diff --git a/bin/update_test_reports.sh b/bin/update_test_reports.sh index 1c5028a..e652d71 100644 --- a/bin/update_test_reports.sh +++ b/bin/update_test_reports.sh @@ -1,4 +1,4 @@ -§set -e +set -e vuegen -dir docs/example_data/Basic_example_vuegen_demo_notebook -output_dir tests/report_examples/Basic_example_vuegen_demo_notebook vuegen -dir docs/example_data/Basic_example_vuegen_demo_notebook -output_dir tests/report_examples/Basic_example_vuegen_demo_notebook/html -rt html diff --git a/docs/example_data/Basic_example_vuegen_demo_notebook/description.md b/docs/example_data/Basic_example_vuegen_demo_notebook/description.md index f8a5c17..577dd50 100644 --- a/docs/example_data/Basic_example_vuegen_demo_notebook/description.md +++ b/docs/example_data/Basic_example_vuegen_demo_notebook/description.md @@ -1 +1,6 @@ -A general description of the report. \ No newline at end of file +A general description of the report. + +It should test all major components which are available +to be integrated into VueGen. + +Check our tests folder for examples of report files used to generate actual reports. diff --git a/src/vuegen/config_manager.py b/src/vuegen/config_manager.py index 82b381a..e2194ad 100644 --- a/src/vuegen/config_manager.py +++ b/src/vuegen/config_manager.py @@ -211,7 +211,7 @@ def _read_description_file(self, folder_path: Path) -> str: """ description_file = folder_path / "description.md" if description_file.exists(): - ret = description_file.read_text().strip().replace("\n", "\n ") + ret = description_file.read_text().strip() return f"{ret}\n" return "" diff --git a/src/vuegen/quarto_reportview.py b/src/vuegen/quarto_reportview.py index 32b5599..5a182ce 100644 --- a/src/vuegen/quarto_reportview.py +++ b/src/vuegen/quarto_reportview.py @@ -129,7 +129,7 @@ def generate_report(self, output_dir: Optional[Path] = None) -> None: # Add description of the report if self.report.description: - qmd_content.append(f"""{self.report.description}""") + qmd_content.append(self.report.description) # If available add the graphical abstract if self.report.graphical_abstract: diff --git a/src/vuegen/streamlit_reportview.py b/src/vuegen/streamlit_reportview.py index 36a38a7..cac5b30 100644 --- a/src/vuegen/streamlit_reportview.py +++ b/src/vuegen/streamlit_reportview.py @@ -424,17 +424,19 @@ def _format_text( ) text = text.strip() # get rid of new lines - - return textwrap.dedent( - f""" + text = textwrap.indent(text, " ") + ret = textwrap.dedent( + f"""\ st.markdown( - ( - "<{tag} style='text-align: {text_align}; " - "color: {color};'>{text}" - ), + ''' + <{tag} style='text-align: {text_align}; + color: {color};'>\n{text} + + ''', unsafe_allow_html=True) """ ) + return ret def _generate_home_section( self, diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/docx/quarto_report/quarto_report.qmd b/tests/report_examples/Basic_example_vuegen_demo_notebook/docx/quarto_report/quarto_report.qmd index d17143d..e719b37 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/docx/quarto_report/quarto_report.qmd +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/docx/quarto_report/quarto_report.qmd @@ -27,6 +27,11 @@ report_dir = Path().cwd() A general description of the report. +It should test all major components which are available +to be integrated into VueGen. + +Check our tests folder for examples of report files used to generate actual reports. + ![](../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/home_image.png){fig-alt= width=90%} # Plots diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/html/quarto_report/quarto_report.qmd b/tests/report_examples/Basic_example_vuegen_demo_notebook/html/quarto_report/quarto_report.qmd index 0946b7d..a76287b 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/html/quarto_report/quarto_report.qmd +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/html/quarto_report/quarto_report.qmd @@ -53,6 +53,11 @@ report_dir = Path().cwd() A general description of the report. +It should test all major components which are available +to be integrated into VueGen. + +Check our tests folder for examples of report files used to generate actual reports. + ![](../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/home_image.png){fig-alt= width=90%} # Plots diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/jupyter/quarto_report/quarto_report.qmd b/tests/report_examples/Basic_example_vuegen_demo_notebook/jupyter/quarto_report/quarto_report.qmd index eb86015..19eb27c 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/jupyter/quarto_report/quarto_report.qmd +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/jupyter/quarto_report/quarto_report.qmd @@ -53,6 +53,11 @@ report_dir = Path().cwd() A general description of the report. +It should test all major components which are available +to be integrated into VueGen. + +Check our tests folder for examples of report files used to generate actual reports. + ![](../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/home_image.png){fig-alt= width=90%} # Plots diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/odt/quarto_report/quarto_report.qmd b/tests/report_examples/Basic_example_vuegen_demo_notebook/odt/quarto_report/quarto_report.qmd index 7e77432..bd4126e 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/odt/quarto_report/quarto_report.qmd +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/odt/quarto_report/quarto_report.qmd @@ -27,6 +27,11 @@ report_dir = Path().cwd() A general description of the report. +It should test all major components which are available +to be integrated into VueGen. + +Check our tests folder for examples of report files used to generate actual reports. + ![](../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/home_image.png){fig-alt= width=90%} # Plots diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/pdf/quarto_report/quarto_report.qmd b/tests/report_examples/Basic_example_vuegen_demo_notebook/pdf/quarto_report/quarto_report.qmd index 76fe18d..c858855 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/pdf/quarto_report/quarto_report.qmd +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/pdf/quarto_report/quarto_report.qmd @@ -39,6 +39,11 @@ report_dir = Path().cwd() A general description of the report. +It should test all major components which are available +to be integrated into VueGen. + +Check our tests folder for examples of report files used to generate actual reports. + ![](../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/home_image.png){fig-alt= width=90%} # Plots diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/pptx/quarto_report/quarto_report.qmd b/tests/report_examples/Basic_example_vuegen_demo_notebook/pptx/quarto_report/quarto_report.qmd index bfe6edf..7b637b8 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/pptx/quarto_report/quarto_report.qmd +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/pptx/quarto_report/quarto_report.qmd @@ -28,6 +28,11 @@ report_dir = Path().cwd() A general description of the report. +It should test all major components which are available +to be integrated into VueGen. + +Check our tests folder for examples of report files used to generate actual reports. + ![](../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/home_image.png){fig-alt= width=90%} # Plots diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/revealjs/quarto_report/quarto_report.qmd b/tests/report_examples/Basic_example_vuegen_demo_notebook/revealjs/quarto_report/quarto_report.qmd index ce6e15e..491dbfb 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/revealjs/quarto_report/quarto_report.qmd +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/revealjs/quarto_report/quarto_report.qmd @@ -54,6 +54,11 @@ report_dir = Path().cwd() A general description of the report. +It should test all major components which are available +to be integrated into VueGen. + +Check our tests folder for examples of report files used to generate actual reports. + ![](../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/home_image.png){fig-alt= width=90%} # Plots diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Dataframes/All_Formats.py b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Dataframes/All_Formats.py index 2babf56..ea9a3b5 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Dataframes/All_Formats.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Dataframes/All_Formats.py @@ -6,20 +6,22 @@ df_index = 1 section_dir = Path(__file__).resolve().parent.parent - st.markdown( - ( - "

