feat(primo): Boards rail toggle, facet rename, ScientaLab data repos

README.md

@@ -37,7 +37,7 @@ that does not exist.
 
 🌐 Website: http://primomics.org/ ·
 📄 Paper: https://openreview.net/forum?id=v2SA8gHwqo ·
-📦 Data: https://huggingface.co/datasets/PRIMOmics/primo
+📦 Data: https://huggingface.co/datasets/ScientaLab/primo
 
 ## What's in the data
 
@@ -133,8 +133,8 @@ pushed by `benchmark/public_benchmark/baselines.py --score --publish`.
 - **`hf_oauth: true`** (set above) turns on the Submit tab's *Sign in with
   Hugging Face* button; submitting requires a logged-in HF account.
 - Set an **`HF_TOKEN`** Space secret (fine-grained) with: **read** on
-  `PRIMOmics/primo` (the public `datasets.yaml` manifest) and
-  `PRIMOmics/primo-labels` (the private `tasks.yaml` registry +
+  `ScientaLab/primo` (the public `datasets.yaml` manifest) and
+  `ScientaLab/primo-labels` (the private `tasks.yaml` registry +
   `<task_id>/labels.csv`), and **read + write** on
   `ScientaLab/primo-results` (the persisted leaderboard).
 - Results persist as one normalized `task_results.csv` (`model_name, task_id,

boards.py

@@ -37,8 +37,8 @@ MODALITY_LABEL = {
     "single-cell RNA": "single-cell RNAseq",
 }
 
-MODALITY_GROUP = "Modality"
-AREA_GROUP = "Therapeutic Areas"
+MODALITY_GROUP = "Per modality"
+AREA_GROUP = "Per therapeutic areas"
 CATEGORY_GROUP = "Task Category"
 
 GROUP_NOTE = {

evaluator.py

@@ -47,7 +47,7 @@ SPLIT = "split"
 SPLIT_TRAIN = "train"
 SPLIT_TEST = "test"
 
-ORG = "PRIMOmics"
+ORG = "ScientaLab"
 PUBLIC_REPO = f"{ORG}/primo"
 LABELS_REPO = f"{ORG}/primo-labels"
 # Keep the established leaderboard history available until it is migrated.

pages/about.md

@@ -16,7 +16,7 @@ diseases**, and we ask the same three questions of each patient:
 
 | Task family | The question | Metric |
 |---|---|---|
-| **Treatment outcome** | Will this patient respond to anti-TNF therapy? | AUROC |
+| **Treatment outcome** | Will this patient respond to treatment (for example, anti-TNF therapy)? | AUROC |
 | **Clinical scores** | How severe is this patient's disease? | Pearson r |
 | **Endotype** | Which molecular subtype is this patient? | AUROC |
 
@@ -85,6 +85,6 @@ modality or therapeutic area, or work with us on the methodology? The
 ## Links
 
 - 🌐 **Website**: [primomics.org](http://primomics.org/)
-- 📦 **Data**: [PRIMOmics/primo](https://huggingface.co/datasets/PRIMOmics/primo)
+- 📦 **Data**: [ScientaLab/primo](https://huggingface.co/datasets/ScientaLab/primo)
 - 📄 **Paper**: [OpenReview](https://openreview.net/forum?id=v2SA8gHwqo)
 - 💬 **Questions**: [karim.elkanbi@scientalab.com](mailto:karim.elkanbi@scientalab.com)

pages/contribute.md

@@ -53,4 +53,4 @@ methodology, co-signature on what we publish, and early access to the results.
 - **Question the method.** Open a thread in the Space's **Community** tab.
 - **Submit a model.** Baselines are on the leaderboard already; beat them.
 - **Read the paper**: [OpenReview](https://openreview.net/forum?id=v2SA8gHwqo)
-- **Look at the data**: [PRIMOmics/primo](https://huggingface.co/datasets/PRIMOmics/primo)
+- **Look at the data**: [ScientaLab/primo](https://huggingface.co/datasets/ScientaLab/primo)

pages/submit.md

@@ -15,7 +15,7 @@ python quickstart.py --out submission.parquet
 
 Or do it by hand, in **three steps**:
 
-1. **Get the data** → download the datasets from [PRIMOmics/primo](https://huggingface.co/datasets/PRIMOmics/primo) (start with its `datasets.yaml`).
+1. **Get the data** → download the datasets from [ScientaLab/primo](https://huggingface.co/datasets/ScientaLab/primo) (start with its `datasets.yaml`).
 2. **Embed every dataset** → build **one** file: `dataset_id`, `sample_id`, then one column per embedding dim (`e0`, `e1`, …). CSV / TSV / Parquet, or NPZ.
 3. **Sign in, fill the form, and hit Evaluate.** A fixed linear probe scores each hidden task (AUROC or Pearson), reported per task category in its native metric.
 

primo.css

@@ -59,7 +59,18 @@ footer { display: none !important; }
 .pm-brand b { font: 700 1.125rem/1 var(--font-title); letter-spacing: -.04em; }
 .pm-brand span { font: 500 1.25rem/0 var(--font-title); letter-spacing: -.04em; color: var(--sidebar-sub-fg); }
 
