jats-convert 1.0.13 → 1.0.15

package/README.md

@@ -1,18 +1,18 @@
 # jats-convert
 
 [![jats-convert on npm](https://img.shields.io/npm/v/jats-convert.svg)](https://www.npmjs.com/package/jats-convert)
-[![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/curvenote/jats/blob/main/LICENSE)
-[![CI](https://github.com/curvenote/jats/workflows/CI/badge.svg)](https://github.com/curvenote/jats-cli/actions)
+[![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/continuous-foundation/jats/blob/main/LICENSE)
+[![CI](https://github.com/continuous-foundation/jats/workflows/CI/badge.svg)](https://github.com/continuous-foundation/jats-cli/actions)
 
 Convert a JATS XML document to a MyST AST.
 
-Portions of this package were created for `jats-to-myst` and [committed](https://github.com/jupyter-book/mystmd/commits/mystmd%401.3.12/packages/jats-to-myst/src) to project Jupyter's `mystmd` project by Curvenote team members. The work is licensed MIT in both places, `jats-convert` has additional functionality and nuance depending on the publisher.
+Portions of this package were created for `jats-to-myst` and [committed](https://github.com/jupyter-book/mystmd/commits/mystmd%401.3.12/packages/jats-to-myst/src) to project Jupyter's `mystmd` project. The work is licensed MIT in both places, `jats-convert` has additional functionality and nuance depending on the publisher.
 
 ---
 
 <p style="text-align: center; color: #aaa; padding-top: 50px">
   Made with love by
-  <a href="https://curvenote.com" target="_blank" style="color: #aaa">
-    <img src="https://cdn.curvenote.com/brand/logo-blue-icon.png" style="height: 1em" /> Curvenote
+  <a href="https://continuous.foundation" target="_blank" style="color: #aaa">
+    Continuous Science Foundation <img src="https://continuous.foundation/images/logo-small.svg" style="height: 1em" />
   </a>
 </p>

package/dist/index.d.ts

@@ -1,7 +1,7 @@
-import type { Root } from 'myst-spec';
 import type { Plugin } from 'unified';
 import { VFile } from 'vfile';
-import type { MessageInfo, GenericNode } from 'myst-common';
+import type { MessageInfo, GenericNode, GenericParent } from 'myst-common';
+import type { Body } from 'jats-tags';
 import type { ISession } from 'jats-xml';
 import { Jats } from 'jats-xml';
 import type { Handler, IJatsParser, Options, StateData } from './types.js';
@@ -30,14 +30,12 @@ export declare class JatsParser implements IJatsParser {
     openNode(name: string, attributes?: Attributes, isLeaf?: boolean): void;
     closeNode(): GenericNode | undefined;
 }
-export declare const jatsConvertPlugin: Plugin<[Jats, Options?], Root, Root>;
-export declare function jatsConvertTransform(data: string | Jats, opts?: Options): Promise<{
-    tree: Root;
-    jats: Jats;
-    references: any;
+export declare const jatsConvertPlugin: Plugin<[Jats, Options?], Body, Body>;
+export declare function jatsConvertTransform(jats: Jats, opts?: Options): {
+    tree: GenericParent;
     frontmatter: ProjectFrontmatter;
-}>;
-export declare function jatsConvert(session: ISession, input: string, opts?: {
+};
+export declare function jatsConvert(session: ISession, input?: string, opts?: {
     frontmatter?: 'page' | 'project';
     dois?: boolean;
     bibtex?: boolean;

package/dist/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAGtC,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,SAAS,CAAC;AACtC,OAAO,EAAE,KAAK,EAAE,MAAM,OAAO,CAAC;AAE9B,OAAO,KAAK,EAAE,WAAW,EAAE,WAAW,EAAiB,MAAM,aAAa,CAAC;AAM3E,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,UAAU,CAAC;AACzC,OAAO,EAAE,IAAI,EAAE,MAAM,UAAU,CAAC;AAGhC,OAAO,KAAK,EAAE,OAAO,EAAE,WAAW,EAAc,OAAO,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAMvF,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AAyD3D,KAAK,UAAU,GAAG,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC;AA8UtC,qBAAa,UAAW,YAAW,WAAW;IAC5C,IAAI,EAAE,KAAK,CAAC;IACZ,IAAI,EAAE,SAAS,CAAC;IAChB,OAAO,EAAE,OAAO,CAAC;IACjB,QAAQ,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAClC,KAAK,EAAE,WAAW,EAAE,CAAM;IAC1B,IAAI,EAAE,IAAI,CAAC;IAEX,SAAS,EAAE,MAAM,EAAE,CAAM;gBAEb,IAAI,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,EAAE,OAAO;IASnD,GAAG;IAIH,IAAI,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,WAAW;IAQzD,KAAK,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,WAAW;IAQ1D,QAAQ,CAAC,EAAE,CAAC,EAAE,WAAW;IAMzB,IAAI,CAAC,IAAI,CAAC,EAAE,MAAM;;;;IAelB,cAAc,CAAC,IAAI,EAAE,WAAW;IAYhC,YAAY,CAAC,IAAI,EAAE,WAAW,EAAE,IAAI,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,UAAU;IAUrE,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,UAAU;IAK7C,QAAQ,CAAC,IAAI,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,UAAU,EAAE,MAAM,UAAQ;IAM9D,SAAS;CAIV;AAED,eAAO,MAAM,iBAAiB,EAAE,MAAM,CAAC,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,EAAE,IAAI,EAAE,IAAI,CA0ElE,CAAC;AAEF,wBAAsB,oBAAoB,CACxC,IAAI,EAAE,MAAM,GAAG,IAAI,EACnB,IAAI,CAAC,EAAE,OAAO,GACb,OAAO,CAAC;IACT,IAAI,EAAE,IAAI,CAAC;IACX,IAAI,EAAE,IAAI,CAAC;IACX,UAAU,EAAE,GAAG,CAAC;IAChB,WAAW,EAAE,kBAAkB,CAAC;CACjC,CAAC,CAsED;AAED,wBAAsB,WAAW,CAC/B,OAAO,EAAE,QAAQ,EACjB,KAAK,EAAE,MAAM,EACb,IAAI,CAAC,EAAE;IAAE,WAAW,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAAC,IAAI,CAAC,EAAE,OAAO,CAAC;IAAC,MAAM,CAAC,EAAE,OAAO,CAAA;CAAE,iBAkD9E"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,SAAS,CAAC;AACtC,OAAO,EAAE,KAAK,EAAE,MAAM,OAAO,CAAC;AAE9B,OAAO,KAAK,EAAE,WAAW,EAAE,WAAW,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAI3E,OAAO,KAAK,EAAE,IAAI,EAAsB,MAAM,WAAW,CAAC;AAE1D,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,UAAU,CAAC;AACzC,OAAO,EAAE,IAAI,EAAE,MAAM,UAAU,CAAC;AAGhC,OAAO,KAAK,EAAE,OAAO,EAAE,WAAW,EAAc,OAAO,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAEvF,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AAiF3D,KAAK,UAAU,GAAG,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC;AA0ZtC,qBAAa,UAAW,YAAW,WAAW;IAC5C,IAAI,EAAE,KAAK,CAAC;IACZ,IAAI,EAAE,SAAS,CAAC;IAChB,OAAO,EAAE,OAAO,CAAC;IACjB,QAAQ,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAClC,KAAK,EAAE,WAAW,EAAE,CAAM;IAC1B,IAAI,EAAE,IAAI,CAAC;IAEX,SAAS,EAAE,MAAM,EAAE,CAAM;gBAEb,IAAI,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,EAAE,OAAO;IASnD,GAAG;IAIH,IAAI,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,WAAW;IAQzD,KAAK,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,WAAW;IAQ1D,QAAQ,CAAC,EAAE,CAAC,EAAE,WAAW;IAMzB,IAAI,CAAC,IAAI,CAAC,EAAE,MAAM;;;;IAelB,cAAc,CAAC,IAAI,EAAE,WAAW;IAYhC,YAAY,CAAC,IAAI,EAAE,WAAW,EAAE,IAAI,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,UAAU;IAUrE,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,UAAU;IAK7C,QAAQ,CAAC,IAAI,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,UAAU,EAAE,MAAM,UAAQ;IAM9D,SAAS;CAIV;AAED,eAAO,MAAM,iBAAiB,EAAE,MAAM,CAAC,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,EAAE,IAAI,EAAE,IAAI,CA+DlE,CAAC;AAEF,wBAAgB,oBAAoB,CAClC,IAAI,EAAE,IAAI,EACV,IAAI,CAAC,EAAE,OAAO,GACb;IACD,IAAI,EAAE,aAAa,CAAC;IACpB,WAAW,EAAE,kBAAkB,CAAC;CACjC,CAuDA;AAED,wBAAsB,WAAW,CAC/B,OAAO,EAAE,QAAQ,EACjB,KAAK,CAAC,EAAE,MAAM,EACd,IAAI,CAAC,EAAE;IAAE,WAAW,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAAC,IAAI,CAAC,EAAE,OAAO,CAAC;IAAC,MAAM,CAAC,EAAE,OAAO,CAAA;CAAE,iBA+D9E"}

