@ca-plant-list/ca-plant-list 0.1.12 → 0.1.14

package/build-site.js

@@ -1,6 +1,5 @@
 #!/usr/bin/env node
 
-import { Config } from "./lib/config.js";
 import { DataLoader } from "./lib/dataloader.js";
 import { ErrorLog } from "./lib/errorlog.js";
 import { PageRenderer } from "./lib/pagerenderer.js";
@@ -8,11 +7,9 @@ import commandLineArgs from "command-line-args";
 
 const options = commandLineArgs( DataLoader.getOptionDefs() );
 
-const CONFIG_DATA_DIR = "./data";
 const OUTPUT_DIR = "./output";
 
-Config.init( CONFIG_DATA_DIR );
 DataLoader.load( options );
 PageRenderer.render( OUTPUT_DIR );
 
-ErrorLog.write( OUTPUT_DIR + "/errors.txt" );
+ErrorLog.write( OUTPUT_DIR + "/errors.tsv" );

package/data/genera.json

@@ -11,6 +11,10 @@
         "family": "Lycopodiaceae",
         "id": "9179"
     },
+    "Rhinotropis": {
+        "family": "Polygalaceae",
+        "id": 99965
+    },
     "Selaginella": {
         "family": "Selaginellaceae",
         "id": "8877"

package/jekyll/_layouts/html.html

@@ -47,6 +47,9 @@
 
     {%if page.js%}
     <script src="{{site.baseurl}}/assets/js/{{page.js}}" type="module"></script>{%endif%}
+
+    <script src="{{site.baseurl}}/assets/js/ui.js" type="module"></script>
+
     {%include analytics.html%}
 </body>
 

package/jekyll/assets/css/main.css

@@ -17,10 +17,6 @@
     background-color: #3D550C;
 }
 
-span[title] {
-    text-decoration: underline dotted;
-}
-
 span.label {
     font-weight: 600;
     padding-right: .5rem;

package/jekyll/assets/js/ui.js

@@ -0,0 +1,10 @@
+class UI {
+
+    static init() {
+        const tooltips = document.querySelectorAll( "span[title]" );
+        [ ...tooltips ].map( tooltipTriggerEl => new bootstrap.Tooltip( tooltipTriggerEl ) );
+    }
+
+}
+
+UI.init();

package/lib/basepagerenderer.js

@@ -1,19 +1,19 @@
-import * as fs from "node:fs";
 import { Config } from "./config.js";
 import { Families } from "./families.js";
+import { Files } from "./files.js";
 
 class BasePageRenderer {
 
-    static render( outputDir, Taxa ) {
+    static render( outputDir, Taxa, familyCols ) {
 
         // Copy static files
-        fs.rmSync( outputDir, { force: true, recursive: true, maxRetries: 2, retryDelay: 1000 } );
+        Files.rmDir( outputDir );
         // First copy default Jekyll files from package.
-        fs.cpSync( Config.getPackageDir() + "/jekyll", outputDir, { recursive: true } );
+        Files.copyDir( Config.getPackageDir() + "/jekyll", outputDir );
         // Then copy Jekyll files from current dir (which may override default files).
-        fs.cpSync( "jekyll", outputDir, { recursive: true } );
+        Files.copyDir( "jekyll", outputDir );
 
-        Families.renderPages( outputDir );
+        Families.renderPages( outputDir, familyCols );
 
         this.renderTools( outputDir, Taxa );
 
@@ -39,7 +39,7 @@ class BasePageRenderer {
             names.push( row );
         }
 
-        fs.writeFileSync( outputDir + "/_includes/names.json", JSON.stringify( names ) );
+        Files.write( outputDir + "/_includes/names.json", JSON.stringify( names ) );
 
     }
 

package/lib/config.js

@@ -1,12 +1,20 @@
 import * as path from "node:path";
 import * as url from "node:url";
-import * as fs from "node:fs";
+import { Files } from "./files.js";
 
 class Config {
 
     static #config = {};
     static #packageDir = path.dirname( path.dirname( url.fileURLToPath( import.meta.url ) ) );
 
