upload_data_files_to_figshare.py add missing figshare.publish_article()

scripts/upload_data_files_to_figshare.py

@@ -33,8 +33,10 @@ def main(
             article will be created.
         pyproject (dict[str, Any]): Dictionary containing the project metadata.
         max_file_size (int): Maximum file size in bytes to be uploaded automatically.
-        files (list[DataFiles] | None): List of DataFiles to upload.
+        files (list[DataFiles] | None): Which attributes of DataFiles to upload.
+            Defaults to all.
     """
+    article_is_new = False
     if article_id is not None:
         # Check if article exists and is accessible
         if figshare.article_exists(article_id):
@@ -71,10 +73,12 @@ def main(
 
     if article_id is None:
         article_id = figshare.create_article(metadata)
+        article_is_new = True
         print(
             f"\n⚠️ Created new Figshare article with {article_id=}"
             f"\nUpdate FIGSHARE_ARTICLE_ID in {__file__} with this ID!"
         )
+    article_url = f"{figshare.ARTICLE_URL_PREFIX}/{article_id}"
 
     try:
         # Load existing YAML data if available
@@ -158,6 +162,18 @@ def main(
                 print("\nUpdated files:")
                 for idx, (data_file, url) in enumerate(updated_files.items(), start=1):
                     print(f"{idx}. {data_file}: {url}")
+
+            # Publish the article if any new files were added and it's not newly created
+            if article_is_new:
+                print(
+                    "\n⚠️ Article was newly created. Please review it at "
+                    f"{article_url} before publishing manually."
+                )
+            else:
+                print(
+                    f"\nFiles were added or updated. Publishing article {article_url}"
+                )
+                figshare.publish_article(article_id)
         else:
             print("\nNo files were added or updated.")
 

scripts/upload_model_preds_to_figshare.py

@@ -150,6 +150,7 @@ def update_one_modeling_task_article(
 ) -> None:
     """Update or create a Figshare article for a modeling task."""
     article_id = figshare.ARTICLE_IDS[f"model_preds_{task}"]
+    article_is_new = False
 
     if article_id is not None:
         # Check if article exists and is accessible
@@ -166,6 +167,7 @@ def update_one_modeling_task_article(
         else:
             metadata = get_article_metadata(task)
             article_id = figshare.create_article(metadata)
+            article_is_new = True
             print(
                 f"\n⚠️ Created new Figshare article for {task=} with {article_id=}"
                 f"\nUpdate figshare.ARTICLE_IDS with this ID!"
@@ -335,10 +337,16 @@ def find_file_keys(data: dict[str, Any], prefix: str = "") -> dict[str, str]:
             ):
                 print(f"{idx}. {model.name} {filename}: {url}")
 
-        # Publish the article if any new files were added and it's not a dry run
-        if (new_files or updated_files) and not dry_run:
-            print("\nNew or updated files were added. Publishing the article...")
+        # Publish the article if any new files were added, it's not a dry run,
+        # and the article wasn't newly created
+        if (new_files or updated_files) and not dry_run and not article_is_new:
+            print(f"\nFiles were added or updated. Publishing article {article_url}")
             figshare.publish_article(article_id)
+        elif article_is_new:
+            print(
+                "\n⚠️ Article was newly created. Please review it at "
+                f"{article_url} before publishing manually."
+            )
     else:
         print("\nNo files were added or updated.")
 

site/package.json

@@ -19,24 +19,24 @@
   },
   "devDependencies": {
     "@rollup/plugin-yaml": "^4.1.2",
-    "@stylistic/eslint-plugin": "^3.1.0",
+    "@stylistic/eslint-plugin": "^4.2.0",
     "@sveltejs/adapter-static": "^3.0.8",
-    "@sveltejs/kit": "^2.17.2",
-    "@sveltejs/vite-plugin-svelte": "^4.0.3",
+    "@sveltejs/kit": "^2.20.2",
+    "@sveltejs/vite-plugin-svelte": "^5.0.3",
     "d3-array": "^3.2.4",
     "d3-scale": "^4.0.2",
     "d3-scale-chromatic": "^3.1.0",
-    "elementari": "^0.2.7",
-    "eslint": "^9.20.1",
-    "eslint-plugin-svelte": "^2.46.1",
-    "hastscript": "^9.0.0",
+    "elementari": "^0.3.0",
+    "eslint": "^9.23.0",
+    "eslint-plugin-svelte": "^3.3.3",
+    "hastscript": "^9.0.1",
     "iconify-icon": "^2.3.0",
     "js-yaml": "^4.1.0",
     "jsdom": "^26.0.0",
     "json-schema-to-typescript": "^15.0.4",
     "katex": "^0.16.21",
     "mdsvex": "^0.12.3",
-    "prettier": "^3.5.1",
+    "prettier": "^3.5.3",
     "prettier-plugin-svelte": "^3.3.3",
     "rehype-autolink-headings": "^7.1.0",
     "rehype-katex-svelte": "^1.2.0",
@@ -45,19 +45,19 @@
     "remark-math": "6.0.0",
     "remark-parse": "^11.0.0",
     "remark-rehype": "^11.1.1",
-    "svelte": "^5.20.1",
-    "svelte-check": "^4.1.4",
+    "svelte": "^5.25.3",
+    "svelte-check": "^4.1.5",
     "svelte-multiselect": "11.0.0-rc.1",
     "svelte-preprocess": "^6.0.3",
     "svelte-toc": "^0.5.9",
     "svelte-zoo": "^0.4.17",
-    "svelte2tsx": "^0.7.34",
+    "svelte2tsx": "^0.7.35",
     "tslib": "^2.8.1",
-    "typescript": "5.7.3",
-    "typescript-eslint": "^8.24.1",
+    "typescript": "5.8.2",
+    "typescript-eslint": "^8.28.0",
     "unified": "^11.0.5",
-    "vite": "^5.4.11",
-    "vitest": "^3.0.5"
+    "vite": "^6.2.3",
+    "vitest": "^3.0.9"
   },
   "prettier": {
     "semi": false,

