maxima,quaking grass,X,16135,1165,57157
 Briza minor,little quaking grass,X,16137,1166,57162
@@ -1075,11 +1075,11 @@ Linanthus dichotomus subsp. meridianus,,N,51287,10625,80001
 Linanthus pungens subsp. pulchriflorus,granite prickly phlox,N,98684,14586,861790,,perennial,"white,pink",5,8
 Linum bienne,,X,31144,4906,55679
 Linum lewisii var. lewisii,blue flax,N,60912,4910,60495,Prairie Flax
-Lithophragma affine,woodland star,N,31236,4922,50803,San Francisco Woodland Star,,white,3,4
-Lithophragma bolanderi,,N,31238,4923,77787,Bolander's Woodland Star
-Lithophragma cymbalaria,,N,31241,4925,58323,Mission Woodland Star
-Lithophragma heterophyllum,hill starflower,N,31244,4927,53124,Hillside Woodland Star,,white
-Lithophragma parviflorum var. parviflorum,,N,60952,4930,81027,Smallflower Woodland-star,,"white,pink",3,7
+Lithophragma affine,woodland star,N,31236,4922,50803,San Francisco Woodland Star,perennial,white,3,4
+Lithophragma bolanderi,,N,31238,4923,77787,Bolander's Woodland Star,perennial,white,2,7
+Lithophragma cymbalaria,,N,31241,4925,58323,Mission Woodland Star,perennial,white,3,5
+Lithophragma heterophyllum,hill starflower,N,31244,4927,53124,Hillside Woodland Star,perennial,white,2,6
+Lithophragma parviflorum var. parviflorum,,N,60952,4930,81027,Smallflower Woodland-star,perennial,"white,pink",3,7
 Lobularia maritima,sweet alyssum,X,31347,4939,56992
 Logfia filaginoides,herba impia,N,81847,10960,64254,California Cottonrose,annual,red,2,5
 Logfia gallica,,X,31363,9521,56949,,annual,"brown,yellow",3,7
@@ -1285,9 +1285,10 @@ Osmorhiza berteroi,wood cicely,N,35560,10164,53166,Sweet Cicely
 Osmorhiza brachypoda,California cicely,N,35564,6000,58793,California Sweetcicely
 Oxalis corniculata,creeping wood sorrel,X,35609,6010,53168,,,yellow,1,12
 Oxalis incarnata,crimson wood sorrel,X,35636,6012,61776,,,"white,pink",3,6
-Oxalis oregana,redwood sorrel,N,35641,6015,47757,Redwood Sorrel,,"white,pink",2,8
+Oxalis oregana,Oregon wood sorrel,N,35641,6015,47757,Redwood Sorrel,perennial,white,2,10
 Oxalis pes-caprae,Bermuda-buttercup,X,35642,6016,53169,,,yellow,1,5
 Oxalis pilosa,hairy wood sorrel,N,35601,11895,78300,Radishroot Woodsorrel,,yellow,2,9
+Oxalis smalliana,redwood sorrel,N,8615,14752,1464017,,perennial,"white,pink,blue",1,8
 Packera breweri,Brewer groundsel,N,77383,9613,56983,Groundsel
 Panicum acuminatum,Pacific panic grass,N,35923,6044,128949,Western Panicgrass
 Panicum capillare,witchgrass,N,36094,6048,78337,Witch Grass
@@ -1563,17 +1564,17 @@ Rubus pensilvanicus,,X,42114,7202,78894
 Rubus spectabilis,,N,42231,7203,47543,Salmon Berry
 Rubus ulmifolius var. anoplothyrsus,,X,91783,11997,81352
 Rubus ursinus,California blackberry,N,42267,7206,53445,California Blackberry
-Rumex acetosella,sheep sorrel,X,42362,7213,53195
-Rumex californicus,,N,42423,11058,78901,California Dock
-Rumex conglomeratus,green dock,X,42385,7214,57215
-Rumex crassus,,N,42422,11059,61087,Willow Dock
-Rumex crispus,curly dock,X,42386,7215,53197
-Rumex fueginus,golden dock,N,42405,10679,78903,Golden Dock
-Rumex obtusifolius,bitter dock,X,42409,7220,63371
-Rumex occidentalis,western dock,N,42376,7221,61086,Western Dock
-Rumex pulcher,fiddle dock,X,42419,7224,60232
-Rumex salicifolius,willow dock,N,42421,7225,60233,Willow Dock
-Rumex transitorius,,N,42429,11999,78910
+Rumex acetosella,sheep sorrel,X,42362,7213,53195,,perennial,,4,7
+Rumex californicus,,N,42423,11058,78901,California Dock,perennial,,5,9
+Rumex conglomeratus,green dock,X,42385,7214,57215,,perennial,,5,8
+Rumex crassus,,N,42422,11059,61087,Willow Dock,perennial,,2,7
+Rumex crispus,curly dock,X,42386,7215,53197,,perennial,,1,12
+Rumex fueginus,golden dock,N,42405,10679,78903,Golden Dock,annual,,5,8
+Rumex obtusifolius,bitter dock,X,42409,7220,63371,,perennial,,5,9
+Rumex occidentalis,western dock,N,42376,7221,61086,Western Dock,perennial,,5,8
+Rumex pulcher,fiddle dock,X,42419,7224,60232,,perennial,,5,9
+Rumex salicifolius,willow dock,N,42421,7225,60233,Willow Dock,perennial,,5,7
+Rumex transitorius,,N,42429,11999,78910,,perennial,,4,6
 Rupertia physodes,California tea,N,42446,7236,53198,Common Rupertia
 Ruppia cirrhosa,ditch-grass,N,42449,7238,61089,Spiral Ditchgrass
 Ruppia maritima,ditch-grass,N,42451,7239,61090,Beaked Tasselweed

