diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
index a04c287..191de5c 100644
--- a/.github/workflows/python-publish.yml
+++ b/.github/workflows/python-publish.yml
@@ -9,8 +9,8 @@
name: Upload Python Package
on:
- release:
- types: [published]
+ push:
+ branches: [ "main" ]
permissions:
contents: read
diff --git a/docs/index.html b/docs/index.html
index 6eec80e..c1fdbe5 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -5,4 +5,4 @@
-
\ No newline at end of file
+
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index e2586d2..ce2d27e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,12 +15,13 @@ license = { text = "BSD 3-Clause License" }
authors = [
{ email = "rhoadesj@hhmi.org", name = "Jeff Rhoades" },
]
-version = "0.0.0"
+version = "0.0.1"
dependencies = [
'torch',
'torchvision',
'numpy',
- "tqdm",
+ 'tqdm',
+ 'cellpose'
]
[project.optional-dependencies]
@@ -32,8 +33,9 @@ dev = [
'mypy',
'pdoc',
'pre-commit',
- 'cellpose[gui]'
]
+pretrained = ['cellpose[gui]']
+all = ["cellmap-models[dev,pretrained]"]
[project.urls]
homepage = "https://janelia-cellmap.github.io/cellmap-models"
diff --git a/src/cellmap_models/pytorch/cosem/README.md b/src/cellmap_models/pytorch/cosem/README.md
index 8ff020b..ef9c8e3 100755
--- a/src/cellmap_models/pytorch/cosem/README.md
+++ b/src/cellmap_models/pytorch/cosem/README.md
@@ -20,12 +20,12 @@ Available models can be seen with the following code:
cosem_models.models_list
```
-Each model has a separate unet backbone and single layer prediction head. The `unet` and `head` objects are both PyTorch modules and can be used as such. You can access the separate components of the model using the following code:
+Each model has a separate backbone and single layer prediction head. The `backbone` and `head` objects are both PyTorch modules and can be used as such. You can access the separate components of the model using the following code:
```python
import cellmap_models.cosem as cosem_models
model = cosem_models.load_model('setup04/1820500')
-unet = model.unet
+backnone = model.backbone
head = model.prediction_head
```
diff --git a/src/cellmap_models/pytorch/cosem/load_model.py b/src/cellmap_models/pytorch/cosem/load_model.py
index 6be1fe9..5d0c8b6 100755
--- a/src/cellmap_models/pytorch/cosem/load_model.py
+++ b/src/cellmap_models/pytorch/cosem/load_model.py
@@ -127,7 +127,7 @@ def __init__(self, model_params):
kernel_size=(1,) * 3,
)
model = torch.nn.Sequential(*layers)
- self.unet = model
+ self.backbone = model
self.prediction_head = prediction_head
for k, v in model_params.__dict__.items():
setattr(self, k, v)
@@ -136,7 +136,7 @@ def __init__(self, model_params):
self.compute_minimal_shapes()
def forward(self, x):
- return self.prediction_head(self.unet(x))
+ return self.prediction_head(self.backbone(x))
def compute_minimal_shapes(self):
"""