package/dist/index.js

@@ -1,7 +1,6 @@
 import fs from 'node:fs';
 import path from 'node:path';
 import { unified } from 'unified';
-import { doi } from 'doi-utils';
 import { VFile } from 'vfile';
 import yaml from 'js-yaml';
 import { copyNode, fileError, RuleId, normalizeLabel } from 'myst-common';
@@ -11,15 +10,31 @@ import { RefType } from 'jats-tags';
 import { Jats } from 'jats-xml';
 import { MathMLToLaTeX } from 'mathml-to-latex';
 import { js2xml } from 'xml-js';
-import { basicTransformations, citationToMixedCitation, journalTransforms, } from './transforms/index.js';
+import { basicTransformations, journalTransforms } from './transforms/index.js';
 import { abstractTransform, descriptionFromAbstract } from './transforms/abstract.js';
-import { processJatsReferences, resolveJatsCitations } from './transforms/references.js';
-import { backToBodyTransform } from './transforms/footnotes.js';
+import { getPMIDLookup, processJatsReferences, resolveJatsCitations, } from './transforms/references.js';
+import { backToBodyTransform, tableFootnotesToLegend } from './transforms/footnotes.js';
 import version from './version.js';
 import { logMessagesFromVFile, toText } from './utils.js';
 import { inlineCitationsTransform } from './myst/inlineCitations.js';
-import { abbreviationSectionTransform } from './transforms/abbreviations.js';
+import { abbreviationFootnoteTransform, abbreviationSectionTransform, } from './transforms/abbreviations.js';
 import { floatToEndTransform } from './transforms/supplementary.js';
+import { dataAvailabilityTransform } from './transforms/parts.js';
+import { abbreviationsFromTree } from './myst/abbreviations.js';
+const MEDIA_FIGURE_EXTENSIONS = [
+    '.png',
+    '.jpg',
+    '.jpeg',
+    '.svg',
+    '.gif',
+    '.tiff',
+    '.tif',
+    '.eps',
+    '.webp',
+    '.mp4',
+    '.mov',
+    '.avi',
+];
 function refTypeToReferenceKind(kind) {
     switch (kind) {
         case RefType.sec:
@@ -79,10 +94,12 @@ const handlers = {
         state.renderInline(node, 'paragraph');
     },
     heading(node, state) {
+        var _a;
+        const { label, identifier } = (_a = normalizeLabel(node.id)) !== null && _a !== void 0 ? _a : {};
         state.renderInline(node, 'heading', {
             enumerated: true,
-            label: node.id,
-            identifier: node.id,
+            label,
+            identifier,
             depth: node.depth,
         });
     },
@@ -119,12 +136,14 @@ const handlers = {
         state.renderInline(node, 'listItem');
     },
     ['inline-formula'](node, state) {
+        var _a;
         const texMath = texMathFromNode(node);
         if (texMath) {
+            const { label, identifier } = (_a = normalizeLabel(node.id)) !== null && _a !== void 0 ? _a : {};
             state.addLeaf('inlineMath', {
                 value: texMath,
-                label: node.id,
-                identifier: node.id,
+                label,
+                identifier,
             });
         }
         else {
@@ -132,16 +151,26 @@ const handlers = {
         }
     },
     ['disp-formula'](node, state) {
+        var _a;
         const texMath = texMathFromNode(node);
+        const { label, identifier } = (_a = normalizeLabel(node.id)) !== null && _a !== void 0 ? _a : {};
         if (texMath) {
             state.addLeaf('math', {
                 value: texMath,
-                label: node.id,
-                identifier: node.id,
+                label,
+                identifier,
             });
         }
         else {
+            if (node.id) {
+                state.openNode('div', { label, identifier });
+            }
+            state.openNode('paragraph');
             state.renderChildren(node);
+            state.closeNode();
+            if (node.id) {
+                state.closeNode();
+            }
         }
     },
     bold(node, state) {
@@ -184,7 +213,15 @@ const handlers = {
         state.renderInline(node, 'link', { url: node['xlink:href'] });
     },
     ['boxed-text'](node, state) {
+        var _a;
+        if (node.id) {
+            const { label, identifier } = (_a = normalizeLabel(node.id)) !== null && _a !== void 0 ? _a : {};
+            state.openNode('div', { label, identifier });
+        }
         state.renderInline(node, 'admonition', { kind: 'info' });
+        if (node.id) {
+            state.closeNode();
+        }
     },
     admonitionTitle(node, state) {
         // This is created in a transform!
@@ -359,6 +396,9 @@ const handlers = {
                     kind: 'narrative',
                 });
                 return;
+            case RefType.app:
+            case RefType.boxedText:
+            case RefType.media:
             case RefType.supplementaryMaterial:
             case RefType.sec:
             case RefType.fig:
@@ -381,6 +421,59 @@ const handlers = {
         }
     },
     ['supplementary-material'](node, state) {
+        var _a, _b, _c, _d, _e;
+        const { label, identifier } = (_a = normalizeLabel(node.id)) !== null && _a !== void 0 ? _a : {};
+        let maybeCaption;
+        let media;
+        if (((_b = node.children) === null || _b === void 0 ? void 0 : _b.length) === 1 && node.children[0].type === 'media') {
+            media = node.children[0];
+        }
+        else if (((_c = node.children) === null || _c === void 0 ? void 0 : _c.length) === 2 &&
+            node.children[0].type === 'label' &&
+            node.children[1].type === 'media') {
+            maybeCaption = node.children[0];
+            media = node.children[1];
+        }
+        const url = media === null || media === void 0 ? void 0 : media['xlink:href'];
+        let caption = ((_d = select('caption', media)) !== null && _d !== void 0 ? _d : maybeCaption);
+        if (((_e = caption === null || caption === void 0 ? void 0 : caption.children) === null || _e === void 0 ? void 0 : _e.length) === 1 && caption.children[0].type === 'p') {
+            caption = caption.children[0];
+        }
+        if (url && MEDIA_FIGURE_EXTENSIONS.find((ext) => url.endsWith(ext))) {
+            const title = select('title', media);
+            state.openNode('container', { label, identifier, kind: 'figure' });
+            const wasInContainer = state.data.isInContainer;
+            state.data.isInContainer = true;
+            state.addLeaf('image', { url });
+            state.openNode('caption');
+            state.openNode('link', { url });
+            if (title) {
+                state.openNode('strong');
+                state.renderChildren(title);
+                state.closeNode();
+            }
+            if (caption) {
+                state.renderChildren(caption);
+            }
+            state.closeNode();
+            state.closeNode();
+            state.closeNode();
+            state.data.isInContainer = wasInContainer;
+        }
+        else {
+            if (node.id) {
+                state.openNode('div', { label, identifier });
+            }
+            state.renderChildren(node);
+            if (node.id) {
+                state.closeNode();
+            }
+        }
+    },
+    ['app-group'](node, state) {
+        state.renderChildren(node);
+    },
+    app(node, state) {
         var _a;
         if (node.id) {
             const { label, identifier } = (_a = normalizeLabel(node.id)) !== null && _a !== void 0 ? _a : {};
@@ -400,6 +493,9 @@ const handlers = {
     caption(node, state) {
         state.renderChildren(node);
     },
+    email(node, state) {
+        state.renderInline(node, 'link', { url: `mailto:${toText(node)}` });
+    },
     // These nodes can be safely ignored
     label() { },
     comment() { },
@@ -503,68 +599,57 @@ export class JatsParser {
     }
 }
 export const jatsConvertPlugin = function (jats, opts) {
-    this.Compiler = (node, file) => {
-        if (jats.abstract)
+    this.Compiler = (body, file) => {
+        if (jats.abstract) {
             abstractTransform(jats.abstract);
-        const tree = jats.abstract
-            ? {
-                type: 'root',
-                children: [
-                    u('block', { part: 'abstract' }, copyNode(jats.abstract).children),
