🚧 start to explore adding subsections to homesection

.github/workflows/cdci.yml

@@ -109,6 +109,15 @@ jobs:
           cd docs
           vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt jupyter
           vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt jupyter
+      - name: quarto html report based on predefined config file
+        run: |
+          cd docs
+          vuegen -c example_config_files/Basic_example_vuegen_demo_notebook_config.yaml -output_dir ../tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/html -rt html
+          # Check for changes
+          if git diff ../tests/report_examples | grep .; then
+            echo "Error: One or more protected files have been modified."
+            exit 1
+          fi
       - name: check for changes in report files
         run: |
           # write streamlit report to test folder 
@@ -118,7 +127,18 @@ jobs:
             echo "Error: One or more protected files have been modified."
             exit 1
           fi
-
+      - name: check for changes in quarto report files 
+        run: |
+          # write quarto based report to test folder
+          for format in html pdf docx odt revealjs pptx jupyter; do
+            vuegen -dir docs/example_data/Basic_example_vuegen_demo_notebook -output_dir tests/report_examples/Basic_example_vuegen_demo_notebook/$format  -rt $format 
+            # Check for changes
+            if git diff tests/report_examples | grep .; then
+              echo Failed for report: $format
+              echo "Error: One or more protected files have been modified."
+              exit 1
+            fi
+          done
 
   publish:
     name: Publish package to PyPI

README.md

@@ -126,6 +126,9 @@ vuegen --directory docs/example_data/Earth_microbiome_vuegen_demo_notebook --rep
 
 > [!NOTE]
 > By default, the `streamlit_autorun` argument is set to False, but you can use it in case you want to automatically run the streamlit app.
+> You can also specify the output directory with the `--output_directory` argumument, which defaults to the current working directory.
+> See all available arguments with the `--help` option.
+
 
 ### Folder structure
 
@@ -154,6 +157,8 @@ report_folder/
 The titles for sections, subsections, and components are extracted from the corresponding folder and file names, and afterward, users can add descriptions, captions, and other details to the configuration file. Component types are inferred from the file extensions and names.
 The order of sections, subsections, and components can be defined using numerical suffixes in folder and file names.
 
