Style and format codebase

docs/README.md

@@ -1,10 +1,10 @@
 # Docs creation
 
-In order to build the docs you need to 
+In order to build the docs you need to
 
-  1. Install sphinx and additional support packages
-  2. Build the package reference files
-  3. Run sphinx to create a local html version
+1. Install sphinx and additional support packages
+2. Build the package reference files
+3. Run sphinx to create a local html version
 
 The documentation is build using readthedocs automatically.
 
@@ -18,12 +18,13 @@ poetry install --with docs
 
 ## Build docs using Sphinx command line tools
 
-Command to be run from `path/to/docs`, i.e. from within the `docs` package folder: 
+Command to be run from `path/to/docs`, i.e. from within the `docs` package folder:
 
 Options:
-  - `--separate` to build separate pages for each (sub-)module
 
-```bash	
+- `--separate` to build separate pages for each (sub-)module
+
+```bash
 # pwd: docs
 # apidoc
 sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../src/vuegen
@@ -38,4 +39,3 @@ The README is included in the `Overview` section of the docs. We created a [Pyth
 Relative links are used in the main README, which need to be resolved when building. It's
 possible to include the a `relative-docs` option if one uses `index.md` ([see docs](https://myst-parser.readthedocs.io/en/latest/faq/index.html#include-a-file-from-outside-the-docs-folder-like-readme-md)). This does not work
 with `href` links, only native markdown links.
-

docs/vuegen_basic_case_study_configfile.md

@@ -1,6 +1,6 @@
 # Predefined Directory Case Study - Configuration File
 
-The [configuration file](https://github.com/Multiomics-Analytics-Group/vuegen/blob/main/docs/example_config_files/Basic_example_vuegen_demo_notebook_config.yaml) of the basic case study using a predefined directory is presented below: 
+The [configuration file](https://github.com/Multiomics-Analytics-Group/vuegen/blob/main/docs/example_config_files/Basic_example_vuegen_demo_notebook_config.yaml) of the basic case study using a predefined directory is presented below:
 
 ```yaml
 report:
@@ -9,168 +9,169 @@ 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
 sections:
-- title: Plots
-  description: This section contains example plots.
-  subsections:
-  - title: Interactive Plots
-    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
-      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
-      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
-      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
-      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
-      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
-      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
-      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
-      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
-      description: ''
-      caption: ''
-      component_type: plot
-      plot_type: static
-    - title: "Graphical overview of VueGen workflow and components"
-      file_path: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_graph_abstract.png
-      description: ''
-      caption: The diagram illustrates the processing pipeline of VueGen, starting
-        from either a directory or a YAML configuration file. Reports consist of hierarchical
-        sections and subsections, each containing various components such as plots,
-        dataframes, Markdown, HTML, and data retrieved via API calls.
-      component_type: plot
-      plot_type: static
-- title: Dataframes
-  description: ''
-  subsections:
-  - title: All Formats
-    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
-      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
-      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
-      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
-      description: ''
-      caption: ''
-      component_type: dataframe
-      file_format: parquet
-- title: Networks
-  description: ''
-  subsections:
-  - title: Interactive Networks
-    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
-      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
-      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
-      description: ''
-      caption: ''
-      component_type: plot
-      plot_type: static
-- title: Html
-  description: ''
-  subsections:
-  - title: All Html
-    description: ''
-    components:
-    - title: Plot
-      file_path: 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
-      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
-      description: ''
-      caption: ''
-      component_type: html
-- title: Markdown
-  description: ''
-  subsections:
-  - title: All Markdown
-    description: ''
-    components:
-    - title: Readme
-      file_path: example_data/Basic_example_vuegen_demo_notebook/5_Markdown/1_All_markdown/README.md
-      description: ''
-      caption: ''
-      component_type: markdown
+  - title: Plots
+    description: This section contains example plots.
+    subsections:
+      - title: Interactive Plots
+        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
+            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
+            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
+            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
+            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
+            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
+            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
+            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
+            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
+            description: ""
+            caption: ""
+            component_type: plot
+            plot_type: static
+          - title: "Graphical overview of VueGen workflow and components"
+            file_path: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_graph_abstract.png
+            description: ""
+            caption:
+              The diagram illustrates the processing pipeline of VueGen, starting
+              from either a directory or a YAML configuration file. Reports consist of hierarchical
+              sections and subsections, each containing various components such as plots,
+              dataframes, Markdown, HTML, and data retrieved via API calls.
+            component_type: plot
+            plot_type: static
+  - title: Dataframes
+    description: ""
+    subsections:
+      - title: All Formats
+        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
+            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
+            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
+            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
+            description: ""
+            caption: ""
+            component_type: dataframe
+            file_format: parquet
+  - title: Networks
+    description: ""
+    subsections:
+      - title: Interactive Networks
+        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
+            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
+            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
+            description: ""
+            caption: ""
+            component_type: plot
+            plot_type: static
+  - title: Html
+    description: ""
+    subsections:
+      - title: All Html
+        description: ""
+        components:
+          - title: Plot
+            file_path: 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
+            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
+            description: ""
+            caption: ""
+            component_type: html
+  - title: Markdown
+    description: ""
+    subsections:
+      - title: All Markdown
+        description: ""
+        components:
+          - title: Readme
+            file_path: example_data/Basic_example_vuegen_demo_notebook/5_Markdown/1_All_markdown/README.md
+            description: ""
+            caption: ""
+            component_type: markdown
 ```
 
 The directory with he example data is available in the [GitHub repository](https://github.com/Multiomics-Analytics-Group/vuegen/blob/main/docs/example_data/Basic_example_vuegen_demo_notebook).

pyproject.toml

@@ -74,3 +74,6 @@ vuegen = "vuegen.__main__:main"
 
 [tool.isort]
 profile = "black"
+
+[tool.jupytext]
+formats = "ipynb,py:percent"

setup.cfg

@@ -0,0 +1,4 @@
+[flake8]
+exclude = docs
+max-line-length = 90
+aggressive = 2

src/vuegen/__init__.py

@@ -1 +1,6 @@
+"""VueGen automates the creation of reports from bioinformatics outputs,
+supporting formats like PDF, HTML, DOCX, ODT, PPTX, Reveal.js, Jupyter notebooks,
+and Streamlit web applications. Users simply provide a directory with output files
+and VueGen compiles them into a structured report."""
+
 __version__ = "1.0.0"