Update docs and workflow

NsquaredLab · Sep 11, 2024 · 00e5704 · 00e5704
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diff --git a/.github/workflows/sphinx.yml b/.github/workflows/sphinx.yml
@@ -22,7 +22,8 @@ jobs:
         sudo apt-get install -y libegl1-mesa libgl1-mesa-glx
         python -m pip install --upgrade pip
         python -m pip install poetry
-        poetry install -E cpu --with docs
+        poetry install --with docs
+        pip install torch torchvision --upgrade
 
     - name: Build the docs
       run: |

diff --git a/README.md b/README.md
@@ -11,31 +11,14 @@ DocOctopy , the **research** library for kinematics, kinetics, and everything el
 > **Important**  
 > Be aware that this project is used for **research**. Do not expect the same stability as from numpy for example.
 
-## What papers use this package?
-<p float="left">
-  <a href="https://doi.org/10.1109/TBME.2024.3432800" target="_blank"> <img src="docs/source/_static/papers/Learning.jpg" width="31%" /> </a>
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-  <a href="https://doi.org/10.33965/ijcsis_2024190101" target="_blank"> <img src="docs/source/_static/papers/Analysis.jpg" width="28.4%" /> </a>
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-  <a href="https://doi.org/10.1101/2024.05.28.24307964" target="_blank"> <img src="docs/source/_static/papers/Identification.jpg" width="31%" /> </a>
-</p>
-
-<p float="left">
-<a href="https://doi.org/10/gtm4bt" target="_blank"> <img src="docs/source/_static/papers/Influence.jpg" width="28.4%" /> </a>
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-  <a href="https://doi.org/10/gsgk4s" target="_blank"> <img src="docs/source/_static/papers/Proportional.jpg" width="31%" /> </a>
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-  <a href="https://doi.org/10/gq2f47" target="_blank"> <img src="docs/source/_static/papers/Accurate.jpg" width="31%" /> </a>
-</p>
-
 ## How to install?
 > **WARNING**   
 > Order matters!
 - clone
 - install [poetry](https://python-poetry.org/docs/#installation)
 - based on your hardware:
-  - GPU (NVIDIA): `poetry install
-  - CPU: run `pip install torch torchvision` after `poetry install`
+  - GPU (NVIDIA): `poetry install`
+  - CPU: run `pip install torch torchvision --upgrade` after `poetry install`
 - for building the documentation add `docs` to the *with* flag: `poetry install --with docs`
 
 ## What is what?
@@ -46,4 +29,14 @@ This projects uses the following structure:
   - utils: Various utilities from training loggers to constants.
 - docs: Contains the documentation.
 - examples: Contains examples on how to use the package.
-- tests: Contains tests for the package.
+- tests: Contains tests for the package.
+
+## What papers/preprints use this package?
+| Journal / Preprint Server                                                                              | DOI                                                                              |
+|--------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------|
+| IEEE Transactions on Biomedical Engineering                                                            | [10.1109/TBME.2024.3432800](https://doi.org/10.1109/TBME.2024.3432800)           |
+| International Journal of Computer Science and Information Security                                     | [10.33965/ijcsis_2024190101](https://doi.org/10.33965/ijcsis_2024190101)         |
+| medRxiv                                                                                                | [10.1101/2024.05.28.24307964](https://doi.org/10.1101/2024.05.28.24307964)       |
+| Journal of Neural Engineering                                                                          | [10.1088/1741-2552/ad3498](https://doi.org/10.1088/1741-2552/ad3498)                            |
+| IEEE Transactions on Neural Systems and Rehabilitation Engineering                                     | [10.1109/TNSRE.2023.3295060](https://doi.org/10.1109/TNSRE.2023.3295060)         |
+| 2022 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC) | [10.1109/EMBC48229.2022.9870937](https://doi.org/10.1109/EMBC48229.2022.9870937) |
diff --git a/docs/source/README.md b/docs/source/README.md
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -33,7 +33,32 @@
 with (HERE.parent.parent / "README.md").open() as f:
     out = f.read()
 
-out = out.replace("docs/source/", "")
+out = out.split("\n")
+
+# find the index of the line that contains "## What papers/preprints use this package?"
+idx = out.index("## What papers/preprints use this package?")
+# remove everything after that line
+out = out[: idx + 1]
+
+to_add = """<p float="middle">
+  <a href="https://doi.org/10.1109/TBME.2024.3432800" target="_blank"> <img src="_static/papers/Learning.jpg" width="31%" /> </a>
+  &nbsp;
+  <a href="https://doi.org/10.33965/ijcsis_2024190101" target="_blank"> <img src="_static/papers/Analysis.jpg" width="28.4%" /> </a>
+  &nbsp;
+  <a href="https://doi.org/10.1101/2024.05.28.24307964" target="_blank"> <img src="_static/papers/Identification.jpg" width="31%" /> </a>
+</p>
+
+<p float="middle">
+<a href="https://doi.org/10/gtm4bt" target="_blank"> <img src="_static/papers/Influence.jpg" width="28.4%" /> </a>
+  &nbsp;
+  <a href="https://doi.org/10/gsgk4s" target="_blank"> <img src="_static/papers/Proportional.jpg" width="31%" /> </a>
+  &nbsp
+  <a href="https://doi.org/10/gq2f47" target="_blank"> <img src="_static/papers/Accurate.jpg" width="31%" /> </a>
+</p>"""
+
+out.extend(to_add.split("\n"))
+
+out = "\n".join(out)
 
 with (HERE / "README.md").open("w+") as f:
     f.write(out)