+    static {
+        try {
+            this.#config = JSON.parse( Files.read( "./data/config.json" ) );
+        } catch ( e ) {
+            console.log( e );
+        }
+    }
+
     static getConfigValue( prefix, name, subcat, dflt ) {
         const obj = this.#config[ prefix ];
         if ( obj ) {
@@ -26,6 +34,10 @@ class Config {
         return dflt;
     }
 
+    static getCountyCodes() {
+        return this.#config[ "counties" ];
+    }
+
     static getLabel( name, dflt ) {
         return this.getConfigValue( "labels", name, undefined, dflt );
     }
@@ -34,14 +46,6 @@ class Config {
         return this.#packageDir;
     }
 
-    static init( dir ) {
-        try {
-            this.#config = JSON.parse( fs.readFileSync( dir + "/config.json" ) );
-        } catch ( e ) {
-            console.log( e );
-        }
-    }
-
 }
 
 export { Config };

package/lib/exceptions.js

@@ -1,35 +1,39 @@
-import * as fs from "node:fs";
+import { Files } from "./files.js";
 
 class Exceptions {
 
     static #exceptions = {};
 
-    static hasException( name, cat, subcat ) {
+    static getExceptions() {
+        return Object.entries( this.#exceptions );
+    }
+
+    static getValue( name, cat, subcat, defaultValue ) {
         const taxonData = this.#exceptions[ name ];
         if ( taxonData ) {
             const catData = taxonData[ cat ];
             if ( catData ) {
-                return catData[ subcat ] !== undefined;
+                const val = catData[ subcat ];
+                return ( val === undefined ) ? defaultValue : val;
             }
         }
-        return false;
+        return defaultValue;
     }
 
-    static getValue( name, cat, subcat, defaultValue ) {
+    static hasException( name, cat, subcat ) {
         const taxonData = this.#exceptions[ name ];
         if ( taxonData ) {
             const catData = taxonData[ cat ];
             if ( catData ) {
-                const val = catData[ subcat ];
-                return ( val === undefined ) ? defaultValue : val;
+                return catData[ subcat ] !== undefined;
             }
         }
-        return defaultValue;
+        return false;
     }
 
     static init( dir ) {
         try {
-            this.#exceptions = JSON.parse( fs.readFileSync( dir + "/exceptions.json" ) );
+            this.#exceptions = JSON.parse( Files.read( dir + "/exceptions.json" ) );
         } catch ( e ) {
             console.log( e );
         }

package/lib/families.js

@@ -19,12 +19,12 @@ class Families {
         }
     }
 
-    static renderPages( outputDir ) {
+    static renderPages( outputDir, columns ) {
         new PageFamilyList( Object.values( this.#families ) ).render( outputDir );
 
         for ( const family of Object.values( this.#families ) ) {
             if ( family.getTaxa() ) {
-                new PageFamily( family ).render( outputDir );
+                new PageFamily( family ).render( outputDir, columns );
             }
         }
     }
@@ -48,15 +48,25 @@ class PageFamilyList extends HTMLPage {
 
         html += HTML.textElement( "h1", title );
 
-        html += "<ul>";
+        html += "<table>";
+        html += "<thead>";
+        html += HTML.textElement( "th", "Family" );
+        html += HTML.textElement( "th", "Number of Species", { class: "right" } );
+        html += "</thead>";
+
+        html += "<tbody>";
         for ( const family of this.#families ) {
             const taxa = family.getTaxa();
-            if ( taxa ) {
-                const link = HTML.getLink( "./" + family.getFileName(), family.getName() );
-                html += "<li>" + link + " (" + taxa.length + ")" + "</li>";
+            if ( !taxa ) {
+                continue;
             }
+            let cols = HTML.wrap( "td", HTML.getLink( "./" + family.getFileName(), family.getName() ) );
+            cols += HTML.wrap( "td", taxa.length, { class: "right" } );
+            html += HTML.wrap( "tr", cols );
         }
-        html += "</ul>";
+        html += "</tbody>";
+
+        html += "</table>";
 
         this.writeFile( outputDir, "list_families.html", html );
     }
@@ -71,7 +81,7 @@ class PageFamily extends HTMLPage {
         this.#family = family;
     }
 