package/data/text/Brassica-nigra.md

@@ -0,0 +1 @@
+Upper leaves not clasping stem. Usually hairy.

package/data/text/Brassica-rapa.md

@@ -0,0 +1 @@
+Upper leaves clasping stem. Usually not hairy.

package/data/text/Oxalis-oregana.footer.md

@@ -0,0 +1,3 @@
+## Resources
+
+- Brinegar, Chris. (2023). [THE TRUE REDWOOD SORREL: REINSTATEMENT OF OXALIS SMALLIANA (OXALIDACEAE) AS A SPECIES SEPARATE FROM OXALIS OREGANA](https://www.researchgate.net/publication/369602947_THE_TRUE_REDWOOD_SORREL_REINSTATEMENT_OF_OXALIS_SMALLIANA_OXALIDACEAE_AS_A_SPECIES_SEPARATE_FROM_OXALIS_OREGANA). Madroño. 69. 10.3120/0024-9637-69.4.304.

package/data/text/Oxalis-smalliana.footer.md

@@ -0,0 +1,3 @@
+## Resources
+
+- Brinegar, Chris. (2023). [THE TRUE REDWOOD SORREL: REINSTATEMENT OF OXALIS SMALLIANA (OXALIDACEAE) AS A SPECIES SEPARATE FROM OXALIS OREGANA](https://www.researchgate.net/publication/369602947_THE_TRUE_REDWOOD_SORREL_REINSTATEMENT_OF_OXALIS_SMALLIANA_OXALIDACEAE_AS_A_SPECIES_SEPARATE_FROM_OXALIS_OREGANA). Madroño. 69. 10.3120/0024-9637-69.4.304.

package/data/text/Rumex-acetosella.md

@@ -0,0 +1 @@
+Leaves with lobes at base. Plants unisexual.

package/lib/csv.js

@@ -85,9 +85,10 @@ class CSV {
     }
 
     /**
+     * @template T
      * @param {string} fileName
      * @param {string} [delimiter]
-     * @returns {{headers:string[],data:Object<string,any>[]}}
+     * @returns {{headers:string[],data:T[]}}
      */
     static readFileAndHeaders(fileName, delimiter) {
         let headers;

package/lib/exceptions.js

@@ -30,6 +30,9 @@ class Exceptions {
         }
     }
 
+    /**
+     * @returns {[string,Object<string,Object<string,string>>][]}
+     */
     getExceptions() {
         return Object.entries(this.#exceptions);
     }

package/lib/index.d.ts

@@ -24,6 +24,13 @@ export class ErrorLog {
 
 export class Exceptions {
     constructor(dataDir: string);
+    getExceptions(): [string, Record<string, Record<string, string>>][];
+    getValue(
+        name: string,
+        cat: string,
+        subcat: string,
+        defaultValue?: string | undefined,
+    ): string | undefined;
     hasException(name: string, cat: string, subcat: string): boolean;
 }
 
