chore: 💩 Change name to cellmap-models (from cellmap.models)

.github/ISSUE_TEMPLATE.md

@@ -1,4 +1,4 @@
-* cellmap.models version or commit:
+* cellmap-models version or commit:
 * Python version:
 * Operating System:
 

.github/workflows/black.yaml

@@ -14,4 +14,4 @@ jobs:
       - name: Lint with Black
         run: |
           pip install black
-          black --diff --check src/cellmap.models tests
+          black --diff --check src/cellmap-models tests

.github/workflows/mypy.yaml

@@ -15,4 +15,4 @@ jobs:
         run: |
           pip install .
           pip install --upgrade mypy
-          mypy src/cellmap.models
+          mypy src/cellmap-models

pyproject.toml

@@ -3,7 +3,7 @@ build-backend = "setuptools.build_meta"
 requires = ["setuptools", "wheel"]
 
 [project]
-name = "cellmap-models"
+name = "cellmap_models"
 description = "Repository of model architectures and network weights used for CellMap segmentations."
 readme = "README.md"
 requires-python = ">=3.7"
@@ -19,7 +19,8 @@ dynamic = ["version"]
 dependencies = [
   'torch',
   'torchvision',
-  'numpy'
+  'numpy',
+  "tqdm",
 ]
 
 [project.optional-dependencies]

src/cellmap_models.egg-info/PKG-INFO

@@ -0,0 +1,56 @@
+Metadata-Version: 2.1
+Name: cellmap_models
+Version: 0.0.0
+Summary: Repository of model architectures and network weights used for CellMap segmentations.
+Author-email: CellMap <[email protected]>
+License: BSD 3-Clause License
+Project-URL: homepage, https://github.com/janelia-cellmap/cellmap-models
+Project-URL: repository, https://github.com/janelia-cellmap/cellmap-models
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+Requires-Dist: torch
+Requires-Dist: torchvision
+Requires-Dist: numpy
+Requires-Dist: tqdm
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pdoc; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+
+# cellmap-models
+
+[![tests](https://github.com/janelia-cellmap/cellmap-models/actions/workflows/tests.yaml/badge.svg)](https://github.com/janelia-cellmap/cellmap-models/actions/workflows/tests.yaml)
+[![black](https://github.com/janelia-cellmap/cellmap-models/actions/workflows/black.yaml/badge.svg)](https://github.com/janelia-cellmap/cellmap-models/actions/workflows/black.yaml)
+[![mypy](https://github.com/janelia-cellmap/cellmap-models/actions/workflows/mypy.yaml/badge.svg)](https://github.com/janelia-cellmap/cellmap-models/actions/workflows/mypy.yaml)
+[![codecov](https://codecov.io/gh/janelia-cellmap/cellmap-models/branch/main/graph/badge.svg)](https://codecov.io/gh/janelia-cellmap/cellmap-models)
+
+This package contains the models used for segmention by the CellMap project team at HHMI Janelia.
+
+## Installation
+
+```bash
+git clone https://github.com/janelia-cellmap/cellmap-models
+cd cellmap-models
+conda env create -n cellmap python=3.10
+conda activate cellmap
+pip install .
+```
+
+## Usage
+
+```python
+import cellmap-models
+```
+
+Different models are available in the `cellmap-models` module. For example, to use the models produced by the `COSEM` pilot project team, and published as part of [Whole-cell organelle segmentation in volume electron microscopy](https://doi.org/10.1038/s41586-021-03977-3):
+
+```python
+import cellmap-models.cosem as cosem_models
+model = cosem_models.load_model('setup04/1820500')
+```
+
+More information on each set of models and how to use them is available in the `README.md` file in the corresponding subdirectory.

src/cellmap_models.egg-info/SOURCES.txt

@@ -0,0 +1,21 @@
+README.md
+pyproject.toml
+src/cellmap_models/__init__.py
+src/cellmap_models/utils.py
+src/cellmap_models.egg-info/PKG-INFO
+src/cellmap_models.egg-info/SOURCES.txt
+src/cellmap_models.egg-info/dependency_links.txt
+src/cellmap_models.egg-info/requires.txt
+src/cellmap_models.egg-info/top_level.txt
+src/cellmap_models/pytorch/__init__.py
+src/cellmap_models/pytorch/cosem/__init__.py
+src/cellmap_models/pytorch/cosem/load_model.py
+src/cellmap_models/pytorch/cosem/setup04/__init__.py
+src/cellmap_models/pytorch/cosem/setup04/model.py
+src/cellmap_models/pytorch/cosem/setup28/__init__.py
+src/cellmap_models/pytorch/cosem/setup28/model.py
+src/cellmap_models/pytorch/cosem/setup36/__init__.py
+src/cellmap_models/pytorch/cosem/setup36/model.py
+src/cellmap_models/pytorch/cosem/setup45/__init__.py
+src/cellmap_models/pytorch/cosem/setup45/model.py
+tests/test_assert.py

src/cellmap_models.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

src/cellmap_models.egg-info/requires.txt

@@ -0,0 +1,12 @@
+torch
+torchvision
+numpy
+tqdm
+
+[dev]
+pytest
+pytest-cov
+black
+mypy
+pdoc
+pre-commit

src/cellmap_models.egg-info/top_level.txt

@@ -0,0 +1 @@
+cellmap_models

src/cellmap-models/pytorch/cosem/setup04/model.py → src/cellmap_models/pytorch/cosem/setup04/model.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 import numpy as np
-from cellmap.models import download_url_to_file
+from cellmap-models import download_url_to_file
 
 # voxel size parameters
 voxel_size_output = np.array((4,) * 3)

src/cellmap-models/pytorch/cosem/setup26.1/model.py → src/cellmap_models/pytorch/cosem/setup26.1/model.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 import numpy as np
-from cellmap.models import download_url_to_file
+from cellmap-models import download_url_to_file
 
 # voxel size parameters
 voxel_size_output = np.array((4,) * 3)

src/cellmap-models/pytorch/cosem/setup28/model.py → src/cellmap_models/pytorch/cosem/setup28/model.py

@@ -1,6 +1,6 @@
 import numpy as np
 from pathlib import Path
-from cellmap.models import download_url_to_file
+from cellmap-models import download_url_to_file
 
 # voxel size parameters
 voxel_size_output = np.array((4,) * 3)

src/cellmap-models/pytorch/cosem/setup36/model.py → src/cellmap_models/pytorch/cosem/setup36/model.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 import numpy as np
-from cellmap.models import download_url_to_file
+from cellmap-models import download_url_to_file
 
 # voxel size parameters
 voxel_size_output = np.array((4,) * 3)

src/cellmap-models/pytorch/cosem/setup45/model.py → src/cellmap_models/pytorch/cosem/setup45/model.py

@@ -1,6 +1,6 @@
 import numpy as np
 from pathlib import Path
-from cellmap.models import download_url_to_file
+from cellmap-models import download_url_to_file
 
 # voxel size parameters
 voxel_size_output = np.array((4,) * 3)