From ae93e6b30d9ed832f3f54144b52de06dafa633f9 Mon Sep 17 00:00:00 2001 From: "samira.vandenbogaard" Date: Mon, 16 Dec 2024 12:10:04 +0100 Subject: [PATCH] bugfixes --- docs/{docs => }/PAM_setup_guide.md | 0 docs/{docs => }/PAModelpy_UML.svg | 0 docs/{docs => }/api.rst | 0 docs/{docs => }/api_reference/CatalyticEvent.md | 0 docs/{docs => }/api_reference/Constraints.md | 0 docs/{docs => }/api_reference/Enzyme.md | 0 docs/{docs => }/api_reference/EnzymeSectors.md | 0 docs/{docs => }/api_reference/PAMValidator.md | 0 docs/{docs => }/api_reference/PAModel.md | 0 docs/{docs => }/api_reference/_category_.json | 0 docs/{docs => }/api_reference/configuration.md | 0 docs/{docs => }/api_reference/sidebar.json | 0 docs/conf.py | 4 ---- docs/{docs => }/example.md | 2 +- docs/{docs => }/index.rst | 0 docs/{docs => }/introduction.md | 0 16 files changed, 1 insertion(+), 5 deletions(-) rename docs/{docs => }/PAM_setup_guide.md (100%) rename docs/{docs => }/PAModelpy_UML.svg (100%) rename docs/{docs => }/api.rst (100%) rename docs/{docs => }/api_reference/CatalyticEvent.md (100%) rename docs/{docs => }/api_reference/Constraints.md (100%) rename docs/{docs => }/api_reference/Enzyme.md (100%) rename docs/{docs => }/api_reference/EnzymeSectors.md (100%) rename docs/{docs => }/api_reference/PAMValidator.md (100%) rename docs/{docs => }/api_reference/PAModel.md (100%) rename docs/{docs => }/api_reference/_category_.json (100%) rename docs/{docs => }/api_reference/configuration.md (100%) rename docs/{docs => }/api_reference/sidebar.json (100%) rename docs/{docs => }/example.md (99%) rename docs/{docs => }/index.rst (100%) rename docs/{docs => }/introduction.md (100%) diff --git a/docs/docs/PAM_setup_guide.md b/docs/PAM_setup_guide.md similarity index 100% rename from docs/docs/PAM_setup_guide.md rename to docs/PAM_setup_guide.md diff --git a/docs/docs/PAModelpy_UML.svg b/docs/PAModelpy_UML.svg similarity index 100% rename from docs/docs/PAModelpy_UML.svg rename to docs/PAModelpy_UML.svg diff --git a/docs/docs/api.rst b/docs/api.rst similarity index 100% rename from docs/docs/api.rst rename to docs/api.rst diff --git a/docs/docs/api_reference/CatalyticEvent.md b/docs/api_reference/CatalyticEvent.md similarity index 100% rename from docs/docs/api_reference/CatalyticEvent.md rename to docs/api_reference/CatalyticEvent.md diff --git a/docs/docs/api_reference/Constraints.md b/docs/api_reference/Constraints.md similarity index 100% rename from docs/docs/api_reference/Constraints.md rename to docs/api_reference/Constraints.md diff --git a/docs/docs/api_reference/Enzyme.md b/docs/api_reference/Enzyme.md similarity index 100% rename from docs/docs/api_reference/Enzyme.md rename to docs/api_reference/Enzyme.md diff --git a/docs/docs/api_reference/EnzymeSectors.md b/docs/api_reference/EnzymeSectors.md similarity index 100% rename from docs/docs/api_reference/EnzymeSectors.md rename to docs/api_reference/EnzymeSectors.md diff --git a/docs/docs/api_reference/PAMValidator.md b/docs/api_reference/PAMValidator.md similarity index 100% rename from docs/docs/api_reference/PAMValidator.md rename to docs/api_reference/PAMValidator.md diff --git a/docs/docs/api_reference/PAModel.md b/docs/api_reference/PAModel.md similarity index 100% rename from docs/docs/api_reference/PAModel.md rename to docs/api_reference/PAModel.md diff --git a/docs/docs/api_reference/_category_.json b/docs/api_reference/_category_.json similarity index 100% rename from docs/docs/api_reference/_category_.json rename to docs/api_reference/_category_.json diff --git a/docs/docs/api_reference/configuration.md b/docs/api_reference/configuration.md similarity index 100% rename from docs/docs/api_reference/configuration.md rename to docs/api_reference/configuration.md diff --git a/docs/docs/api_reference/sidebar.json b/docs/api_reference/sidebar.json similarity index 100% rename from docs/docs/api_reference/sidebar.json rename to docs/api_reference/sidebar.json diff --git a/docs/conf.py b/docs/conf.py index 9672235..6331342 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,7 +1,3 @@ -# Configuration file for the Sphinx documentation builder. -import os -import sys -sys.path.insert(0, os.path.abspath('../docs/docs')) # Adjust the path to where your documentation files are # Set the source directory for your Sphinx documentation files source_suffix = ['.rst', '.md'] # If using Markdown files with MyST diff --git a/docs/docs/example.md b/docs/example.md similarity index 99% rename from docs/docs/example.md rename to docs/example.md index 9f3f6dd..9cf1d54 100644 --- a/docs/docs/example.md +++ b/docs/example.md @@ -238,7 +238,7 @@ sensitivities can help us explain concepts of protein allocation.
-![toy_model_image](./assets/toy-model.png) +![toy_model_image](assetsoy-model.png)
**Figure 1. Toy model network and parameters** *This toy model represents a schematic overview of a microbial metabolism, diff --git a/docs/docs/index.rst b/docs/index.rst similarity index 100% rename from docs/docs/index.rst rename to docs/index.rst diff --git a/docs/docs/introduction.md b/docs/introduction.md similarity index 100% rename from docs/docs/introduction.md rename to docs/introduction.md