@@ -100,7 +107,9 @@ export class Taxon {
     getGenusName(): string;
     getINatID(): string;
     getINatTaxonLink(): string;
+    getJepsonID(): string;
     getName(): string;
+    getRPIRankAndThreat(): string;
     getRPITaxonLink(): string;
     getSynonyms(): string[];
 }

package/lib/taxon.js

@@ -264,6 +264,9 @@ class Taxon {
         return this.#iNatSyn ? link + " (" + this.#iNatSyn + ")" : link;
     }
 
+    /**
+     * @returns {string}
+     */
     getJepsonID() {
         return this.#jepsonID;
     }
@@ -287,6 +290,9 @@ class Taxon {
         return this.#rankRPI.split(".")[0];
     }
 
+    /**
+     * @returns {string}
+     */
     getRPIRankAndThreat() {
         return this.#rankRPI;
     }

package/lib/tools/jepsoneflora.js

@@ -1,10 +1,17 @@
 import { scrape } from "@htmltools/scrape";
 import { Files } from "../files.js";
+import { SynCSV } from "./syncsv.js";
 
 /**
- * @typedef {{id:string,name:string,common?:string,type:string,under:string}} JepsonInfo
+ * @typedef {{
+ * id:string,
+ * name:string,
+ * common?:string,
+ * type:string,
+ * }} JepsonTaxon
  */
 
+/** @type {Object<string,string>} */
 const TYPES = {
     EX_ALIEN: "Extirpated alien",
     HYBRID_SPONT: "Spontaneous hybrid",
@@ -32,44 +39,47 @@ const TYPES = {
     WEED: "* weed*",
 };
 
-class JepsonEFlora {
+export class JepsonEFlora {
     #toolsDataPath;
     #taxa;
     #errorLog;
-    #shouldLogNotes;
 
-    /** @type {Map<string,JepsonInfo>} */
+    /** @type {Map<string,JepsonTaxon>} */
     #nameInfo = new Map();
-    /** @type {Set<string>} */
-    #loadedLetters = new Set();
+    /** @type {Map<string,string[]>} */
+    #synInfo = new Map();
+    /** @type {import("./syncsv.js").SynData[]} */
+    #synonymsToAdd = [];
 
     /**
      * @param {string} toolsDataDir
      * @param {Taxa} taxa
      * @param {ErrorLog} errorLog
-     * @param {boolean} shouldLogNotes
      */
-    constructor(toolsDataDir, taxa, errorLog, shouldLogNotes) {
+    constructor(toolsDataDir, taxa, errorLog) {
         this.#toolsDataPath = toolsDataDir + "/jepson-eflora";
         this.#taxa = taxa;
         this.#errorLog = errorLog;
-        this.#shouldLogNotes = shouldLogNotes;
     }
 
     /**
      * @param {import("../exceptions.js").Exceptions} exceptions
+     * @param {boolean} update
      */
-    async analyze(exceptions) {
+    async analyze(exceptions, update) {
         // Create data directory if it's not there.
         Files.mkdir(this.#toolsDataPath);
 
+        // Retrieve all Jepson indexes.
+        await this.#loadIndexPages();
+
         for (const taxon of this.#taxa.getTaxonList()) {
             const name = taxon.getName();
             if (name.includes(" unknown")) {
                 continue;
             }
 
-            const jepsInfo = await this.#getJepsInfo(name);
+            const jepsInfo = this.#getJepsInfo(name);
             if (jepsInfo === undefined) {
                 // Not found in the index.
                 if (!exceptions.hasException(name, "jepson", "notineflora")) {
@@ -87,12 +97,6 @@ class JepsonEFlora {
                 );
             }
 
-            if (this.#isSynonym(jepsInfo)) {
-                if (!exceptions.hasException(name, "jepson", "allowsynonym")) {
-                    this.#errorLog.log(name, "is synonym for", jepsInfo.under);
-                }
-            }
-
             const efStatus = this.#getStatusCode(jepsInfo);
             const taxonStatus = taxon.getStatus();
             if (
@@ -108,8 +112,12 @@ class JepsonEFlora {
             }
         }
 
