Merge pull request #6 from DataAnalyticsEngineering/FANS-v0.1.0

Release v0.1.0

.clang-format

@@ -0,0 +1,119 @@
+---
+Language:        Cpp
+AccessModifierOffset: -2
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: true
+AlignConsecutiveDeclarations: true
+AlignEscapedNewlines: Right
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Empty
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: MultiLine
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   true
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  AfterExternBlock: false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Custom
+BreakBeforeInheritanceComma: false
+BreakInheritanceList: BeforeColon
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: BeforeColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     0
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IncludeBlocks:   Preserve
+IncludeCategories:
+  - Regex:           '^(<|"(gtest|isl|json)/)'
+    Priority:        1
+  - Regex:           '.*'
+    Priority:        2
+  - Regex:           '.*'
+    Priority:        1
+IncludeIsMainRegex: '$'
+IndentCaseLabels: false
+IndentPPDirectives: None
+IndentWidth:     4
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBinPackProtocolList: Auto
+ObjCBlockIndentWidth: 4
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 100
+PointerAlignment: Right
+ReflowComments:  true
+SortIncludes:    true
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: true
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Cpp11
+StatementMacros:
+  - Q_UNUSED
+  - QT_REQUIRE_VERSION
+TabWidth:        4
+UseTab:          Never
+...

.github/workflows/clang-format-check.yml

@@ -0,0 +1,21 @@
+name: clang-format Check
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+
+jobs:
+  formatting-check:
+    name: Formatting Check
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Run clang-format style check for C/C++/Protobuf programs.
+      uses: jidicula/[email protected]
+      with:
+        clang-format-version: '13'
+        check-path: ${{ matrix.path }}
+        exclude-regex: 'include/json.hpp'
+        fallback-style: 'Mozilla' # optional

.pre-commit-config.yaml

@@ -1,4 +1,6 @@
 repos:
+# Official repo for the clang-format hook
+repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v2.3.0
   hooks:

CHANGELOG.md

@@ -0,0 +1,6 @@
+# FANS Changelog
+
+## v0.1.0
+
+- Add release guide and a Changelog file https://github.com/DataAnalyticsEngineering/FANS/pull/4
+- Add clang-format check and format all relevant files https://github.com/DataAnalyticsEngineering/FANS/pull/1

CMakeLists.txt

@@ -5,7 +5,7 @@ cmake_minimum_required(VERSION 3.0...3.28)
 # ##############################################################################
 
 project(FANS
-        VERSION 0.0.0
+        VERSION 0.1.0
         LANGUAGES C CXX
 )
 

