jupyter-book · rowanc1 · Jul 10, 2023 · Jul 10, 2023 · Jul 10, 2023 · Jul 10, 2023
diff --git a/.changeset/dry-poems-repeat.md b/.changeset/dry-poems-repeat.md
@@ -0,0 +1,6 @@
+---
+'myst-to-tex': patch
+'myst-cli': patch
+---
+
+Clean up tex errors associated with legends and empty outputs
diff --git a/.changeset/fast-plants-wave.md b/.changeset/fast-plants-wave.md
@@ -0,0 +1,6 @@
+---
+'myst-to-jats': patch
+'myst-cli': patch
+---
+
+Consolidate id deduplication/simplification for JATS to isolated myst-to-jats transforms
diff --git a/package-lock.json b/package-lock.json
diff --git a/packages/jats-to-myst/package.json b/packages/jats-to-myst/package.json
@@ -38,8 +38,8 @@
     "doi-utils": "^2.0.0",
     "jats-tags": "^1.0.0",
     "jats-xml": "^1.0.1",
-    "myst-common": "^1.0.2",
-    "myst-frontmatter": "^1.0.2",
+    "myst-common": "^1.0.3",
+    "myst-frontmatter": "^1.0.3",
     "myst-spec": "^0.0.4",
     "myst-spec-ext": "^1.0.2",
     "myst-transforms": "^1.0.3",

diff --git a/packages/jtex/package.json b/packages/jtex/package.json
@@ -48,7 +48,7 @@
     "commander": "^10.0.1",
     "js-yaml": "^4.1.0",
     "myst-cli-utils": "^2.0.1",
-    "myst-frontmatter": "^1.0.2",
+    "myst-frontmatter": "^1.0.3",
     "myst-templates": "^1.0.2",
     "node-fetch": "^3.3.1",
     "nunjucks": "^3.2.4",

diff --git a/packages/myst-cli/src/process/notebook.ts b/packages/myst-cli/src/process/notebook.ts
@@ -20,11 +20,9 @@ function createOutputDirective(): { myst: string; id: string } {
   return { myst: `\`\`\`{output}\n:id: ${id}\n\`\`\``, id };
 }
 
-function blockDivider(cell: ICell, index: number) {
-  const id =
-    cell.metadata.id ?? `nb-cell-${index}-${computeHash(JSON.stringify(cell)).substring(0, 10)}`;
+function blockDivider(cell: ICell) {
   const type = cell.cell_type === CELL_TYPES.code ? NotebookCell.code : NotebookCell.content;
-  return `+++ ${JSON.stringify({ id, type, ...cell.metadata })}\n\n`;
+  return `+++ ${JSON.stringify({ type, ...cell.metadata })}\n\n`;
 }
 
 export async function processNotebook(
@@ -55,10 +53,10 @@ export async function processNotebook(
       const cellContent = asString(cell.source);
       // If the first cell is a frontmatter block, do not put a block break above it
       const omitBlockDivider = index === 0 && cellContent.startsWith('---\n');
-      return acc.concat(`${omitBlockDivider ? '' : blockDivider(cell, index)}${cellContent}`);
+      return acc.concat(`${omitBlockDivider ? '' : blockDivider(cell)}${cellContent}`);
     }
     if (cell.cell_type === CELL_TYPES.raw) {
-      return acc.concat(`${blockDivider(cell, index)}\`\`\`\n${asString(cell.source)}\n\`\`\``);
+      return acc.concat(`${blockDivider(cell)}\`\`\`\n${asString(cell.source)}\n\`\`\``);
     }
     if (cell.cell_type === CELL_TYPES.code) {
       const code = `\`\`\`{code-cell} ${language}\n${asString(cell.source)}\n\`\`\``;
@@ -73,7 +71,7 @@ export async function processNotebook(
       } else {
         outputMap[id] = [];
       }
-      return acc.concat(`${blockDivider(cell, index)}${code}\n\n${myst}`);
+      return acc.concat(`${blockDivider(cell)}${code}\n\n${myst}`);
     }
     return acc;
   }, Promise.resolve([] as string[]));