-        await this.#checkSynonyms();
+        this.#checkSynonyms();
         this.#checkExceptions(exceptions);
+
+        if (update) {
+            this.#updateSynCSV();
+        }
     }
 
     /**
@@ -140,15 +148,6 @@ class JepsonEFlora {
             for (const [k] of Object.entries(exceptions)) {
                 const jepsonData = this.#nameInfo.get(name);
                 switch (k) {
-                    case "allowsynonym":
-                        // Make sure it really is a synonym.
-                        if (!this.#isSynonym(jepsonData)) {
-                            this.#errorLog.log(
-                                name,
-                                "has Jepson allowsynonym exception but is not a synonym",
-                            );
-                        }
-                        break;
                     case "notineflora":
                         // Make sure it is really not in eFlora.
                         if (jepsonData) {
@@ -169,42 +168,43 @@ class JepsonEFlora {
         }
     }
 
-    async #checkSynonyms() {
+    #checkSynonyms() {
         // Make sure all synonyms in eFlora are in our list.
-        for (const jepsonInfo of Object.values(this.#nameInfo)) {
-            if (!this.#isSynonym(jepsonInfo)) {
-                continue;
-            }
+        for (const [synName, targetNames] of this.#synInfo.entries()) {
+            for (const targetName of targetNames) {
+                const taxon = this.#taxa.getTaxon(targetName);
+                if (!taxon) {
+                    // We're not tracking the target.
+                    continue;
+                }
 
-            const target = jepsonInfo.under;
-            const taxon = this.#taxa.getTaxon(target);
-            if (!taxon) {
-                // We're not tracking the target.
-                continue;
-            }
+                if (taxon.getSynonyms().includes(synName)) {
+                    // Already have it.
+                    continue;
+                }
 
-            if (taxon.getSynonyms().includes(jepsonInfo.name)) {
-                // Already have it.
-                continue;
+                this.#errorLog.log(
+                    targetName,
+                    "does not have synonym",
+                    synName + "," + targetName,
+                );
+                this.#synonymsToAdd.push({
+                    Former: synName,
+                    Current: targetName,
+                });
             }
-
-            this.#errorLog.log(
-                target,
-                "does not have synonym",
-                jepsonInfo.name + "," + target,
-            );
         }
 
         // Make sure everything in our list is in eFlora.
         for (const taxon of this.#taxa.getTaxonList()) {
             for (const synonym of taxon.getSynonyms()) {
-                const jepsonInfo = await this.#getJepsInfo(synonym);
-                if (!jepsonInfo || !this.#isSynonym(jepsonInfo)) {
+                const synInfo = this.#synInfo.get(synonym);
+                if (!synInfo || !synInfo.includes(taxon.getName())) {
                     // Ignore iNat synonyms.
                     if (synonym !== taxon.getINatSyn()) {
                         this.#errorLog.log(
                             synonym,
-                            "is in synonyms.csv but is not a synonym in eFlora",
+                            `is in synonyms.csv but is not a synonym for ${taxon.getName()} in eFlora`,
                         );
                     }
                 }
@@ -214,31 +214,17 @@ class JepsonEFlora {
 
     /**
      * @param {string} name
-     * @returns {Promise<JepsonInfo|undefined>}
+     * @returns {JepsonTaxon|undefined}
      */
-    async #getJepsInfo(name) {
-        const firstLetter = name[0];
-        // See if this index has been loaded.
-        if (!this.#loadedLetters.has(firstLetter)) {
-            await this.#loadNameIndex(firstLetter);
-        }
-
+    #getJepsInfo(name) {
         return this.#nameInfo.get(name);
     }
 
     /**
-     * @param {JepsonInfo} jepsInfo
+     * @param {JepsonTaxon} jepsInfo
      * @returns {StatusCode|undefined}
      */
     #getStatusCode(jepsInfo) {
-        // If it's a synonym, return status of the target.
-        if (this.#isSynonym(jepsInfo)) {
-            const targetInfo = this.#nameInfo.get(jepsInfo.under);
-            if (!targetInfo) {
-                return;
-            }
-            return this.#getStatusCode(targetInfo);
-        }
         switch (jepsInfo.type) {
             case TYPES.NATIVE:
                 return "N";
@@ -249,19 +235,12 @@ class JepsonEFlora {
         }
     }
 
