@ca-plant-list/ca-plant-list 0.4.35 → 0.4.37

package/data/text/Hieracium-albiflorum.md

@@ -0,0 +1 @@
+In forested areas.

package/data/text/Hieracium-horridum.md

@@ -0,0 +1 @@
+In rocky areas. Leaves densely hairy.

package/data/text/Hieracium-triste.md

@@ -0,0 +1 @@
+Usually in moist or forested areas. [Phyllaries](./g/phyllary.html) with black hairs.

package/data/text/Lupinus-lepidus-var-lobbii.md

@@ -0,0 +1 @@
+Leaves hairy. Plant mostly prostrate; inflorescence low.

package/data/text/Pedicularis-attollens.md

@@ -0,0 +1 @@
+Inflorescence hairy. Beak 3-5 mm (shorter than _P. groenlandica_).

package/data/text/Pedicularis-groenlandica.md

@@ -0,0 +1 @@
+Inflorescence not hairy. Beak 6-13 mm (longer than _P. attolens_).

package/data/text/Pseudognaphalium-beneolens.md

@@ -0,0 +1 @@
+Leaves gray. Scented.

package/data/text/Pseudognaphalium-californicum.md

@@ -0,0 +1 @@
+Leaves green. Scented.

package/data/text/Pseudognaphalium-ramosissimum.md

@@ -0,0 +1 @@
+Leaves green. Scented.

package/data/text/Salix-lemmonii.md

@@ -1 +1 @@
-Leaves generally narrow and pointed at both ends.
+Leaves generally pointed at both ends. Older leaves usually hairless; younger leaves often somewhat hairy.

package/ebook/css/main.css

@@ -1,48 +1,47 @@
 * {
-    font-family: Georgia, 'Times New Roman', Times, serif;
+  font-family: Georgia, 'Times New Roman', Times, serif;
 }
 
 div.flr {
-    background-color: lightgray;
-    display: flex;
-    align-items: center;
+  background-color: lightgray;
+  display: flex;
+  align-items: center;
 }
 
 div.hdr {
-    display: flex;
-    column-gap: 2rem;
-    row-gap: .5rem;
-    flex-flow: row wrap;
-    justify-content: space-between;
+  display: flex;
+  column-gap: 2rem;
+  row-gap: .5rem;
+  flex-flow: row wrap;
+  justify-content: space-between;
 }
 
 div.section {
-    margin-bottom: .5rem;
+  margin-bottom: .5rem;
 }
 
 div.photos {
-    display: flex;
+  display: flex;
 }
 
 figure {
-    margin: auto;
+  margin: auto;
 }
 
 img.flr-color {
-    padding-right: .25rem;
-    width: 1rem;
+  padding-right: .25rem;
+  width: 1rem;
 }
 
 span.flr-time,
 span.lc {
-    font-weight: bold;
+  font-weight: bold;
 }
 
 span.lcs {
-    margin-right: 1rem;
+  margin-right: 1rem;
 }
 
-/* Glossary */
 div.glossary img {
-    max-height: 300px;
+  width: 100%
 }

package/lib/csv.js

@@ -134,7 +134,6 @@ export class CSV {
     }
 
     /**
-     *
      * @param {string} fileName
      * @param {string[][]} data
      * @param {string[]} [headerData]
@@ -146,7 +145,6 @@ export class CSV {
     }
 
     /**
-     *
      * @param {string} fileName
      * @param {Object<string,any>[]} data
      * @param {string[]} headerData

package/lib/htmltaxon.js

@@ -252,12 +252,19 @@ class HTMLTaxon {
      * @returns {string}
      */
     static getFooterHTML(taxon) {
-        const footerTextPath = path.join(
+        const footerTextPathCommon = path.join(
             Config.getPackageDir(),
             "/data/text/",
             `${taxon.getBaseFileName()}.footer.md`,
         );
-        return HTMLFragments.getMarkdownSection(footerTextPath);
+        const footerTextPathLocal = path.join(
+            "./data/footers/",
+            `${taxon.getBaseFileName()}.md`,
+        );
+        return (
+            HTMLFragments.getMarkdownSection(footerTextPathCommon) +
+            HTMLFragments.getMarkdownSection(footerTextPathLocal)
+        );
     }
 
