Navigate to model pages from GitHub activity scatter plot (#316)

* Bump pre-commit hooks and site dependencies

- ruff v0.14.13 -> v0.14.14
- eslint v10.0.0-rc.0 -> v10.0.0-rc.2
- check-jsonschema 0.36.0 -> 0.36.1
- typos v1.42.0 -> v1.42.3
- svelte 5.47.0 -> 5.49.1
- svelte-check -> svelte-check-rs 0.7.3
- matterviz 0.2.2 -> 0.2.3
- vitest 4.0.17 -> 4.0.18
- typescript-eslint 8.53.0 -> 8.54.0

* Remove unnecessary type: ignore comments

- SevenNetCalculator kwargs typing fixed upstream
- mace_calc.models typing fixed
- pmv.structure_3d typing fixed
- FrechetCellFilter typing fixed
- PET calculator compute_energy typing fixed

* Replace abc.abstractmethod with NotImplementedError in Files enum

Files base class can't use abc.abstractmethod since it uses a custom
metaclass (MetaFiles), not ABCMeta. Replace with explicit
NotImplementedError to enforce implementation in subclasses.

- Remove abc import from enums.py
- Add type annotation to energy.py dict access
- Update test SubFiles to implement url/label properties

* Navigate to model pages from GitHub activity scatter plot and set color scale to log

Add model_key field to GitHub activity data to enable direct navigation
to model detail pages when clicking points in the scatter plot.

- fetch-mlip-repos-github-activity.ts: Extract model_key from YAML,
  skip superseded/aborted models, update cache with current model info
- GitHubActivityScatter.svelte: Use goto() to navigate to /models/{slug},
  add color_scale prop, fix GitHubMetricKey type to exclude model_key,
  improve tooltip null checks
- types.ts: Add model_key to GitHubActivityData type
- TableControls.svelte: Remove obsolete ts-expect-error, fix Label type
- Regenerate mlip-github-activity.json with model_key fields

Cleanup site routes and tests

- +error.svelte: Add light theme filter for images
- +layout.svelte: Simplify heading selector, remove redundant CSS,
  adjust breakpoint and nav styling
- +page.svelte: Consolidate matterviz imports
- data/+page.svelte: Add types to snapshot restore
- models/+page.svelte: Add types to snapshot restore, consolidate imports
- test_fetch.py: Fix iter_content mock signature (add decode_unicode)

DRY improvements across codebase

- test_fetch.py: Extract make_mock_response() helper (removes 3x duplication)
- fetch-mlip-repos-github-activity.ts: Extract is_cache_fresh() helper,
  use update_info() for consistent object spreading
- GitHubActivityScatter.svelte: Extract format string constant,
  consolidate point_label object to single line
- data/+page.svelte, models/+page.svelte: Use ReturnType<typeof capture_state>
  to infer snapshot restore type instead of manual duplication

* Fix svelte-check warnings and TypeScript errors

- Fix a11y heading hierarchy: change h3 to h2 in phonons, discovery, model pages
- Fix RadarChart a11y: add role="button", keyboard handler, tabindex for interactive SVG
- Fix +error.svelte type narrowing: use !online instead of online === false
- Fix api/+page.svelte: add typed import.meta.glob for markdown modules
- Simplify GitHubActivityScatter tooltip type assertion
- Update table-export tests with proper html-to-image mocking

* Fix test failures after heading hierarchy changes

- Update PhononsPage test to expect h2 instead of h3
- Remove vi.resetModules() from table-export tests (interferes with vi.mock)

Make h2 assertion resilient to additional headings

Fix table-export test isolation issues

- Add async beforeEach to re-establish html-to-image mocks after clearAllMocks
- Use vi.restoreAllMocks() in afterEach to ensure clean spy state between tests
- Fix mock leakage between parameterized test iterations

Fix RadarChart keyboard handler to use proper coordinates

- Extract move_to_position helper for shared click/keyboard logic
- Add handle_keyboard_click that moves to SVG center (equal weights)
- Fixes NaN coordinates from casting KeyboardEvent to MouseEvent

Author: janosh

.github/workflows/gh-pages.yml

@@ -19,9 +19,4 @@ jobs:
       uv-version: latest
       deno-version: 2.3.7 # https://github.com/pngwn/MDsveX/issues/743
       working-directory: site
-      pre-build: |
-        uv run --with-editable .. ../scripts/make_api_docs.py
-        git clone --depth 1 https://github.com/janosh/matterviz ../matterviz
-        (cd ../matterviz && deno install && deno run -A npm:@sveltejs/kit sync && deno task package)
-        rm -rf node_modules/.deno/matterviz* node_modules/matterviz
-        ln -s ../../matterviz node_modules/matterviz
+      pre-build: uv run --with-editable .. ../scripts/make_api_docs.py