-    /**
-     * @param {JepsonInfo|undefined} jepsInfo
-     * @returns {boolean}
-     */
-    #isSynonym(jepsInfo) {
-        if (!jepsInfo) {
-            return false;
-        }
-        switch (jepsInfo.type) {
-            case TYPES.SYNONYM:
-                return true;
+    async #loadIndexPages() {
+        for (let index = 0; index < 26; index++) {
+            await this.#loadNameIndex(
+                String.fromCharCode("A".charCodeAt(0) + index),
+            );
         }
-        return false;
     }
 
     /**
@@ -293,32 +272,6 @@ class JepsonEFlora {
 
         const document = scrape.parseFile(filePath);
         this.#parseIndex(document);
-
-        this.#loadedLetters.add(firstLetter);
-    }
-
-    /**
-     * @param {JepsonInfo} taxonData
-     */
-    #logNotes(taxonData) {
-        // If we're tracking the source, log it.
-        if (this.#taxa.getTaxon(taxonData.name)) {
-            this.#errorLog.log(
-                taxonData.name,
-                "has eFlora note (as source)",
-                taxonData.type + " for",
-                taxonData.under,
-            );
-        }
-        // If we're tracking the target, log it.
-        if (this.#taxa.getTaxon(taxonData.under)) {
-            this.#errorLog.log(
-                taxonData.under,
-                "has eFlora note (as target)",
-                taxonData.type + " for",
-                taxonData.name,
-            );
-        }
     }
 
     /**
@@ -370,71 +323,83 @@ class JepsonEFlora {
                 );
             }
 
-            const under = scrape.getTextContent(cols[0]);
             const common = scrape.getTextContent(cols[1]);
+            const name = linkText;
 
-            /** @type {JepsonInfo} */
-            const taxonData = {};
-
-            taxonData.name = linkText;
             const href = scrape.getAttr(links[0], "href");
             if (!href) {
                 throw new Error();
             }
-            taxonData.id = href.split("=")[1];
-            taxonData.type = type;
-            if (taxonData.common) {
-                taxonData.common = common;
-            }
+            const id = href.split("=")[1];
 
-            if (under) {
-                const m = under.match(reUnder);
+            const sciNameText = scrape.getTextContent(cols[0]);
+            let under;
+            if (sciNameText) {
+                const m = sciNameText.match(reUnder);
                 if (m) {
-                    taxonData.under = m[1];
+                    under = m[1];
                 }
             }
 
-            // If we're not tracking either the source or target, ignore this entry.
-            if (
-                !this.#taxa.getTaxon(taxonData.name) &&
-                !this.#taxa.getTaxon(taxonData.under) &&
-                !this.#taxa.hasSynonym(taxonData.name)
-            ) {
-                continue;
+            switch (type) {
+                case TYPES.NATIVE:
+                case TYPES.NATIVITY_UNCERTAIN:
+                case TYPES.NATURALIZED:
+                case TYPES.NATURALIZED_UW:
+                case TYPES.SYNONYM:
+                case TYPES.WAIF:
+                case TYPES.WEED:
+                    break;
+                default:
+                    continue;
             }
 
-            switch (type) {
-                case TYPES.ILLEGITIMATE:
-                case TYPES.INVALID:
-                case TYPES.INVALID_NOTED:
-                case TYPES.INVALID_SUPERFLUOUS:
-                case TYPES.MISAPPLIED:
-                case TYPES.MISAPP_PART:
-                case TYPES.MISAPP_UNABRIDGED:
-                case TYPES.SYN_INED:
-                case TYPES.SYN_ORTH_VARIANT:
-                case TYPES.SYN_PART:
-                case TYPES.SYN_PART_UN:
-                case TYPES.MENTIONED:
-                    // Not a valid synonym or active taxon. Log it for further investigation.
-                    if (this.#shouldLogNotes) {
-                        this.#logNotes(taxonData);
-                    }
+            if (type === TYPES.SYNONYM) {
+                // Should have "under".
+                if (!under) {
+                    throw new Error();
+                }
+                // If we're not tracking the target, ignore this entry.
+                if (!this.#taxa.getTaxon(under)) {
                     continue;
+                }
+
+                // Add to synonyms.
+                let targetNames = this.#synInfo.get(name);
+                if (!targetNames) {
+                    targetNames = [];
+                    this.#synInfo.set(name, targetNames);
+                }
+                targetNames.push(under);
+                continue;
             }
 
