reorganization of content to focus on a smaller number of categories

IUPAC · Jan 16, 2024 · 0b09fa4 · 0b09fa4
1 parent c30daa0
commit 0b09fa4
Show file tree

Hide file tree

Showing 28 changed files with 29 additions and 37 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,9 +1,9 @@
 .idea
 .DS_Store
 book/_build
-book/recipes/hiddensettings.py
+book/manipulations/hiddensettings.py
 book/howtos/inchikeys.md
 book/.DS_Store
 Pipfile.lock
-book/ingredients/conformer1.txt
-book/ingredients/conformer2.txt
+book/datasources/conformer1.txt
+book/datasources/conformer2.txt
diff --git a/book/_toc.yml b/book/_toc.yml
@@ -8,48 +8,39 @@ parts:
     chapters:
     - file: about_cookbook
       title: About this Cookbook
-      sections:
-        - file: iupacfair
+    - file: use_cookbook
     - file: contributions
     - file: feedback
   - caption: The FAIR Chemistry Cookbook
     chapters:
     - file: cooking
       title: The Joy of Cooking
     - file: techniques
-      title: Cooking Techniques
+      title: FAIR Techniques
       sections:
         - glob: techniques/*
-    - file: utensils
-      title: Utensils to Use
+    - file: tools
+      title: Tools & Web Services
       sections:
-        - glob: utensils/*
-    - file: ingredients
-      title: Finding Ingredients
+        - glob: tools/*
+    - file: data_sources
+      title: Data Sources
       sections:
-        - glob: ingredients/[!pubchem]*
-        - file: ingredients/pubchem
-        - file: ingredients/pubchem_pugrest
+        - glob: datasources/[!pubchem]*
+        - file: datasources/pubchem
+        - file: datasources/pubchem_pugrest
           sections:
-            - file: ingredients/pubchem_pugrest1
-            - file: ingredients/pubchem_pugrest2
-            - file: ingredients/pubchem_pugrest3
-    - file: recipes
-      title: Data Recipes
-      sections:
-        - glob: recipes/*
-    - file: menus
-      title: FAIR Menus
-      sections:
-        - glob: menus/*
-    - file: school
-      title: Culinary School
+            - file: datasources/pubchem_pugrest1
+            - file: datasources/pubchem_pugrest2
+            - file: datasources/pubchem_pugrest3
+    - file: manipulations
+      title: Data Manipulations
       sections:
-        - glob: school/*
-    - file: plating
-      title: Data Plating
+        - glob: manipulations/*
+    - file: usecases
+      title: Use Cases & Workflows
       sections:
-        - glob: standards/*
+        - glob: usecases/*
   - caption: Reference
     chapters:
       - file: about_project

diff --git a/book/cooking.md b/book/cooking.md
@@ -1,3 +1,3 @@
-# Cooking up FAIR Chemical Data
+# The Joy of Cooking (FAIR data)
 
 Add more content
diff --git a/book/ingredients.md → book/data_sources.md b/book/ingredients.md → book/data_sources.md
@@ -1,5 +1,4 @@
-> **This is an outline of the section. Detailed content is coming soon.** 
-# Data standards and formats for Chemistry
+# Sources of FAIR Chemical Data
 
 This section will provide descriptions of standard notation and file formats available for sharing and reusing chemical data that are referred to in recipes throughout this book. 
 

