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actions/checkout@v2->3 github/codeql-action/init@v1->2 github/codeql-action/autobuild@v1->2 github/codeql-action/analyze@v1->2
materialsproject · May 2, 2023 · bf7aedd · bf7aedd
1 parent 2d87ecb
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diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -7,48 +7,47 @@ on:
     # The branches below must be a subset of the branches above
     branches: [main]
   schedule:
-    - cron: '0 13 * * 3' # run at 13:00 every Wednesday
+    - cron: "0 13 * * 3" # run at 13:00 every Wednesday
 
 jobs:
   CodeQL-Build:
-
     runs-on: ubuntu-latest
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v2
-      with:
-        # We must fetch at least the immediate parents so that if this is
-        # a pull request then we can checkout the head.
-        fetch-depth: 2
-
-    # If this run was triggered by a pull request event, then checkout
-    # the head of the pull request instead of the merge commit.
-    - run: git checkout HEAD^2
-      if: github.event_name == 'pull_request'
-
-    # Initializes the CodeQL tools for scanning.
-    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
-      # Override language selection by uncommenting this and choosing your languages
-      # with:
-      #   languages: go, javascript, csharp, python, cpp, java
-
-    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
-    # If this step fails, then you should remove it and run the build manually (see below)
-    - name: Autobuild
-      uses: github/codeql-action/autobuild@v1
-
-    # ℹ️ Command-line programs to run using the OS shell.
-    # 📚 https://git.io/JvXDl
-
-    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
-    #    and modify them (or add more) to build your code if your project
-    #    uses a compiled language
-
-    #- run: |
-    #   make bootstrap
-    #   make release
-
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          # We must fetch at least the immediate parents so that if this is
+          # a pull request then we can checkout the head.
+          fetch-depth: 2
+
+      # If this run was triggered by a pull request event, then checkout
+      # the head of the pull request instead of the merge commit.
+      - run: git checkout HEAD^2
+        if: github.event_name == 'pull_request'
+
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        # Override language selection by uncommenting this and choosing your languages
+        # with:
+        #   languages: go, javascript, csharp, python, cpp, java
+
+      # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+      # If this step fails, then you should remove it and run the build manually (see below)
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v2
+
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 https://git.io/JvXDl
+
+      # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+      #    and modify them (or add more) to build your code if your project
+      #    uses a compiled language
+
+      #- run: |
+      #   make bootstrap
+      #   make release
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2
diff --git a/crystal_toolkit/components/phonon.py b/crystal_toolkit/components/phonon.py
@@ -432,15 +432,13 @@ def get_ph_dos_traces(dos: CompletePhononDos, freq_range: tuple[float, float]):
     def get_figure(
         ph_bs: PhononBandStructureSymmLine | None = None,
         ph_dos: CompletePhononDos | None = None,
-        freq_range: tuple[float, float] | tuple[None, None] = (None, None),
+        freq_range: tuple[float | None, float | None] = (None, None),
     ) -> go.Figure:
-        y_range = list(freq_range)
-
         if freq_range[0] is None:
-            y_range[0] = np.min(ph_bs.bands) * 1.05
+            freq_range = (np.min(ph_bs.bands) * 1.05, freq_range[1])
 
         if freq_range[1] is None:
-            y_range[1] = np.max(ph_bs.bands) * 1.05
+            freq_range = (freq_range[0], np.max(ph_bs.bands) * 1.05)
 
         if (not ph_dos) and (not ph_bs):
             empty_plot_style = {
@@ -457,12 +455,12 @@ def get_figure(
                 bs_traces,
                 bs_data,
             ) = PhononBandstructureAndDosComponent.get_ph_bandstructure_traces(
-                ph_bs, freq_range=y_range
+                ph_bs, freq_range=freq_range
             )
 
         if ph_dos:
             dos_traces = PhononBandstructureAndDosComponent.get_ph_dos_traces(
-                ph_dos, freq_range=y_range
+                ph_dos, freq_range=freq_range
             )
 