-    render( outputDir ) {
+    render( outputDir, columns ) {
 
         let html = this.getFrontMatter( this.#family.getName() );
 
@@ -83,7 +93,7 @@ class PageFamily extends HTMLPage {
             { class: "section" }
         );
 
-        html += Taxa.getHTMLTable( this.#family.getTaxa() );
+        html += Taxa.getHTMLTable( this.#family.getTaxa(), columns );
 
         this.writeFile( outputDir, this.#family.getFileName(), html );
 

package/lib/files.js

@@ -3,6 +3,10 @@ import { default as unzipper } from "unzipper";
 
 class Files {
 
+    static copyDir( srcDir, targetDir ) {
+        fs.cpSync( srcDir, targetDir, { recursive: true } );
+    }
+
     static createFileFromStream( fileName, inStream ) {
 
         function implementation( fileName, inStream, resolve ) {
@@ -18,11 +22,30 @@ class Files {
         return fs.existsSync( path );
     }
 
-    static async fetch( url, targetFileName ) {
-        const response = await fetch( url );
+    /**
+     * Retrieve data from a URL and write it to a file.
+     * @param {string|URL} url 
+     * @param {string|undefined} targetFileName If targetFileName is undefined, the data will be retrieved but not written to a file.
+     * @param {Object} [headers={}] Request Headers.
+     */
+    static async fetch( url, targetFileName, headers = {} ) {
+        const response = await fetch( url, headers );
         const data = await response.blob();
-        const buffer = await data.arrayBuffer();
-        fs.writeFileSync( targetFileName, Buffer.from( buffer ) );
+        const arrayBuffer = await data.arrayBuffer();
+        const buffer = Buffer.from( arrayBuffer );
+        if ( targetFileName ) {
+            fs.writeFileSync( targetFileName, buffer );
+        }
+    }
+
+    /**
+     * Retrieve data from a URL and return the Response Header.
+     * @param {string|URL} url 
+     * @returns {Headers}
+     */
+    static async fetchHeaders( url ) {
+        const response = await fetch( url );
+        return response.headers;
     }
 
     static mkdir( path ) {
@@ -33,8 +56,12 @@ class Files {
         return fs.readFileSync( path, "utf8" );
     }
 
-    static write( path, data ) {
-        if ( this.exists( path ) ) {
+    static rmDir( dir ) {
+        fs.rmSync( dir, { force: true, recursive: true, maxRetries: 2, retryDelay: 1000 } );
+    }
+
+    static write( path, data, overwrite = false ) {
+        if ( !overwrite && this.exists( path ) ) {
             throw new Error( path + " already exists" );
         }
         fs.writeFileSync( path, data );

package/lib/genericpage.js

@@ -0,0 +1,48 @@
+import { Files, HTML, Jekyll } from "@ca-plant-list/ca-plant-list";
+
+class GenericPage {
+
+    #outputDir;
+    #title;
+    #baseFileName;
+    #js;
+
+    constructor( outputDir, title, baseFileName, js ) {
+        this.#outputDir = outputDir;
+        this.#title = title;
+        this.#baseFileName = baseFileName;
+        this.#js = js;
+    }
+
+    getDefaultIntro() {
+        let html = this.#getFrontMatter();
+        html += HTML.textElement( "h1", this.#title );
+        const introPath = "lists/" + this.#baseFileName + "-intro.md";
+        if ( Jekyll.hasInclude( this.#outputDir, introPath ) ) {
+            html += HTML.wrap( "div", Jekyll.include( introPath ), { class: "section" } );
+        }
+        return html;
+    }
+
+    #getFrontMatter() {
+        return "---\n"
+            + "title: \"" + this.#title + "\"\n"
+            + ( this.#js ? ( "js: " + this.#js + "\n" ) : "" )
+            + "---\n";
+    }
+
+    getOutputDir() {
+        return this.#outputDir;
+    }
+
+    getTitle() {
+        return this.#title;
+    }
+
+    writeFile( html ) {
+        Files.write( this.#outputDir + "/" + this.#baseFileName + ".html", html );
+    }
+
+}
+
+export { GenericPage };

