Merge branch 'main' into test_all_os

Author: enryH

.github/workflows/cdci.yml

@@ -74,8 +74,8 @@ jobs:
       - name: quarto pdf report
         run: |
           cd docs
-          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt pdf
-          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt pdf
+          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt pdf -qt_checks
+          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt pdf -qt_checks
       - name: quarto docx report
         run: |
           cd docs
@@ -169,13 +169,32 @@ jobs:
         with:
           name: vuegen_gui_${{ matrix.os.label }}
           path: gui/dist/
-      - name: Upload Executable to a GitHub Release
-        if: startsWith(github.ref, 'refs/tags')
+      - name: Upload MacOS Executable to a GitHub Release)
+        if: startsWith(matrix.os.runner, 'macos') && startsWith(github.ref, 'refs/tags')
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          TAG_NAME=${GITHUB_REF#refs/tags/}
-          cp 
-          gh release upload "$TAG_NAME" gui/dist/vuegen_gui.*#vuegen_gui_${{ matrix.os.label }}
+          echo GITHUB_REF_NAME $GITHUB_REF_NAME
+          echo "Uploading vuegen_gui_${{ matrix.os.label }} to release $GITHUB_REF_NAME"
+          echo "Available files in build folder: gui/dist/"
+          cd gui/dist/
+          ls -lh
+          echo "Zip .app folder"
+          zip -r vuegen_gui_${{ matrix.os.label }}.zip vuegen_gui.app/
+          echo "Uploading..."
+          gh release upload $GITHUB_REF_NAME vuegen_gui_${{ matrix.os.label }}.zip
+        # .app is folder that needs to be zipped
+      - name: Upload Windows Executable to a GitHub Release
+        if: startsWith(matrix.os.runner, 'windows') && startsWith(github.ref, 'refs/tags')
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          echo "GITHUB_REF_NAME in env $env:GITHUB_REF_NAME"
+          $GITHUB_REF_NAME = $env:GITHUB_REF_NAME
+          echo "Uploading vuegen_gui_${{ matrix.os.label }} to release $GITHUB_REF_NAME"
+          echo "Available files in build folder: gui/dist/"
+          ls gui/dist/
+          echo "Uploading..."
+          gh release upload $GITHUB_REF_NAME gui/dist/vuegen_gui.exe#vuegen_gui_${{ matrix.os.label }}.exe
         # https://cli.github.com/manual/gh_release_upload
-        # either .app or .exe depending on the OS
+        # .exe is a single file already

.gitignore

@@ -118,6 +118,7 @@ logs/
 vuegen/logs/
 streamlit_report/
 quarto_report/
+output_docker/
 
 # VS Code
 .DS_Store

README.md

@@ -0,0 +1,81 @@
+{
+  "visdat": {
+    "ac2421aa47": ["function () ", "plotlyVisDat"]
+  },
+  "cur_data": "ac2421aa47",
+  "attrs": {
+    "ac2421aa47": {
+      "x": {},
+      "y": {},
+      "mode": "markers",
+      "alpha_stroke": 1,
+      "sizes": [10, 100],
+      "spans": [1, 20],
+      "type": "scatter"
+    }
+  },
+  "layout": {
+    "margin": {
+      "b": 40,
+      "l": 60,
+      "t": 25,
+      "r": 10
+    },
+    "xaxis": {
+      "domain": [0, 1],
+      "automargin": true,
+      "title": "mpg"
+    },
+    "yaxis": {
+      "domain": [0, 1],
+      "automargin": true,
+      "title": "hp"
+    },
+    "hovermode": "closest",
+    "showlegend": false
+  },
+  "source": "A",
+  "config": {
+    "modeBarButtonsToAdd": ["hoverclosest", "hovercompare"],
+    "showSendToCloud": false
+  },
+  "data": [
+    {
+      "x": [21, 21, 22.800000000000001, 21.399999999999999, 18.699999999999999, 18.100000000000001, 14.300000000000001, 24.399999999999999, 22.800000000000001, 19.199999999999999, 17.800000000000001, 16.399999999999999, 17.300000000000001, 15.199999999999999, 10.4, 10.4, 14.699999999999999, 32.399999999999999, 30.399999999999999, 33.899999999999999, 21.5, 15.5, 15.199999999999999, 13.300000000000001, 19.199999999999999, 27.300000000000001, 26, 30.399999999999999, 15.800000000000001, 19.699999999999999, 15, 21.399999999999999],
+      "y": [110, 110, 93, 110, 175, 105, 245, 62, 95, 123, 123, 180, 180, 180, 205, 215, 230, 66, 52, 65, 97, 150, 150, 245, 175, 66, 91, 113, 264, 175, 335, 109],
+      "mode": "markers",
+      "type": "scatter",
+      "marker": {
+        "color": "rgba(31,119,180,1)",
+        "line": {
+          "color": "rgba(31,119,180,1)"
+        }
+      },
+      "error_y": {
+        "color": "rgba(31,119,180,1)"
+      },
+      "error_x": {
+        "color": "rgba(31,119,180,1)"
+      },
+      "line": {
+        "color": "rgba(31,119,180,1)"
+      },
+      "xaxis": "x",
+      "yaxis": "y",
+      "frame": null
+    }
+  ],
+  "highlight": {
+    "on": "plotly_click",
+    "persistent": false,
+    "dynamic": false,
+    "selectize": false,
+    "opacityDim": 0.20000000000000001,
+    "selected": {
+      "opacity": 1
+    },
+    "debounce": 0
+  },
+  "shinyEvents": ["plotly_hover", "plotly_click", "plotly_selected", "plotly_relayout", "plotly_brushed", "plotly_brushing", "plotly_clickannotation", "plotly_doubleclick", "plotly_deselect", "plotly_afterplot", "plotly_sunburstclick"],
+  "base_url": "https://plot.ly"
+}