site/src/lib/MetricScatter.svelte

@@ -80,8 +80,7 @@
 </script>
 
 <ScatterPlot
-  {x}
-  {y}
+  series={[{ x, y }]}
   x_format="%b %y"
   {y_label}
   bind:tooltip_point

site/src/lib/ModelCard.svelte

@@ -72,7 +72,7 @@
     </span>
   {/each}
 </nav>
-<p>
+<section class="metadata">
   <span title="Date added">
     <iconify-icon icon="ion:ios-calendar" inline></iconify-icon>
     Added {model.date_added}
@@ -135,7 +135,7 @@
       {/each}
     </span>
   {/if}
-</p>
+</section>
 {#if show_details}
   <div transition:fade|fly={{ duration: 200 }}>
     <section transition:slide={{ duration: 200 }}>
@@ -244,7 +244,7 @@
     gap: 6pt;
     place-items: center;
   }
-  p {
+  section.metadata {
     display: grid;
     gap: 5pt;
     grid-template-columns: 1fr 1fr;

site/src/lib/Nav.svelte

@@ -1,16 +1,16 @@
 <script lang="ts">
-  import { page } from '$app/stores'
+  import { page } from '$app/state'
 
   interface Props {
-    routes: (string | [string, string])[];
-    style?: string | null;
+    routes: (string | [string, string])[]
+    style?: string | null
   }
 
-  let { routes, style = null }: Props = $props();
+  let { routes, style = null }: Props = $props()
 
   let is_current = $derived((path: string) => {
-    if (path === $page.url.pathname) return `page`
-    if (path !== `/` && $page.url.pathname.includes(path)) return `page`
+    if (path === page.url.pathname) return `page`
+    if (path !== `/` && page.url.pathname.includes(path)) return `page`
     return undefined
   })
 </script>

site/src/lib/PtableHeatmap.svelte

@@ -6,20 +6,20 @@
   import type { Snapshot } from './$types'
 
   interface Props {
-    heatmap_values: Record<string, number>;
-    color_scale?: string;
-    active_element: ChemicalElement;
-    log?: boolean; // log color scale
-    color_bar_props?: ComponentProps<ColorBar>;
+    heatmap_values: Record<string, number>
+    color_scale?: string
+    active_element: ChemicalElement | null
+    log?: boolean // log color scale
+    color_bar_props?: ComponentProps<typeof ColorBar>
   }
 
   let {
     heatmap_values,
     color_scale = $bindable(`Viridis`),
-    active_element = $bindable(),
+    active_element = $bindable(null),
     log = $bindable(false),
-    color_bar_props = {}
-  }: Props = $props();
+    color_bar_props = {},
+  }: Props = $props()
 
   export const snapshot: Snapshot = {
     capture: () => ({ color_scale, log }),
@@ -35,7 +35,7 @@
   show_photo={false}
 >
   {#snippet inset()}
-    <TableInset >
+    <TableInset>
       <label for="log">Log color scale<Toggle id="log" bind:checked={log} /></label>
       <PtableInset element={active_element} elem_counts={heatmap_values} />
       <ColorBar

site/src/routes/+error.svelte

@@ -1,20 +1,20 @@
 <script lang="ts">
-  import { page } from '$app/stores'
+  import { page } from '$app/state'
   import { homepage, name } from '$site/package.json'
   import 'iconify-icon'
 
   let online: boolean = $state(true)
 </script>
 
 <svelte:head>
-  <title>Error {$page.status} &bull; {name}</title>
+  <title>Error {page.status} &bull; {name}</title>
 </svelte:head>
 
