Merge branch 'main' into fix_electron_diffraction

Author: minhsueh

.github/workflows/issue-metrics.yml

@@ -1,8 +1,6 @@
 name: Monthly issue metrics
 on:
   workflow_dispatch:
-  schedule:
-    - cron: '3 2 1 * *'
 
 permissions:
   contents: read

.github/workflows/pull-request.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
 
     steps:
       - uses: actions/checkout@v4
@@ -46,7 +46,7 @@ jobs:
           PERCY_TOKEN: ${{ secrets.PERCY_TOKEN }}
         run: python${{ matrix.python-version }} -m pytest --cov=crystal_toolkit --cov-report=xml --color=yes --webdriver Chrome --headless crystal_toolkit/apps/examples/tests/
       - uses: codecov/codecov-action@v1
-        if: matrix.python-version == 3.10
+        if: matrix.python-version == 3.11
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml

.github/workflows/pytest-docs.yml

@@ -17,14 +17,14 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'

.github/workflows/upgrade-dependencies.yml

@@ -3,9 +3,6 @@ name: upgrade dependencies
 
 on:
   workflow_dispatch: # Allow running on-demand
-  schedule:
-    # Runs every Monday at 8:00 UTC (4:00 Eastern)
-    - cron: "0 8 * * 1"
 
 jobs:
   upgrade:
@@ -71,6 +68,8 @@ jobs:
           git checkout -b auto-dependency-upgrades
           git branch -r | grep auto-dependency-upgrades- | xargs -I {} git merge {}
           git rebase ${GITHUB_REF##*/}
+          git reset $(git merge-base ${GITHUB_REF##*/} HEAD)
+          git commit -a -m "auto dependency upgrades"
           git push -f origin auto-dependency-upgrades
           git branch -r | grep auto-dependency-upgrades- | cut -d/ -f2 | xargs -I {} git push origin :{}
       - name: Open pull request if needed

.github/workflows/url-check.yml

@@ -14,7 +14,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Check for broken links
-        uses: lycheeverse/lychee-action@v1
+        uses: lycheeverse/lychee-action@v2.0.2
         with:
           # --exclude-loopback ensures we don't check localhost URLs
           args: --exclude-loopback './**/*.md' './**/*.rst'

crystal_toolkit/components/diffraction.py

@@ -56,28 +56,26 @@ def __init__(
     # Default XRD plot style settings
     default_xrd_plot_style = frozendict(
         xaxis={
-            "title": "2𝜃 / º",
+            "title": {"text": "2θ (°)", "font": {"size": 16}},
             "anchor": "y",
             "nticks": 8,
             "showgrid": True,
             "showline": True,
             "side": "bottom",
             "tickfont": {"size": 16.0},
             "ticks": "inside",
-            "titlefont": {"size": 16.0},
             "type": "linear",
             "zeroline": False,
         },
         yaxis={
-            "title": "Intensity / arb. units",
+            "title": {"text": "Intensity / arb. units", "font": {"size": 16}},
             "anchor": "x",
             "nticks": 7,
             "showgrid": True,
             "showline": True,
             "side": "left",
             "tickfont": {"size": 16.0},
             "ticks": "inside",
-            "titlefont": {"size": 16.0},
             "type": "linear",
             "zeroline": False,
         },

crystal_toolkit/core/scene.py

@@ -214,6 +214,7 @@ def merge(cls, sphere_list):
             visible=sphere_list[0].visible,
             clickable=sphere_list[0].clickable,
             tooltip=sphere_list[0].tooltip,
+            _meta=sphere_list[0]._meta,
         )
 
 
@@ -320,13 +321,18 @@ def merge(cls, cylinder_list):
             chain.from_iterable([cylinder.positionPairs for cylinder in cylinder_list])
         )
 
+        new_meta_list = list(
+            chain.from_iterable([[cylinder._meta] for cylinder in cylinder_list])
+        )
+
         return cls(
             positionPairs=new_positionPairs,
             color=cylinder_list[0].color,
             radius=cylinder_list[0].radius,
             visible=cylinder_list[0].visible,
             clickable=cylinder_list[0].clickable,
             tooltip=cylinder_list[0].tooltip,
+            _meta=new_meta_list,
         )
 
     @property

crystal_toolkit/renderables/site.py

@@ -47,6 +47,7 @@ def get_site_scene(
     visualize_bond_orders: bool = False,
     magmom_scale: float = 1.0,
     legend: Legend | None = None,
+    retain_atom_idx: bool = False,
 ) -> Scene:
     """Get a Scene object for a Site.
 
@@ -70,6 +71,7 @@ def get_site_scene(
         visualize_bond_orders (bool, optional): Defaults to False.
         magmom_scale (float, optional): Defaults to 1.0.
         legend (Legend | None, optional): Defaults to None.
+        retain_atom_idx (bool, optional): Defaults to False.
 
     Returns:
         Scene: The scene object containing atoms, bonds, polyhedra, magmoms.
@@ -135,6 +137,7 @@ def get_site_scene(
                 phiEnd=phiEnd,
                 clickable=True,
                 tooltip=name,
+                _meta=[site_idx] if retain_atom_idx else None,
             )
             atoms.append(sphere)
 
@@ -207,6 +210,9 @@ def get_site_scene(
                                     radius=bond_radius / 2,
                                     clickable=True,
                                     tooltip=name_cyl,
+                                    _meta=[site_idx, connected_site.index]
+                                    if retain_atom_idx
+                                    else None,
                                 )
                             )
                             trans_vector = trans_vector + 0.25 * max_radius
@@ -218,6 +224,9 @@ def get_site_scene(
                             radius=bond_radius,
                             clickable=True,
                             tooltip=name_cyl,
+                            _meta=[site_idx, connected_site.index]
+                            if retain_atom_idx
+                            else None,
                         )
                         bonds.append(cylinder)
 
@@ -228,6 +237,7 @@ def get_site_scene(
                     radius=bond_radius,
                     clickable=True,
                     tooltip=name_cyl,
+                    _meta=[site_idx, connected_site.index] if retain_atom_idx else None,
                 )
                 bonds.append(cylinder)
             all_positions.append(connected_position.tolist())
@@ -251,6 +261,7 @@ def get_site_scene(
                     positionPairs=[[position, bond_midpoint.tolist()]],
                     color=color,
                     radius=bond_radius,
+                    _meta=[site_idx, connected_site.index] if retain_atom_idx else None,
                 )
                 bonds.append(cylinder)
                 all_positions.append(connected_position.tolist())

crystal_toolkit/renderables/structuregraph.py

@@ -197,6 +197,8 @@ def get_weight_color(weight):
             explicitly_calculate_polyhedra_hull=explicitly_calculate_polyhedra_hull,
             legend=legend,
             bond_radius=bond_radius,
+            site_idx=idx,
+            show_atom_idx=True,
             **(site_get_scene_kwargs or {}),
         )