+### Configuration file
+
 It's also possible to provide a configuration file instead of a directory:
 
 ```bash
@@ -162,6 +167,8 @@ vuegen --config docs/example_config_files/Earth_microbiome_vuegen_demo_notebook.
 
 If a configuration file is given, users can specify titles and descriptions for sections and subsections, as well as component paths and required attributes, such as file format and delimiter for dataframes, plot types, and other details.
 
+The component paths in the configuration file can be absolute or relative to the execution directory.
+
 The current report types supported by VueGen are:
 
 - Streamlit

docs/example_config_files/Basic_example_vuegen_demo_notebook_config.yaml

@@ -1,8 +1,8 @@
 report:
   title: Basic Example Vuegen Demo Notebook
   description: A general description of the report.
-  graphical_abstract: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg
-  logo: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg
+  graphical_abstract: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png
+  logo: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png
 sections:
 - title: Plots
   description: This section contains example plots.
@@ -11,57 +11,57 @@ sections:
     description: Optional description for section.
     components:
     - title: Top Species Plot By Biome Plotly
-      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/1_top_species_plot_by_biome_plotly.json
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/1_top_species_plot_by_biome_plotly.json
       description: ''
       caption: ''
       component_type: plot
       plot_type: plotly
     - title: Multiline Plot Altair
-      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/2_multiline_plot_altair.json
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/2_multiline_plot_altair.json
       description: ''
       caption: ''
       component_type: plot
       plot_type: altair
     - title: Pie Plot Countries Plotly
-      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/3_pie_plot_countries_plotly.json
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/3_pie_plot_countries_plotly.json
       description: ''
       caption: ''
       component_type: plot
       plot_type: plotly
     - title: Pie Plots Biomes Plotly
-      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/4_pie_plots_biomes_plotly.json
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/4_pie_plots_biomes_plotly.json
       description: ''
       caption: ''
       component_type: plot
       plot_type: plotly
     - title: Saline Metagenomics Samples Map Altair
-      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/5_saline_metagenomics_samples_map_altair.json
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/5_saline_metagenomics_samples_map_altair.json
       description: ''
       caption: ''
       component_type: plot
       plot_type: altair
     - title: Description
-      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/description.md
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/1_Plots/1_Interactive_plots/description.md
       description: ''
       caption: ''
       component_type: markdown
   - title: Static Plots
     description: ''
     components:
     - title: Number Samples Per Study
-      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/1_number_samples_per_study.png
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/1_number_samples_per_study.png
       description: ''
       caption: ''
       component_type: plot
       plot_type: static
     - title: Animal Metagenomics Samples Map
-      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/2_animal_metagenomics_samples_map.png
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/2_animal_metagenomics_samples_map.png
       description: ''
       caption: ''
       component_type: plot
       plot_type: static
     - title: Alpha Diversity Host Associated Samples
-      file_path: example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/3_alpha_diversity_host_associated_samples.png
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/3_alpha_diversity_host_associated_samples.png
       description: ''
       caption: ''
       component_type: plot
@@ -82,27 +82,27 @@ sections:
     description: This subsection contains example dataframes.
     components:
     - title: Phyla Correlation Network Csv
-      file_path: example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/1_phyla_correlation_network_csv.csv
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/1_phyla_correlation_network_csv.csv
       description: ''
       caption: ''
       component_type: dataframe
       file_format: csv
       delimiter: ','
     - title: Abundance Table Example Xls
-      file_path: example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/2_abundance_table_example_xls.xls
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/2_abundance_table_example_xls.xls
       description: ''
       caption: ''
       component_type: dataframe
       file_format: xls
     - title: Sample Info Example Txt
-      file_path: example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/3_sample_info_example_txt.txt
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/3_sample_info_example_txt.txt
       description: ''
       caption: ''
       component_type: dataframe
       file_format: txt
       delimiter: \t
     - title: Sample Info Example Parquet
-      file_path: example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/4_sample_info_example_parquet.parquet
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/4_sample_info_example_parquet.parquet
       description: ''
       caption: ''
       component_type: dataframe
@@ -114,21 +114,21 @@ sections:
     description: Optional description for subsection
     components:
     - title: Man Example
-      file_path: example_data/Basic_example_vuegen_demo_notebook/3_Networks/1_Interactive_networks/1_man_example.graphml
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/3_Networks/1_Interactive_networks/1_man_example.graphml
       description: ''
       caption: ''
       component_type: plot
       plot_type: interactive_network
     - title: Description
-      file_path: example_data/Basic_example_vuegen_demo_notebook/3_Networks/1_Interactive_networks/description.md
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/3_Networks/1_Interactive_networks/description.md
       description: ''
       caption: ''
       component_type: markdown
   - title: Static Networks
     description: ''
     components:
     - title: Phyla Correlation Network
-      file_path: example_data/Basic_example_vuegen_demo_notebook/3_Networks/2_Static_networks/1_phyla_correlation_network.png
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/3_Networks/2_Static_networks/1_phyla_correlation_network.png
       description: ''
       caption: ''
       component_type: plot
@@ -140,18 +140,18 @@ sections:
     description: ''
     components:
     - title: Plot
-      file_path: example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/1_plot.html
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/1_plot.html
       description: ''
       caption: ''
       component_type: html
     - title: Ckg Network
-      file_path: example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/2_ckg_network.html
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/2_ckg_network.html