-            if (this.#nameInfo.get(taxonData.name)) {
-                this.#errorLog.log(
-                    taxonData.name,
-                    "has multiple entries in eFlora",
-                );
-                // Disable the current entry, since we don't know which one is correct.
-                this.#nameInfo.delete(taxonData.name);
+            // Not a synonym. Should not have "under".
+            if (under) {
+                throw new Error(`under = ${under} for ${name}`);
+            }
+
+            // If we're not tracking either the source, ignore this entry.
+            if (!this.#taxa.getTaxon(name)) {
                 continue;
             }
-            this.#nameInfo.set(taxonData.name, taxonData);
+
+            if (this.#nameInfo.get(name)) {
+                throw new Error();
+            }
+            this.#nameInfo.set(name, {
+                id: id,
+                type: type,
+                name: name,
+                common: common,
+            });
         }
     }
-}
 
-export { JepsonEFlora };
+    #updateSynCSV() {
+        const csv = new SynCSV("./data");
+        const data = csv.getData();
+        data.push(...this.#synonymsToAdd);
+        csv.write();
+    }
+}

package/lib/tools/syncsv.js

@@ -0,0 +1,41 @@
+import path from "path";
+import { CSV } from "../csv.js";
+
+/**
+ * @typedef {{Former:string,Current:string,Type?:"INAT"|undefined}} SynData
+ */
+
+export class SynCSV {
+    #filePath;
+    #headers;
+    /** @type {SynData[]} */
+    #data;
+
+    /**
+     * @param {string} dataDir
+     */
+    constructor(dataDir) {
+        this.#filePath = path.join(dataDir, "synonyms.csv");
+        const csv = CSV.readFileAndHeaders(this.#filePath);
+        this.#data = csv.data;
+        this.#headers = csv.headers;
+    }
+
+    /**
+     * @returns {SynData[]}
+     */
+    getData() {
+        return this.#data;
+    }
+
+    write() {
+        this.#data.sort((a, b) => {
+            const former = a.Former.localeCompare(b.Former);
+            if (former !== 0) {
+                return former;
+            }
+            return a.Current.localeCompare(b.Current);
+        });
+        CSV.writeFileObject(this.#filePath, this.#data, this.#headers);
+    }
+}

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.4.17",
+    "version": "0.4.18",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {
@@ -35,6 +35,7 @@
         "inatobsphotos": "scripts/inatobsphotos.js"
     },
     "dependencies": {
+        "@htmltools/scrape": "^0.1.0",
         "archiver": "^5.3.1",
         "cli-progress": "^3.12.0",
         "commander": "^12.1.0",
@@ -48,7 +49,6 @@
         "unzipper": "^0.12.3"
     },
     "devDependencies": {
-        "@htmltools/scrape": "^0.1.0",
         "@types/archiver": "^6.0.2",
         "@types/cli-progress": "^3.11.6",
         "@types/markdown-it": "^14.1.2",

package/scripts/cpl-tools.js

@@ -85,13 +85,8 @@ async function build(program, options) {
                 );
                 break;
             case TOOLS.JEPSON_EFLORA: {
-                const eflora = new JepsonEFlora(
-                    TOOLS_DATA_DIR,
-                    taxa,
-                    errorLog,
-                    options.efLognotes,
-                );
-                await eflora.analyze(exceptions);
+                const eflora = new JepsonEFlora(TOOLS_DATA_DIR, taxa, errorLog);
+                await eflora.analyze(exceptions, !!options.update);
                 break;
             }
             case TOOLS.JEPSON_FAM:
@@ -130,10 +125,6 @@ program.option(
     "The name of the file containing the iNaturalist taxa. Can be used for testing on a smaller subset of the iNaturalist data.",
     "inat_taxa.csv",
 );
-program.option(
-    "--ef-lognotes",
-    "When running the jepson-eflora tool, include eFlora notes, invalid names, etc. in the log file.",
-);
 program.option("--update", "Update taxa.csv to remove errors if possible.");
 program.addHelpText(
     "after",