     /**

package/lib/index.d.ts

@@ -231,6 +231,7 @@ export class Taxa<T> {
         extraTaxa?: TaxonOverrides[],
         extraSynonyms?: Record<string, string>[],
     );
+    static getIncludeList(dataDir: string): true | Record<string, TaxonData>;
     getTaxon(name: string): T;
     getTaxonList(): T[];
 }

package/lib/markdown.js

@@ -2,7 +2,7 @@ import markdownIt from "markdown-it";
 import { Files } from "./files.js";
 
 export class Markdown {
-    static #md = new markdownIt({ xhtmlOut: true });
+    static #md = new markdownIt({ html: true, xhtmlOut: true });
 
     /**
      * @param {string} filePath

package/lib/program.js

@@ -1,7 +1,4 @@
 import { Command } from "commander";
-import { Files } from "./files.js";
-import { CSV } from "./csv.js";
-import path from "node:path";
 
 /**
  * @typedef {{
@@ -12,29 +9,6 @@ import path from "node:path";
  */
 
 class Program {
-    /**
-     * @param {string} dataDir
-     */
-    static getIncludeList(dataDir) {
-        // Read inclusion list.
-        const includeFileName = "taxa_include.csv";
-        const includeFilePath = dataDir + "/" + includeFileName;
-        if (!Files.exists(includeFilePath)) {
-            console.log(includeFilePath + " not found; loading all taxa");
-            return true;
-        }
-
-        /** @type {import("./index.js").TaxonData[]} */
-        // @ts-ignore
-        const includeCSV = CSV.readFile(path.join(dataDir, includeFileName));
-        /** @type {Object<string,import("./index.js").TaxonData>} */
-        const include = {};
-        for (const row of includeCSV) {
-            include[row["taxon_name"]] = row;
-        }
-        return include;
-    }
-
     static getProgram() {
         const program = new Command();
         program

package/lib/sitegenerator.js

@@ -56,16 +56,16 @@ export class SiteGenerator {
                 Config.getPackageDir() + "/data/illustrations/inkscape";
             const entries = Files.getDirEntries(srcDir);
             for (const entry of entries) {
-                const srcFile = Files.join(srcDir, entry);
+                const srcFile = path.join(srcDir, entry);
                 const srcSVG = Files.read(srcFile);
                 const result = optimize(srcSVG, {
-                    plugins: ["preset-default", "removeDimensions"],
+                    enable: ["removeDimensions"],
                 });
-                Files.write(Files.join(outputDir, entry), result.data);
+                Files.write(path.join(outputDir, entry), result.data);
             }
         }
 
-        const outputDir = Files.join(this.#baseDir, "i");
+        const outputDir = path.join(this.#baseDir, "i");
         Files.mkdir(outputDir);
 
         optimizeSVG(outputDir);

package/lib/taxonomy/taxa.js

@@ -9,8 +9,8 @@ import { Families } from "./families.js";
 import { FlowerColor } from "../flowercolor.js";
 import { TaxaCSV } from "../tools/taxacsv.js";
 import { ErrorLog } from "../errorlog.js";
-import { Program } from "../program.js";
 import { Photo } from "../photo.js";
+import { Files } from "../files.js";
 
 /**
  * @typedef {{Current: string;Former: string;Type: string;}} SynonymData
@@ -28,7 +28,7 @@ const FLOWER_COLORS = [
     { name: "brown", color: "brown" },
 ];
 
-class Taxa {
+export class Taxa {
     #families;
     #errorLog;
     /** @type {Object<string,Taxon>} */
@@ -152,6 +152,29 @@ class Taxa {
         );
     }
 
+    /**
+     * @param {string} dataDir
+     * @returns {true|Object<string,import("../index.js").TaxonData>}
+     */
+    static getIncludeList(dataDir) {
+        // Read inclusion list.
+        const includeFileName = "taxa_include.csv";
+        const includeFilePath = dataDir + "/" + includeFileName;
+        if (!Files.exists(includeFilePath)) {
+            console.log(includeFilePath + " not found; loading all taxa");
+            return true;
+        }
+
+        /** @type {import("../index.js").TaxonData[]} */
+        const includeCSV = CSV.readFile(path.join(dataDir, includeFileName));
+        /** @type {Object<string,import("../index.js").TaxonData>} */
+        const include = {};
+        for (const row of includeCSV) {
+            include[row["taxon_name"]] = row;
+        }
+        return include;
+    }
+
     /**
      * @param {string} name
      */
@@ -193,7 +216,7 @@ class Taxa {
             taxa = await taxaLoaderClass.TaxaLoader.loadTaxa(options, errorLog);
         } else {
             taxa = new Taxa(
-                Program.getIncludeList(options.datadir),
+                Taxa.getIncludeList(options.datadir),
                 errorLog,
                 options.showFlowerErrors,
             );
@@ -297,5 +320,3 @@ class Taxa {
         }
     }
 }
-
-export { Taxa };