.github/workflows/test.yml

@@ -41,12 +41,6 @@ jobs:
       working-directory: site
       test-cmd: npx vitest run
       deno-version: 2.3.7 # https://github.com/denoland/deno/issues/29968
-      install-cmd: |
-        git clone --depth 1 https://github.com/janosh/matterviz ../matterviz
-        (cd ../matterviz && deno install && deno run -A npm:@sveltejs/kit sync && deno task package)
-        deno install
-        rm -rf node_modules/.deno/matterviz* node_modules/matterviz
-        ln -s ../../matterviz node_modules/matterviz
 
   scripts:
     runs-on: ubuntu-latest

.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: v0.14.13
+    rev: v0.14.14
     hooks:
       - id: ruff-check
         args: [--fix]
@@ -82,7 +82,7 @@ repos:
         exclude: changelog\.md$
 
   - repo: https://github.com/pre-commit/mirrors-eslint
-    rev: v10.0.0-rc.0
+    rev: v10.0.0-rc.2
     hooks:
       - id: eslint
         types: [file]
@@ -97,7 +97,7 @@ repos:
           - '@stylistic/eslint-plugin'
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.36.0
+    rev: 0.36.1
     hooks:
       - id: check-jsonschema
         files: ^models/.+/.+\.yml$
@@ -108,7 +108,7 @@ repos:
       - id: check-github-actions
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.42.0
+    rev: v1.42.3
     hooks:
       - id: typos
         types: [text]

matbench_discovery/energy.py

@@ -112,7 +112,7 @@ def calc_energy_from_e_refs(
         ValueError: If missing reference energies for some elements
     """
     if isinstance(struct_or_entry, dict):  # entry dict case
-        energy = struct_or_entry["energy"]
+        energy: float = struct_or_entry["energy"]
         comp = Composition(struct_or_entry["composition"])
     # Entry/ComputedEntry/ComputedStructureEntry instance case
     elif isinstance(struct_or_entry, Entry):

matbench_discovery/enums.py

@@ -1,6 +1,5 @@
 """Enums used as keys/accessors for dicts and dataframes across Matbench Discovery."""
 
-import abc
 import builtins
 import functools
 import os
@@ -232,14 +231,18 @@ def __str__(self) -> str:
         return self.name
 
     @property
-    @abc.abstractmethod
     def url(self) -> str:
         """URL associated with the file."""
+        raise NotImplementedError(
+            f"{type(self).__name__} must implement 'url' property"
+        )
 
     @property
-    @abc.abstractmethod
     def label(self) -> str:
         """Label associated with the file."""
+        raise NotImplementedError(
+            f"{type(self).__name__} must implement 'label' property"
+        )
 
     @property
     def rel_path(self) -> str:

models/eqV2/test_fairchem_discovery.py

@@ -164,7 +164,7 @@ def _ase_relax(
 
                 filtered_atoms = atoms if filter_cls is None else filter_cls(atoms)
                 optim_inst = optim_cls(
-                    filtered_atoms,  # type: ignore[arg-type]
+                    filtered_atoms,
                     logfile=None,
                     **optimizer_params,
                 )

models/mace/test_mace_discovery.py

@@ -112,7 +112,7 @@
     "force_max": force_max,
     "ase_optimizer": ase_optimizer,
     "device": device,
-    Key.model_params: count_parameters(mace_calc.models[0]),  # type: ignore[arg-type]
+    Key.model_params: count_parameters(mace_calc.models[0]),
     "model_name": model_name,
     "dtype": dtype,
     "cell_filter": "FrechetCellFilter",

models/pet/thermal_conductivity.py

@@ -94,9 +94,7 @@ def calculate_fc2_set(
             )
             for supercell in batch_displacements
         ]
-        res = calculator.compute_energy(  # type: ignore[attr-defined]
-            batch_atoms, compute_forces_and_stresses=True
-        )
+        res = calculator.compute_energy(batch_atoms, compute_forces_and_stresses=True)
         f = res["forces"]
         forces.extend(f)
 
@@ -144,9 +142,7 @@ def calculate_fc3_set(
             )
             for supercell in batch_displacements
         ]
-        res = calculator.compute_energy(  # type: ignore[attr-defined]
-            batch_atoms, compute_forces_and_stresses=True
-        )
+        res = calculator.compute_energy(batch_atoms, compute_forces_and_stresses=True)
         f = res["forces"]
         forces.extend(f)
 

models/sevennet/test_sevennet_diatomics.py

@@ -58,7 +58,7 @@
     calc_kwargs["model"] = str(checkpoint_path)
 
 dtype = "float32"
-calculator = SevenNetCalculator(**calc_kwargs)  # type: ignore[arg-type]
+calculator = SevenNetCalculator(**calc_kwargs)
 
 json_path = f"{ROOT}/models/{model_name}/{model_variant}/{today}-diatomics.json.gz"
 existing_paths = glob(json_path.replace(today, "*-*-*"))

models/sevennet/test_sevennet_discovery.py

@@ -93,7 +93,7 @@
 print(f"{data_path=}", flush=True)
 
 # Initialize ASE SevenNet Calculator from checkpoint
-seven_net_calc = SevenNetCalculator(**calc_kwargs)  # type: ignore[arg-type]
+seven_net_calc = SevenNetCalculator(**calc_kwargs)
 
 
 # %%