All Formats

" - ), + ''' +

+ All Formats +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Phyla Correlation Network Csv

" - ), + ''' +

+ Phyla Correlation Network Csv +

+ ''', unsafe_allow_html=True) file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/1_phyla_correlation_network_csv.csv').resolve().as_posix() @@ -53,12 +55,13 @@ mime='text/csv', key=f"download_button_{df_index}") df_index += 1 - st.markdown( - ( - "

Abundance Table Example Xls

" - ), + ''' +

+ Abundance Table Example Xls +

+ ''', unsafe_allow_html=True) selected_sheet = 0 @@ -99,12 +102,13 @@ mime='text/csv', key=f"download_button_{df_index}") df_index += 1 - st.markdown( - ( - "

Sample Info Example Txt

" - ), + ''' +

+ Sample Info Example Txt +

+ ''', unsafe_allow_html=True) file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/3_sample_info_example_txt.txt').resolve().as_posix() @@ -138,12 +142,13 @@ mime='text/csv', key=f"download_button_{df_index}") df_index += 1 - st.markdown( - ( - "

Sample Info Example Parquet

" - ), + ''' +

+ Sample Info Example Parquet +

+ ''', unsafe_allow_html=True) file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/4_sample_info_example_parquet.parquet').resolve().as_posix() @@ -177,12 +182,13 @@ mime='text/csv', key=f"download_button_{df_index}") df_index += 1 - st.markdown( - ( - "

Example Xlsx

" - ), + ''' +

+ Example Xlsx +

+ ''', unsafe_allow_html=True) selected_sheet = 0 diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Home/Homepage.py b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Home/Homepage.py index 060aec6..3e5401e 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Home/Homepage.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Home/Homepage.py @@ -1,10 +1,16 @@ import streamlit as st - st.markdown( - ( - "

A general description of the report.

" - ), + ''' +

+ A general description of the report. + + It should test all major components which are available + to be integrated into VueGen. + + Check our tests folder for examples of report files used to generate actual reports. +

+ ''', unsafe_allow_html=True) diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Html/All_Html.py b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Html/All_Html.py index e44d890..bb20fc3 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Html/All_Html.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Html/All_Html.py @@ -3,20 +3,22 @@ import streamlit as st section_dir = Path(__file__).resolve().parent.parent - st.markdown( - ( - "

All Html

" - ), + ''' +

+ All Html +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Plot

" - ), + ''' +

+ Plot +

+ ''', unsafe_allow_html=True) file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/1_plot.html').resolve().as_posix() @@ -25,12 +27,13 @@ st.components.v1.html(html_content, height=600, scrolling=True) - st.markdown( - ( - "

Ckg Network

" - ), + ''' +

+ Ckg Network +

+ ''', unsafe_allow_html=True) @@ -53,12 +56,13 @@ # Load HTML into HTML component for display on Streamlit st.components.v1.html(html_content, height=net_html_height) - st.markdown( - ( - "

Multiqc Report

" - ), + ''' +

+ Multiqc Report +

+ ''', unsafe_allow_html=True) file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/3_multiqc_report.html').resolve().as_posix() diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Markdown/All_Markdown.py b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Markdown/All_Markdown.py index 40b331d..5d8dd86 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Markdown/All_Markdown.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Markdown/All_Markdown.py @@ -3,20 +3,22 @@ import streamlit as st section_dir = Path(__file__).resolve().parent.parent - st.markdown( - ( - "

All Markdown

" - ), + ''' +

+ All Markdown +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Readme

" - ), + ''' +

+ Readme +

+ ''', unsafe_allow_html=True) diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Networks/Interactive_Networks.py b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Networks/Interactive_Networks.py index 7eaa895..852bdc0 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Networks/Interactive_Networks.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Networks/Interactive_Networks.py @@ -3,28 +3,31 @@ import streamlit as st section_dir = Path(__file__).resolve().parent.parent - st.markdown( - ( - "

Interactive Networks

" - ), + ''' +

+ Interactive Networks +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Optional description for subsection.