       description: ''
       caption: ''
       component_type: plot
       plot_type: interactive_network
     - title: Multiqc Report
-      file_path: example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/3_multiqc_report.html
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/3_multiqc_report.html
       description: ''
       caption: ''
       component_type: html
@@ -162,7 +162,7 @@ sections:
     description: ''
     components:
     - title: Readme
-      file_path: example_data/Basic_example_vuegen_demo_notebook/5_Markdown/1_All_markdown/README.md
+      file_path: ./docs/example_data/Basic_example_vuegen_demo_notebook/5_Markdown/1_All_markdown/README.md
       description: ''
       caption: ''
       component_type: markdown

docs/example_config_files/Earth_microbiome_vuegen_demo_notebook_config.yaml

@@ -22,26 +22,26 @@ sections:
     description: ''
     components:
     - title: Metadata Random Subset
-      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/1_metadata_random_subset.csv
+      file_path: ./docs/example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/1_metadata_random_subset.csv
       description: ''
       caption: ''
       component_type: DATAFRAME
       file_format: CSV
       delimiter: ','
     - title: Animal Samples Map
-      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/2_animal_samples_map.png
+      file_path: ./docs/example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/2_animal_samples_map.png
       description: ''
       caption: ''
       component_type: PLOT
       plot_type: STATIC
     - title: Plant Samples Map
-      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/3_plant_samples_map.json
+      file_path: ./docs/example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/3_plant_samples_map.json
       description: ''
       caption: ''
       component_type: PLOT
       plot_type: PLOTLY
     - title: Saline Samples Map
-      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/4_saline_samples_map.json
+      file_path: ./docs/example_data/Earth_microbiome_vuegen_demo_notebook/1_Exploratory_data_analysis/1_sample_exploration/4_saline_samples_map.json
       description: ''
       caption: ''
       component_type: PLOT
@@ -62,13 +62,13 @@ sections:
       dataset.
     components:
     - title: Alpha Diversity Host Associated Samples
-      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/1_alpha_diversity/1_alpha_diversity_host_associated_samples.png
+      file_path: ./docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/1_alpha_diversity/1_alpha_diversity_host_associated_samples.png
       description: ''
       caption: ''
       component_type: PLOT
       plot_type: STATIC
     - title: Alpha Diversity Free Living Samples
-      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/1_alpha_diversity/2_alpha_diversity_free_living_samples.json
+      file_path: ./docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/1_alpha_diversity/2_alpha_diversity_free_living_samples.json
       description: ''
       caption: ''
       component_type: PLOT
@@ -77,13 +77,13 @@ sections:
     description: ''
     components:
     - title: Average Copy Number Emp Ontology Level2
-      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/2_average_copy_number/1_average_copy_number_emp_ontology_level2.png
+      file_path: ./docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/2_average_copy_number/1_average_copy_number_emp_ontology_level2.png
       description: ''
       caption: ''
       component_type: PLOT
       plot_type: STATIC
     - title: Average Copy Number Emp Ontology Level3
-      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/2_average_copy_number/2_average_copy_number_emp_ontology_level3.json
+      file_path: ./docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/2_average_copy_number/2_average_copy_number_emp_ontology_level3.json
       description: ''
       caption: ''
       component_type: PLOT
@@ -92,39 +92,38 @@ sections:
     description: ''
     components:
     - title: Nestedness Random Subset
-      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/1_nestedness_random_subset.csv
+      file_path: ./docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/1_nestedness_random_subset.csv
       description: ''
       caption: ''
       component_type: DATAFRAME
       file_format: CSV
       delimiter: ','
     - title: All Samples
-      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/2_all_samples.json
+      file_path: ./docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/2_all_samples.json
       description: ''
       caption: ''
       component_type: PLOT
       plot_type: PLOTLY
     - title: Plant Samples
-      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/3_plant_samples.json
+      file_path: ./docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/3_plant_samples.json
       description: ''
       caption: ''
       component_type: PLOT
       plot_type: PLOTLY
     - title: Animal Samples
-      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/4_animal_samples.png
+      file_path: ./docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/4_animal_samples.png
       description: ''
       caption: ''
       component_type: PLOT
       plot_type: STATIC
     - title: Non Saline Samples
-      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/5_non_saline_samples.png
+      file_path: ./docs/example_data/Earth_microbiome_vuegen_demo_notebook/2_Metagenomics/3_nestedness/5_non_saline_samples.png
       description: ''
       caption: ''
       component_type: PLOT
       plot_type: STATIC
   - title: Shanon entropy analysis
-    description: This subsection contains the Shannon entropy analysis of the EMP
-    dataset.
+    description: This subsection contains the Shannon entropy analysis of the EMP dataset.
     components:
     - title: Specificity of sequences and higher taxonomic groups for environment
       file_path: https://raw.githubusercontent.com/biocore/emp/master/methods/images/figure4_entropy.png
@@ -140,21 +139,21 @@ sections:
     description: ''
     components:
     - title: Phyla Counts Subset
-      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/1_phyla_counts_subset.csv
+      file_path: ./docs/example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/1_phyla_counts_subset.csv
       description: ''
       caption: ''
       component_type: DATAFRAME
       file_format: CSV
       delimiter: ','
     - title: Phyla Correlation Network With 0.5 Threshold Edgelist
-      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/2_phyla_correlation_network_with_0.5_threshold_edgelist.csv
+      file_path: ./docs/example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/2_phyla_correlation_network_with_0.5_threshold_edgelist.csv
       description: ''
       caption: ''
       component_type: PLOT
       plot_type: INTERACTIVE_NETWORK
       csv_network_format: EDGELIST
     - title: Phyla Correlation Network With 0.5 Threshold
-      file_path: example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/3_phyla_correlation_network_with_0.5_threshold.png
+      file_path: ./docs/example_data/Earth_microbiome_vuegen_demo_notebook/3_Network_analysis/1_phyla_association_networks/3_phyla_correlation_network_with_0.5_threshold.png
       description: ''
       caption: ''
       component_type: PLOT