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🎨 format example notebooks in documentation with black #82

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6e8374d
:art: format example notebooks in documentation with black
enryH Mar 3, 2025
6a70eb5
Merge branch 'main' into format_nbs
enryH Mar 17, 2025
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18 changes: 10 additions & 8 deletions .github/workflows/cdci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ on:
branches: [main]
release:
types: [published]

jobs:
test:
name: Unittests+streamlit
Expand All @@ -17,14 +17,16 @@ jobs:
python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
steps:
- uses: actions/checkout@v4
- uses: psf/black@stable
- uses: psf/black@stable
# with:
# jupyter: true
- uses: isort/isort-action@v1
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
cache: 'pip' # caching pip dependencies
cache-dependency-path: '**/pyproject.toml'
cache: "pip" # caching pip dependencies
cache-dependency-path: "**/pyproject.toml"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
Expand All @@ -37,7 +39,7 @@ jobs:
cd docs
vuegen --directory example_data/Earth_microbiome_vuegen_demo_notebook
vuegen --config example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml

other-reports:
name: Integration tests
runs-on: ubuntu-latest
Expand All @@ -50,8 +52,8 @@ jobs:
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
cache: 'pip' # caching pip dependencies
cache-dependency-path: '**/pyproject.toml'
cache: "pip" # caching pip dependencies
cache-dependency-path: "**/pyproject.toml"
- name: Install dependencies
run: |
pip install --upgrade pip
Expand Down Expand Up @@ -110,7 +112,7 @@ jobs:

steps:
- uses: actions/checkout@v4

- uses: actions/setup-python@v5
with:
python-version: "3.11"
Expand Down
77 changes: 52 additions & 25 deletions docs/vuegen_basic_case_study.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@
},
"outputs": [],
"source": [
"# Vuegen library \n",
"# Vuegen library\n",
"%pip install vuegen"
]
},
Expand All @@ -78,6 +78,7 @@
"outputs": [],
"source": [
"import os\n",
"\n",
"IN_COLAB = \"COLAB_GPU\" in os.environ"
]
},
Expand Down Expand Up @@ -164,7 +165,9 @@
"source": [
"# Generate the report\n",
"report_type = \"streamlit\"\n",
"report_generator.get_report(dir_path = base_output_dir, report_type = report_type, logger = None)"
"report_generator.get_report(\n",
" dir_path=base_output_dir, report_type=report_type, logger=None\n",
")"
]
},
{
Expand All @@ -185,14 +188,20 @@
"# run_streamlit = True # uncomment line to run the streamlit report\n",
"# Launch the Streamlit report depneding on the platform\n",
"if not IN_COLAB and run_streamlit:\n",
" !streamlit run streamlit_report/sections/report_manager.py\n",
" !streamlit run streamlit_report/sections/report_manager.py\n",
"elif run_streamlit:\n",
" # see: https://discuss.streamlit.io/t/how-to-launch-streamlit-app-from-google-colab-notebook/42399\n",
" print(\"Password/Enpoint IP for localtunnel is:\",urllib.request.urlopen('https://ipv4.icanhazip.com').read().decode('utf8').strip(\"\\n\"))\n",
" # Run the Streamlit app in the background\n",
" !streamlit run streamlit_report/sections/report_manager.py --server.address=localhost &>/content/logs.txt &\n",
" # Expose the Streamlit app on port 8501\n",
" !npx localtunnel --port 8501 --subdomain vuegen-demo\n",
" # see: https://discuss.streamlit.io/t/how-to-launch-streamlit-app-from-google-colab-notebook/42399\n",
" print(\n",
" \"Password/Enpoint IP for localtunnel is:\",\n",
" urllib.request.urlopen(\"https://ipv4.icanhazip.com\")\n",
" .read()\n",
" .decode(\"utf8\")\n",
" .strip(\"\\n\"),\n",
" )\n",
" # Run the Streamlit app in the background\n",
" !streamlit run streamlit_report/sections/report_manager.py --server.address=localhost &>/content/logs.txt &\n",
" # Expose the Streamlit app on port 8501\n",
" !npx localtunnel --port 8501 --subdomain vuegen-demo\n",
"else:\n",
" print(\"Streamlit report not executed, set run_streamlit to True to run the report\")"
]
Expand All @@ -212,7 +221,9 @@
"source": [
"# Generate the report\n",
"report_type = \"html\"\n",
"report_generator.get_report(dir_path = base_output_dir, report_type = report_type, logger = None)"
"report_generator.get_report(\n",
" dir_path=base_output_dir, report_type=report_type, logger=None\n",
")"
]
},
{
Expand All @@ -239,11 +250,15 @@
"vuegen_logo_path = \"https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg\"\n",
"\n",
"# Load the YAML file\n",
"config_path = os.path.join(base_output_dir, \"Basic_example_vuegen_demo_notebook_config.yaml\")\n",
"config_path = os.path.join(\n",
" base_output_dir, \"Basic_example_vuegen_demo_notebook_config.yaml\"\n",
")\n",
"config = load_yaml_config(config_path)\n",
"\n",
"# Update the logo and graphical abstract with the URL\n",
"config[\"report\"].update({\"logo\": vuegen_logo_path, \"graphical_abstract\": vuegen_logo_path})"
"config[\"report\"].update(\n",
" {\"logo\": vuegen_logo_path, \"graphical_abstract\": vuegen_logo_path}\n",
")"
]
},
{
Expand All @@ -261,15 +276,17 @@
"source": [
"# Update the description for the EDA section\n",
"for section in config[\"sections\"]:\n",
" if section[\"title\"] == \"Plots\": \n",
" if section[\"title\"] == \"Plots\":\n",
" section[\"description\"] = \"This section contains example plots\"\n",
"\n",
"# Update the description for the alpha diversity subsection from the Metagenomics section\n",
"for section in config[\"sections\"]:\n",
" if section[\"title\"] == \"Dataframes\":\n",
" for subsection in section[\"subsections\"]:\n",
" if subsection[\"title\"] == \"All Formats\":\n",
" subsection[\"description\"] = \"This subsection contains example dataframes.\"\n"
" subsection[\"description\"] = (\n",
" \"This subsection contains example dataframes.\"\n",
" )"
]
},
{
Expand All @@ -288,11 +305,11 @@
"# Define new plot with a URL as the file path\n",
"vuegen_abst_fig = {\n",
" \"title\": \"Graphical overview of VueGen’s workflow and components\",\n",
" \"file_path\": \"https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_graph_abstract.png\", \n",
" \"file_path\": \"https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_graph_abstract.png\",\n",
" \"description\": \"\",\n",
" \"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.\",\n",
" \"component_type\": \"plot\",\n",
" \"plot_type\": \"static\"\n",
" \"plot_type\": \"static\",\n",
"}\n",
"\n",
"# Add the plot to the Sample Provenance subsection in the EDA section\n",
Expand Down Expand Up @@ -324,7 +341,9 @@
"source": [
"# Test the changes by generarating the report from the modified YAML file\n",
"report_type = \"streamlit\"\n",
"report_generator.get_report(config_path = config_path, report_type = report_type, logger = None)"
"report_generator.get_report(\n",
" config_path=config_path, report_type=report_type, logger=None\n",
")"
]
},
{
Expand All @@ -337,14 +356,20 @@
"# run_streamlit = True # uncomment line to run the streamlit report\n",
"# Launch the Streamlit report depneding on the platform\n",
"if not IN_COLAB and run_streamlit:\n",
" !streamlit run streamlit_report/sections/report_manager.py\n",
" !streamlit run streamlit_report/sections/report_manager.py\n",
"elif run_streamlit:\n",
" # see: https://discuss.streamlit.io/t/how-to-launch-streamlit-app-from-google-colab-notebook/42399\n",
" print(\"Password/Enpoint IP for localtunnel is:\",urllib.request.urlopen('https://ipv4.icanhazip.com').read().decode('utf8').strip(\"\\n\"))\n",
" # Run the Streamlit app in the background\n",
" !streamlit run streamlit_report/sections/report_manager.py --server.address=localhost &>/content/logs.txt &\n",
" # Expose the Streamlit app on port 8501\n",
" !npx localtunnel --port 8501 --subdomain vuegen-demo\n",
" # see: https://discuss.streamlit.io/t/how-to-launch-streamlit-app-from-google-colab-notebook/42399\n",
" print(\n",
" \"Password/Enpoint IP for localtunnel is:\",\n",
" urllib.request.urlopen(\"https://ipv4.icanhazip.com\")\n",
" .read()\n",
" .decode(\"utf8\")\n",
" .strip(\"\\n\"),\n",
" )\n",
" # Run the Streamlit app in the background\n",
" !streamlit run streamlit_report/sections/report_manager.py --server.address=localhost &>/content/logs.txt &\n",
" # Expose the Streamlit app on port 8501\n",
" !npx localtunnel --port 8501 --subdomain vuegen-demo\n",
"else:\n",
" print(\"Streamlit report not executed, set run_streamlit to True to run the report\")"
]
Expand All @@ -364,7 +389,9 @@
"source": [
"# Test the changes by generarating the report from the modified YAML file\n",
"report_type = \"html\"\n",
"report_generator.get_report(config_path = config_path, report_type = report_type, logger = None)"
"report_generator.get_report(\n",
" config_path=config_path, report_type=report_type, logger=None\n",
")"
]
}
],
Expand Down
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