diff --git a/src/devvi/__init__.py b/src/devvi/__init__.py index c3de13d..e56028f 100644 --- a/src/devvi/__init__.py +++ b/src/devvi/__init__.py @@ -1,7 +1,7 @@ from importlib.metadata import version -from . import pl, pp, tl +from . import model -__all__ = ["pl", "pp", "tl"] +__all__ = ["model"] __version__ = version("devVI") diff --git a/src/devvi/model/__init__.py b/src/devvi/model/__init__.py new file mode 100644 index 0000000..7bc0159 --- /dev/null +++ b/src/devvi/model/__init__.py @@ -0,0 +1 @@ +from .devvi_model import BasicClass, basic_plot diff --git a/src/devvi/model/devvi_model.py b/src/devvi/model/devvi_model.py new file mode 100644 index 0000000..d91dee1 --- /dev/null +++ b/src/devvi/model/devvi_model.py @@ -0,0 +1,124 @@ +# import lightning as L +# import torch +# import torch.nn.functional as F +# from torch.utils.data import DataLoader + +from torch import nn + + +def basic_plot(adata: nn.Module) -> int: + """Generate a basic plot for an AnnData object. + + Parameters + ---------- + adata + The AnnData object to preprocess. + + Returns + ------- + Some integer value. + """ + print("Import matplotlib and implement a plotting function here.") + return 0 + + +class Encoder(nn.Module): + """A basic class. + + Parameters + ---------- + adata + The AnnData object to preprocess. + """ + + def __init__(self): + super().__init__() + self.l1 = nn.Sequential(nn.Linear(28 * 28, 64), nn.ReLU(), nn.Linear(64, 3)) + + def forward(self, x): + """Generate a basic plot for an AnnData object. + + Parameters + ---------- + adata + The AnnData object to preprocess. + + Returns + ------- + Some integer value. + """ + return self.l1(x) + + +class Decoder(nn.Module): + """A basic class. + + Parameters + ---------- + adata + The AnnData object to preprocess. + """ + + def __init__(self): + super().__init__() + self.l1 = nn.Sequential(nn.Linear(3, 64), nn.ReLU(), nn.Linear(64, 28 * 28)) + + def forward(self, x): + """Generate a basic plot for an AnnData object. + + Parameters + ---------- + adata + The AnnData object to preprocess. + + Returns + ------- + Some integer value. + """ + return self.l1(x) + + +class BasicClass: + """A basic class. + + Parameters + ---------- + adata + The AnnData object to preprocess. + """ + + my_attribute: str = "Some attribute." + my_other_attribute: int = 0 + + def __init__(self, adata: nn.Module): + print("Implement a class here.") + + def my_method(self, param: int) -> int: + """A basic method. + + Parameters + ---------- + param + A parameter. + + Returns + ------- + Some integer value. + """ + print("Implement a method here.") + return 0 + + def my_other_method(self, param: str) -> str: + """Another basic method. + + Parameters + ---------- + param + A parameter. + + Returns + ------- + Some integer value. + """ + print("Implement a method here.") + return "" diff --git a/src/devvi/pl/__init__.py b/src/devvi/pl/__init__.py deleted file mode 100644 index c2315dd..0000000 --- a/src/devvi/pl/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from .basic import BasicClass, basic_plot diff --git a/src/devvi/pl/basic.py b/src/devvi/pl/basic.py deleted file mode 100644 index ed390ef..0000000 --- a/src/devvi/pl/basic.py +++ /dev/null @@ -1,63 +0,0 @@ -from anndata import AnnData - - -def basic_plot(adata: AnnData) -> int: - """Generate a basic plot for an AnnData object. - - Parameters - ---------- - adata - The AnnData object to preprocess. - - Returns - ------- - Some integer value. - """ - print("Import matplotlib and implement a plotting function here.") - return 0 - - -class BasicClass: - """A basic class. - - Parameters - ---------- - adata - The AnnData object to preprocess. - """ - - my_attribute: str = "Some attribute." - my_other_attribute: int = 0 - - def __init__(self, adata: AnnData): - print("Implement a class here.") - - def my_method(self, param: int) -> int: - """A basic method. - - Parameters - ---------- - param - A parameter. - - Returns - ------- - Some integer value. - """ - print("Implement a method here.") - return 0 - - def my_other_method(self, param: str) -> str: - """Another basic method. - - Parameters - ---------- - param - A parameter. - - Returns - ------- - Some integer value. - """ - print("Implement a method here.") - return "" diff --git a/src/devvi/pp/__init__.py b/src/devvi/pp/__init__.py deleted file mode 100644 index 5e7e293..0000000 --- a/src/devvi/pp/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from .basic import basic_preproc diff --git a/src/devvi/pp/basic.py b/src/devvi/pp/basic.py deleted file mode 100644 index 5db1ec0..0000000 --- a/src/devvi/pp/basic.py +++ /dev/null @@ -1,17 +0,0 @@ -from anndata import AnnData - - -def basic_preproc(adata: AnnData) -> int: - """Run a basic preprocessing on the AnnData object. - - Parameters - ---------- - adata - The AnnData object to preprocess. - - Returns - ------- - Some integer value. - """ - print("Implement a preprocessing function here.") - return 0 diff --git a/src/devvi/tl/__init__.py b/src/devvi/tl/__init__.py deleted file mode 100644 index 95a32cd..0000000 --- a/src/devvi/tl/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from .basic import basic_tool diff --git a/src/devvi/tl/basic.py b/src/devvi/tl/basic.py deleted file mode 100644 index d215ade..0000000 --- a/src/devvi/tl/basic.py +++ /dev/null @@ -1,17 +0,0 @@ -from anndata import AnnData - - -def basic_tool(adata: AnnData) -> int: - """Run a tool on the AnnData object. - - Parameters - ---------- - adata - The AnnData object to preprocess. - - Returns - ------- - Some integer value. - """ - print("Implement a tool to run on the AnnData object.") - return 0