docs/example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/6_plotly_plot_R.json

@@ -36,7 +36,7 @@
 
 # from vuegen.__main__ import main
 from vuegen.report import ReportType
-from vuegen.utils import get_logger, print_completion_message
+from vuegen.utils import get_completion_message, get_logger
 
 customtkinter.set_appearance_mode("system")
 customtkinter.set_default_color_theme("dark-blue")
@@ -159,6 +159,7 @@ def inner():
             kwargs["logger"].info("logfile: %s", log_file)
             kwargs["logger"].debug("sys.path: %s", sys.path)
             kwargs["logger"].debug("PATH (in app): %s ", os.environ["PATH"])
+            kwargs["quarto_checks"] = True  # for gui check local quarto installation
             report_dir, gen_config_path = report_generator.get_report(**kwargs)
             kwargs["logger"].info("Report generated at %s", report_dir)
             messagebox.showinfo(
@@ -169,7 +170,7 @@ def inner():
                 f"\n\nConfiguration file at:\n{gen_config_path}",
             )
             global hash_config_app  # ! fix this
-            print_completion_message(report_type.get())
+            get_completion_message(report_type.get())
             if hash(yaml.dump(config_app)) != hash_config_app:
                 with open(config_file, "w", encoding="utf-8") as f:
                     yaml.dump(config_app, f)

docs/images/vuegen_logo.png

@@ -2,7 +2,7 @@
 from pathlib import Path
 
 from vuegen import report_generator
-from vuegen.utils import get_logger, get_parser, print_completion_message
+from vuegen.utils import get_completion_message, get_logger, get_parser
 
 
 def main():
@@ -14,7 +14,9 @@ def main():
     config_path = args.config
     dir_path = args.directory
     report_type = args.report_type
+    output_dir = args.output_directory
     streamlit_autorun = args.streamlit_autorun
+    quarto_cheks = args.quarto_checks
 
     # Determine the report name for logger suffix
     if config_path:
@@ -38,18 +40,21 @@ def main():
     # Initialize logger
     logger, logfile = get_logger(f"{logger_suffix}")
     logger.info("logfile: %s", logfile)
+
     # Generate the report
     _, _ = report_generator.get_report(
         report_type=report_type,
         logger=logger,
         config_path=config_path,
         dir_path=dir_path,
+        output_dir=output_dir,
         streamlit_autorun=streamlit_autorun,
+        quarto_checks=quarto_cheks,
     )
 
     # Print completion message
     # ! Could use now report_dir and config_path as information
-    print_completion_message(report_type)
+    print(get_completion_message(report_type, config_path))
 
 
 if __name__ == "__main__":

docs/images/vuegen_logo.svg

@@ -20,8 +20,14 @@ class QuartoReportView(r.ReportView):
     BASE_DIR = Path("quarto_report")
     STATIC_FILES_DIR = BASE_DIR / "static"
 