-.pm-rail-group { padding: 16px 16px 0; }
+/* "Boards" collapses the facet groups so the foot links stay above the fold */
+.pm-rail-section { margin: 8px 0 0; }
+.pm-rail-summary { display: flex; align-items: center; justify-content: space-between; gap: 8px;
+  height: 2.5rem; padding: 8px; margin: 0; cursor: pointer; list-style: none;
+  border-radius: var(--radius-md); font: 600 13px/1 var(--font-sans); color: var(--sidebar-fg); }
+.pm-rail-summary::-webkit-details-marker { display: none; }
+.pm-rail-summary:hover { background: var(--sidebar-highlight); }
+.pm-rail-summary.pm-active { background: var(--sidebar-accent); color: #fff; }
+.pm-rail-summary .pm-chevron { flex: none; color: var(--sidebar-sub-fg); transition: transform .15s ease; }
+.pm-rail-section[open] > .pm-rail-summary .pm-chevron { transform: rotate(90deg); }
+
+.pm-rail-group { padding: 8px 16px 0; }
 .pm-rail-label { display: flex; align-items: center; height: 2.5rem; padding: 8px;
   font: 400 10px/1 var(--font-mono); letter-spacing: .08em; text-transform: uppercase; color: var(--sidebar-sub-fg); }
 
@@ -86,11 +97,11 @@ footer { display: none !important; }
    force the rail's inner text to take the link/brand colour instead. */
 #pm-rail .pm-link .pm-label, #pm-rail .pm-link .pm-count, #pm-rail .pm-brand b { color: inherit !important; }
 
-.pm-rail-foot { margin-top: auto; padding: 16px; border-top: 1px solid var(--sidebar-border); }
+.pm-rail-foot { margin: 8px 0 0; padding: 12px 16px 16px; border-top: 1px solid var(--sidebar-border); }
 #pm-rail .pm-foot-link {
   display: flex !important; align-items: center; width: 100%; height: 2.5rem; padding: 8px; margin: 0 0 2px;
   border: 0 !important; border-radius: var(--radius-md); background: transparent !important; box-shadow: none !important;
-  font: 500 14px/1 var(--font-sans); color: var(--sidebar-fg) !important; text-align: left;
+  font: 600 14px/1 var(--font-sans); color: var(--sidebar-fg) !important; text-align: left;
 }
 #pm-rail .pm-foot-link:hover { background: var(--sidebar-highlight) !important; color: #fff !important; }
 #pm-rail .pm-foot-link.pm-active { background: var(--sidebar-accent) !important; color: #fff !important; }

quickstart.py

@@ -22,7 +22,7 @@ import yaml
 from huggingface_hub import snapshot_download
 from sklearn.decomposition import PCA
 
-PUBLIC_REPO = "PRIMOmics/primo"
+PUBLIC_REPO = "ScientaLab/primo"
 MANIFEST_FILENAME = "datasets.yaml"
 
 DATASET_ID = "dataset_id"

render.py

@@ -61,17 +61,37 @@ STRONG_COLUMNS = frozenset({"Task"})
 METRIC_COLUMNS = frozenset({"Metric"})
 RIGHT_COLUMNS = frozenset({"Rank", "Patients"})
 
+CHEVRON = (
+    '<svg class="pm-chevron" viewBox="0 0 16 16" width="12" height="12" '
+    'aria-hidden="true"><path d="M6 4l4 4-4 4" fill="none" stroke="currentColor" '
+    'stroke-width="1.6" stroke-linecap="round" stroke-linejoin="round"/></svg>'
+)
+
 
 # --------------------------------------------------------------------- rail
 def rail_html(
     boards: list[Board], active_slug: str | None, active_tab: str | None
 ) -> str:
-    """The left navigation: brand, one link per board grouped by facet, foot links.
+    """The left navigation: brand, a collapsible "Boards" menu, then the foot links.
+
+    The board groups live inside a ``<details>`` toggle so the four foot links
+    (Tasks, Submit, Contribute, Method) stay visible without scrolling. The toggle
+    is pure HTML/CSS, keeping navigation reload-based and JavaScript-free.
 
     ``active_slug`` highlights the board a visitor is on; ``active_tab`` highlights
-    a foot link. Open boards link to Contribute, mirroring the overview cards.
+    a foot link, and its absence means we are on a board or the overview, so the
+    "Boards" menu is the active one. Open boards link to Contribute, mirroring the
+    overview cards.
     """
-    parts = ['<div class="pm-rail-inner">', BRAND]
+    on_boards = active_tab is None
+    summary_cls = "pm-rail-summary pm-active" if on_boards else "pm-rail-summary"
+    parts = [
+        '<div class="pm-rail-inner">',
+        BRAND,
+        '<details class="pm-rail-section" open>',
+        f'<summary class="{summary_cls}"><span>Boards</span>{CHEVRON}</summary>',
+        '<div class="pm-rail-sections">',
+    ]
     for group in SECTIONS:
         cards, opens = in_group(boards, group), open_in_group(boards, group)
         if not cards and not opens:
@@ -93,6 +113,7 @@ def rail_html(
                 '<span class="pm-badge pm-badge--quiet">open</span></a>'
             )
         parts.append("</div>")
+    parts.append("</div></details>")
     parts.append('<div class="pm-rail-foot">')
     for tab, label in FOOT_LINKS:
         cls = "pm-foot-link pm-active" if tab == active_tab else "pm-foot-link"