-                    ...copyNode(node).children,
-                ],
-            }
-            : copyNode(node);
+            body.children = [
+                u('block', { part: 'abstract' }, copyNode(jats.abstract).children),
+                ...body.children,
+            ];
+        }
         // Can do better than this in the future, but for now, just put them at the end!
         const floatsGroup = selectAll('floats-group', jats.tree);
         if (floatsGroup.length > 0) {
             floatsGroup.forEach((g) => {
-                tree.children.push(...g.children);
+                body.children.push(...g.children);
             });
         }
-        basicTransformations(tree, file);
-        citationToMixedCitation(tree);
-        journalTransforms(tree);
-        const state = new JatsParser(file, jats, opts !== null && opts !== void 0 ? opts : { handlers });
-        state.renderChildren(tree);
+        floatToEndTransform(body);
+        backToBodyTransform(body, jats.back);
+        dataAvailabilityTransform(body);
+        const refLookup = processJatsReferences(body, jats.references, opts);
+        basicTransformations(body, file);
+        journalTransforms(body);
+        const state = new JatsParser(file, jats, opts);
+        state.renderChildren(body);
         while (state.stack.length > 1)
             state.closeNode();
+        const tree = state.stack[0];
         if (state.unhandled.length && (opts === null || opts === void 0 ? void 0 : opts.logInfo)) {
             opts.logInfo.unhandled = [...new Set(state.unhandled)];
         }
-        const referenceData = Object.fromEntries(jats.references.map((bibr) => {
-            const id = bibr.id;
-            const names = selectAll('name,string-name', bibr)
-                .map((n) => `${toText(select('surname', n))}, ${toText(select('given-names', n))}`)
-                .join(', ');
-            const year = toText(select('year', bibr));
-            const title = toText(select('article-title', bibr));
-            const source = toText(select('source', bibr));
-            const volume = toText(select('volume', bibr));
-            const fpage = toText(select('fpage', bibr));
-            const lpage = toText(select('lpage', bibr));
-            const doiElement = selectAll('ext-link,[pub-id-type=doi]', bibr).find((e) => doi.validate(toText(e)));
-            const doiString = doiElement ? toText(doiElement) : undefined;
-            const doiLink = doiString ? ` <a href=${doi.buildUrl(doiString)}>${doiString}</a>` : '';
-            return [
-                id,
-                {
-                    html: `${names}. (${year}). ${title}. <i>${source}</i>, <i>${volume}</i>, ${fpage}-${lpage}.${doiLink}`,
-                    doi: doiString,
-                },
-            ];
-        }));
-        const referenceOrder = [];
-        const xrefs = selectAll('xref[ref-type=bibr]', jats.body);
-        xrefs.forEach((xref) => {
-            const rid = xref.rid;
-            if (!referenceOrder.includes(rid)) {
-                referenceOrder.push(rid);
-            }
+        resolveJatsCitations(tree, refLookup);
+        inlineCitationsTransform(tree, jats.references
+            .map(({ id }) => {
+            var _a;
+            const { identifier } = (_a = normalizeLabel(id)) !== null && _a !== void 0 ? _a : {};
+            return identifier;
+        })
+            .filter((id) => !!id));
+        const { frontmatter } = jats;
+        abbreviationSectionTransform(tree, frontmatter);
+        abbreviationFootnoteTransform(tree, frontmatter);
+        abbreviationsFromTree(tree, frontmatter);
+        tableFootnotesToLegend(tree);
+        const abstract = selectAll('block', tree).find((block) => {
+            return block.data && block.data.part === 'abstract';
         });
+        if (abstract) {
+            frontmatter.description = descriptionFromAbstract(toText(abstract));
+        }
         const result = {
-            references: { order: referenceOrder, data: referenceData },
-            tree: state.stack[0],
+            tree,
+            frontmatter,
         };
         file.result = result;
         return file;
@@ -573,9 +658,8 @@ export const jatsConvertPlugin = function (jats, opts) {
         return node;
     };
 };
-export async function jatsConvertTransform(data, opts) {
+export function jatsConvertTransform(jats, opts) {
     var _a, _b, _c;
-    const jats = typeof data === 'string' ? new Jats(data) : data;
     if (opts === null || opts === void 0 ? void 0 : opts.logInfo) {
         opts.logInfo.publisher = toText(select('publisher-name', jats.tree)) || null;
         opts.logInfo.journal = toText(select('journal-title', jats.tree)) || null;
@@ -599,24 +683,10 @@ export async function jatsConvertTransform(data, opts) {
         }
         opts.logInfo.license = licenseString;
     }
-    const { frontmatter } = jats;
     const file = (_b = opts === null || opts === void 0 ? void 0 : opts.vfile) !== null && _b !== void 0 ? _b : new VFile();
-    const refLookup = await processJatsReferences(jats, opts);
-    floatToEndTransform(jats);
-    backToBodyTransform(jats);
     const pipe = unified().use(jatsConvertPlugin, jats, opts);
-    pipe.stringify(((_c = jats.body) !== null && _c !== void 0 ? _c : { type: 'body', children: [] }), file);
-    const references = file.result.references;
-    const tree = file.result.tree;
-    resolveJatsCitations(tree, refLookup);
-    inlineCitationsTransform(tree, [...Object.keys(references.data)]);
-    abbreviationSectionTransform(tree, frontmatter);
-    const abstract = selectAll('block', tree).find((node) => {
-        return node.data && node.data.part === 'abstract';
-    });
-    if (abstract) {
-        frontmatter.description = descriptionFromAbstract(toText(abstract));
-    }
+    pipe.stringify(copyNode((_c = jats.body) !== null && _c !== void 0 ? _c : { type: 'body', children: [] }), file);
+    const { tree, frontmatter } = file.result;
     if (opts === null || opts === void 0 ? void 0 : opts.logInfo) {
         opts.logInfo.figures = {
             body: selectAll('fig', jats.body).length,
@@ -646,17 +716,30 @@ export async function jatsConvertTransform(data, opts) {
             myst: selectAll('footnoteDefinition', tree).length,
         };
     }
-    return { tree, jats, references, frontmatter }; //, kind };
+    return { tree, frontmatter };
 }
 export async function jatsConvert(session, input, opts) {
     const logInfo = { jatsVersion: version };
+    if (!input) {
+        const xmls = fs.readdirSync('.').filter((file) => path.extname(file) === '.xml');
+        if (xmls.length === 0) {
+            throw new Error('No JATS xml file found in current directory; please specify input');
+        }
+        if (xmls.length > 1) {
+            throw new Error('Multiple XML files found in current directory; please specify input');
+        }
+        input = xmls[0];
+    }
     const dir = path.dirname(input);
     const vfile = new VFile();
     vfile.path = input;
-    const { tree, frontmatter } = await jatsConvertTransform(fs.readFileSync(input).toString(), {
+    const jats = new Jats(fs.readFileSync(input).toString());
+    const pmidCache = await getPMIDLookup(jats.references, dir);
+    const { tree, frontmatter } = jatsConvertTransform(jats, {
         vfile,
         dir,
         logInfo,
+        pmidCache,
         dois: opts === null || opts === void 0 ? void 0 : opts.dois,
         bibtex: opts === null || opts === void 0 ? void 0 : opts.bibtex,
     });

package/dist/myst/abbreviations.d.ts

@@ -0,0 +1,11 @@
+import type { GenericParent } from 'myst-common';
+import type { ProjectFrontmatter } from 'myst-frontmatter';
+/**
+ * Attempt to pull abbreviations out of tree
+ *
+ * This looks for parenthesized letters and tries to match them to the
+ * previous words.
+ */
+export declare function abbreviationsFromTree(tree: GenericParent, frontmatter: Pick<ProjectFrontmatter, 'abbreviations'>): void;
+export declare function abbreviationsFromText(text: string): Record<string, string>;
+//# sourceMappingURL=abbreviations.d.ts.map