 <svelte:window bind:online />
 
 <div>
-  <h1>Error {String($page.status).replace(`0`, `😵`)}: {$page.error?.message}</h1>
-  {#if $page.status >= 500}
+  <h1>Error {String(page.status).replace(`0`, `😵`)}: {page.error?.message}</h1>
+  {#if page.status >= 500}
     <p>
       If page reloading doesn't help, please raise an issue on
       <a href="{homepage}/issues" target="_blank" rel="noreferrer">GitHub</a>. Thanks! 🙏

site/src/routes/+layout.svelte

@@ -1,25 +1,24 @@
 <script lang="ts">
-  import { afterNavigate, goto } from '$app/navigation'
-  import { page } from '$app/stores'
+  import { goto } from '$app/navigation'
+  import { page } from '$app/state'
   import { Footer, Nav } from '$lib'
   import { repository } from '$site/package.json'
-  import type { Snippet } from 'svelte'
+  import { type Snippet } from 'svelte'
   import { CmdPalette } from 'svelte-multiselect'
   import Toc from 'svelte-toc'
-  import { CopyButton, GitHubCorner } from 'svelte-zoo'
+  import { GitHubCorner } from 'svelte-zoo'
   import '../app.css'
 
   interface Props {
     children?: Snippet
   }
-
   let { children }: Props = $props()
 
   const routes = Object.keys(import.meta.glob(`./*/+page.{svelte,md}`)).map(
     (filename) => `/` + filename.split(`/`)[1],
   )
 
-  let url = $derived($page.url.pathname)
+  let url = $derived(page.url.pathname)
   let headingSelector = $derived(
     `main :is(${{ '/api': `h1, ` }[url] ?? ``}h2, h3, h4):not(.toc-exclude)`,
   )
@@ -50,26 +49,13 @@
       return { label: route, action: () => goto(route) }
     },
   )
-  afterNavigate(({ to }) => {
-    if (to?.route.id == `/models`) {
+  $effect.pre(() => {
+    if (page.url.pathname == `/models`) {
       document.documentElement.style.setProperty(`--main-max-width`, `90em`)
     } else {
       document.documentElement.style.setProperty(`--main-max-width`, `50em`)
     }
-
-    for (const node of document.querySelectorAll(`pre > code`)) {
-      // skip if <pre> already contains a button (presumably for copy)
-      const pre = node.parentElement
-      if (!pre || pre.querySelector(`button`)) continue
-
-      new CopyButton({
-        target: pre,
-        props: {
-          content: node.textContent ?? ``,
-          style: `position: absolute; top: 1ex; right: 1ex;`,
-        },
-      })
-    }
+    // TODO restore svelte-zoo CopyButton to code blocks
   })
 </script>
 

site/src/routes/data/+page.svelte

@@ -17,10 +17,7 @@
 
   const elem_counts = import.meta.glob(
     `./*-element-counts-by-{occurrence,composition}*.json`,
-    {
-      eager: true,
-      import: `default`,
-    },
+    { eager: true, import: `default` },
   )
 
   let log = $state(false) // log color scale
@@ -109,8 +106,10 @@
 
   {#snippet spacegroup_sunbursts()}
     {#if browser}
-      <SpacegroupSunburstMp />
-      <SpacegroupSunburstWbm />
+      <div style="display: flex; gap: 2em; place-content: center;">
+        <SpacegroupSunburstMp />
+        <SpacegroupSunburstWbm />
+      </div>
     {/if}
   {/snippet}
 </DataReadme>

site/src/routes/data/mptrj/MPtrjElemCountsPtable.svelte

@@ -5,17 +5,20 @@
   interface Props extends ComponentProps<typeof PtableHeatmap> {
     count_mode?: string
   }
-
   let { count_mode = `occurrence`, ...rest }: Props = $props()
 
   const elem_counts = import.meta.glob(`../mp-trj-element-counts-by-*.json`, {
     eager: true,
     import: `default`,
-  })
+  }) as Record<string, Record<string, number>>
+
+  let mp_trj_elem_counts = elem_counts[`../mp-trj-element-counts-by-${count_mode}.json`]
 
-  let mp_trj_elem_counts = $derived(
-    elem_counts[`../mp-trj-element-counts-by-${count_mode}.json`],
-  )
+  $effect(() => {
+    if (!(`mp_trj_json_gz` in data_files)) {
+      throw `mp_trj_json_gz not found in data-files.yml`
+    }
+  })
 </script>
 
 <p>
@@ -25,7 +28,7 @@
 </p>
 
 <PtableHeatmap
-  heatmap_values={mp_trj_elem_counts}
   {...rest}
+  heatmap_values={mp_trj_elem_counts}
   color_bar_props={{ label: `MPtrj element counts by ${count_mode}` }}
 />