" - ), + ''' +

+ Optional description for subsection. +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Man Example

" - ), + ''' +

+ Man Example +

+ ''', unsafe_allow_html=True) @@ -47,12 +50,13 @@ # Load HTML into HTML component for display on Streamlit st.components.v1.html(html_content, height=net_html_height) - st.markdown( - ( - "

Description

" - ), + ''' +

+ Description +

+ ''', unsafe_allow_html=True) diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Networks/Static_Networks.py b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Networks/Static_Networks.py index fce1380..92ec024 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Networks/Static_Networks.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Networks/Static_Networks.py @@ -2,20 +2,22 @@ import streamlit as st section_dir = Path(__file__).resolve().parent.parent - st.markdown( - ( - "

Static Networks

" - ), + ''' +

+ Static Networks +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Phyla Correlation Network

" - ), + ''' +

+ Phyla Correlation Network +

+ ''', unsafe_allow_html=True) plot_file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/3_Networks/2_Static_networks/1_phyla_correlation_network.png').resolve().as_posix() diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Plots/Interactive_Plots.py b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Plots/Interactive_Plots.py index 534be34..cb5916e 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Plots/Interactive_Plots.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Plots/Interactive_Plots.py @@ -5,28 +5,31 @@ import streamlit as st section_dir = Path(__file__).resolve().parent.parent - st.markdown( - ( - "

Interactive Plots

" - ), + ''' +

+ Interactive Plots +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Optional description for section.

" - ), + ''' +

+ Optional description for section. +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Top Species Plot By Biome Plotly

" - ), + ''' +

+ Top Species Plot By Biome Plotly +

+ ''', unsafe_allow_html=True) @@ -43,12 +46,13 @@ for entry in plot_json.get('data', [])] st.plotly_chart(plot_json, use_container_width=True) - st.markdown( - ( - "

Multiline Plot Altair

" - ), + ''' +

+ Multiline Plot Altair +

+ ''', unsafe_allow_html=True) @@ -60,12 +64,13 @@ st.vega_lite_chart(json.loads(altair_plot.to_json()), use_container_width=True) - st.markdown( - ( - "

Pie Plot Countries Plotly

" - ), + ''' +

+ Pie Plot Countries Plotly +

+ ''', unsafe_allow_html=True) @@ -82,12 +87,13 @@ for entry in plot_json.get('data', [])] st.plotly_chart(plot_json, use_container_width=True) - st.markdown( - ( - "

Pie Plots Biomes Plotly

" - ), + ''' +

+ Pie Plots Biomes Plotly +

+ ''', unsafe_allow_html=True) @@ -104,12 +110,13 @@ for entry in plot_json.get('data', [])] st.plotly_chart(plot_json, use_container_width=True) - st.markdown( - ( - "

Saline Metagenomics Samples Map Altair

" - ), + ''' +

+ Saline Metagenomics Samples Map Altair +

+ ''', unsafe_allow_html=True) @@ -121,12 +128,13 @@ st.vega_lite_chart(json.loads(altair_plot.to_json()), use_container_width=True) - st.markdown( - ( - "

Plotly Plot R

" - ), + ''' +

+ Plotly Plot R +

+ ''', unsafe_allow_html=True) @@ -143,12 +151,13 @@ for entry in plot_json.get('data', [])] st.plotly_chart(plot_json, use_container_width=True) - st.markdown( - ( - "

Description

" - ), + ''' +

+ Description +

+ ''', unsafe_allow_html=True) diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Plots/Static_Plots.py b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Plots/Static_Plots.py index 4c2304c..47084f6 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Plots/Static_Plots.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/Plots/Static_Plots.py @@ -2,42 +2,46 @@ import streamlit as st section_dir = Path(__file__).resolve().parent.parent - st.markdown( - ( - "

Static Plots

" - ), + ''' +

+ Static Plots +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Number Samples Per Study

" - ), + ''' +

+ Number Samples Per Study +

+ ''', unsafe_allow_html=True) plot_file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/1_number_samples_per_study.png').resolve().as_posix() st.image(plot_file_path, caption='', use_column_width=True) - st.markdown( - ( - "

