From f6b14b9c115543f56a36e7eb4650719d3efd9daf Mon Sep 17 00:00:00 2001 From: anu <63437899+ae-bii@users.noreply.github.com> Date: Mon, 15 Jul 2024 12:19:33 -0500 Subject: [PATCH 1/5] Update autoencoder.py docstring formatting --- nlgm/autoencoder.py | 81 +++++++++++++++++++++++++++++++++------------ 1 file changed, 59 insertions(+), 22 deletions(-) diff --git a/nlgm/autoencoder.py b/nlgm/autoencoder.py index cfd3ee0..5356b03 100644 --- a/nlgm/autoencoder.py +++ b/nlgm/autoencoder.py @@ -12,9 +12,16 @@ def __init__(self, hidden_dim=20, latent_dim=2): """ Encoder class for the geometric autoencoder. - Args: - hidden_dim (int): Number of hidden dimensions. - latent_dim (int): Number of latent dimensions. + Parameters + ---------- + hidden_dim : int + Number of hidden dimensions. + latent_dim : int + Number of latent dimensions. + + Attributes + ---------- + encoder """ super(Encoder, self).__init__() @@ -45,11 +52,15 @@ def forward(self, x): """ Forward pass of the encoder. - Args: - x (torch.Tensor): Input tensor. + Parameters + ---------- + x : torch.Tensor + Input tensor. - Returns: - torch.Tensor: Encoded output tensor. + Returns + ------- + tensor : torch.Tensor + Encoded output tensor. """ z = self.encoder(x) return z @@ -60,9 +71,17 @@ def __init__(self, hidden_dim=20, latent_dim=2): """ Decoder class for the geometric autoencoder. - Args: - hidden_dim (int): Number of hidden dimensions. - latent_dim (int): Number of latent dimensions. + Parameters + ---------- + hidden_dim : int + Number of hidden dimensions. + latent_dim : int + Number of latent dimensions. + + + Attributes + ---------- + decoder """ super(Decoder, self).__init__() @@ -88,11 +107,15 @@ def forward(self, z): """ Forward pass of the decoder. - Args: - z (torch.Tensor): Encoded input tensor. + Parameters + ---------- + z : torch.Tensor + Encoded input tensor. - Returns: - torch.Tensor: Decoded output tensor. + Returns + ------- + tensor : torch.Tensor + Decoded output tensor. """ x_recon = self.decoder(z) return x_recon @@ -103,10 +126,20 @@ def __init__(self, signature, hidden_dim=20, latent_dim=2): """ Geometric Autoencoder class. - Args: - signature (list): List of signature dimensions. - hidden_dim (int): Number of hidden dimensions. - latent_dim (int): Number of latent dimensions. + Parameters + ---------- + signature : list + List of signature dimensions. + hidden_dim : int + Number of hidden dimensions. + latent_dim : int + Number of latent dimensions. + + Attributes + ---------- + geometry + encoder + decoder """ super(GeometricAutoencoder, self).__init__() self.geometry = ProductManifold(signature) @@ -117,11 +150,15 @@ def forward(self, x): """ Forward pass of the geometric autoencoder. - Args: - x (torch.Tensor): Input tensor. + Parameters + ---------- + x : torch.Tensor + Input tensor. - Returns: - torch.Tensor: Decoded output tensor. + Returns + ------- + tensor : torch.Tensor + Decoded output tensor. """ z = self.encoder(x) z = self.geometry.exponential_map(z) From 1e12fe0396e2b34eef6c01a157e68f605dc0f474 Mon Sep 17 00:00:00 2001 From: anu <63437899+ae-bii@users.noreply.github.com> Date: Mon, 15 Jul 2024 12:24:45 -0500 Subject: [PATCH 2/5] remove extra new line --- nlgm/autoencoder.py | 1 - 1 file changed, 1 deletion(-) diff --git a/nlgm/autoencoder.py b/nlgm/autoencoder.py index 5356b03..49e1a45 100644 --- a/nlgm/autoencoder.py +++ b/nlgm/autoencoder.py @@ -77,7 +77,6 @@ def __init__(self, hidden_dim=20, latent_dim=2): Number of hidden dimensions. latent_dim : int Number of latent dimensions. - Attributes ---------- From 2ccbf7609871f2a43c6c4a06750bb758c6aa9c93 Mon Sep 17 00:00:00 2001 From: anu <63437899+ae-bii@users.noreply.github.com> Date: Mon, 15 Jul 2024 12:28:32 -0500 Subject: [PATCH 3/5] reformat with ruff --- nlgm/autoencoder.