-    def __init__(self, report: r.Report, report_type: r.ReportType):
+    def __init__(
+        self,
+        report: r.Report,
+        report_type: r.ReportType,
+        quarto_checks: bool = False,
+    ):
         super().__init__(report=report, report_type=report_type)
+        self.quarto_checks = quarto_checks
         self.BUNDLED_EXECUTION = False
         self.quarto_path = "quarto"
         # self.env_vars = os.environ.copy()
@@ -186,11 +192,15 @@ def run_report(self, output_dir: str = BASE_DIR) -> None:
         self.report.logger.info(
             f"Running '{self.report.title}' '{self.report_type}' report with {args!r}"
         )
-        if self.report_type in [
-            r.ReportType.PDF,
-            r.ReportType.DOCX,
-            r.ReportType.ODT,
-        ]:
+        if (
+            self.report_type
+            in [
+                r.ReportType.PDF,
+                r.ReportType.DOCX,
+                r.ReportType.ODT,
+            ]
+            and self.quarto_checks
+        ):
             subprocess.run(
                 [self.quarto_path, "install", "tinytex", "--no-prompt"],
                 check=True,
@@ -204,11 +214,17 @@ def run_report(self, output_dir: str = BASE_DIR) -> None:
                 args,
                 check=True,
             )
-            out_path = file_path_to_qmd.with_suffix(f".{self.report_type.lower()}")
-            if self.report_type in [r.ReportType.REVEALJS, r.ReportType.JUPYTER]:
+            if self.report_type == r.ReportType.REVEALJS:
+                out_path = file_path_to_qmd.with_name(
+                    f"{file_path_to_qmd.stem}_revealjs.html"
+                )
+            elif self.report_type == r.ReportType.JUPYTER:
                 out_path = file_path_to_qmd.with_suffix(".html")
+            else:
+                out_path = file_path_to_qmd.with_suffix(f".{self.report_type.lower()}")
             if not out_path.exists():
                 raise FileNotFoundError(f"Report file could not be created: {out_path}")
+
             if self.report_type == r.ReportType.JUPYTER:
                 args = [self.quarto_path, "convert", str(file_path_to_qmd)]
                 subprocess.run(
@@ -571,14 +587,25 @@ def _generate_plot_code(self, plot, output_file="") -> str:
         else:  # If it's a local file
             plot_code += f"""
 with open('{(Path("..") / plot.file_path).as_posix()}', 'r') as plot_file:
-    plot_json = plot_file.read()\n"""
+    plot_json = json.load(plot_file)\n"""
         # Add specific code for each visualization tool
         if plot.plot_type == r.PlotType.PLOTLY:
             plot_code += """
-fig_plotly = pio.from_json(plot_json)
+# Keep only 'data' and 'layout' sections
+plot_json = {key: plot_json[key] for key in plot_json if key in ['data', 'layout']}\n
+# Remove 'frame' section in 'data'
+plot_json['data'] = [{k: v for k, v in entry.items() if k != 'frame'} for entry in plot_json.get('data', [])]\n
+# Convert JSON to string
+plot_json_str = json.dumps(plot_json)\n
+# Create the plotly plot
+fig_plotly = pio.from_json(plot_json_str)
 fig_plotly.update_layout(width=950, height=500)\n"""
         elif plot.plot_type == r.PlotType.ALTAIR:
-            plot_code += """fig_altair = alt.Chart.from_json(plot_json).properties(width=900, height=400)"""
+            plot_code += """
+# Convert JSON to string
+plot_json_str = json.dumps(plot_json)\n
+# Create the plotly plot
+fig_altair = alt.Chart.from_json(plot_json_str).properties(width=900, height=400)\n"""
         elif plot.plot_type == r.PlotType.INTERACTIVE_NETWORK:
             # Generate the HTML embedding for interactive networks
             if is_url(plot.file_path) and plot.file_path.endswith(".html"):
@@ -834,7 +861,7 @@ def _show_dataframe(
             # Generate path for the DataFrame image
             df_image = Path(static_dir) / f"{dataframe.title.replace(' ', '_')}.png"
             dataframe_content.append(
-                f"df.dfi.export('{Path(df_image).resolve().as_posix()}', max_rows=10, max_cols=5)\n```\n"
+                f"df.dfi.export('{Path(df_image).resolve().as_posix()}', max_rows=10, max_cols=5, table_conversion='matplotlib')\n```\n"
             )
             # Use helper method to add centered image content
             dataframe_content.append(self._generate_image_content(df_image))
@@ -866,8 +893,16 @@ def _generate_component_imports(self, component: r.Component) -> List[str]:
         # Dictionary to hold the imports for each component type
         components_imports = {
             "plot": {
-                r.PlotType.ALTAIR: ["import altair as alt", "import requests"],
-                r.PlotType.PLOTLY: ["import plotly.io as pio", "import requests"],
+                r.PlotType.ALTAIR: [
+                    "import altair as alt",
+                    "import requests",
+                    "import json",
+                ],
+                r.PlotType.PLOTLY: [
+                    "import plotly.io as pio",
+                    "import requests",
+                    "import json",
+                ],
             },
             "dataframe": [
                 "import pandas as pd",