Animal Metagenomics Samples Map

" - ), + ''' +

+ Animal Metagenomics Samples Map +

+ ''', unsafe_allow_html=True) plot_file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/2_animal_metagenomics_samples_map.png').resolve().as_posix() st.image(plot_file_path, caption='', use_column_width=True) - st.markdown( - ( - "

Alpha Diversity Host Associated Samples

" - ), + ''' +

+ Alpha Diversity Host Associated Samples +

+ ''', unsafe_allow_html=True) plot_file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/3_alpha_diversity_host_associated_samples.png').resolve().as_posix() diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/report_manager.py b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/report_manager.py index 5ea3ad3..8356035 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/report_manager.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/streamlit_report/sections/report_manager.py @@ -7,12 +7,13 @@ st.set_page_config(layout="wide", page_title="Basic Example Vuegen Demo Notebook") - st.markdown( - ( - "

Basic Example Vuegen Demo Notebook

" - ), + ''' +

+ Basic Example Vuegen Demo Notebook +

+ ''', unsafe_allow_html=True) diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Dataframes/All_Formats.py b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Dataframes/All_Formats.py index 1d3b43b..956f869 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Dataframes/All_Formats.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Dataframes/All_Formats.py @@ -6,28 +6,31 @@ df_index = 1 section_dir = Path(__file__).resolve().parent.parent - st.markdown( - ( - "

All Formats

" - ), + ''' +

+ All Formats +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

This subsection contains example dataframes.

" - ), + ''' +

+ This subsection contains example dataframes. +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Phyla Correlation Network Csv

" - ), + ''' +

+ Phyla Correlation Network Csv +

+ ''', unsafe_allow_html=True) file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/1_phyla_correlation_network_csv.csv').resolve().as_posix() @@ -61,12 +64,13 @@ mime='text/csv', key=f"download_button_{df_index}") df_index += 1 - st.markdown( - ( - "

Abundance Table Example Xls

" - ), + ''' +

+ Abundance Table Example Xls +

+ ''', unsafe_allow_html=True) selected_sheet = 0 @@ -107,12 +111,13 @@ mime='text/csv', key=f"download_button_{df_index}") df_index += 1 - st.markdown( - ( - "

Sample Info Example Txt

" - ), + ''' +

+ Sample Info Example Txt +

+ ''', unsafe_allow_html=True) file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/3_sample_info_example_txt.txt').resolve().as_posix() @@ -146,12 +151,13 @@ mime='text/csv', key=f"download_button_{df_index}") df_index += 1 - st.markdown( - ( - "

Sample Info Example Parquet

" - ), + ''' +

+ Sample Info Example Parquet +

+ ''', unsafe_allow_html=True) file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/2_Dataframes/1_All_formats/4_sample_info_example_parquet.parquet').resolve().as_posix() diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Home/Homepage.py b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Home/Homepage.py index 0131be5..d1b7796 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Home/Homepage.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Home/Homepage.py @@ -1,10 +1,11 @@ import streamlit as st - st.markdown( - ( - "

A general description of the report.

" - ), + ''' +

+ A general description of the report. +

+ ''', unsafe_allow_html=True) diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Html/All_Html.py b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Html/All_Html.py index e44d890..bb20fc3 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Html/All_Html.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Html/All_Html.py @@ -3,20 +3,22 @@ import streamlit as st section_dir = Path(__file__).resolve().parent.parent - st.markdown( - ( - "

All Html

" - ), + ''' +

+ All Html +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Plot

" - ), + ''' +

+ Plot +

+ ''', unsafe_allow_html=True) file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/1_plot.html').resolve().as_posix() @@ -25,12 +27,13 @@ st.components.v1.html(html_content, height=600, scrolling=True) - st.markdown( - ( - "

Ckg Network

" - ), + ''' +

+ Ckg Network +

+ ''', unsafe_allow_html=True) @@ -53,12 +56,13 @@ # Load HTML into HTML component for display on Streamlit st.components.v1.html(html_content, height=net_html_height) - st.markdown( - ( - "