diff --git a/packages/myst-cli/src/transforms/outputs.ts b/packages/myst-cli/src/transforms/outputs.ts
@@ -4,6 +4,7 @@ import { computeHash } from 'myst-cli-utils';
 import { SourceFileKind } from 'myst-common';
 import type { GenericNode } from 'myst-common';
 import stripAnsi from 'strip-ansi';
+import { remove } from 'unist-util-remove';
 import { selectAll } from 'unist-util-select';
 import type { IOutput } from '@jupyterlab/nbformat';
 import { extFromMimeType, minifyCellOutput, walkOutputs } from 'nbtx';
@@ -66,6 +67,10 @@ export async function transformOutputs(
 export function reduceOutputs(mdast: Root, writeFolder: string) {
   const outputs = selectAll('output', mdast) as GenericNode[];
   outputs.forEach((node) => {
+    if (!node.data?.length) {
+      node.type = '__delete__';
+      return;
+    }
     let selectedOutput: { content_type: string; path: string; hash: string } | undefined;
     walkOutputs(node.data, (obj: any) => {
       if (selectedOutput || !obj.path || !obj.hash) return;
@@ -94,4 +99,5 @@ export function reduceOutputs(mdast: Root, writeFolder: string) {
       delete node.id;
     }
   });
+  remove(mdast, '__delete__');
 }
diff --git a/packages/myst-config/package.json b/packages/myst-config/package.json
@@ -31,7 +31,7 @@
     "url": "https://github.com/executablebooks/mystmd/issues"
   },
   "dependencies": {
-    "myst-frontmatter": "^1.0.2",
+    "myst-frontmatter": "^1.0.3",
     "simple-validators": "^1.0.1"
   },
   "devDependencies": {

diff --git a/packages/myst-directives/package.json b/packages/myst-directives/package.json
@@ -31,7 +31,7 @@
   },
   "dependencies": {
     "js-yaml": "^4.1.0",
-    "myst-common": "^1.0.2",
+    "myst-common": "^1.0.3",
     "myst-spec-ext": "^1.0.2",
     "vfile": "^5.3.7"
   },

diff --git a/packages/myst-ext-card/package.json b/packages/myst-ext-card/package.json
@@ -32,7 +32,7 @@
     "url": "https://github.com/executablebooks/mystmd/issues"
   },
   "dependencies": {
-    "myst-common": "^1.0.2"
+    "myst-common": "^1.0.3"
   },
   "devDependencies": {
     "myst-parser": "^1.0.3"

diff --git a/packages/myst-ext-exercise/package.json b/packages/myst-ext-exercise/package.json
@@ -32,7 +32,7 @@
     "url": "https://github.com/executablebooks/mystmd/issues"
   },
   "dependencies": {
-    "myst-common": "^1.0.2"
+    "myst-common": "^1.0.3"
   },
   "devDependencies": {
     "myst-parser": "^1.0.3"

diff --git a/packages/myst-ext-grid/package.json b/packages/myst-ext-grid/package.json
@@ -32,7 +32,7 @@
     "url": "https://github.com/executablebooks/mystmd/issues"
   },
   "dependencies": {
-    "myst-common": "^1.0.2"
+    "myst-common": "^1.0.3"
   },
   "devDependencies": {
     "myst-parser": "^1.0.3"

diff --git a/packages/myst-ext-proof/package.json b/packages/myst-ext-proof/package.json
@@ -32,7 +32,7 @@
     "url": "https://github.com/executablebooks/mystmd/issues"
   },
   "dependencies": {
-    "myst-common": "^1.0.2"
+    "myst-common": "^1.0.3"
   },
   "devDependencies": {
     "myst-parser": "^1.0.3"

diff --git a/packages/myst-ext-reactive/package.json b/packages/myst-ext-reactive/package.json
@@ -32,7 +32,7 @@
     "url": "https://github.com/executablebooks/mystmd/issues"
   },
   "dependencies": {
-    "myst-common": "^1.0.2"
+    "myst-common": "^1.0.3"
   },
   "devDependencies": {
     "myst-parser": "^1.0.3"

diff --git a/packages/myst-ext-tabs/package.json b/packages/myst-ext-tabs/package.json
@@ -32,7 +32,7 @@
     "url": "https://github.com/executablebooks/mystmd/issues"
   },
   "dependencies": {
-    "myst-common": "^1.0.2"
+    "myst-common": "^1.0.3"
   },
   "devDependencies": {
     "myst-parser": "^1.0.3"