Merge pull request #10 from kabilar/main

Fix docs

Author: kushalbakshi

CHANGELOG.md

@@ -3,6 +3,10 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.1.3] - 2023-05-12
+
++ Fix - Docs
+
 ## [0.1.2] - 2023-05-11
 
 + Fix - `.ipynb` dark mode output for all notebooks.
@@ -16,6 +20,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 
 + Add - Table structure and basic docs (changelog, contribution guidelines, etc.)
 
-[0.1.2](https://github.com/datajoint/element-optogenetics/releases/tag/0.1.2)
-[0.1.1](https://github.com/datajoint/element-optogenetics/releases/tag/0.1.1)
-[0.1.0](https://github.com/datajoint/element-optogenetics/releases/tag/0.1.0)
+[0.1.3]: https://github.com/datajoint/element-optogenetics/releases/tag/0.1.3
+[0.1.2]: https://github.com/datajoint/element-optogenetics/releases/tag/0.1.2
+[0.1.1]: https://github.com/datajoint/element-optogenetics/releases/tag/0.1.1
+[0.1.0]: https://github.com/datajoint/element-optogenetics/releases/tag/0.1.0

README.md

@@ -25,3 +25,7 @@ fully functional pipeline.
 + [Interactive tutorial on GitHub Codespaces](https://github.com/datajoint/workflow-optogenetics#interactive-tutorial)
 
 + [Documentation](https://datajoint.com/docs/elements/element-optogenetics)
+
+## Support
+
++ If you need help getting started or run into any errors, please contact our team by email at [email protected].

docs/.docker/pip_requirements.txt

@@ -8,4 +8,5 @@ mkdocs-gen-files
 mkdocs-literate-nav
 mkdocs-exclude-search
 mkdocs-markdownextradata-plugin
-mkdocs-jupyter
+mkdocs-jupyter
+mkdocs-section-index

docs/mkdocs.yaml

@@ -86,7 +86,6 @@ theme:
       toggle:
         icon: material/brightness-4
         name: Switch to light mode
-
 plugins:
   - markdownextradata: {}
   - search
@@ -109,7 +108,7 @@ plugins:
   - mkdocs-jupyter:
       ignore_h1_titles: True
       ignore: ["*make_pages.py"]
-
+  - section-index
 markdown_extensions:
   - attr_list
   - toc:

docs/src/api/make_pages.py

@@ -18,7 +18,7 @@
 for path in sorted(Path(package).glob("**/*.py")) + sorted(
     Path(f"workflow_{element}").glob("**/*.py")
 ):
-    if path.stem == "__init__":
+    if path.stem == "__init__" or path.stem == "version":
         continue
     with mkdocs_gen_files.open(f"api/{path.with_suffix('')}.md", "w") as f:
         module_path = ".".join(

docs/src/concepts.md

@@ -2,13 +2,11 @@
 
 ## Optogenetic Research
 
-The seminal 2005 paper[^1] by Karl Deisseroth and colleagues established a strategy for
+The seminal work by Karl Deisseroth and colleagues established a strategy for
 using light (*opto-*) to directly regulate the activation of genetically modified
-(*-genetics*) neurons. By incorporating genes from photosensitive algae, neurons become
-sensitive to different wavelengths for either excitation or inhibition.
-Scientists now use this technology to draw more direct
-causal links between the activity of neuronal populations and corresponding animal behavior.
-
-[^1]: Boyden, E. S., Zhang, F., Bamberg, E., Nagel, G., & Deisseroth, K. (2005).
-    [Millisecond-timescale, genetically targeted optical control of neural activity](https://www.nature.com/articles/nn1525).
-    Nature neuroscience, 8(9), 1263-1268.
+(*-genetics*) neurons 
+([Boyden et al., Nature Neuroscience 2005](https://doi.org/10.1038/nn1525){:target="_blank"}).
+By incorporating genes from photosensitive algae, neurons become sensitive to different 
+wavelengths for either excitation or inhibition. Scientists now use this technology to 
+draw more direct causal links between the activity of neuronal populations and 
+corresponding animal behavior.

docs/src/index.md

@@ -10,7 +10,7 @@ fully functional pipeline.
 
 ![flowchart](https://raw.githubusercontent.com/datajoint/element-optogenetics/main/images/flowchart.svg)
 
-## Data Pipeline
+## Data Pipeline Diagram
 
 ![pipeline](https://raw.githubusercontent.com/datajoint/element-optogenetics/main/images/pipeline.svg)
 
@@ -27,3 +27,7 @@ fully functional pipeline.
 + [Tutorials](./tutorials/index.md) - Start building your data pipeline
 
 + [Code Repository](https://github.com/datajoint/element-optogenetics/){:target="_blank"}
+
+## Support
+
++ If you need help getting started or run into any errors, please contact our team by email at [email protected].

docs/src/pipeline.md

@@ -7,7 +7,7 @@ documentation on each table, see the API docs for the respective schemas.
 
 ![pipeline](https://raw.githubusercontent.com/datajoint/element-optogenetics/main/images/pipeline.svg)
 
-## `reference` schema ([API docs](../api/workflow_Optogenetics/pipeline/#workflow_Optogenetics.reference.Device))
+## `reference` schema ([API docs](https://datajoint.com/docs/elements/element-optogenetics/latest/api/workflow_optogenetics/reference))
 
 | Table | Description |
 | --- | --- |
@@ -35,7 +35,7 @@ documentation on each table, see the API docs for the respective schemas.
 | --- | --- |
 | Session | Unique experimental session identifier |
 
-## `optogenetics` schema ([API docs](../api/element_optogenetics/optogenetics))
+## `optogenetics` schema ([API docs](https://datajoint.com/docs/elements/element-optogenetics/latest/api/element_optogenetics/optogenetics))
 
 | Table               | Description |
 | ---                 |   ---       |

docs/src/tutorials/index.md

@@ -1,10 +1,10 @@
 # Tutorials
 
-+ DataJoint Elements are modular pipelines that can be connected into a complete workflow.  [Workflow Optogenetics](https://github.com/datajoint/workflow-optogenetics)) is an example that combines four DataJoint Elements - Lab, Animal, Session, and Optogenetics.
++ DataJoint Elements are modular pipelines that can be connected into a complete workflow.  [Workflow Optogenetics](https://github.com/datajoint/workflow-optogenetics) is an example that combines four DataJoint Elements - Lab, Animal, Session, and Optogenetics.
 
 + Workflow Optogenetics includes an [interactive tutorial on GitHub Codespaces](https://github.com/datajoint/workflow-optogenetics#interactive-tutorial), which is configured for users to run the pipeline.
 
-+ In the interactive tutorial, the [example notebook](https://github.com/datajoint/workflow-optogenetics/tree/main/notebooks.tutorial.ipynb) describes the pipeline and provides instructions for adding data to the pipeline.
++ In the interactive tutorial, the [example notebook](https://github.com/datajoint/workflow-optogenetics/tree/main/notebooks/tutorial.ipynb) describes the pipeline and provides instructions for adding data to the pipeline.
 
 ## Installation Instructions for Active Projects
 

element_optogenetics/version.py

@@ -1,2 +1,2 @@
 """Package metadata"""
-__version__ = "0.1.2"
+__version__ = "0.1.3"