Multiqc Report

" - ), + ''' +

+ Multiqc Report +

+ ''', unsafe_allow_html=True) file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/4_Html/1_All_html/3_multiqc_report.html').resolve().as_posix() diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Markdown/All_Markdown.py b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Markdown/All_Markdown.py index 40b331d..5d8dd86 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Markdown/All_Markdown.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Markdown/All_Markdown.py @@ -3,20 +3,22 @@ import streamlit as st section_dir = Path(__file__).resolve().parent.parent - st.markdown( - ( - "

All Markdown

" - ), + ''' +

+ All Markdown +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Readme

" - ), + ''' +

+ Readme +

+ ''', unsafe_allow_html=True) diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Networks/Interactive_Networks.py b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Networks/Interactive_Networks.py index 0b29029..f99c144 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Networks/Interactive_Networks.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Networks/Interactive_Networks.py @@ -3,28 +3,31 @@ import streamlit as st section_dir = Path(__file__).resolve().parent.parent - st.markdown( - ( - "

Interactive Networks

" - ), + ''' +

+ Interactive Networks +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Optional description for subsection

" - ), + ''' +

+ Optional description for subsection +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Man Example

" - ), + ''' +

+ Man Example +

+ ''', unsafe_allow_html=True) @@ -47,12 +50,13 @@ # Load HTML into HTML component for display on Streamlit st.components.v1.html(html_content, height=net_html_height) - st.markdown( - ( - "

Description

" - ), + ''' +

+ Description +

+ ''', unsafe_allow_html=True) diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Networks/Static_Networks.py b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Networks/Static_Networks.py index fce1380..92ec024 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Networks/Static_Networks.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Networks/Static_Networks.py @@ -2,20 +2,22 @@ import streamlit as st section_dir = Path(__file__).resolve().parent.parent - st.markdown( - ( - "

Static Networks

" - ), + ''' +

+ Static Networks +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Phyla Correlation Network

" - ), + ''' +

+ Phyla Correlation Network +

+ ''', unsafe_allow_html=True) plot_file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/3_Networks/2_Static_networks/1_phyla_correlation_network.png').resolve().as_posix() diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Plots/Interactive_Plots.py b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Plots/Interactive_Plots.py index 94f5177..8b98d7d 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Plots/Interactive_Plots.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Plots/Interactive_Plots.py @@ -5,28 +5,31 @@ import streamlit as st section_dir = Path(__file__).resolve().parent.parent - st.markdown( - ( - "

Interactive Plots

" - ), + ''' +

+ Interactive Plots +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Optional description for section.

" - ), + ''' +

+ Optional description for section. +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Top Species Plot By Biome Plotly

" - ), + ''' +

+ Top Species Plot By Biome Plotly +

+ ''', unsafe_allow_html=True) @@ -43,12 +46,13 @@ for entry in plot_json.get('data', [])] st.plotly_chart(plot_json, use_container_width=True) - st.markdown( - ( - "

Multiline Plot Altair

" - ), + ''' +

+ Multiline Plot Altair +

+ ''', unsafe_allow_html=True) @@ -60,12 +64,13 @@ st.vega_lite_chart(json.loads(altair_plot.to_json()), use_container_width=True) - st.markdown( - ( - "

Pie Plot Countries Plotly

" - ), + ''' +

+ Pie Plot Countries Plotly +

+ ''', unsafe_allow_html=True) @@ -82,12 +87,13 @@ for entry in plot_json.get('data', [])] st.plotly_chart(plot_json, use_container_width=True) - st.markdown( - ( - "

Pie Plots Biomes Plotly

" - ), + ''' +

+ Pie Plots Biomes Plotly +

+ ''', unsafe_allow_html=True) @@ -104,12 +110,13 @@ for entry in plot_json.get('data', [])] st.plotly_chart(plot_json, use_container_width=True) - st.markdown( - ( - "