package/lib/tools/rpi.js

@@ -1,30 +1,53 @@
 import path from "node:path";
 import { CSV } from "../csv.js";
 import { Files } from "../files.js";
+import { TaxaCSV } from "./taxacsv.js";
+
+/**
+ * @typedef {"CESA"|"CNDDB"|"FESA"|"Global"} Rank
+ * @typedef {Map<string,Map<Rank,string|undefined>>} RanksToUpdate
+ */
 
 const HTML_FILE_NAME = "rpi.html";
 const URL_RPI_LIST =
     "https://rareplants.cnps.org/Search/result?frm=T&life=tree:herb:shrub:vine:leaf:stem";
 
-class RPI {
+export class RPI {
     /** @type {Object<string,Object<string,string>>} */
     static #rpiData = {};
 
     /**
      * @param {string} toolsDataDir
+     * @param {string} dataDir
      * @param {import("../types.js").Taxa} taxa
      * @param {import("../config.js").Config} config
      * @param {import("../exceptions.js").Exceptions} exceptions
      * @param {import("../errorlog.js").ErrorLog} errorLog
+     * @param {boolean} update
      */
-    static async analyze(toolsDataDir, taxa, config, exceptions, errorLog) {
+    static async analyze(
+        toolsDataDir,
+        dataDir,
+        taxa,
+        config,
+        exceptions,
+        errorLog,
+        update,
+    ) {
         /**
          * @param {string} name
-         * @param {string} label
+         * @param {Rank} label
          * @param {string|undefined} rpiRank
          * @param {string|undefined} taxonRank
+         * @param {RanksToUpdate} ranksToUpdate
          */
-        function checkStatusMatch(name, label, rpiRank, taxonRank) {
+        function checkStatusMatch(
+            name,
+            label,
+            rpiRank,
+            taxonRank,
+            ranksToUpdate,
+        ) {
             if (rpiRank !== taxonRank) {
                 errorLog.log(
                     name,
@@ -34,6 +57,12 @@ class RPI {
                     String(taxonRank),
                     String(rpiRank),
                 );
+                let map = ranksToUpdate.get(name);
+                if (map === undefined) {
+                    map = new Map();
+                    ranksToUpdate.set(name, map);
+                }
+                map.set(label, rpiRank);
             }
         }
 
@@ -67,6 +96,9 @@ class RPI {
         const ignoreGlobalRank = config.getConfigValue("rpi", "ignoreglobal");
         const ignoreCNDDBRank = config.getConfigValue("rpi", "ignorecnddb");
 
+        /** @type {RanksToUpdate} */
+        const ranksToUpdate = new Map();
+
         const csv = CSV.readFile(path.join(toolsDataPath, fileName));
         for (const row of csv) {
             const rpiName = row["ScientificName"].replace(" ssp.", " subsp.");
@@ -145,10 +177,28 @@ class RPI {
                     );
                 }
             }
-            checkStatusMatch(name, "CESA", cesa, taxon.getCESA());
-            checkStatusMatch(name, "FESA", fesa, taxon.getFESA());
+            checkStatusMatch(
+                name,
+                "CESA",
+                cesa,
+                taxon.getCESA(),
+                ranksToUpdate,
+            );
+            checkStatusMatch(
+                name,
+                "FESA",
+                fesa,
+                taxon.getFESA(),
+                ranksToUpdate,
+            );
             if (!ignoreCNDDBRank) {
-                checkStatusMatch(name, "CNDDB", cnddb, taxon.getCNDDBRank());
+                checkStatusMatch(
+                    name,
+                    "CNDDB",
+                    cnddb,
+                    taxon.getCNDDBRank(),
+                    ranksToUpdate,
+                );
             }
             if (!ignoreGlobalRank) {
                 checkStatusMatch(
@@ -156,6 +206,7 @@ class RPI {
                     "Global",
                     globalRank,
                     taxon.getGlobalRank(),
+                    ranksToUpdate,
                 );
             }
 
@@ -199,6 +250,10 @@ class RPI {
         this.#checkExceptions(taxa, config, exceptions, errorLog);
 
         this.#scrape(toolsDataDir, taxa, exceptions, errorLog);
+
+        if (update) {
+            this.#updateRanks(dataDir, ranksToUpdate);
+        }
     }
 
     /**
@@ -429,6 +484,34 @@ class RPI {
         }
         return false;
     }
-}
 
-export { RPI };
+    /**
+     * @param {string} dataDir
+     * @param {RanksToUpdate} ranksToUpdate
+     */
+    static #updateRanks(dataDir, ranksToUpdate) {
+        const taxa = new TaxaCSV(dataDir);
+
+        for (const taxonData of taxa.getTaxa()) {
+            const ranks = ranksToUpdate.get(taxonData.taxon_name);
+            if (!ranks) {
+                continue;
+            }
+            for (const [k, v] of ranks.entries()) {
+                switch (k) {
+                    case "CNDDB":
+                        taxonData["SRank"] = v ?? "";
+                        break;
+                    case "Global":
+                        taxonData["GRank"] = v ?? "";
+                        break;
+                    default:
+                        taxonData[k] = v ?? "";
+                        break;
+                }
+            }
+        }
+
+        taxa.write();
+    }
+}

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@ca-plant-list/ca-plant-list",
-    "version": "0.4.35",
+    "version": "0.4.37",
     "description": "Tools to create files for a website listing plants in an area of California.",
     "license": "MIT",
     "repository": {
@@ -40,14 +40,14 @@
         "@htmltools/scrape": "^0.1.1",
         "archiver": "^5.3.1",
         "cli-progress": "^3.12.0",
-        "commander": "^13.1.0",
+        "commander": "^14.0.1",
         "csv-parse": "^5.6.0",
         "csv-stringify": "^6.5.2",
         "exceljs": "^4.4.0",
         "image-size": "^1.1.1",
         "markdown-it": "^14.1.0",
         "sharp": "^0.33.5",
-        "svgo-ll": "^5.6.0",
+        "svgo-ll": "^6.0.1",
         "unzipper": "^0.12.3"
     },
     "devDependencies": {
@@ -57,10 +57,10 @@
         "@types/markdown-it": "^14.1.2",
         "@types/node": "^22.10.7",
         "@types/unzipper": "^0.10.9",
-        "eslint": "^9.20.1",
+        "eslint": "^9.35.0",
         "jest": "^29.7.0",
-        "prettier": "^3.5.1",
+        "prettier": "^3.6.2",
         "puppeteer": "^24.1.1",
-        "typescript": "^5.7.3"
+        "typescript": "^5.9.2"
     }
 }

package/scripts/build-ebook.js

@@ -71,7 +71,7 @@ async function buildBook(outputDir, dataDir, showFlowerErrors, maxTaxa) {
     const errorLog = new ErrorLog(outputDir + "/errors.tsv");
 
     const taxa = new Taxa(
-        Program.getIncludeList(dataDir),
+        Taxa.getIncludeList(dataDir),
         errorLog,
         showFlowerErrors,
     );

package/scripts/build-site.js

@@ -16,7 +16,7 @@ async function build(options) {
     Files.rmDir(outputDir);
     const errorLog = new ErrorLog(outputDir + "/errors.tsv");
     const taxa = new Taxa(
-        Program.getIncludeList(options.datadir),
+        Taxa.getIncludeList(options.datadir),
         errorLog,
         options.showFlowerErrors,
     );

package/scripts/cpl-photos.js

@@ -506,7 +506,7 @@ async function getTaxa(options) {
         taxa = await taxaLoaderClass.TaxaLoader.loadTaxa(options, errorLog);
     } else {
         taxa = new Taxa(
-            Program.getIncludeList(options.datadir),
+            Taxa.getIncludeList(options.datadir),
             errorLog,
             options.showFlowerErrors,
         );

package/scripts/cpl-tools.js

@@ -145,10 +145,12 @@ async function build(program, options) {
             case TOOLS.RPI:
                 await RPI.analyze(
                     TOOLS_DATA_DIR,
+                    options.datadir,
                     taxa,
                     config,
                     exceptions,
                     errorLog,
+                    !!options.update,
                 );
                 break;
             case TOOLS.TEXT:

package/scripts/inattaxonphotos.js

@@ -44,7 +44,7 @@ async function fetchInatTaxa(taxa) {
 async function getTaxonPhotos(options) {
     const errorLog = new ErrorLog(options.outputdir + "/errors.tsv");
     const taxa = new Taxa(
-        Program.getIncludeList(options.datadir),
+        Taxa.getIncludeList(options.datadir),
         errorLog,
         false,
     );