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nlgm/autoencoder.py b/nlgm/autoencoder.py index 49e1a45..97071c8 100644 --- a/nlgm/autoencoder.py +++ b/nlgm/autoencoder.py @@ -77,7 +77,7 @@ def __init__(self, hidden_dim=20, latent_dim=2): Number of hidden dimensions. latent_dim : int Number of latent dimensions. - + Attributes ---------- decoder @@ -133,7 +133,7 @@ def __init__(self, signature, hidden_dim=20, latent_dim=2): Number of hidden dimensions. latent_dim : int Number of latent dimensions. - + Attributes ---------- geometry From 2e0aeb88528133bf77672e90a1a2e4804d5fc939 Mon Sep 17 00:00:00 2001 From: Anupam Bhakta Date: Wed, 17 Jul 2024 21:45:39 -0500 Subject: [PATCH 4/5] Add numpydoc extension and update Encoder and Decoder classes --- doc/requirements.txt | 3 +- doc/source/conf.py | 2 +- nlgm/autoencoder.py | 103 +++++++++++++++++++++++++------------------ 3 files changed, 62 insertions(+), 46 deletions(-) diff --git a/doc/requirements.txt b/doc/requirements.txt index 7bc001d..245e831 100644 --- a/doc/requirements.txt +++ b/doc/requirements.txt @@ -1,2 +1,3 @@ sphinx -sphinx_book_theme \ No newline at end of file +sphinx_book_theme +numpydoc \ No newline at end of file diff --git a/doc/source/conf.py b/doc/source/conf.py index 66c040e..7014456 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -21,7 +21,7 @@ # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration -extensions = ["sphinx.ext.todo", "sphinx.ext.viewcode", "sphinx.ext.autodoc"] +extensions = ["sphinx.ext.todo", "sphinx.ext.viewcode", "sphinx.ext.autodoc", "sphinx.ext.autosummary", "numpydoc"] templates_path = ["_templates"] exclude_patterns = [] diff --git a/nlgm/autoencoder.py b/nlgm/autoencoder.py index 97071c8..9f47eaa 100644 --- a/nlgm/autoencoder.py +++ b/nlgm/autoencoder.py @@ -8,21 +8,26 @@ class Encoder(nn.Module): - def __init__(self, hidden_dim=20, latent_dim=2): - """ - Encoder class for the geometric autoencoder. + """ + Encoder class for the geometric autoencoder. - Parameters - ---------- - hidden_dim : int - Number of hidden dimensions. - latent_dim : int - Number of latent dimensions. + Parameters + ---------- + hidden_dim : int + Number of hidden dimensions. + latent_dim : int + Number of latent dimensions. - Attributes - ---------- - encoder - """ + Methods + ------- + forward + + Attributes + ---------- + encoder + """ + + def __init__(self, hidden_dim=20, latent_dim=2): super(Encoder, self).__init__() self.encoder = nn.Sequential( @@ -67,21 +72,26 @@ def forward(self, x): class Decoder(nn.Module): - def __init__(self, hidden_dim=20, latent_dim=2): - """ - Decoder class for the geometric autoencoder. + """ + Decoder class for the geometric autoencoder. - Parameters - ---------- - hidden_dim : int - Number of hidden dimensions. - latent_dim : int - Number of latent dimensions. + Parameters + ---------- + hidden_dim : int + Number of hidden dimensions. + latent_dim : int + Number of latent dimensions. - Attributes - ---------- - decoder - """ + Methods + ------- + forward + + Attributes + ---------- + decoder + """ + + def __init__(self, hidden_dim=20, latent_dim=2): super(Decoder, self).__init__() self.decoder = nn.Sequential( @@ -121,25 +131,30 @@ def forward(self, z): class GeometricAutoencoder(nn.Module): - def __init__(self, signature, hidden_dim=20, latent_dim=2): - """ - Geometric Autoencoder class. + """ + Geometric Autoencoder class. + + Parameters + ---------- + signature : list + List of signature dimensions. + hidden_dim : int + Number of hidden dimensions. + latent_dim : int + Number of latent dimensions. + + Methods + ------- + forward + + Attributes + ---------- + geometry + encoder + decoder + """ - Parameters - ---------- - signature : list - List of signature dimensions. - hidden_dim : int - Number of hidden dimensions. - latent_dim : int - Number of latent dimensions. - - Attributes - ---------- - geometry - encoder - decoder - """ + def __init__(self, signature, hidden_dim=20, latent_dim=2): super(GeometricAutoencoder, self).__init__() self.geometry = ProductManifold(signature) self.encoder = Encoder(hidden_dim, latent_dim) From 2331e68a7ef8439010056b1f841b2bad615f20a5 Mon Sep 17 00:00:00 2001 From: Anupam Bhakta Date: Wed, 17 Jul 2024 21:47:33 -0500 Subject: [PATCH 5/5] Update formatting in conf.py --- doc/source/conf.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/doc/source/conf.py b/doc/source/conf.py index 7014456..d82c505 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -21,7 +21,13 @@ # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration -extensions = ["sphinx.ext.todo", "sphinx.ext.viewcode", "sphinx.ext.autodoc", "sphinx.ext.autosummary", "numpydoc"] +extensions = [ + "sphinx.ext.todo", + "sphinx.ext.viewcode", + "sphinx.ext.autodoc", + "sphinx.ext.autosummary", + "numpydoc", +] templates_path = ["_templates"] exclude_patterns = []