package/lib/html.js

@@ -45,21 +45,40 @@ export class HTML {
         return html;
     }
 
-    static getLink( href, linkText, attributes = {}, options = 0 ) {
+    /**
+     * 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.
+     * @returns {string} an HTML <a> element.
+     */
+    static getLink( href, linkText, attributes = {}, openInNewWindow ) {
         let html = "<a";
         if ( href !== undefined ) {
             html += this.renderAttribute( "href", href );
         }
         html += this.renderAttributes( attributes );
-        if ( options & HTML_OPTIONS.OPEN_NEW ) {
+        if ( openInNewWindow ) {
             html += this.renderAttribute( "target", "_blank" );
         }
         return html + ">" + this.escapeText( linkText ) + "</a >";
     }
 
-    static getToolTip( text, tooltip ) {
+    /**
+     * Get a Bootstrap formatted tooltip element.
+     * @param {string} text - The text or HTML that should trigger the tooltip on hover.
+     * @param {string} tooltip - The tooltip text or HTML.
+     * @param {Object} options
+     * @param {boolean} options.icon [true] display an icon after the text
+     * @returns {string} A &lt;span> element to be used as a Bootstrap tooltip.
+     */
+    static getToolTip( text, tooltip, options = {} ) {
         const func = text.charAt( 0 ) === "<" ? HTML.wrap : HTML.textElement;
-        return func( "span", text + " ⓘ", { title: tooltip } );
+        if ( options.icon !== false ) {
+            text += " ⓘ";
+        }
+        return func( "span", text, { "data-bs-html": "true", "title": tooltip } );
     }
 
     static renderAttribute( n, v ) {

package/lib/htmlpage.js

@@ -1,5 +1,8 @@
-import * as fs from "node:fs";
+import { Files } from "./files.js";
 
+/**
+ * @deprecated
+ */
 class HTMLPage {
 
     getFrontMatter( title, js ) {
@@ -10,7 +13,7 @@ class HTMLPage {
     }
 
     writeFile( outputDir, fileName, html ) {
-        fs.writeFileSync( outputDir + "/" + fileName, html );
+        Files.write( outputDir + "/" + fileName, html );
     }
 
 }

package/lib/index.d.ts

@@ -1,10 +1,24 @@
 export class Files {
+    static copyDir(srcDir: any, targetDir: any): void;
     static createFileFromStream(fileName: any, inStream: any): Promise<any>;
     static exists(path: any): boolean;
-    static fetch(url: any, targetFileName: any): Promise<void>;
+    /**
+     * Retrieve data from a URL and write it to a file.
+     * @param {string|URL} url
+     * @param {string|undefined} targetFileName If targetFileName is undefined, the data will be retrieved but not written to a file.
+     * @param {Object} [headers={}] Request Headers.
+     */
+    static fetch(url: string | URL, targetFileName: string | undefined, headers?: any): Promise<void>;
+    /**
+     * Retrieve data from a URL and return the Response Header.
+     * @param {string|URL} url
+     * @returns {Headers}
+     */
+    static fetchHeaders(url: string | URL): Headers;
     static mkdir(path: any): void;
     static read(path: any): string;
-    static write(path: any, data: any): void;
+    static rmDir(dir: any): void;
+    static write(path: any, data: any, overwrite?: boolean): void;
     static zipFileExtract(zipFilePath: any, fileNameToUnzip: any, targetFilePath: any): Promise<void>;
 }
 export namespace HTML_OPTIONS {
@@ -21,8 +35,26 @@ export class HTML {
      */
     static getElement(elName: any, text: any, attributes?: {}, options?: number): string;
     static "__#2@#getElement"(elName: any, text: any, attributes: any, escape: any): string;
-    static getLink(href: any, linkText: any, attributes?: {}, options?: number): string;
-    static getToolTip(text: any, tooltip: any): string;
+    /**
+     * 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.
+     * @returns {string} an HTML &lt;a> element.
+     */
+    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.
+     * @param {string} tooltip - The tooltip text or HTML.
+     * @param {Object} options
+     * @param {boolean} options.icon [true] display an icon after the text
+     * @returns {string} A &lt;span> element to be used as a Bootstrap tooltip.
+     */
+    static getToolTip(text: string, tooltip: string, options?: {
+        icon: boolean;
+    }): string;
     static renderAttribute(n: any, v: any): string;
     static renderAttributes(attributes: any): string;
     static textElement(elName: any, text: any, attributes?: {}): string;