package/dist/myst/abbreviations.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"abbreviations.d.ts","sourceRoot":"","sources":["../../src/myst/abbreviations.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAGjD,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AAE3D;;;;;GAKG;AACH,wBAAgB,qBAAqB,CACnC,IAAI,EAAE,aAAa,EACnB,WAAW,EAAE,IAAI,CAAC,kBAAkB,EAAE,eAAe,CAAC,QAYvD;AAgCD,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CA+B1E"}

package/dist/myst/abbreviations.js

@@ -0,0 +1,80 @@
+import { selectAll } from 'unist-util-select';
+import { toText } from '../utils.js';
+/**
+ * Attempt to pull abbreviations out of tree
+ *
+ * This looks for parenthesized letters and tries to match them to the
+ * previous words.
+ */
+export function abbreviationsFromTree(tree, frontmatter) {
+    let abbreviations = {};
+    const paragraphs = selectAll('paragraph', tree);
+    paragraphs.forEach((paragraph) => {
+        const text = toText(paragraph);
+        abbreviations = {
+            ...abbreviations,
+            ...abbreviationsFromText(text),
+        };
+    });
+    frontmatter.abbreviations = { ...frontmatter.abbreviations, ...abbreviations };
+}
+function maybeStopWord(word) {
+    return word.length < 5;
+}
+function exploreAbbrPossibilities(letter, possibilities) {
+    const newPossibilities = [];
+    possibilities.forEach(({ prev, next }) => {
+        if (prev === null || prev === void 0 ? void 0 : prev.includes(letter)) {
+            newPossibilities.push({
+                prev: prev.slice(prev.indexOf(letter) + 1),
+                next,
+            });
+        }
+        for (const [i, n] of next.entries()) {
+            if (n.startsWith(letter)) {
+                newPossibilities.push({
+                    prev: next[i].slice(1),
+                    next: next.slice(i + 1),
+                });
+            }
+            if (!prev || !maybeStopWord(n)) {
+                break;
+            }
+        }
+    });
+    return newPossibilities;
+}
+export function abbreviationsFromText(text) {
+    const abbreviations = {};
+    const textList = text.split(' ');
+    textList.forEach((word, index) => {
+        var _a;
+        const abbr = (_a = word.match(/^\(([^\s]{2,})\).{0,1}/)) === null || _a === void 0 ? void 0 : _a[1];
+        if (!abbr)
+            return;
+        const possibleWords = [];
+        let wordIndex = index - 1;
+        while (textList[wordIndex] && possibleWords.filter((w) => w.length > 4).length < abbr.length) {
+            possibleWords.unshift(textList[wordIndex]);
+            wordIndex--;
+        }
+        for (const i of Array(possibleWords.length).keys()) {
+            let possibilities = [
+                {
+                    next: possibleWords.slice(i).map((w) => w.toLowerCase()),
+                },
+            ];
+            abbr
+                .split('')
+                .filter((letter) => letter.match(/^[a-zA-Z]$/))
+                .forEach((letter) => {
+                possibilities = exploreAbbrPossibilities(letter.toLowerCase(), possibilities);
+            });
+            if (possibilities.filter(({ next }) => next.length === 0).length) {
+                abbreviations[abbr] = possibleWords.slice(i).join(' ');
+                break;
+            }
+        }
+    });
+    return abbreviations;
+}

package/dist/myst/inlineCitations.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"inlineCitations.d.ts","sourceRoot":"","sources":["../../src/myst/inlineCitations.ts"],"names":[],"mappings":"AAAA,OAAO,EAA0C,KAAK,aAAa,EAAE,MAAM,aAAa,CAAC;AAuKzF,wBAAgB,wBAAwB,CAAC,IAAI,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,EAAE,QAenF"}
+{"version":3,"file":"inlineCitations.d.ts","sourceRoot":"","sources":["../../src/myst/inlineCitations.ts"],"names":[],"mappings":"AAAA,OAAO,EAA0C,KAAK,aAAa,EAAE,MAAM,aAAa,CAAC;AAwMzF,wBAAgB,wBAAwB,CAAC,IAAI,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,EAAE,QAiBnF"}

package/dist/myst/inlineCitations.js

@@ -174,6 +174,44 @@ function expandHyphenatedCites(tree, referenceList) {
     });
     remove(tree, '__delete__');
 }
+/**
+ * Remove superscript around citations
+ */
+function removeCiteSuperscript(tree) {
+    const citeGroupParents = selectAll(':has(> citeGroup)', tree);
+    citeGroupParents.forEach((parent) => {
+        if (parent.type !== 'superscript')
+            return;
+        if (parent.children.length !== 1)
+            return;
+        parent.type = '__lift__';
+    });
+    liftChildren(tree, '__lift__');
+}
+/**
+ * Ensure there are spaces before citations
+ *
+ * This is a problem, for example, when citations are removed from superscript and there
+ * was no space before the citation.
+ */
+function ensureSpaceBeforeCite(tree) {
+    const citeGroupParents = selectAll(':has(> text + citeGroup)', tree);
+    citeGroupParents.forEach((parent) => {
+        parent.children.forEach((child, index) => {
+            var _a, _b;
+            if (child.type !== 'text')
+                return;
+            const citeChild = parent.children[index + 1];
+            if ((citeChild === null || citeChild === void 0 ? void 0 : citeChild.type) !== 'citeGroup')
+                return;
+            if ((_a = child.value) === null || _a === void 0 ? void 0 : _a.match(/\s+$/))
+                return;
+            if ((_b = child.value) === null || _b === void 0 ? void 0 : _b.match(/[[(]$/))
+                return;
+            child.value = `${child.value} `;
+        });
+    });
+}
 export function inlineCitationsTransform(tree, referenceIds) {
     let before = '';
     let current = JSON.stringify(tree);
@@ -187,6 +225,8 @@ export function inlineCitationsTransform(tree, referenceIds) {
         removeCiteSeparators(tree);
         expandHyphenatedCites(tree, referenceIds);
         removeCiteParentheses(tree);
+        removeCiteSuperscript(tree);
+        ensureSpaceBeforeCite(tree);
         current = JSON.stringify(tree);
     }
 }

package/dist/transforms/abbreviations.d.ts

@@ -14,4 +14,9 @@ import type { ProjectFrontmatter } from 'myst-frontmatter';
  * CER, ceramides; FASN, fatty acid synthase; FDR, false discovery rate.
  */
 export declare function abbreviationSectionTransform(tree: GenericParent, frontmatter: Pick<ProjectFrontmatter, 'abbreviations'>): void;
+/**
+ * If there is a footnote that starts with "abbreviations:" try to move abbreviatons to frontmatter
+ *
+ */
+export declare function abbreviationFootnoteTransform(tree: GenericParent, frontmatter: Pick<ProjectFrontmatter, 'abbreviations'>): void;
 //# sourceMappingURL=abbreviations.d.ts.map

package/dist/transforms/abbreviations.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"abbreviations.d.ts","sourceRoot":"","sources":["../../src/transforms/abbreviations.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AACjD,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AAK3D;;;;;;;;;;;;GAYG;AACH,wBAAgB,4BAA4B,CAC1C,IAAI,EAAE,aAAa,EACnB,WAAW,EAAE,IAAI,CAAC,kBAAkB,EAAE,eAAe,CAAC,QAuBvD"}
+{"version":3,"file":"abbreviations.d.ts","sourceRoot":"","sources":["../../src/transforms/abbreviations.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAe,aAAa,EAAE,MAAM,aAAa,CAAC;AAC9D,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AAK3D;;;;;;;;;;;;GAYG;AACH,wBAAgB,4BAA4B,CAC1C,IAAI,EAAE,aAAa,EACnB,WAAW,EAAE,IAAI,CAAC,kBAAkB,EAAE,eAAe,CAAC,QAuBvD;AAED;;;GAGG;AACH,wBAAgB,6BAA6B,CAC3C,IAAI,EAAE,aAAa,EACnB,WAAW,EAAE,IAAI,CAAC,kBAAkB,EAAE,eAAe,CAAC,QA4BvD"}

