clean up for sepes 0.12 (#102)

ASEM000 · Apr 2, 2024 · d3b2389 · d3b2389
1 parent 533d390
commit d3b2389
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Showing 33 changed files with 614 additions and 1,142 deletions.
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -25,7 +25,6 @@ jobs:
       - name: Install dependencies
         run: |
           sudo apt-get update
-          sudo apt install graphviz graphviz-dev
           sudo apt install -y pandoc
           python -m pip install --upgrade pip
           pip install .

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -22,10 +22,10 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install sepes>=0.10.0
-          python -m pip install keras_nightly==3.0.0.dev2023110103
+          python -m pip install sepes>=0.12.0
+          python -m pip install keras>=0.3.0
           python -m pip install scikit-learn
-          python -m pip install pytest wheel optax jaxlib coverage kernex
+          python -m pip install pytest wheel optax jaxlib coverage
       - name: Pytest Check
         run: |
           python -m pip install .

diff --git a/docs/API/activations.rst b/docs/API/activations.rst
@@ -2,10 +2,6 @@ Activations
 ---------------------------------
 .. currentmodule:: serket.nn
 
-.. autoclass:: AdaptiveLeakyReLU
-.. autoclass:: AdaptiveReLU
-.. autoclass:: AdaptiveSigmoid
-.. autoclass:: AdaptiveTanh
 .. autoclass:: CeLU
 .. autoclass:: ELU
 .. autoclass:: GELU
@@ -28,7 +24,6 @@ Activations
 .. autoclass:: SoftSign
 .. autoclass:: SquarePlus
 .. autoclass:: Swish
-.. autoclass:: Snake
 .. autoclass:: Tanh
 .. autoclass:: TanhShrink
 .. autoclass:: ThresholdedReLU
diff --git a/docs/API/common.rst b/docs/API/common.rst
@@ -5,8 +5,6 @@
 
 .. autofunction:: tree_state
 .. autofunction:: tree_eval
-.. autofunction:: def_init_entry
-.. autofunction:: def_act_entry
 
 .. autoclass:: Sequential
 .. autoclass:: RandomChoice
diff --git a/docs/API/constructor.rst b/docs/API/constructor.rst
@@ -0,0 +1,10 @@
+🏗️ Constructor utils API
+=============================
+
+
+.. currentmodule:: serket 
+
+.. autofunction:: field
+.. autofunction:: fields
+.. autofunction:: autoinit
+.. autofunction:: leafwise
diff --git a/docs/API/core.rst b/docs/API/core.rst
diff --git a/docs/API/linear.rst b/docs/API/linear.rst
@@ -5,4 +5,6 @@ Linear
 .. autoclass:: Linear
 .. autoclass:: Identity
 .. autoclass:: Embedding
-.. autoclass:: MLP
+.. autoclass:: MLP
+
+.. autofunction:: linear
diff --git a/docs/API/masking.rst b/docs/API/masking.rst
@@ -3,9 +3,6 @@
 
 .. currentmodule:: serket 
 
-.. autofunction:: is_nondiff
-.. autofunction:: freeze
-.. autofunction:: unfreeze
-.. autofunction:: is_frozen
+.. autofunction:: is_masked
 .. autofunction:: tree_mask
 .. autofunction:: tree_unmask
diff --git a/docs/API/module.rst b/docs/API/module.rst
@@ -0,0 +1,10 @@
+📍 Module API
+=============================
+
+
+.. currentmodule:: serket 
+
+.. autoclass:: TreeClass 
+    :members:
+        at
+
diff --git a/docs/API/pretty_print.rst b/docs/API/pretty_print.rst
@@ -4,8 +4,6 @@
 .. currentmodule:: serket 
 
 .. autofunction:: tree_diagram
-.. autofunction:: tree_graph
-.. autofunction:: tree_mermaid 
 .. autofunction:: tree_repr 
 .. autofunction:: tree_str
 .. autofunction:: tree_summary
diff --git a/docs/API/recurrent.rst b/docs/API/recurrent.rst
@@ -6,7 +6,7 @@ Recurrent
 .. autoclass:: LSTMCell
 .. autoclass:: GRUCell
 .. autoclass:: SimpleRNNCell
-.. autoclass:: DenseCell
+.. autoclass:: LinearCell
 
 .. autoclass:: ConvLSTM1DCell
 .. autoclass:: ConvLSTM2DCell

diff --git a/docs/API/sepes.rst b/docs/API/sepes.rst
@@ -2,13 +2,15 @@
 =============================
 
 .. note::
-    `sepes <https://sepes.readthedocs.io/en/latest/?badge=latest>`_ API is fully re-exported under the ``serket`` namespace.
-    `Check the docs <https://sepes.readthedocs.io/en/latest/?badge=latest>`_ for full details.
+    `sepes <https://sepes.readthedocs.io/>`_ API is fully re-exported under the ``serket`` namespace.
+    `Check the docs <https://sepes.readthedocs.io/>`_ for full details.
 
 .. toctree::
    :maxdepth: 2
    :caption: API Documentation
 
-   core
+   module
    masking
+   tree
+   constructor
    pretty_print
diff --git a/docs/API/tree.rst b/docs/API/tree.rst
@@ -0,0 +1,17 @@
+🌲 Tree utils API
+=============================
+
+
+.. currentmodule:: serket 
+
+.. autoclass:: at
+    :members:
+        get,
+        set,
+        apply,
+        scan,
+        reduce,
+        pluck,
+
+.. autofunction:: value_and_tree
+.. autofunction:: bcmap