FANS_Dashboard/FANS_Dashboard.ipynb

@@ -32,7 +32,7 @@
     "- `collections`\n",
     "- `argparse`\n",
     "- `lxml`\n",
-    "- `re`",
+    "- `re`\n",
     "- `nbformat`"
    ]
   },
@@ -232,11 +232,11 @@
    "outputs": [],
    "source": [
     "# Plot stress average vs strain average for each component\n",
-    "\n",
-    "plot_subplots(strain_average, stress_average, labels_x=['Strain']*6, labels_y=['Stress']*6, \n",
-    "              subplot_titles=['component - 11', 'component - 22', 'component - 33', 'component - 12', 'component - 13', 'component - 23'], \n",
-    "              title='Stress average vs strain average', \n",
-    "              nrows=2, ncols=3, linewidth=1, markersize=4, linecolor='blue', markercolor='blue', fontsize=12)\n"
+    "fig = plot_subplots(strain_average, stress_average, labels_x=['Strain']*6, labels_y=['Stress']*6, \n",
+    "                    subplot_titles=['component - 11', 'component - 22', 'component - 33', 'component - 12', 'component - 13', 'component - 23'], \n",
+    "                    title='Stress average vs strain average', \n",
+    "                    nrows=2, ncols=3, linewidth=1, markersize=4, linecolor=[\"blue\"]*6, markercolor=[\"blue\"]*6, fontsize=16)\n",
+    "fig.show()"
    ]
   },
   {
@@ -246,10 +246,11 @@
    "outputs": [],
    "source": [
     "# Plot deviatoric stress average vs strain average for each component\n",
-    "plot_subplots(strain_average, stress_average_deviatoric, labels_x=['Strain']*6, labels_y=['Stress_dev']*6,\n",
-    "                subplot_titles=['component - 11', 'component - 22', 'component - 33', 'component - 12', 'component - 13', 'component - 23'],\n",
-    "                title='Deviatoric stress average vs strain average',\n",
-    "                nrows=2, ncols=3, linewidth=1, markersize=4, linecolor='blue', markercolor='blue', fontsize=12)"
+    "fig = plot_subplots(strain_average, stress_average_deviatoric, labels_x=['Strain']*6, labels_y=['Stress_dev']*6,\n",
+    "                    subplot_titles=['component - 11', 'component - 22', 'component - 33', 'component - 12', 'component - 13', 'component - 23'],\n",
+    "                    title='Deviatoric stress average vs strain average',\n",
+    "                    nrows=2, ncols=3, linewidth=1, markersize=4, linecolor=[\"blue\"]*6, markercolor=[\"blue\"]*6, fontsize=16)\n",
+    "fig.show()"
    ]
   },
   {
@@ -260,10 +261,11 @@
    "source": [
     "# Plot deviatoric stress average vs time\n",
     "time_broadcasted = np.tile(time_steps[:, np.newaxis], (1, stress_average.shape[1]))\n",
-    "plot_subplots(time_broadcasted, stress_average_deviatoric, labels_x=['Time']*6, labels_y=['Stress_dev']*6,\n",
-    "                subplot_titles=['component - 11', 'component - 22', 'component - 33', 'component - 12', 'component - 13', 'component - 23'],\n",
-    "                title='Deviatoric stress average vs time',\n",
-    "                nrows=2, ncols=3, linewidth=1, markersize=4, linecolor='blue', markercolor='blue', fontsize=12)\n"
+    "fig = plot_subplots(time_broadcasted, stress_average_deviatoric, labels_x=['Time']*6, labels_y=['Stress_dev']*6,\n",
+    "                    subplot_titles=['component - 11', 'component - 22', 'component - 33', 'component - 12', 'component - 13', 'component - 23'],\n",
+    "                    title='Deviatoric stress average vs time',\n",
+    "                    nrows=2, ncols=3, linewidth=1, markersize=4, linecolor=[\"blue\"]*6, markercolor=[\"blue\"]*6, fontsize=16)\n",
+    "fig.show()"
    ]
   },
   {
@@ -272,12 +274,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "plot_subplots(\n",
-    "    np.column_stack((strain_average[:, 0], strain_average[:, 0])), \n",
-    "    np.column_stack((stress_average[:, 0], stress_average_deviatoric[:, 0])), \n",
-    "    labels_x=['Strain_11']*2, labels_y=['Stress_11', 'Stress_dev_11'],\n",
-    "    subplot_titles=['Stress_11 vs Strain_11', 'Stress_dev_11 vs Strain_11'],\n",
-    "    nrows=1, ncols=2, linewidth=1, markersize=4, linecolor='blue', markercolor='blue', fontsize=12)"
+    "fig = plot_subplots(np.column_stack((strain_average[:, 0], strain_average[:, 0])), \n",
+    "                    np.column_stack((stress_average[:, 0], stress_average_deviatoric[:, 0])), \n",
+    "                    labels_x=['Strain_11']*2, labels_y=['Stress_11', 'Stress_dev_11'],\n",
+    "                    subplot_titles=['Stress_11 vs Strain_11', 'Stress_dev_11 vs Strain_11'],\n",
+    "                    nrows=1, ncols=2, linewidth=1, markersize=4, linecolor=[\"blue\"]*2, markercolor=[\"blue\"]*2, fontsize=16)\n",
+    "fig.show()"
    ]
   },
   {
@@ -335,7 +337,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.4"
+   "version": "3.12.0"
   }
  },
  "nbformat": 4,

FANS_Dashboard/README.md

@@ -1,5 +1,5 @@
 # FANS Dashboard
 
-This folder contains a Jupyter Notebook designed to post-process, interpret, and visualize results generated by FANS. The notebook provides tools for exploring the hierarchical structure of HDF5 files, extracting and summarizing simulation data, and preparing the results for visualization in ParaView.
+The FANS Dashboard is a comprehensive tool designed to streamline the post-processing, interpretation, and visualization of results generated by the FANS solver. This jupyter notebook provides a user-friendly environment to work with complex simulation data stored in HDF5 format, offering a step-by-step workflow that covers data extraction, postprocessing, visualization, and preparation for 3D visualization in tools like ParaView.
 
-For further details follow along `FANS_Dashboard.ipynb`
+For further details follow along [`FANS_Dashboard.ipynb`](FANS_Dashboard.ipynb)

FANS_Dashboard/plotting.py

@@ -9,14 +9,15 @@ def plot_subplots(
     labels_x=None,
     labels_y=None,
     subplot_titles=None,
-    title="Subplot Grid",
+    title="",
     nrows=None,
     ncols=None,
     linewidth=1,
     markersize=4,
-    linecolor="blue",
-    markercolor="red",
+    linecolor=None,
+    markercolor=None,
     fontsize=12,
+    fig=None,
 ):
     """
     Plot a grid of subplots using Plotly, handling both single-component (scalar vs scalar) and multi-component data.
@@ -32,9 +33,10 @@ def plot_subplots(
     - ncols: int, number of columns in the subplot grid (optional)
     - linewidth: int, line width for the plots (optional, default=1)
     - markersize: int, size of the markers (optional, default=4)
-    - linecolor: string, color of the lines (optional, default="blue")
-    - markercolor: string, color of the markers (optional, default="red")
+    - linecolor: list of strings, colors of the lines for each subplot (optional, default=None, all blue)
+    - markercolor: list of strings, colors of the markers for each subplot (optional, default=None, all blue)
     - fontsize: int, font size for axis labels, subplot titles, and tick labels (optional, default=12)
+    - fig: existing Plotly figure to overlay the new subplots (optional, default=None, creates a new figure)
     """
     # Validate data shapes
     if not isinstance(data1, np.ndarray) or not isinstance(data2, np.ndarray):
@@ -53,6 +55,21 @@ def plot_subplots(
     # Set the number of components based on data shape
     n_components = data1.shape[1]
 
+    # Initialize linecolor and markercolor lists if not provided
+    if linecolor is None:
+        linecolor = ["blue"] * n_components
+    elif len(linecolor) != n_components:
+        raise ValueError(
+            f"The length of linecolor must match the number of components ({n_components})."
+        )
+
+    if markercolor is None:
+        markercolor = ["blue"] * n_components
+    elif len(markercolor) != n_components:
+        raise ValueError(
+            f"The length of markercolor must match the number of components ({n_components})."
+        )
+
     # If nrows or ncols is not specified, determine an optimal grid layout
     if nrows is None or ncols is None:
         nrows = int(np.ceil(np.sqrt(n_components)))
@@ -81,8 +98,9 @@ def plot_subplots(
             f"The length of labels_y must match the number of components ({n_components})."
         )
 
-    # Create the subplot figure
-    fig = make_subplots(rows=nrows, cols=ncols, subplot_titles=subplot_titles)
+    # Create the subplot figure if not provided
+    if fig is None:
+        fig = make_subplots(rows=nrows, cols=ncols, subplot_titles=subplot_titles)
 
     # Add traces for each component
     for i in range(n_components):
@@ -93,8 +111,8 @@ def plot_subplots(
                 x=data1[:, i],
                 y=data2[:, i],
                 mode="lines+markers",
-                marker=dict(symbol="x", size=markersize, color=markercolor),
-                line=dict(width=linewidth, color=linecolor),
+                marker=dict(symbol="x", size=markersize, color=markercolor[i]),
+                line=dict(width=linewidth, color=linecolor[i]),
                 name=f"Component {i+1}",
             ),
             row=row,
@@ -113,6 +131,7 @@ def plot_subplots(
             ticklen=6,
             title_font=dict(size=fontsize),
             tickfont=dict(size=fontsize),
+            automargin=True,
         )
         fig.update_yaxes(
             title_text=labels_y[i],
@@ -125,17 +144,18 @@ def plot_subplots(
             ticklen=6,
             title_font=dict(size=fontsize),
             tickfont=dict(size=fontsize),
+            automargin=True,
         )
 
     # Update layout with the overall plot title and styling
     fig.update_layout(
-        height=600,
-        width=900,
+        height=1000,
+        width=1600,
         title_text=title,
         title_font=dict(size=fontsize),
-        showlegend=False,
+        showlegend=False,  # Legends removed
         template="plotly_white",
-        margin=dict(l=20, r=20, t=50, b=20),
+        margin=dict(l=50, r=50, t=50, b=50),  # Adjust margins to prevent overlap
         title_x=0.5,
         autosize=False,
     )
@@ -161,12 +181,5 @@ def plot_subplots(
     for annotation in fig["layout"]["annotations"]:
         annotation["font"] = dict(size=fontsize)
 
-    # Increase the DPI/quality of the plots by setting higher resolution dimensions
-    fig.update_layout(
-        height=1200,
-        width=1800,
-        autosize=False,
-    )
-
-    # Show the plot
-    fig.show()
+    # Return the figure for further customization or overlaying
+    return fig