package/dist/transforms/abbreviations.js

@@ -45,3 +45,41 @@ export function abbreviationSectionTransform(tree, frontmatter) {
     });
     remove(tree, '__delete__');
 }
+/**
+ * If there is a footnote that starts with "abbreviations:" try to move abbreviatons to frontmatter
+ *
+ */
+export function abbreviationFootnoteTransform(tree, frontmatter) {
+    const fnDefs = selectAll('footnoteDefinition', tree);
+    const fnRefs = selectAll('footnoteReference', tree).map(({ identifier }) => identifier);
+    fnDefs.forEach((fnDef) => {
+        var _a;
+        if (fnDef.identifier && fnRefs.includes(fnDef.identifier))
+            return;
+        if (((_a = fnDef.children) === null || _a === void 0 ? void 0 : _a.length) !== 1)
+            return;
+        if (fnDef.children[0].type !== 'paragraph')
+            return;
+        const fnText = toText(fnDef.children[0]);
+        const abbrPrefix = 'abbreviations: ';
+        if (!fnText.toLowerCase().startsWith(abbrPrefix))
+            return;
+        const abbreviations = fnText.slice(abbrPrefix.length).replace(/\.$/, '').split(/;\s*/g);
+        const entries = abbreviations.map((abbr) => {
+            const parts = abbr.split(/[,:]\s*/g);
+            if (parts.length !== 2)
+                return undefined;
+            // Spaces in abbreviation value are not allowed
+            if (parts[0].match(/\s/))
+                return undefined;
+            return [parts[0], parts[1]];
+        });
+        // There cannot be a single invalid abbreviation
+        if (entries.findIndex((entry) => !entry) !== -1)
+            return;
+        const newAbbreviations = Object.fromEntries(entries);
+        frontmatter.abbreviations = { ...frontmatter.abbreviations, ...newAbbreviations };
+        fnDef.type = '__delete__';
+    });
+    remove(tree, '__delete__');
+}

package/dist/transforms/footnotes.d.ts

@@ -1,9 +1,13 @@
-import type { Jats } from 'jats-xml';
+import type { GenericParent } from 'myst-common';
+import type { Back, Body } from 'jats-tags';
 /**
- * Move footnotes and sections from back to body
+ * Copy footnotes and sections from back into body tree
  *
- * Currently we only pass body to JATS convert plugin, so we move parts of
- * the backmatter that need parsing to body.
+ * Back is not modified.
  */
-export declare function backToBodyTransform(jats: Jats): void;
+export declare function backToBodyTransform(body: Body, back?: Back): void;
+/**
+ * Leave table footnotes in legend if they are not referenced anywhere
+ */
+export declare function tableFootnotesToLegend(tree: GenericParent): void;
 //# sourceMappingURL=footnotes.d.ts.map

package/dist/transforms/footnotes.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"footnotes.d.ts","sourceRoot":"","sources":["../../src/transforms/footnotes.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,IAAI,EAAE,MAAM,UAAU,CAAC;AAErC;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,IAAI,QAW7C"}
+{"version":3,"file":"footnotes.d.ts","sourceRoot":"","sources":["../../src/transforms/footnotes.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAe,aAAa,EAAE,MAAM,aAAa,CAAC;AAE9D,OAAO,KAAK,EAAE,IAAI,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAG5C;;;;GAIG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,EAAE,IAAI,QAO1D;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,IAAI,EAAE,aAAa,QASzD"}

package/dist/transforms/footnotes.js

@@ -1,23 +1,30 @@
 import { copyNode } from 'myst-common';
-import { remove } from 'unist-util-remove';
+import { selectAll } from 'unist-util-select';
 /**
- * Move footnotes and sections from back to body
+ * Copy footnotes and sections from back into body tree
  *
- * Currently we only pass body to JATS convert plugin, so we move parts of
- * the backmatter that need parsing to body.
+ * Back is not modified.
  */
-export function backToBodyTransform(jats) {
-    var _a, _b;
-    if (!jats.back)
+export function backToBodyTransform(body, back) {
+    var _a;
+    if (!back)
         return;
-    const backNodes = (_a = jats.back.children) === null || _a === void 0 ? void 0 : _a.filter((node) => {
-        return ['fn-group', 'sec', 'ack'].includes(node.type);
+    const backNodes = (_a = back.children) === null || _a === void 0 ? void 0 : _a.filter((node) => {
+        return ['fn-group', 'sec', 'ack', 'app-group'].includes(node.type);
     });
-    if (!((_b = jats.body) === null || _b === void 0 ? void 0 : _b.children) || backNodes.length === 0)
+    if (!(body === null || body === void 0 ? void 0 : body.children) || backNodes.length === 0)
         return;
-    jats.body.children.push({ type: 'hr' }, ...copyNode(backNodes));
-    backNodes.forEach((node) => {
-        node.type = '__delete__';
+    body.children.push({ type: 'hr' }, ...copyNode(backNodes));
+}
+/**
+ * Leave table footnotes in legend if they are not referenced anywhere
+ */
+export function tableFootnotesToLegend(tree) {
+    const tableFns = selectAll('legend > footnoteDefinition', tree);
+    const fnRefs = selectAll('footnoteReference', tree).map(({ identifier }) => identifier);
+    tableFns.forEach((tableFn) => {
+        if (tableFn.identifier && fnRefs.includes(tableFn.identifier))
+            return;
+        tableFn.type = 'paragraph';
     });
-    remove(jats.back, '__delete__');
 }

package/dist/transforms/index.d.ts

@@ -1,17 +1,16 @@
-import type { GenericParent, GenericNode } from 'myst-common';
 import type { Plugin } from 'unified';
 import type { VFile } from 'vfile';
+import type { Body } from 'jats-tags';
 export * from './abbreviations.js';
 export * from './abstract.js';
 export * from './admonitions.js';
 export * from './biorxiv.js';
-export * from './citations.js';
 export * from './figureCaptions.js';
 export * from './footnotes.js';
 export * from './references.js';
 export * from './sections.js';
 export * from './typography.js';
-export declare function basicTransformations(tree: GenericParent, file: VFile): void;
-export declare const basicTransformationsPlugin: Plugin<[], GenericParent, GenericParent>;
-export declare function journalTransforms(tree?: GenericNode): void;
+export declare function basicTransformations(body: Body, file: VFile): void;
+export declare const basicTransformationsPlugin: Plugin<[], Body, Body>;
+export declare function journalTransforms(body: Body): void;
 //# sourceMappingURL=index.d.ts.map

package/dist/transforms/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/transforms/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AAC9D,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,SAAS,CAAC;AACtC,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,OAAO,CAAC;AAQnC,cAAc,oBAAoB,CAAC;AACnC,cAAc,eAAe,CAAC;AAC9B,cAAc,kBAAkB,CAAC;AACjC,cAAc,cAAc,CAAC;AAC7B,cAAc,gBAAgB,CAAC;AAC/B,cAAc,qBAAqB,CAAC;AACpC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,iBAAiB,CAAC;AAChC,cAAc,eAAe,CAAC;AAC9B,cAAc,iBAAiB,CAAC;AAEhC,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,KAAK,QAKpE;AAED,eAAO,MAAM,0BAA0B,EAAE,MAAM,CAAC,EAAE,EAAE,aAAa,EAAE,aAAa,CAG7E,CAAC;AAEJ,wBAAgB,iBAAiB,CAAC,IAAI,CAAC,EAAE,WAAW,QAEnD"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/transforms/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,SAAS,CAAC;AACtC,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,OAAO,CAAC;AACnC,OAAO,KAAK,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAOtC,cAAc,oBAAoB,CAAC;AACnC,cAAc,eAAe,CAAC;AAC9B,cAAc,kBAAkB,CAAC;AACjC,cAAc,cAAc,CAAC;AAC7B,cAAc,qBAAqB,CAAC;AACpC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,iBAAiB,CAAC;AAChC,cAAc,eAAe,CAAC;AAC9B,cAAc,iBAAiB,CAAC;AAEhC,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,KAAK,QAK3D;AAED,eAAO,MAAM,0BAA0B,EAAE,MAAM,CAAC,EAAE,EAAE,IAAI,EAAE,IAAI,CAE7D,CAAC;AAEF,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,IAAI,QAE3C"}

package/dist/transforms/index.js

@@ -7,21 +7,20 @@ export * from './abbreviations.js';
 export * from './abstract.js';
 export * from './admonitions.js';
 export * from './biorxiv.js';
-export * from './citations.js';
 export * from './figureCaptions.js';
 export * from './footnotes.js';
 export * from './references.js';
 export * from './sections.js';
 export * from './typography.js';
-export function basicTransformations(tree, file) {
-    sectionTransform(tree);
-    typographyTransform(tree);
-    admonitionTransform(tree, file);
-    figCaptionTitleTransform(tree);
+export function basicTransformations(body, file) {
+    sectionTransform(body);
+    typographyTransform(body);
+    admonitionTransform(body, file);
+    figCaptionTitleTransform(body);
 }
-export const basicTransformationsPlugin = () => (tree, file) => {
-    basicTransformations(tree, file);
+export const basicTransformationsPlugin = () => (body, file) => {
+    basicTransformations(body, file);
 };
-export function journalTransforms(tree) {
-    graphicToBioRxivUrl(tree);
+export function journalTransforms(body) {
+    graphicToBioRxivUrl(body);
 }

package/dist/transforms/parts.d.ts

@@ -0,0 +1,6 @@
+import type { GenericParent } from 'myst-common';
+/**
+ * Remove duplicate Data Availability title from data-availability part
+ */
+export declare function dataAvailabilityTransform(tree: GenericParent): void;
+//# sourceMappingURL=parts.d.ts.map

package/dist/transforms/parts.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"parts.d.ts","sourceRoot":"","sources":["../../src/transforms/parts.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAe,aAAa,EAAE,MAAM,aAAa,CAAC;AAK9D;;GAEG;AACH,wBAAgB,yBAAyB,CAAC,IAAI,EAAE,aAAa,QAW5D"}

package/dist/transforms/parts.js

@@ -0,0 +1,18 @@
+import { toText } from 'myst-common';
+import { remove } from 'unist-util-remove';
+import { selectAll } from 'unist-util-select';
+/**
+ * Remove duplicate Data Availability title from data-availability part
+ */
+export function dataAvailabilityTransform(tree) {
+    const dataAvailability = selectAll('sec[sec-type=data-availability]', tree);
+    dataAvailability.forEach((node) => {
+        const titles = selectAll('title', node);
+        titles.forEach((title) => {
+            if (toText(title).toLowerCase() === 'data availability') {
+                title.type = '__delete__';
+            }
+        });
+    });
+    remove(tree, '__delete__');
+}

package/dist/transforms/references.d.ts

@@ -1,6 +1,6 @@
 import 'dotenv/config.js';
+import type { Body, Reference } from 'jats-tags';
 import type { GenericParent } from 'myst-common';
-import type { Jats } from 'jats-xml';
 import type { Options } from '../types.js';
 type ProcessedReference = {
     cite?: string;
@@ -18,7 +18,16 @@ type ProcessedReference = {
  * This function also writes a bibtex file if necessary and appends footnotes
  * to the jats tree.
  */
-export declare function processJatsReferences(jats: Jats, opts?: Options): Promise<Record<string, ProcessedReference[]>>;
+export declare function processJatsReferences(body: Body, references: Reference[], opts?: Options): Record<string, ProcessedReference[]>;
+/**
+ * Generate a DOI lookup dictionary for a list of References with PubMed IDs
+ *
+ * This will load lookup dictionary cached on path, if available,
+ * then query (and cache) NIH APIs for other PMIDs
+ *
+ * Returns PMID -> DOI lookup dictionary
+ */
+export declare function getPMIDLookup(refs: Reference[], dir: string): Promise<Record<string, string | null>>;
 /**
  * Resolve cite nodes using reference lookup
  *

package/dist/transforms/references.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"references.d.ts","sourceRoot":"","sources":["../../src/transforms/references.ts"],"names":[],"mappings":"AAAA,OAAO,kBAAkB,CAAC;AAM1B,OAAO,KAAK,EAAe,aAAa,EAAE,MAAM,aAAa,CAAC;AAI9D,OAAO,KAAK,EAAE,IAAI,EAAE,MAAM,UAAU,CAAC;AACrC,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,aAAa,CAAC;AAW3C,KAAK,kBAAkB,GAAG;IACxB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB,CAAC;AA6RF;;;;;;;;;;;GAWG;AACH,wBAAsB,qBAAqB,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,EAAE,OAAO,iDA2DrE;AAsCD;;;;;GAKG;AACH,wBAAsB,oBAAoB,CACxC,IAAI,EAAE,aAAa,EACnB,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,kBAAkB,EAAE,CAAC,iBAqChD"}
+{"version":3,"file":"references.d.ts","sourceRoot":"","sources":["../../src/transforms/references.ts"],"names":[],"mappings":"AAAA,OAAO,kBAAkB,CAAC;AAI1B,OAAO,KAAK,EAAE,IAAI,EAAE,SAAS,EAAE,MAAM,WAAW,CAAC;AACjD,OAAO,KAAK,EAAe,aAAa,EAAE,MAAM,aAAa,CAAC;AAI9D,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,aAAa,CAAC;AAW3C,KAAK,kBAAkB,GAAG;IACxB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB,CAAC;AA6RF;;;;;;;;;;;GAWG;AACH,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,IAAI,EAAE,UAAU,EAAE,SAAS,EAAE,EAAE,IAAI,CAAC,EAAE,OAAO,wCA0DxF;AAED;;;;;;;GAOG;AACH,wBAAsB,aAAa,CAAC,IAAI,EAAE,SAAS,EAAE,EAAE,GAAG,EAAE,MAAM,0CAejE;AAaD;;;;;GAKG;AACH,wBAAsB,oBAAoB,CACxC,IAAI,EAAE,aAAa,EACnB,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,kBAAkB,EAAE,CAAC,iBAqChD"}

package/dist/transforms/references.js

@@ -1,7 +1,6 @@
 import 'dotenv/config.js';
 import fs from 'node:fs';
 import path from 'node:path';
-// import OpenAI from 'openai';
 import { convertPMIDs2DOIs, normalizePMID } from 'jats-fetch';
 import { copyNode, liftChildren, normalizeLabel } from 'myst-common';
 import { select, selectAll } from 'unist-util-select';
@@ -183,7 +182,7 @@ function bibtexFromCite(key, cite, counts, doi) {
     }
     if (bibtexLines.length === 1) {
         counts.unprocessed += 1;
-        // console.log(`This needs addressing: ${key}`);
+        bibtexLines.push(`  note = {${toText(cite)}}`);
     }
     else {
         counts.bibtex += 1;
@@ -266,7 +265,7 @@ function processRef(ref, pmidCache, fnCount, counts, dois) {
     const footnotes = [];
     const bibtexEntries = [];
     (_b = ref.children) === null || _b === void 0 ? void 0 : _b.forEach((child) => {
-        if (['element-citation', 'mixed-citation'].includes(child.type)) {
+        if (['element-citation', 'mixed-citation', 'citation'].includes(child.type)) {
             if (!toText(child))
                 return;
             const cite = processRefCite(child, identifier, pmidCache, counts, dois);
@@ -307,15 +306,14 @@ function processRef(ref, pmidCache, fnCount, counts, dois) {
  * This function also writes a bibtex file if necessary and appends footnotes
  * to the jats tree.
  */
-export async function processJatsReferences(jats, opts) {
+export function processJatsReferences(body, references, opts) {
     var _a, _b;
     const dir = (_a = opts === null || opts === void 0 ? void 0 : opts.dir) !== null && _a !== void 0 ? _a : '.';
     const bibfile = path.join(dir, 'main.bib');
-    const refs = jats.references;
+    const pmidCache = (_b = opts === null || opts === void 0 ? void 0 : opts.pmidCache) !== null && _b !== void 0 ? _b : {};
     let refLookup = {};
     const footnotes = [];
     const bibtexEntries = [];
-    const pmidCache = await getPMIDLookup(refs, dir);
     const counts = {
         dois: 0,
         bibtex: 0,
@@ -323,7 +321,7 @@ export async function processJatsReferences(jats, opts) {
         lostRefs: [],
         lostRefItems: [],
     };
-    refs.forEach((ref) => {
+    references.forEach((ref) => {
         const { refLookup: newRefLookup, footnotes: newFootnotes, bibtexEntries: newBibtexEntries, } = processRef(ref, pmidCache, footnotes.length + 1, counts, opts === null || opts === void 0 ? void 0 : opts.dois);
         refLookup = { ...refLookup, ...newRefLookup };
         bibtexEntries.push(...newBibtexEntries);
@@ -331,7 +329,7 @@ export async function processJatsReferences(jats, opts) {
     });
     if (opts === null || opts === void 0 ? void 0 : opts.logInfo) {
         opts.logInfo.references = {
-            total: refs.length,
+            total: references.length,
             dois: counts.dois,
             bibtex: counts.bibtex,
             footnotes: footnotes.length,
@@ -362,7 +360,7 @@ export async function processJatsReferences(jats, opts) {
         fs.writeFileSync(bibfile, bibtexEntries.join('\n\n'));
     }
     if (footnotes.length) {
-        (_b = jats.body) === null || _b === void 0 ? void 0 : _b.children.push({ type: 'fn-group', children: footnotes });
+        body.children.push({ type: 'fn-group', children: footnotes });
     }
     return refLookup;
 }
@@ -374,7 +372,7 @@ export async function processJatsReferences(jats, opts) {
  *
  * Returns PMID -> DOI lookup dictionary
  */
-async function getPMIDLookup(refs, dir) {
+export async function getPMIDLookup(refs, dir) {
     const pmids = refs
         .map((ref) => {
         const pmidElement = select('ext-link,[pub-id-type=pmid]', ref);