         # TODO: add logic to handle if bs_traces and/or dos_traces not present
@@ -503,7 +501,7 @@ def get_figure(
         yaxis_style = dict(
             **in_common_axis_styles,
             mirror="ticks",
-            range=y_range,
+            range=freq_range,
             title=dict(text="Frequency (THz)", font=dict(size=16)),
             zeroline=True,
             zerolinecolor="white",
@@ -526,7 +524,7 @@ def get_figure(
             showticklabels=False,
             mirror="ticks",
             zerolinewidth=2,
-            range=y_range,
+            range=freq_range,
             zerolinecolor="white",
             matches="y",
             anchor="x2",

diff --git a/crystal_toolkit/components/pourbaix.py b/crystal_toolkit/components/pourbaix.py
@@ -162,7 +162,7 @@ class PourbaixDiagramComponent(MPComponent):
     #
     #         if not heatmap_as_contour:
     #             # Plotly needs a list here for validation
-    #             hmap = go.Heatmap(
+    #             h_map = go.Heatmap(
     #                 x=list(ph_range),
     #                 y=list(v_range),
     #                 z=decomposition_e,
@@ -176,11 +176,11 @@ class PourbaixDiagramComponent(MPComponent):
     #                 zmin=0,
     #                 zmax=1,
     #             )
-    #             data.append(hmap)
+    #             data.append(h_map)
     #
     #         else:
     #
-    #             hmap = go.Contour(
+    #             h_map = go.Contour(
     #                 z=decomposition_e,
     #                 x=list(ph_range),
     #                 y=list(v_range),
@@ -193,18 +193,18 @@ class PourbaixDiagramComponent(MPComponent):
     #                 contours_coloring="heatmap",
     #                 text=hovertexts,
     #             )
-    #             data.insert(0, hmap)
+    #             data.insert(0, h_map)
     #
     #     shapes = []
-    #     xydata = []
+    #     xy_data = []
     #     labels = []
     #
     #     for entry, vertices in pourbaix_diagram._stable_domain_vertices.items():
     #         formula = entry.name
     #         clean_formula = PourbaixDiagramComponent.clean_formula(formula)
     #
     #         # Generate annotation
-    #         xydata.append(np.average(vertices, axis=0))
+    #         xy_data.append(np.average(vertices, axis=0))
     #         labels.append(clean_formula)
     #
     #         # Info on SVG paths: https://developer.mozilla.org/en-US/docs/Web/SVG/Tutorial/Paths
@@ -262,11 +262,11 @@ class PourbaixDiagramComponent(MPComponent):
     #                     "y": y,
     #                     "yref": "y",
     #                 }
-    #                 for (x, y), label in zip(xydata, labels)
+    #                 for (x, y), label in zip(xy_data, labels)
     #             ]
     #             layout.update({"annotations": annotations})
     #         else:
-    #             x, y = zip(*xydata)
+    #             x, y = zip(*xy_data)
     #             data.append(
     #                 go.Scatter(x=x, y=y, text=labels, hoverinfo="text", mode="markers")
     #             )
@@ -292,7 +292,7 @@ def get_figure(
         data = []
 
         shapes = []
-        xydata = []
+        xy_data = []
         labels = []
         domain_heights = []
 
@@ -309,7 +309,7 @@ def get_figure(
 
             # Ensure label is within plot area
             # TODO: remove hard-coded value here and make sure it's set dynamically
-            xydata.append([centroid.x, centroid.y])
+            xy_data.append([centroid.x, centroid.y])
             labels.append(clean_formula)
             domain_heights.append(height)
 
@@ -389,7 +389,7 @@ def get_figure(
         layout.update({"shapes": shapes})
 
         if heatmap_entry is None:
-            x, y = zip(*xydata)
+            x, y = zip(*xy_data)
             data.append(
                 go.Scatter(
                     x=x, y=y, text=labels, hoverinfo="text", mode="text", name="Labels"
@@ -437,7 +437,7 @@ def get_text_size(available_vertical_space):
                     "y": y,
                     "yref": "y",
                 }
-                for (x, y), label, height in zip(xydata, labels, domain_heights)
+                for (x, y), label, height in zip(xy_data, labels, domain_heights)
             ]
             layout.update({"annotations": annotations})
 
@@ -473,7 +473,7 @@ def get_text_size(available_vertical_space):
                 Composition(heatmap_entry.composition).reduced_formula
             )
 
-            hmap = go.Contour(
+            h_map = go.Contour(
                 z=decomposition_e,
                 x=list(ph_range),
                 y=list(v_range),
@@ -492,7 +492,7 @@ def get_text_size(available_vertical_space):
                 name=f"{heatmap_formula} ({heatmap_entry.entry_id}) Heatmap",
                 showlegend=True,
             )
-            data.append(hmap)
+            data.append(h_map)
 
         if show_water_lines:
             ph_range = [-2, 16]

diff --git a/jupyterlab-extension/.github/workflows/build.yml b/jupyterlab-extension/.github/workflows/build.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
     - name: Install node
       uses: actions/setup-node@v3
       with: