Improve GeoOptMetricsTable and remove duplicate scatter plot controls (#317)

* Improve GeoOptMetricsTable and remove duplicate scatter plot controls

- Add unit (Å) to RMSD and display units in thin font in column headers
- Add (higher/lower=better) hints to column tooltips
- Group columns under Symmetry and Hyperparams headers
- Add initial sort by RMSD ascending, sort_hint, and default_num_format
- Add n_layers and graph_construction_radius as hidden-by-default columns
- Fix z-index of ToggleMenu dropdown above sticky table headers
- Remove duplicate fullscreen buttons and settings panes from
  DynamicScatter and GitHubActivityScatter (use ScatterPlot built-ins)
- Move DynamicScatter controls into controls_extra snippet
- Bump pre-commit hooks and site dependencies
- Use rsplit/maxsplit=1 for safer string splits in Python
- Add tests for units, group headers, hidden columns, and tooltips

* Add RMSD unit and improve GeoOptMetricsTable tests

- Add missing unit: 'Å' to ALL_METRICS.RMSD label definition
- Test units in column headers (RMSD, f_max), group headers
  (Symmetry, Hyperparams), hidden-by-default columns, and
  initial sort via aria-sort attribute
- Test n_layers presence in assemble_row_data output
- Consolidate 3 redundant structure tests into 1

* Update DynamicScatter tests for refactored controls

Custom fullscreen button and DraggablePane were replaced with
ScatterPlot's built-in FullscreenToggle and controls_extra snippet.
Tests now verify component mounting and structure without depending
on removed DOM elements (.settings-toggle, button[title$="fullscreen"]).

* Simplify DynamicScatter and fix GeoOptMetricsTable column handling

- Remove dead size_value date re-conversion (get_label_value already handles it)
- Use isFinite() instead of !isNaN() to also reject Infinity values
- Consolidate axis_options/color_options into single prop_options derived
- Inline date_key/params_key constants (each used only once)
- Remove intermediate color_prop derived (inline into axes)
- Use const for grid/tick settings (PlotControls manages the UI)
- Fix enrich_col override order so enrichments aren't silently discarded
- Use ALL_METRICS.RMSD.key for initial_sort instead of hardcoded string
- Use .key instead of .label for cell_filter in assemble_row_data
- Drop dead ?? col.label fallback in key_remap
- Merge RMSD unit test into test.each, merge overlapping mount tests

* fix lints

Author: janosh

.github/workflows/lint.yml

@@ -21,6 +21,11 @@ jobs:
         with:
           deno-version: 2.3.7
 
+      - name: Set up pnpm
+        uses: pnpm/action-setup@v4
+        with:
+          version: 10
+
       - name: Run prek
         uses: j178/prek-action@v1
         env: # skip eslint because it's additional deps are not installed correctly

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ default_install_hook_types: [pre-commit, commit-msg]
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.14
+    rev: v0.15.0
     hooks:
       - id: ruff-check
         args: [--fix]
@@ -55,7 +55,7 @@ repos:
         language: system
       - id: svelte-check
         name: Svelte type check
-        entry: bash -c 'cd site && deno install --allow-scripts && deno run -A --node-modules-dir npm:@sveltejs/kit sync && deno run -A --node-modules-dir npm:svelte-check-rs@latest --threshold error'
+        entry: bash -c 'cd site && pnpm install && pnpm exec svelte-kit sync && pnpm exec svelte-check-rs --threshold error'
         language: system
         types_or: [ts, svelte]
         pass_filenames: false
@@ -82,7 +82,7 @@ repos:
         exclude: changelog\.md$
 
   - repo: https://github.com/pre-commit/mirrors-eslint
-    rev: v10.0.0-rc.2
+    rev: v10.0.0
     hooks:
       - id: eslint
         types: [file]
@@ -108,7 +108,7 @@ repos:
       - id: check-github-actions
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.42.3
+    rev: v1.43.4
     hooks:
       - id: typos
         types: [text]

data/mp/eda_mp_trj.py

@@ -421,7 +421,7 @@ def info_dict_to_id(info: dict[str, int | str]) -> str:
         xref="x3",
         yref="y3",
     )
-fig.layout.yaxis3.update(showgrid=False, rangemode="tozero")
+fig.update_layout(yaxis3=dict(showgrid=False, rangemode="tozero"))
 
 fig.layout.margin = dict(l=5, r=5, b=5, t=5)
 fig.layout.legend.update(x=0.96, y=0.18, xanchor="right", bgcolor="rgba(0,0,0,0)")

matbench_discovery/__init__.py

@@ -46,7 +46,7 @@
 STABILITY_THRESHOLD = 0
 
 timestamp = f"{datetime.now(tz=UTC):%Y-%m-%d@%H-%M-%S}"
-today = timestamp.split("@")[0]
+today = timestamp.split("@", maxsplit=1)[0]
 
 # filter pymatgen warnings that spam the logs when e.g. applying corrections to
 # ComputedStructureEntries or using PatchedPhaseDiagram to get e_above_hull

matbench_discovery/plots.py

@@ -688,7 +688,7 @@ def cumulative_metrics(
             last_idx = pd.Series(trace.y).last_valid_index()
             last_x = trace.x[last_idx]
             last_y = trace.y[last_idx]
-            color = dict(color=trace.line.color)
+            color = dict(color=trace.line["color"])
 
             fig.add_scatter(
                 x=[last_x],

matbench_discovery/remote/fetch.py

@@ -18,7 +18,7 @@ def download_file(file_path: str, url: str) -> None:
     # Convert Figshare URLs to API download URLs to avoid WAF bot detection
     # https://figshare.com/files/12345 -> https://api.figshare.com/v2/file/download/12345
     if "figshare.com/files/" in url:
-        file_id = url.split("/files/")[-1]
+        file_id = url.rsplit("/files/", maxsplit=1)[-1]
         url = f"https://api.figshare.com/v2/file/download/{file_id}"
 
     try:

models/chgnet/join_chgnet_preds.py

@@ -52,7 +52,7 @@
 
 # %% compute corrected formation energies
 e_pred_col = "chgnet_energy"
-e_form_chgnet_col = f"e_form_per_atom_{e_pred_col.split('_energy')[0]}"
+e_form_chgnet_col = f"e_form_per_atom_{e_pred_col.split('_energy', maxsplit=1)[0]}"
 df_chgnet[Key.formula] = df_preds[Key.formula]
 df_chgnet[e_form_chgnet_col] = [
     get_e_form_per_atom(dict(energy=ene, composition=formula))

models/deepmd/dpa-3.1-3m-ft.yml

@@ -68,7 +68,7 @@ hyperparams:
       virial: 0.02 -> 1
     initial_learning_rate: 0.001
     learning_rate_schedule: ExpLR - start_lr=0.001, decay_steps=5000, stop_lr=0.00001
-    training_steps: 4000000
+    training_steps: 4_000_000
     batch_size: 960 # 120 (gpus) * 8 (batch per gpu) = 960 (total batch size)
     epochs: 23.5
   finetune:
@@ -79,7 +79,7 @@ hyperparams:
       virial: 2.5
     initial_learning_rate: 0.0001
     learning_rate_schedule: ExpLR - start_lr=0.0001, decay_steps=5000, stop_lr=0.000006
-    training_steps: 2000000
+    training_steps: 2_000_000
     batch_size: 256 # 32 (gpus) * 8 (batch per gpu) = 256 (total batch size)
     epochs: 45
   graph_construction_radius: 6.0 # Å

models/deepmd/dpa-3.1-mptrj.yml

@@ -68,7 +68,7 @@ hyperparams:
       virial: 0.02 -> 1
     initial_learning_rate: 0.001
     learning_rate_schedule: ExpLR - start_lr=0.001, decay_steps=5000, stop_lr=0.00001
-    training_steps: 2000000
+    training_steps: 2_000_000
   round2:
     loss: Huber
     loss_weights:
@@ -77,7 +77,7 @@ hyperparams:
       virial: 2.5
     initial_learning_rate: 0.0002
     learning_rate_schedule: ExpLR - start_lr=0.0002, decay_steps=5000, stop_lr=0.00001
-    training_steps: 1000000
+    training_steps: 1_000_000
   batch_size: 64 # 16 (gpus) * 4 (batch per gpu) = 64 (total batch size)
   epochs: 120 # round1 80 + round2 40
   graph_construction_radius: 6.0 # Å

models/deepmd/dpa3-v1-mptrj.yml

@@ -70,7 +70,7 @@ hyperparams:
       virial: 0.02 -> 1
     initial_learning_rate: 0.001
     learning_rate_schedule: ExpLR - start_lr=0.001, decay_steps=5000, stop_lr=0.00001
-    training_steps: 2000000
+    training_steps: 2_000_000
   round2:
     loss: Huber
     loss_weights:
@@ -79,7 +79,7 @@ hyperparams:
       virial: 2.5
     initial_learning_rate: 0.0002
     learning_rate_schedule: ExpLR - start_lr=0.0002, decay_steps=5000, stop_lr=0.00001
-    training_steps: 2000000
+    training_steps: 2_000_000
   batch_size: 64 # 16 (gpus) * 4 (batch per gpu) = 64 (total batch size)
   epochs: 160 # round1 80 + round2 80
   graph_construction_radius: 6.0 # Å