package/lib/pagerenderer.js

@@ -1,14 +1,14 @@
-import * as fs from "node:fs";
 import { HTML } from "./html.js";
-import { Taxa, COLUMNS } from "./taxa.js";
+import { Taxa, TAXA_LIST_COLS } from "./taxa.js";
 import { HTMLPage } from "./htmlpage.js";
 import { PageTaxon } from "./pagetaxon.js";
 import { Config } from "./config.js";
 import { RarePlants } from "./rareplants.js";
 import { BasePageRenderer } from "./basepagerenderer.js";
+import { Files } from "./files.js";
 
-const RPI_CESA = [ COLUMNS.COL_SPECIES, COLUMNS.COL_COMMON_NAME, COLUMNS.COL_CESA ];
-const RPI_COLUMNS = [ COLUMNS.COL_SPECIES, COLUMNS.COL_COMMON_NAME, COLUMNS.COL_CNPS_RANK ];
+const RPI_CESA = [ TAXA_LIST_COLS.SPECIES, TAXA_LIST_COLS.COMMON_NAME, TAXA_LIST_COLS.CESA ];
+const RPI_COLUMNS = [ TAXA_LIST_COLS.SPECIES_BARE, TAXA_LIST_COLS.COMMON_NAME, TAXA_LIST_COLS.CNPS_RANK ];
 
 class PageRenderer extends BasePageRenderer {
 
@@ -20,7 +20,7 @@ class PageRenderer extends BasePageRenderer {
 
         const taxa = Taxa.getTaxa();
         for ( const taxon of taxa ) {
-            new PageTaxon( taxon ).render( outputDir );
+            new PageTaxon( outputDir, taxon ).render();
         }
 
     }
@@ -46,8 +46,8 @@ class PageRenderer extends BasePageRenderer {
                     continue;
                 }
 
-                fs.writeFileSync( outputDir + "/calflora_" + list.filename + ".txt", calfloraTaxa.join( "\n" ) );
-                fs.writeFileSync( outputDir + "/inat_" + list.filename + ".txt", iNatTaxa.join( "\n" ) );
+                Files.write( outputDir + "/calflora_" + list.filename + ".txt", calfloraTaxa.join( "\n" ) );
+                Files.write( outputDir + "/inat_" + list.filename + ".txt", iNatTaxa.join( "\n" ) );
 
                 const cols = columns ? columns : list.columns;
                 new PageTaxonList().render( outputDir, taxa, list.filename, list.name, cols );
@@ -170,7 +170,7 @@ class PageRenderer extends BasePageRenderer {
         html += "</div>";
 
         // Write lists to includes directory so it can be inserted into pages.
-        fs.writeFileSync( outputDir + "/_includes/plantlists.html", html );
+        Files.write( outputDir + "/_includes/plantlists.html", html );
 
     }
 

package/lib/pagetaxon.js

@@ -1,16 +1,16 @@
-import * as fs from "node:fs";
-import { HTML, HTML_OPTIONS } from "./html.js";
+import { HTML } from "./html.js";
 import { Jepson } from "./jepson.js";
-import { HTMLPage } from "./htmlpage.js";
 import { Config } from "./config.js";
 import { RarePlants } from "./rareplants.js";
+import { GenericPage } from "./genericpage.js";
+import { Files } from "./files.js";
 
-class PageTaxon extends HTMLPage {
+class PageTaxon extends GenericPage {
 
     #taxon;
 
