Merge branch 'develop' into options_docs to prepare for merging to de…

…velop
biosustain · Feb 2, 2024 · f2741f6 · f2741f6
2 parents 0683401 + 8d1e08b
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diff --git a/docs/atom_mapping_example_notebook.ipynb b/docs/atom_mapping_example_notebook.ipynb
diff --git a/docs/conf.py b/docs/conf.py
@@ -8,12 +8,12 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'incawrapper'
-copyright = '2021, Biosustain'
-author = 'Biosustain'
+project = "incawrapper"
+copyright = "2021, Biosustain"
+author = "Biosustain"
 
 # The full version, including alpha/beta/rc tags
-release = '0.0.1'
+release = "0.0.1"
 
 
 # -- General configuration ---------------------------------------------------
@@ -25,10 +25,10 @@
     "sphinx.ext.intersphinx",
     "numpydoc",
     "nbsphinx",
-    #"autoapi.extension"
+    "autoapi.extension",
 ]
-templates_path = ['_templates']
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 autosummary_generate = True
 numpydoc_show_class_members = False
 
@@ -42,15 +42,13 @@
 # -- Options for HTML output -------------------------------------------------
 
 html_title = "incawrapper"
-html_theme = 'sphinx_material'
+html_theme = "sphinx_material"
 html_theme_options = {
     "repo_url": "https://github.com/biosustain/incawrapper",
     "repo_name": "incawrapper",
     "color_primary": "indigo",
     "color_accent": "pink",
-    "globaltoc_depth": 3
-}
-html_sidebars = {
-    "**": ["globaltoc.html", "localtoc.html"]
+    "globaltoc_depth": 3,
 }
+html_sidebars = {"**": ["globaltoc.html", "localtoc.html"]}
 html_collapsible_definitions = True
diff --git a/...examples/Literature data/Astrocytes and neural stem cells/11064_2016_1907_MOESM1_ESM.docx b/...examples/Literature data/Astrocytes and neural stem cells/11064_2016_1907_MOESM1_ESM.docx
diff --git a/docs/examples/Literature data/Astrocytes and neural stem cells/MDVs.csv b/docs/examples/Literature data/Astrocytes and neural stem cells/MDVs.csv
diff --git a/docs/examples/Literature data/Astrocytes and neural stem cells/MDVs.xlsx b/docs/examples/Literature data/Astrocytes and neural stem cells/MDVs.xlsx
diff --git a/docs/examples/Literature data/Astrocytes and neural stem cells/Model.xlsx b/docs/examples/Literature data/Astrocytes and neural stem cells/Model.xlsx
diff --git a/...xamples/Literature data/Astrocytes and neural stem cells/Neural_Stem_Cells_estimation.mat b/...xamples/Literature data/Astrocytes and neural stem cells/Neural_Stem_Cells_estimation.mat
diff --git a/docs/examples/Literature data/Astrocytes and neural stem cells/astrocytes_estimation.mat b/docs/examples/Literature data/Astrocytes and neural stem cells/astrocytes_estimation.mat
diff --git a/docs/examples/Literature data/Astrocytes and neural stem cells/exchange_fluxes.csv b/docs/examples/Literature data/Astrocytes and neural stem cells/exchange_fluxes.csv
diff --git a/docs/examples/Literature data/E. coli - Antoniewicz 2015/1-s2.0-S1096717615000038-mmc1.xlsx b/docs/examples/Literature data/E. coli - Antoniewicz 2015/1-s2.0-S1096717615000038-mmc1.xlsx
diff --git a/docs/examples/Literature data/E. coli - Antoniewicz 2015/1-s2.0-S1096717615000038-mmc2.docx b/docs/examples/Literature data/E. coli - Antoniewicz 2015/1-s2.0-S1096717615000038-mmc2.docx
diff --git a/docs/examples/Literature data/E. coli - Antoniewicz 2015/Biomass and glucose.xlsx b/docs/examples/Literature data/E. coli - Antoniewicz 2015/Biomass and glucose.xlsx
diff --git a/docs/examples/Literature data/E. coli - Antoniewicz 2015/MDV.xlsx b/docs/examples/Literature data/E. coli - Antoniewicz 2015/MDV.xlsx
diff --git a/docs/examples/Literature data/E. coli - Antoniewicz 2015/MDV_mod.csv b/docs/examples/Literature data/E. coli - Antoniewicz 2015/MDV_mod.csv
diff --git a/docs/examples/Literature data/E. coli - Antoniewicz 2015/Model.docx b/docs/examples/Literature data/E. coli - Antoniewicz 2015/Model.docx
diff --git a/docs/examples/Literature data/E. coli - Antoniewicz 2015/Model.xlsx b/docs/examples/Literature data/E. coli - Antoniewicz 2015/Model.xlsx
diff --git a/docs/examples/Literature data/Pichia pastoris Jorda 2015/1475-2859-11-57-S1.doc b/docs/examples/Literature data/Pichia pastoris Jorda 2015/1475-2859-11-57-S1.doc
diff --git a/docs/examples/Literature data/Pichia pastoris Jorda 2015/1475-2859-11-57-S3.ppt b/docs/examples/Literature data/Pichia pastoris Jorda 2015/1475-2859-11-57-S3.ppt
diff --git a/docs/examples/Literature data/Pichia pastoris Jorda 2015/1475-2859-11-57-S4.doc b/docs/examples/Literature data/Pichia pastoris Jorda 2015/1475-2859-11-57-S4.doc
diff --git a/docs/examples/Literature data/Pichia pastoris Jorda 2015/Atom Map by the same peepz.docx b/docs/examples/Literature data/Pichia pastoris Jorda 2015/Atom Map by the same peepz.docx
diff --git a/docs/examples/Literature data/Pichia pastoris Jorda 2015/MDV.doc b/docs/examples/Literature data/Pichia pastoris Jorda 2015/MDV.doc
diff --git a/docs/examples/Literature data/Pichia pastoris Jorda 2015/metabolic_model_Pichia.xlsx b/docs/examples/Literature data/Pichia pastoris Jorda 2015/metabolic_model_Pichia.xlsx
diff --git a/docs/index.rst b/docs/index.rst
@@ -37,13 +37,12 @@ Overview of the documentation
    input_data
    multiple_experiments
    monte_carlo_sampling
-   atom_mapping_example_notebook
    incawrapper_and_the_incagui
    options
    Low_level_api
    examples/index
    developer/index
-   API <./autoapi/index.rst> 
+   API </autoapi/incawrapper/index.rst> 
 
 
 References

diff --git a/incawrapper/atommapping/__init__.py b/incawrapper/atommapping/__init__.py