package/dist/transforms/sections.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"sections.d.ts","sourceRoot":"","sources":["../../src/transforms/sections.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,SAAS,CAAC;AACtC,OAAO,KAAK,EAAe,aAAa,EAAE,MAAM,aAAa,CAAC;AAqC9D;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,aAAa,EAAE,SAAS,CAAC,EAAE,SAAS,GAAG,QAAQ,QASrF;AAED,eAAO,MAAM,aAAa,EAAE,MAAM,CAAC,EAAE,EAAE,aAAa,EAAE,aAAa,CAElE,CAAC"}
+{"version":3,"file":"sections.d.ts","sourceRoot":"","sources":["../../src/transforms/sections.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,SAAS,CAAC;AACtC,OAAO,KAAK,EAAe,aAAa,EAAE,MAAM,aAAa,CAAC;AAgD9D;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,aAAa,EAAE,SAAS,CAAC,EAAE,SAAS,GAAG,QAAQ,QAUrF;AAED,eAAO,MAAM,aAAa,EAAE,MAAM,CAAC,EAAE,EAAE,aAAa,EAAE,aAAa,CAElE,CAAC"}

package/dist/transforms/sections.js

@@ -1,9 +1,16 @@
 import { liftChildren, toText } from 'myst-common';
 import { blockNestingTransform } from 'myst-transforms';
-import { select } from 'unist-util-select';
+import { select, selectAll } from 'unist-util-select';
 import { remove } from 'unist-util-remove';
+const SECTION_TYPES = ['sec', 'ack', 'app'];
 function isSection(node) {
-    return node.type === 'sec' || node.type === 'ack';
+    return SECTION_TYPES.includes(node.type);
+}
+function liftApps(tree) {
+    selectAll('app-group', tree).forEach((group) => {
+        group.type = '__lift__';
+    });
+    liftChildren(tree, '__lift__');
 }
 function recurseSections(tree, depth = 1, titleType) {
     var _a;
@@ -34,6 +41,9 @@ function recurseSections(tree, depth = 1, titleType) {
         }
         if (sec.type === 'ack')
             sec.part = 'acknowledgments';
+        if (sec.type === 'app')
+            sec.part = 'appendix';
+        sec.type = 'sec';
         recurseSections(sec, depth + 1, titleType);
     });
 }
@@ -47,6 +57,7 @@ function recurseSections(tree, depth = 1, titleType) {
  */
 export function sectionTransform(tree, titleType) {
     var _a;
+    liftApps(tree);
     recurseSections(tree, 1, titleType);
     remove(tree, '__delete__');
     const topSections = (_a = tree.children) === null || _a === void 0 ? void 0 : _a.filter((n) => isSection(n));

package/dist/transforms/supplementary.d.ts

@@ -1,6 +1,6 @@
-import type { Jats } from 'jats-xml';
+import type { Body } from 'jats-tags';
 /**
  * Move any supplementary-material marked as position=float to end of document
  */
-export declare function floatToEndTransform(jats: Jats): void;
+export declare function floatToEndTransform(body: Body): void;
 //# sourceMappingURL=supplementary.d.ts.map

package/dist/transforms/supplementary.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"supplementary.d.ts","sourceRoot":"","sources":["../../src/transforms/supplementary.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,IAAI,EAAE,MAAM,UAAU,CAAC;AAKrC;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,IAAI,QAY7C"}
+{"version":3,"file":"supplementary.d.ts","sourceRoot":"","sources":["../../src/transforms/supplementary.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAKtC;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,IAAI,QAW7C"}

package/dist/transforms/supplementary.js

@@ -1,23 +1,21 @@
 import { selectAll } from 'unist-util-select';
-import { copyNode } from '../utils.js';
 import { remove } from 'unist-util-remove';
+import { copyNode } from '../utils.js';
 /**
  * Move any supplementary-material marked as position=float to end of document
  */
-export function floatToEndTransform(jats) {
+export function floatToEndTransform(body) {
     var _a;
-    if (!jats.body)
-        return;
-    const floatSupplementaryMaterial = selectAll('supplementary-material[position=float]', jats.body);
+    const floatSupplementaryMaterial = selectAll('supplementary-material[position=float]', body);
     if (floatSupplementaryMaterial.length === 0)
         return;
-    (_a = jats.body.children) === null || _a === void 0 ? void 0 : _a.push({ type: 'hr' });
+    (_a = body.children) === null || _a === void 0 ? void 0 : _a.push({ type: 'hr' });
     floatSupplementaryMaterial.forEach((node) => {
-        var _a, _b;
+        var _a;
         const copy = copyNode(node);
         delete copy.position;
-        (_b = (_a = jats.body) === null || _a === void 0 ? void 0 : _a.children) === null || _b === void 0 ? void 0 : _b.push(copy);
+        (_a = body === null || body === void 0 ? void 0 : body.children) === null || _a === void 0 ? void 0 : _a.push(copy);
         node.type = '__delete__';
     });
-    remove(jats.body, '__delete__');
+    remove(body, '__delete__');
 }

package/dist/types.d.ts

@@ -1,18 +1,11 @@
 import type { PageFrontmatter } from 'myst-frontmatter';
-import type { GenericNode, MessageInfo } from 'myst-common';
+import type { GenericNode, GenericParent, MessageInfo } from 'myst-common';
 import type { Jats } from 'jats-xml';
-import type { Root } from 'myst-spec';
 import type { VFile } from 'vfile';
 export type Handler = (node: GenericNode, state: IJatsParser, parent: any) => void;
 export type JatsResult = {
-    references: {
-        order: string[];
-        data: Record<string, {
-            html: string;
-            doi: string;
-        }>;
-    };
-    tree: Root;
+    tree: GenericParent;
+    frontmatter: PageFrontmatter;
 };
 export type MathPlugins = Required<PageFrontmatter>['math'];
 export type Options = {
@@ -20,6 +13,7 @@ export type Options = {
     handlers?: Record<string, Handler>;
     dir?: string;
     logInfo?: Record<string, any>;
+    pmidCache?: Record<string, string | null>;
     dois?: boolean;
     bibtex?: boolean;
 };