Saline Metagenomics Samples Map Altair

" - ), + ''' +

+ Saline Metagenomics Samples Map Altair +

+ ''', unsafe_allow_html=True) @@ -121,12 +128,13 @@ st.vega_lite_chart(json.loads(altair_plot.to_json()), use_container_width=True) - st.markdown( - ( - "

Description

" - ), + ''' +

+ Description +

+ ''', unsafe_allow_html=True) diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Plots/Static_Plots.py b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Plots/Static_Plots.py index 9eeb920..af6eab8 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Plots/Static_Plots.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/Plots/Static_Plots.py @@ -2,53 +2,58 @@ import streamlit as st section_dir = Path(__file__).resolve().parent.parent - st.markdown( - ( - "

Static Plots

" - ), + ''' +

+ Static Plots +

+ ''', unsafe_allow_html=True) - st.markdown( - ( - "

Number Samples Per Study

" - ), + ''' +

+ Number Samples Per Study +

+ ''', unsafe_allow_html=True) plot_file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/1_number_samples_per_study.png').resolve().as_posix() st.image(plot_file_path, caption='', use_column_width=True) - st.markdown( - ( - "

Animal Metagenomics Samples Map

" - ), + ''' +

+ Animal Metagenomics Samples Map +

+ ''', unsafe_allow_html=True) plot_file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/2_animal_metagenomics_samples_map.png').resolve().as_posix() st.image(plot_file_path, caption='', use_column_width=True) - st.markdown( - ( - "

Alpha Diversity Host Associated Samples

" - ), + ''' +

+ Alpha Diversity Host Associated Samples +

+ ''', unsafe_allow_html=True) plot_file_path = (section_dir / '../../../../../docs/example_data/Basic_example_vuegen_demo_notebook/1_Plots/2_Static_plots/3_alpha_diversity_host_associated_samples.png').resolve().as_posix() st.image(plot_file_path, caption='', use_column_width=True) - st.markdown( - ( - "

Graphical overview of VueGen workflow and components

" - ), + ''' +

+ Graphical overview of VueGen workflow and components +

+ ''', unsafe_allow_html=True) plot_file_path = 'https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_graph_abstract.png' diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/report_manager.py b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/report_manager.py index afb89c3..08a5280 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/report_manager.py +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/report_manager.py @@ -10,12 +10,13 @@ ) st.logo("https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/logo/vuegen_logo.png") - st.markdown( - ( - "

Basic Example Vuegen Demo Notebook

" - ), + ''' +

+ Basic Example Vuegen Demo Notebook +

+ ''', unsafe_allow_html=True) diff --git a/tests/report_examples/chat_bot/streamlit_report/sections/Home/Homepage.py b/tests/report_examples/chat_bot/streamlit_report/sections/Home/Homepage.py index f875979..b1a3fd9 100644 --- a/tests/report_examples/chat_bot/streamlit_report/sections/Home/Homepage.py +++ b/tests/report_examples/chat_bot/streamlit_report/sections/Home/Homepage.py @@ -1,10 +1,11 @@ import streamlit as st - st.markdown( - ( - "

A chatbot example.

" - ), + ''' +

+ A chatbot example. +

+ ''', unsafe_allow_html=True) footer = ''' diff --git a/tests/report_examples/chat_bot/streamlit_report/sections/report_manager.py b/tests/report_examples/chat_bot/streamlit_report/sections/report_manager.py index af3eca1..5b3458b 100644 --- a/tests/report_examples/chat_bot/streamlit_report/sections/report_manager.py +++ b/tests/report_examples/chat_bot/streamlit_report/sections/report_manager.py @@ -7,12 +7,13 @@ st.set_page_config(layout="wide", page_title="Chatbot example") - st.markdown( - ( - "

Chatbot example

" - ), + ''' +

+ Chatbot example +

+ ''', unsafe_allow_html=True)