Fixing doc ophelie

docs/generate_api_reference.sh

@@ -1,12 +1,4 @@
-#/usr/bin/env bash
-set -e
-
 pip install pdoc3
-rm -rf docs/docs/resources
-pdoc --template-dir docs/pdoc_template -o docs/docs/resources client/src/bastionlab
-sed -i '/<p>Generated by <a href="https:\/\/pdoc3.github.io\/pdoc" title="pdoc: Python API documentation generator"><cite>pdoc<\/cite> 0.10.0<\/a>.<\/p>/d' docs/docs/resources/bastionlab/*.md docs/docs/resources/bastionlab/*/*.md
-
-# Fix broken links in the generated documentation
-bash docs/fix_links.sh
-# Generate the structure of the documentation for mkdocs.yml file
-python3 docs/docs/gen_ref_pages.py
+rm -rf docs/resources
+pdoc --html --skip-errors --template-dir docs/pdoc_template -o docs/docs/resources client/src/bastionlab
+sed -i '/<p>Generated by <a href="https:\/\/pdoc3.github.io\/pdoc" title="pdoc: Python API documentation generator"><cite>pdoc<\/cite> 0.10.0<\/a>.<\/p>/d' docs/docs/resources/bastionlab/*.html docs/docs/resources/bastionlab/*/*.html

docs/index.md

@@ -48,7 +48,7 @@ ____________________________________________
 
 - [Concepts](docs/concepts-guides/remote_data_science.md) guides discuss key topics and concepts at a high level. They provide useful background information and explanations, especially on cybersecurity.
 
-- [API Reference](docs/resources/bastionlab/index.md) contains technical references for BastionLab’s API machinery. They describe how it works and how to use it but assume you have a good understanding of key concepts. 
+- [API Reference](docs/resources/bastionlab/index.html) contains technical references for BastionLab’s API machinery. They describe how it works and how to use it but assume you have a good understanding of key concepts. 
 
 - [Security](docs/security/threat_model_data_owner_owns_infrastructure.md) guides contain technical information for security engineers. They explain the threat models and other cybersecurity topics required to audit BastionLab's security standards.
 

mkdocs.yml

@@ -20,7 +20,7 @@ theme:
     - content.tabs.link
     - navigation.sections
     - navigation.indexes
-    # - navigation.expand
+    - navigation.expand
   logo: assets/logo.png
   favicon: assets/logo.png
   palette:
@@ -49,10 +49,6 @@ theme:
 plugins:
   - search
   - mkdocs-jupyter
-  # - gen-files:
-  #   scripts:
-  #     - docs/gen_ref_pages.py
-  # - mkdocstrings
 
 # Customization
 extra:
@@ -72,7 +68,6 @@ extra_css:
 
 extra_javascript:
   - "https://code.jquery.com/jquery-3.3.1.min.js"
-  - javascripts/navbar.js
 
 # Extensions
 markdown_extensions:
@@ -100,36 +95,35 @@ markdown_extensions:
 
 # Documentation tree
 nav:
-  - 🏠 Home: "index.md"
-  - 🚀 Getting started:
-      - Quick tour: "docs/quick-tour/quick-tour.ipynb"
-      - Installation: "docs/getting-started/installation.md"
-  - 📙 Tutorials:
-      - Authentication: "docs/tutorials/authentication.ipynb"
-      - Defining a privacy policy: "docs/tutorials/defining_policy_privacy.ipynb"
-      - Combining datasets: "docs/tutorials/combining_datasets.ipynb"
-      - Data cleaning: "docs/tutorials/data_cleaning.ipynb"
-      - SQL queries: "docs/tutorials/SQL_queries.ipynb"
-      - Data visualization: "docs/tutorials/visualization.ipynb"
-      - Saving DataFrames: "docs/tutorials/saving_dataframes.ipynb"
-      - Normalization: "docs/tutorials/normalization.ipynb"
-  - 🌍 How-to-guides:
-      - Data exploration:
-        - Covid-19 data analysis: "docs/how-to-guides/covid_cleaning_exploration.ipynb"
-        - Fraud detection data analysis: "docs/how-to-guides/fraud_detection.ipynb"
-      - Deep learning:
-          - Fine Tuning DistilBERT: "docs/how-to-guides/distilbert_example_notebook.ipynb"
-  - 💡 Concepts:
-      - Remote data science: "docs/concepts-guides/remote_data_science.md"
-  - 🛠️ API Reference:
-      - Sub-modules:
-  - 🔒 Security:
-      - Threat model: "docs/security/threat_model_data_owner_owns_infrastructure.md"
-      - Authentication specifications: "docs/security/authenticated_sessions.md"
-  - ⚙️ Advanced:
-      - Benchmarks:
-          - Polars: "docs/advanced/benchmarks/polars_benchmarks.md"
-          - Torch: "docs/advanced/benchmarks/torch_benchmarks.md"
-      - Open source:
-          - Contributing: "docs/advanced/contributing/contributing.md"
-          - Code of Conduct: "docs/advanced/contributing/code_of_conduct.md"
+- 🏠 Home: "index.md"
+- 🚀 Getting started:
+  - Quick tour: "docs/quick-tour/quick-tour.ipynb"
+  - Installation: "docs/getting-started/installation.md"
+- 📙 Tutorials:
+  - Authentication: "docs/tutorials/authentication.ipynb"
+  - Defining a privacy policy: "docs/tutorials/defining_policy_privacy.ipynb"
+  - Combining datasets: "docs/tutorials/combining_datasets.ipynb"
+  - Data cleaning: "docs/tutorials/data_cleaning.ipynb"
+  - SQL queries: "docs/tutorials/SQL_queries.ipynb"
+  - Data visualization: "docs/tutorials/visualization.ipynb"
+  - Saving DataFrames: "docs/tutorials/saving_dataframes.ipynb"
+  - Normalization: "docs/tutorials/normalization.ipynb"
+- 🌍 How-to-guides:
+  - Data exploration:
+    - Covid-19 data analysis: "docs/how-to-guides/covid_cleaning_exploration.ipynb"
+    - Fraud detection data analysis: "docs/how-to-guides/fraud_detection.ipynb"
+  - Deep learning:
+    - Fine Tuning DistilBERT: "docs/how-to-guides/distilbert_example_notebook.ipynb"
+- 💡 Concepts:
+  - Remote data science: "docs/concepts-guides/remote_data_science.md"
+- 🛠️ API Reference: "docs/resources/bastionlab/index.html"
+- 🔒 Security:
+  - Threat model: "docs/security/threat_model_data_owner_owns_infrastructure.md"
+  - Authentication specifications: "docs/security/authenticated_sessions.md"
+- ⚙️ Advanced:
+  - Benchmarks:
+    - Polars: "docs/advanced/benchmarks/polars_benchmarks.md"
+    - Torch: "docs/advanced/benchmarks/torch_benchmarks.md"
+  - Open source:
+    - Contributing: "docs/advanced/contributing/contributing.md"
+    - Code of Conduct: "docs/advanced/contributing/code_of_conduct.md"