package/dist/types.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../src/types.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAC;AACxD,OAAO,KAAK,EAAE,WAAW,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AAC5D,OAAO,KAAK,EAAE,IAAI,EAAE,MAAM,UAAU,CAAC;AACrC,OAAO,KAAK,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACtC,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,OAAO,CAAC;AAEnC,MAAM,MAAM,OAAO,GAAG,CAAC,IAAI,EAAE,WAAW,EAAE,KAAK,EAAE,WAAW,EAAE,MAAM,EAAE,GAAG,KAAK,IAAI,CAAC;AAEnF,MAAM,MAAM,UAAU,GAAG;IACvB,UAAU,EAAE;QAAE,KAAK,EAAE,MAAM,EAAE,CAAC;QAAC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE;YAAE,IAAI,EAAE,MAAM,CAAC;YAAC,GAAG,EAAE,MAAM,CAAA;SAAE,CAAC,CAAA;KAAE,CAAC;IACrF,IAAI,EAAE,IAAI,CAAC;CACZ,CAAC;AAEF,MAAM,MAAM,WAAW,GAAG,QAAQ,CAAC,eAAe,CAAC,CAAC,MAAM,CAAC,CAAC;AAE5D,MAAM,MAAM,OAAO,GAAG;IACpB,KAAK,CAAC,EAAE,KAAK,CAAC;IACd,QAAQ,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IACnC,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,OAAO,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC;IAE9B,IAAI,CAAC,EAAE,OAAO,CAAC;IAEf,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB,CAAC;AAEF,MAAM,MAAM,SAAS,GAAG;IACtB,aAAa,CAAC,EAAE,OAAO,CAAC;CACzB,CAAC;AAEF,MAAM,WAAW,WAAW,CAAC,CAAC,SAAS,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,GAAG,SAAS;IACpE,IAAI,EAAE,KAAK,CAAC;IACZ,IAAI,EAAE,CAAC,CAAC;IACR,QAAQ,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAClC,IAAI,EAAE,IAAI,CAAC;IACX,OAAO,EAAE,OAAO,CAAC;IACjB,KAAK,EAAE,WAAW,EAAE,CAAC;IACrB,GAAG,EAAE,MAAM,WAAW,CAAC;IACvB,IAAI,EAAE,CAAC,KAAK,CAAC,EAAE,MAAM,KAAK,IAAI,CAAC;IAC/B,cAAc,EAAE,CAAC,IAAI,EAAE,GAAG,KAAK,IAAI,CAAC;IACpC,YAAY,EAAE,CAAC,IAAI,EAAE,WAAW,EAAE,IAAI,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,KAAK,IAAI,CAAC;IAC1F,OAAO,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,KAAK,IAAI,CAAC;IAClE,QAAQ,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,KAAK,IAAI,CAAC;IACnE,SAAS,EAAE,MAAM,IAAI,CAAC;IACtB,IAAI,EAAE,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,WAAW,KAAK,IAAI,CAAC;IACrE,KAAK,EAAE,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,WAAW,KAAK,IAAI,CAAC;CACvE"}
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../src/types.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAC;AACxD,OAAO,KAAK,EAAE,WAAW,EAAE,aAAa,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AAC3E,OAAO,KAAK,EAAE,IAAI,EAAE,MAAM,UAAU,CAAC;AACrC,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,OAAO,CAAC;AAEnC,MAAM,MAAM,OAAO,GAAG,CAAC,IAAI,EAAE,WAAW,EAAE,KAAK,EAAE,WAAW,EAAE,MAAM,EAAE,GAAG,KAAK,IAAI,CAAC;AAEnF,MAAM,MAAM,UAAU,GAAG;IACvB,IAAI,EAAE,aAAa,CAAC;IACpB,WAAW,EAAE,eAAe,CAAC;CAC9B,CAAC;AAEF,MAAM,MAAM,WAAW,GAAG,QAAQ,CAAC,eAAe,CAAC,CAAC,MAAM,CAAC,CAAC;AAE5D,MAAM,MAAM,OAAO,GAAG;IACpB,KAAK,CAAC,EAAE,KAAK,CAAC;IACd,QAAQ,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IACnC,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,OAAO,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC;IAC9B,SAAS,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC,CAAC;IAE1C,IAAI,CAAC,EAAE,OAAO,CAAC;IAEf,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB,CAAC;AAEF,MAAM,MAAM,SAAS,GAAG;IACtB,aAAa,CAAC,EAAE,OAAO,CAAC;CACzB,CAAC;AAEF,MAAM,WAAW,WAAW,CAAC,CAAC,SAAS,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,GAAG,SAAS;IACpE,IAAI,EAAE,KAAK,CAAC;IACZ,IAAI,EAAE,CAAC,CAAC;IACR,QAAQ,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAClC,IAAI,EAAE,IAAI,CAAC;IACX,OAAO,EAAE,OAAO,CAAC;IACjB,KAAK,EAAE,WAAW,EAAE,CAAC;IACrB,GAAG,EAAE,MAAM,WAAW,CAAC;IACvB,IAAI,EAAE,CAAC,KAAK,CAAC,EAAE,MAAM,KAAK,IAAI,CAAC;IAC/B,cAAc,EAAE,CAAC,IAAI,EAAE,GAAG,KAAK,IAAI,CAAC;IACpC,YAAY,EAAE,CAAC,IAAI,EAAE,WAAW,EAAE,IAAI,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,KAAK,IAAI,CAAC;IAC1F,OAAO,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,KAAK,IAAI,CAAC;IAClE,QAAQ,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,KAAK,IAAI,CAAC;IACnE,SAAS,EAAE,MAAM,IAAI,CAAC;IACtB,IAAI,EAAE,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,WAAW,KAAK,IAAI,CAAC;IACrE,KAAK,EAAE,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,WAAW,KAAK,IAAI,CAAC;CACvE"}

package/dist/version.d.ts

@@ -1,3 +1,3 @@
-declare const version = "1.0.13";
+declare const version = "1.0.15";
 export default version;
 //# sourceMappingURL=version.d.ts.map

package/dist/version.js

@@ -1,2 +1,2 @@
-const version = '1.0.13';
+const version = '1.0.15';
 export default version;

package/package.json

@@ -1,9 +1,9 @@
 {
   "name": "jats-convert",
-  "version": "1.0.13",
+  "version": "1.0.15",
   "description": "Read JATS and convert to MyST-spec frontmatter and AST",
-  "author": "Rowan Cockett <rowan@curvenote.com>",
-  "homepage": "https://github.com/curvenote/jats/tree/main/packages/jats-convert",
+  "author": "Rowan Cockett <rowan@continuous.foundation>",
+  "homepage": "https://github.com/continuous-foundation/jats/tree/main/packages/jats-convert",
   "license": "MIT",
   "type": "module",
   "exports": "./dist/index.js",
@@ -20,7 +20,7 @@
   },
   "repository": {
     "type": "git",
-    "url": "git+https://github.com/curvenote/jats.git"
+    "url": "git+https://github.com/continuous-foundation/jats.git"
   },
   "scripts": {
     "copy:version": "echo \"const version = '\"$npm_package_version\"';\nexport default version;\" > src/version.ts",
@@ -33,14 +33,14 @@
     "build": "npm-run-all -l clean copy:version -p build:esm"
   },
   "bugs": {
-    "url": "https://github.com/curvenote/jats/issues"
+    "url": "https://github.com/continuous-foundation/jats/issues"
   },
   "dependencies": {
     "doi-utils": "^2.0.3",
     "dotenv": "^16.4.5",
-    "jats-fetch": "^1.0.13",
-    "jats-tags": "^1.0.13",
-    "jats-xml": "^1.0.13",
+    "jats-fetch": "^1.0.15",
+    "jats-tags": "^1.0.15",
+    "jats-xml": "^1.0.15",
     "js-yaml": "^4.1.0",
     "mathml-to-latex": "^1.3.0",
     "myst-cli-utils": "^2.0.11",
@@ -48,7 +48,7 @@
     "myst-frontmatter": "^1.7.5",
     "myst-spec": "^0.0.5",
     "myst-spec-ext": "^1.7.5",
-    "myst-transforms": "^1.3.27",
+    "myst-transforms": "^1.3.28",
     "unified": "^10.0.0",
     "unist-builder": "^3.0.0",
     "unist-util-select": "^5.1.0",

package/dist/transforms/citations.d.ts

@@ -1,8 +0,0 @@
-import type { GenericNode } from 'myst-common';
-/**
- * Replace invalid 'citation' element with 'mixed-citation'
- *
- * This occurs in JATS from multiple publishers
- */
-export declare function citationToMixedCitation(tree?: GenericNode): void;
-//# sourceMappingURL=citations.d.ts.map

package/dist/transforms/citations.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"citations.d.ts","sourceRoot":"","sources":["../../src/transforms/citations.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AAG/C;;;;GAIG;AACH,wBAAgB,uBAAuB,CAAC,IAAI,CAAC,EAAE,WAAW,QAIzD"}

package/dist/transforms/citations.js

@@ -1,11 +0,0 @@
-import { selectAll } from 'unist-util-select';
-/**
- * Replace invalid 'citation' element with 'mixed-citation'
- *
- * This occurs in JATS from multiple publishers
- */
-export function citationToMixedCitation(tree) {
-    selectAll('citation', tree).forEach((node) => {
-        node.type = 'mixed-citation';
-    });
-}