-    constructor( taxon ) {
-        super();
+    constructor( outputDir, taxon ) {
+        super( outputDir, taxon.getName(), taxon.getBaseFileName() );
         this.#taxon = taxon;
     }
 
@@ -40,11 +40,11 @@ class PageTaxon extends HTMLPage {
         links.push(
             HTML.getLink(
                 "https://www.calflora.org/entry/observ.html?track=m#srch=t&grezc=5&cols=b&lpcli=t&cc="
-                + Config.getConfigValue( "calflora", "counties" ).join( "!" ) + "&incobs=f&taxon="
+                + Config.getCountyCodes().join( "!" ) + "&incobs=f&taxon="
                 + this.#taxon.getCalfloraName().replaceAll( " ", "+" ),
                 "Calflora",
                 {},
-                HTML_OPTIONS.OPEN_NEW
+                true
             )
         );
         const iNatID = this.#taxon.getINatID();
@@ -55,7 +55,7 @@ class PageTaxon extends HTMLPage {
                     + "&quality_grade=research&subview=map&taxon_id=" + iNatID,
                     "iNaturalist",
                     {},
-                    HTML_OPTIONS.OPEN_NEW
+                    true
                 )
             );
         }
@@ -67,7 +67,7 @@ class PageTaxon extends HTMLPage {
         let html = "";
         if ( list.length > 0 ) {
             html += "<div class=\"section " + className + "\">";
-            html += HTML.getElement( "h2", header );
+            html += HTML.textElement( "h2", header );
             html += "<ul>";
             html += HTML.arrayToLI( list );
             html += "</ul>";
@@ -83,17 +83,16 @@ class PageTaxon extends HTMLPage {
         }
         const ranks = [];
 
-        ranks.push( HTML.getElement( "span", "CNPS Rare Plant Rank:", { class: "label" } )
-            + HTML.getElement( "span", cnpsRank, { title: RarePlants.getRPIRankAndThreatDescriptions( cnpsRank ).join( "\n" ) } ) );
+        ranks.push( HTML.textElement( "span", "CNPS Rare Plant Rank:", { class: "label" } )
+            + HTML.getToolTip( cnpsRank, this.#taxon.getRPIRankAndThreatTooltip() ) );
         if ( this.#taxon.getCESA() ) {
-            ranks.push( HTML.getElement( "span", "CESA:", { class: "label" } ) + RarePlants.getCESADescription( this.#taxon.getCESA() ) );
+            ranks.push( HTML.textElement( "span", "CESA:", { class: "label" } ) + RarePlants.getCESADescription( this.#taxon.getCESA() ) );
         }
 
-        return HTML.getElement(
+        return HTML.wrap(
             "div",
             "<ul>" + HTML.arrayToLI( ranks ) + "</ul>",
-            { class: "section" },
-            HTML_OPTIONS.NO_ESCAPE
+            { class: "section" }
         );
     }
 
@@ -115,27 +114,24 @@ class PageTaxon extends HTMLPage {
         return this.#taxon.getSynonyms();
     }
 
-    render( outputDir ) {
+    render() {
 
-        let html = this.getFrontMatter( this.#taxon.getName() );
-
-        html += HTML.getElement( "h1", this.#taxon.getName() );
+        let html = this.getDefaultIntro();
 
         html += "<div class=\"wrapper\">";
 
         const cn = this.#taxon.getCommonNames();
         if ( cn.length > 0 ) {
-            html += HTML.getElement( "div", cn.join( ", " ), { class: "section common-names" } );
+            html += HTML.textElement( "div", cn.join( ", " ), { class: "section common-names" } );
         }
 
-        html += HTML.getElement( "div", this.#taxon.getStatusDescription(), { class: "section native-status" } );
+        html += HTML.textElement( "div", this.#taxon.getStatusDescription(), { class: "section native-status" } );
 
         const family = this.#taxon.getFamily();
-        html += HTML.getElement(
+        html += HTML.wrap(
             "div",
-            HTML.getElement( "span", "Family:", { class: "label" } ) + HTML.getLink( "./" + family.getFileName(), family.getName() ),
-            { class: "section" },
-            HTML_OPTIONS.NO_ESCAPE
+            HTML.textElement( "span", "Family:", { class: "label" } ) + HTML.getLink( "./" + family.getFileName(), family.getName() ),
+            { class: "section" }
         );
 
         html += this.#getRarityInfo();
@@ -143,8 +139,8 @@ class PageTaxon extends HTMLPage {
         html += "</div>";
 
         const introName = "intros/" + this.#taxon.getFileName( "md" );
-        if ( fs.existsSync( "./jekyll/_includes/" + introName ) ) {
-            html += HTML.getElement(
+        if ( Files.exists( "./jekyll/_includes/" + introName ) ) {
+            html += HTML.wrap(
                 "div",
                 "{% capture my_include %}{% include " + introName + "%}{% endcapture %}{{ my_include | markdownify }}",
                 { class: "section" }
@@ -158,7 +154,7 @@ class PageTaxon extends HTMLPage {
         html += this.#getListSectionHTML( this.#getSynonyms(), "Synonyms", "synonyms" );
         html += "</div>";
 
-        this.writeFile( outputDir, this.#taxon.getFileName(), html );
+        this.writeFile( html );
 
     }
 

package/lib/taxa.js

@@ -4,14 +4,30 @@ import { HTML } from "./html.js";
 import { CSV } from "./csv.js";
 import { RarePlants } from "./rareplants.js";
 
-const COLUMNS = {
-    COL_CESA: "CESA",
-    COL_COMMON_NAME: "Common Name",
-    COL_CNPS_RANK: "CNPS Rank",
-    COL_SPECIES: "Species",
+const TAXA_LIST_COLS = {
+    CESA: {
+        title: "CESA",
+        data: ( t ) => RarePlants.getCESADescription( t.getCESA() )
+    },
+    COMMON_NAME: {
+        title: "Common Name",
+        data: ( t ) => t.getCommonNames().join( ", " )
+    },
+    CNPS_RANK: {
+        title: "CNPS Rank",
+        data: ( t ) => HTML.getToolTip( HTML.textElement( "span", t.getRPIRankAndThreat() ), t.getRPIRankAndThreatTooltip() )
+    },
+    SPECIES: {
+        title: "Species",
+        data: ( t ) => t.getHTMLLink( true, true )
+    },
+    SPECIES_BARE: {
+        title: "Species",
+        data: ( t ) => t.getHTMLLink( true, false )
+    },
 };
 
-const DEFAULT_COLUMNS = [ COLUMNS.COL_SPECIES, COLUMNS.COL_COMMON_NAME ];
+const DEFAULT_COLUMNS = [ TAXA_LIST_COLS.SPECIES, TAXA_LIST_COLS.COMMON_NAME ];
 
 class Taxa {
 
@@ -20,36 +36,22 @@ class Taxa {
 
     static getHTMLTable( taxa, columns = DEFAULT_COLUMNS ) {
 
-        let includeRPI = true;
-
         let html = "<table><thead>";
-        for ( const column of columns ) {
-            html += HTML.textElement( "th", column );
-            if ( column === COLUMNS.COL_CNPS_RANK ) {
-                // Don't show rarity with species link if CNPS Rank column is included.
-                includeRPI = false;
-            }
+        for ( const col of columns ) {
+            const className = col.class;
+            const atts = className ? { class: className } : {};
+            html += HTML.textElement( "th", col.title, atts );
         }
         html += "</thead>";
         html += "<tbody>";
 
         for ( const taxon of taxa ) {
             html += "<tr>";
-            for ( const column of columns ) {
-                switch ( column ) {
-                    case COLUMNS.COL_CESA:
-                        html += HTML.textElement( "td", RarePlants.getCESADescription( taxon.getCESA() ) );
-                        break;
-                    case COLUMNS.COL_COMMON_NAME:
-                        html += HTML.textElement( "td", taxon.getCommonNames().join( ", " ) );
-                        break;
-                    case COLUMNS.COL_CNPS_RANK:
-                        html += HTML.wrap( "td", HTML.wrap( "span", taxon.getRPIRankAndThreat(), taxon.getRPIRankAndThreatTooltip( {} ) ) );
-                        break;
-                    case COLUMNS.COL_SPECIES:
-                        html += HTML.wrap( "td", taxon.getHTMLLink( true, includeRPI ) );
-                        break;
-                }
+            for ( const col of columns ) {
+                const data = col.data( taxon );
+                const className = col.class;
+                const atts = className ? { class: className } : {};
+                html += HTML.wrap( "td", data, atts );
             }
             html += "</tr>";
         }
@@ -120,4 +122,4 @@ class Taxa {
 
 }
 
-export { Taxa, COLUMNS };
+export { Taxa, TAXA_LIST_COLS };

package/lib/taxon.js

@@ -1,6 +1,6 @@
 import { Config } from "./config.js";
 import { Genera } from "./genera.js";
-import { HTML, HTML_OPTIONS } from "./html.js";
+import { HTML } from "./html.js";
 import { RarePlants } from "./rareplants.js";
 
 class Taxon {
@@ -72,7 +72,7 @@ class Taxon {
             "https://www.calflora.org/app/taxon?crn=" + calfloraID,
             "Calflora",
             {},
-            HTML_OPTIONS.OPEN_NEW
+            true
         );
     }
 
@@ -107,10 +107,11 @@ class Taxon {
             className = "rare";
         }
         const attributes = { class: className };
+        const link = HTML.wrap( "span", HTML.getLink( href, this.getName() ), attributes );
         if ( className === "rare" ) {
-            this.getRPIRankAndThreatTooltip( attributes );
+            return HTML.getToolTip( link, this.getRPIRankAndThreatTooltip(), { icon: false } );
         }
-        return HTML.wrap( "span", HTML.getLink( href, this.getName() ), attributes );
+        return link;
     }
 
     getINatID() {
@@ -127,7 +128,7 @@ class Taxon {
         if ( !iNatID ) {
             return "";
         }
-        const link = HTML.getLink( "https://www.inaturalist.org/taxa/" + iNatID, "iNaturalist", {}, HTML_OPTIONS.OPEN_NEW );
+        const link = HTML.getLink( "https://www.inaturalist.org/taxa/" + iNatID, "iNaturalist", {}, true );
         return this.#iNatSyn ? ( link + " (" + this.#iNatSyn + ")" ) : link;
     }
 
@@ -154,9 +155,8 @@ class Taxon {
         return this.#rankRPI;
     }
 
-    getRPIRankAndThreatTooltip( attributes ) {
-        attributes[ "title" ] = RarePlants.getRPIRankAndThreatDescriptions( this.getRPIRankAndThreat() ).join( "\n" );
-        return attributes;
+    getRPIRankAndThreatTooltip() {
+        return RarePlants.getRPIRankAndThreatDescriptions( this.getRPIRankAndThreat() ).join( "<br>" );
     }
 
     getRPITaxonLink() {
@@ -164,7 +164,7 @@ class Taxon {
         if ( !rpiID ) {
             return "";
         }
-        const link = HTML.getLink( "https://rareplants.cnps.org/Plants/Details/" + rpiID, "CNPS Rare Plant Inventory", {}, HTML_OPTIONS.OPEN_NEW );
+        const link = HTML.getLink( "https://rareplants.cnps.org/Plants/Details/" + rpiID, "CNPS Rare Plant Inventory", {}, true );
         return link;
     }
 
@@ -192,6 +192,10 @@ class Taxon {
         return this.#status === "N" || this.#status === "NC";
     }
 
+    /**
+     * Determine whether a species is a local native.
+     * @returns {boolean} true if taxon is a local native; false if not a CA native, or native elsewhere in CA.
+     */
     isNative() {
         return this.#status === "N";
     }

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.1.12",
+    "version": "0.1.14",
     "description": "Tools to create Jekyll files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {

package/jekyll/index_lists.md

@@ -1,7 +0,0 @@
----
-title: Plant Lists
----
-# Plant Lists
-
-Species:
-{%include plantlists.html%}