Add Quarto checks and output dire parameters

* 🦺 Refactor: add quarto_checks argument

* 🐛 Fix: Correct validation for revelajs and jupyter notebooks

* 🎨 Format: add config_path parameter and change the strcuture of the function to print completion message

* 🎨 Format: add black format

* 🎨 Format: order main imports

* 🐛 Fix: fix typo for quarto_checks

* 🐛 Fix: add quarto_checks into the report_generator funcrtion

* 🎨 Format: apply black format and fix quarto_checks typo

* 🐛 Fix: fix quarto_checks typo in quarto_review.py

* 🐛 Fix quarto_checks typo

* 🐛 Fix: add -qt_checks parameter into the CICD file

* 🐛 Fix: add html suffix for jupyter notebook for initial validation

* 🐛 fix import and specify that GUI execution checks tinytex and chromium

* ✨ Feat: add output_dir as an argument

* 🐛 Fix: correct output_dir typo

* 🐛 Fix: add -qt_checks parameter in the CICD processs for the pdf report using a config file

---------

Co-authored-by: Henry Webel <heweb@dtu.dk>

Author: sayalaruano

.github/workflows/cdci.yml

@@ -72,8 +72,8 @@ 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

gui/app.py

@@ -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)

src/vuegen/__main__.py

@@ -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__":

src/vuegen/quarto_reportview.py

@@ -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(

src/vuegen/report_generator.py

@@ -16,6 +16,7 @@ def get_report(
     config_path: str = None,
     dir_path: str = None,
     streamlit_autorun: bool = False,
+    quarto_checks: bool = False,
     output_dir: Path = None,
 ) -> tuple[str, str]:
     """
@@ -97,7 +98,9 @@ def get_report(
             )
         report_dir = output_dir / "quarto_report"
         static_files_dir = report_dir / "static"
-        quarto_report = QuartoReportView(report=report, report_type=report_type)
+        quarto_report = QuartoReportView(
+            report=report, report_type=report_type, quarto_checks=quarto_checks
+        )
         quarto_report.generate_report(
             output_dir=report_dir, static_dir=static_files_dir
         )

src/vuegen/utils.py

@@ -225,14 +225,27 @@ def get_parser(prog_name: str, others: dict = {}) -> argparse.Namespace:
         default="streamlit",
         help="Type of the report to generate (streamlit, html, pdf, docx, odt, revealjs, pptx, or jupyter).",
     )
+    parser.add_argument(
+        "-output_dir",
+        "--output_directory",
+        type=str,
+        default=None,
+        help="Path to the output directory for the generated report.",
+    )
     parser.add_argument(
         "-st_autorun",
         "--streamlit_autorun",
         action="store_true",  # Automatically sets True if the flag is passed
         default=False,
         help="Automatically run the Streamlit app after report generation.",
     )
-
+    parser.add_argument(
+        "-qt_checks",
+        "--quarto_checks",
+        action="store_true",  # Automatically sets True if the flag is passed
+        default=False,
+        help="Check if Quarto is installed and available for report generation.",
+    )
     # Parse arguments
     return parser
 
@@ -731,14 +744,26 @@ def get_logger(
     return logger, log_file
 
 
-def print_completion_message(report_type: str):
+def get_completion_message(report_type: str, config_path: str) -> str:
     """
-    Prints a formatted completion message after report generation.
+    Generate a formatted completion message after report generation.
+
+    Parameters
+    ----------
+    report_type : str
+        The type of report generated (e.g., "streamlit", "html").
+    config_path : str
+        The path to the configuration file used for generating the report.
+
+    Returns
+    -------
+    str
+        A formatted string containing the completion message.
     """
     border = "─" * 65  # Creates a separator line
+
     if report_type == "streamlit":
-        print(
-            """🚀 Streamlit Report Generated!
+        message = f"""🚀 Streamlit Report Generated!
 
 📂 All scripts to build the Streamlit app are available at:
     streamlit_report/sections
@@ -750,11 +775,12 @@ def print_completion_message(report_type: str):
 
 🛠️ Advanced users can modify the Python scripts directly in:
     streamlit_report/sections
+
+⚙️ Configuration file used:
+    {config_path}
 """
-        )
     else:
-        print(
-            f"""🚀 {report_type.capitalize()} Report Generated!
+        message = f"""🚀 {report_type.capitalize()} Report Generated!
 
 📂 Your {report_type} report is available at:
     quarto_report
@@ -763,10 +789,12 @@ def print_completion_message(report_type: str):
 
 🛠️ Advanced users can modify the report template directly in:
     quarto_report/quarto_report.qmd
+
+⚙️ Configuration file used:
+    {config_path}
 """
-        )
 
-    print(border)
+    return f"{message}\n{border}"
 
 
 ## REPORT FORMATTING