fixing links

flatironinstitute · Dec 4, 2024 · 44e61cc · 44e61cc
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diff --git a/docs/background/basis/README.md b/docs/background/basis/README.md
@@ -19,44 +19,44 @@
    * - **B-Spline**
      - .. plot:: scripts/basis_table_figs.py plot_bspline
           :show-source-link: False
-     - `Grid cells <grid_cells_nemos>`_
-     - `EvalBSpline <nemos.basis.basis.EvalBSpline>`_ :raw-html:`<br />`
-       `BSplineConv <nemos.basis.basis.BSplineConv>`_
+     - :ref:`Grid cells <grid_cells_nemos>`
+     - :class:`~nemos.basis.BSplineEval` :raw-html:`<br />`
+       :class:`~nemos.basis.BSplineConv`
      - 🟢 Eval
    * - **Cyclic B-Spline**
      - .. plot:: scripts/basis_table_figs.py plot_cyclic_bspline
           :show-source-link: False
-     - `Place cells <basis_eval_place_cells>`_
-     - `EvalCyclicBSpline <nemos.basis.basis.EvalCyclicBSpline>`_  :raw-html:`<br />`
-       `ConvCyclicBSpline <nemos.basis.basis.ConvCyclicBSpline>`_
+     - :ref:`Place cells <basis_eval_place_cells>`
+     - :class:`~nemos.basis.CyclicBSplineEval`  :raw-html:`<br />`
+       :class:`~nemos.basis.CyclicBSplineConv`
      - 🟢 Eval
    * - **M-Spline**
      - .. plot:: scripts/basis_table_figs.py plot_mspline
           :show-source-link: False
-     - `Place cells <basis_eval_place_cells>`_
-     - `EvalMSpline <nemos.basis.basis.EvalMSpline>`_  :raw-html:`<br />`
-       `ConvMSpline <nemos.basis.basis.ConvMSpline>`_
+     - :ref:`Place cells <basis_eval_place_cells>`
+     - :class:`~nemos.basis.MSplineEval`  :raw-html:`<br />`
+       :class:`~nemos.basis.MSplineConv`
      - 🟢 Eval
    * - **Linearly Spaced Raised Cosine**
      - .. plot:: scripts/basis_table_figs.py plot_raised_cosine_linear
           :show-source-link: False
      - 
-     - `EvalRaisedCosineLinear <nemos.basis.basis.EvalRaisedCosineLinear>`_  :raw-html:`<br />`
-       `ConvRaisedCosineLinear <nemos.basis.basis.ConvRaisedCosineLinear>`_
+     - :class:`~nemos.basis.RaisedCosineLinearEval`  :raw-html:`<br />`
+       :class:`~nemos.basis.RaisedCosineLinearConv`
      - 🟢 Eval
    * - **Log Spaced Raised Cosine**
      - .. plot:: scripts/basis_table_figs.py plot_raised_cosine_log
           :show-source-link: False
-     - `Head Direction <head_direction_reducing_dimensionality>`_
-     - `EvalRaisedCosineLog <nemos.basis.basis.EvalRaisedCosineLog>`_  :raw-html:`<br />`
-       `ConvRaisedCosineLog <nemos.basis.basis.ConvRaisedCosineLog>`_
+     - :ref:`Head Direction <head_direction_reducing_dimensionality>`
+     - :class:`~nemos.basis.RaisedCosineLogEval`  :raw-html:`<br />`
+       :class:`nemos.basis.RaisedCosineLogConv`
      - 🔵 Conv
    * - **Orthogonalized Exponential Decays**
      - .. plot:: scripts/basis_table_figs.py plot_orth_exp_basis
           :show-source-link: False
      - 
-     - `EvalOrthExponential <nemos.basis.basis.EvalOrthExponential>`_  :raw-html:`<br />`
-       `ConvOrthExponential <nemos.basis.basis.ConvOrthExponential>`_
+     - :class:`~nemos.basis.OrthExponentialEval`  :raw-html:`<br />`
+       :class:`~nemos.basis.OrthExponentialConv`
      - 🟢 Eval
 ```
 

diff --git a/docs/background/basis/plot_01_1D_basis_function.md b/docs/background/basis/plot_01_1D_basis_function.md
@@ -156,7 +156,7 @@ Convolution is performed in "valid" mode, and then NaN-padded. The default behav
 is padding left, which makes the output feature causal.
 This is why the first half of the `conv_feature` is full of NaNs and appears as white.
 If you want to learn more about convolutions, as well as how and when to change defaults
-check out the tutorial on [1D convolutions](plot_03_1D_convolution).
+check out the tutorial on [1D convolutions](convolution_background).
 :::
 
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -123,7 +123,11 @@
     "logo": {
       "image_light": "_static/NeMoS_Logo_CMYK_Full.svg",
       "image_dark": "_static/NeMoS_Logo_CMYK_White.svg",
-   }
+   },
+    "secondary_sidebar_items": {
+        "**": ["page-toc", "sourcelink"],
+        "background/basis/README": [],
+    },
 }
 
 html_sidebars = {

diff --git a/docs/scripts/basis_table_figs.py b/docs/scripts/basis_table_figs.py
@@ -24,7 +24,7 @@ def plot_basis(cls):
     cls_params = cls._get_param_names()
     new_kwargs = trim_kwargs(cls, KWARGS.copy(), {cls.__name__: cls_params})
     bas = cls(**new_kwargs)
-    fig, ax = plt.subplots(1, 1, figsize=(5, 2.5))
+    fig, ax = plt.subplots(1, 1, figsize=(5/4, 2.5/4))
     ax.plot(*bas.evaluate_on_grid(300), lw=4)
     for side in ["left", "right", "top", "bottom"]:
         ax.spines[side].set_visible(False)