diff --git a/book/ingredients/commonchem.md → book/datasources/commonchem.md b/book/ingredients/commonchem.md → book/datasources/commonchem.md
diff --git a/book/ingredients/figshare.md → book/datasources/figshare.md b/book/ingredients/figshare.md → book/datasources/figshare.md
diff --git a/book/recipes/goldbook_api.ipynb → book/datasources/goldbook_api.ipynb b/book/recipes/goldbook_api.ipynb → book/datasources/goldbook_api.ipynb
diff --git a/book/ingredients/pubchem.md → book/datasources/pubchem.md b/book/ingredients/pubchem.md → book/datasources/pubchem.md
diff --git a/book/ingredients/pubchem_pugrest.md → book/datasources/pubchem_pugrest.md b/book/ingredients/pubchem_pugrest.md → book/datasources/pubchem_pugrest.md
diff --git a/book/ingredients/pubchem_pugrest1.ipynb → book/datasources/pubchem_pugrest1.ipynb b/book/ingredients/pubchem_pugrest1.ipynb → book/datasources/pubchem_pugrest1.ipynb
diff --git a/book/ingredients/pubchem_pugrest2.ipynb → book/datasources/pubchem_pugrest2.ipynb b/book/ingredients/pubchem_pugrest2.ipynb → book/datasources/pubchem_pugrest2.ipynb
diff --git a/book/ingredients/pubchem_pugrest3.ipynb → book/datasources/pubchem_pugrest3.ipynb b/book/ingredients/pubchem_pugrest3.ipynb → book/datasources/pubchem_pugrest3.ipynb
diff --git a/book/ingredients/zenodo.md → book/datasources/zenodo.md b/book/ingredients/zenodo.md → book/datasources/zenodo.md
diff --git a/book/feedback.md b/book/feedback.md
@@ -1,4 +1,4 @@
-# Help Us! Provide Feedback
+# Feedback on the Cookbook
 
 Please review the book content, provide feedback and share your ideas for additional contributions. 
 * [Questionnaire](https://forms.gle/mnPiXpnWwf7928wi9) 

diff --git a/book/recipes.md → book/manipulations.md b/book/recipes.md → book/manipulations.md
diff --git a/book/recipes/computing_inchis.ipynb → book/manipulations/computing_inchis.ipynb b/book/recipes/computing_inchis.ipynb → book/manipulations/computing_inchis.ipynb
diff --git a/book/techniques/dataset_search.ipynb → book/manipulations/dataset_search.ipynb b/book/techniques/dataset_search.ipynb → book/manipulations/dataset_search.ipynb
diff --git a/book/school/excel_import.md → book/manipulations/excel_import.md b/book/school/excel_import.md → book/manipulations/excel_import.md
diff --git a/book/school/gsheets_citations.md → book/manipulations/gsheets_citations.md b/book/school/gsheets_citations.md → book/manipulations/gsheets_citations.md
diff --git a/book/standards/std_learn_spectra.md b/book/standards/std_learn_spectra.md
@@ -65,7 +65,7 @@ More on this approach can be found at [Preparing Chemical Data for FAIR Sharing
 
 Associated data is critical for reusing spectral data sets. Guidance on this is offered in the reports of the 
 [FAIRSpec IUPAC project](https://iupac.org/project/2019-031-1-024/). Some details are also included in 
-[Creating a UV/Vis (meta)data file structure for small molecule characterisation](../recipes/uvvis_metadata.ipynb).
+[Creating a UV/Vis (meta)data file structure for small molecule characterisation](../usecases/uvvis_metadata.ipynb).
 
 It is always important to include
 

diff --git a/book/techniques.md b/book/techniques.md
@@ -1,3 +1,3 @@
-# FAIR Chemistry Cooking Techniques
+# FAIR Techniques for Chemical Data
 
 Add more content
diff --git a/book/utensils.md → book/tools.md b/book/utensils.md → book/tools.md
diff --git a/book/recipes/opsin_api.ipynb → book/tools/opsin_api.ipynb b/book/recipes/opsin_api.ipynb → book/tools/opsin_api.ipynb
diff --git a/book/utensils/opsin_api.md → book/tools/opsin_api.md b/book/utensils/opsin_api.md → book/tools/opsin_api.md
diff --git a/book/use_cookbook.md b/book/use_cookbook.md
@@ -0,0 +1,2 @@
+# How to use the Cookbook
+
diff --git a/book/menus/iupac_pkadata.ipynb → book/usecases/iupac_pkadata.ipynb b/book/menus/iupac_pkadata.ipynb → book/usecases/iupac_pkadata.ipynb
diff --git a/book/recipes/uvvis_metadata.ipynb → book/usecases/uvvis_metadata.ipynb b/book/recipes/uvvis_metadata.ipynb → book/usecases/uvvis_metadata.ipynb
diff --git a/book/recipes/uvvis_metadata_fig.png → book/usecases/uvvis_metadata_fig.png b/book/recipes/uvvis_metadata_fig.png → book/usecases/uvvis_metadata_fig.png