diff --git a/.github/workflows/conda-build.yml b/.github/workflows/conda-build.yml
index 1509d1eb..70896595 100644
--- a/.github/workflows/conda-build.yml
+++ b/.github/workflows/conda-build.yml
@@ -9,21 +9,20 @@ on:
branches: [master]
jobs:
- build-linux:
- runs-on: ubuntu-latest
-
+ build:
+ strategy:
+ fail-fast: false
+ matrix:
+ os: [macos-latest, windows-latest, ubuntu-latest]
+ runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v2
- - name: Set pytorch-3dunet version
- run: echo "RELEASE_VERSION=$(date +%Y%m%d%H%M%S)" >> $GITHUB_ENV
- - name: Print pytorch-3dunet version
- run: echo $RELEASE_VERSION
- uses: conda-incubator/setup-miniconda@v2
with:
auto-activate-base: true
activate-environment: ""
- channels: local,conda-forge,defaults
- channel-priority: false
+ channel-priority: flexible
+ miniforge-variant: Miniforge3
- shell: bash -l {0}
run: conda info --envs
- name: Build pytorch-3dunet
@@ -33,7 +32,7 @@ jobs:
conda build -c pytorch -c nvidia -c conda-forge conda-recipe
- name: Create pytorch3dunet env
run: |
- conda create -n pytorch3dunet -c pytorch -c nvidia -c conda-forge pytorch-3dunet pytest
+ conda create -n pytorch3dunet -c local -c pytorch -c nvidia -c conda-forge pytorch-3dunet pytest
- name: Run pytest
shell: bash -l {0}
run: |
@@ -41,7 +40,7 @@ jobs:
pytest
conda deactivate
- name: Deploy on conda
- if: ${{ startsWith( github.ref, 'refs/tags/') && success() }}
+ if: ${{ matrix.os == 'ubuntu-latest' && startsWith( github.ref, 'refs/tags/') && success() }}
env:
ANACONDA_SECRET: ${{ secrets.ANACONDA_TOKEN }}
shell: bash -l {0}
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index 43605e71..3c903671 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -1,6 +1,8 @@
+{% set setup_py_data = load_setup_py_data() %}
+
package:
name: pytorch-3dunet
- version: {{ RELEASE_VERSION }}
+ version: {{ setup_py_data['version'] }}
source:
path: ..
diff --git a/resources/3DUnet_multiclass/train_config.yaml b/resources/3DUnet_multiclass/train_config.yaml
index 86a3efae..4d4ca0bc 100644
--- a/resources/3DUnet_multiclass/train_config.yaml
+++ b/resources/3DUnet_multiclass/train_config.yaml
@@ -129,7 +129,7 @@ loaders:
# convert target volume to binary mask
- name: ToTensor
expand_dims: false
- dtype: long
+ dtype: int64
# configuration of the val loader
val:
@@ -158,4 +158,4 @@ loaders:
label:
- name: ToTensor
expand_dims: false
- dtype: long
+ dtype: int64
diff --git a/tests/resources/config_train.yml b/tests/resources/config_train.yml
index 7cd3a044..cf6f031d 100644
--- a/tests/resources/config_train.yml
+++ b/tests/resources/config_train.yml
@@ -54,8 +54,8 @@ loaders:
- name: ToTensor
# do not expand dims for cross-entropy loss
expand_dims: false
- # cross-entropy loss requires target to be of type 'long'
- dtype: 'long'
+ # cross-entropy loss requires target to be of type 'int64'
+ dtype: 'int64'
weight:
- name: ToTensor
expand_dims: false
@@ -76,7 +76,7 @@ loaders:
label:
- name: ToTensor
expand_dims: false
- dtype: 'long'
+ dtype: 'int64'
weight:
- name: ToTensor
expand_dims: false
\ No newline at end of file
diff --git a/tests/resources/config_train_2d.yml b/tests/resources/config_train_2d.yml
index 80a41378..2ef38557 100644
--- a/tests/resources/config_train_2d.yml
+++ b/tests/resources/config_train_2d.yml
@@ -76,8 +76,8 @@ loaders:
- name: ToTensor
# do not expand dims for cross-entropy loss
expand_dims: false
- # cross-entropy loss requires target to be of type 'long'
- dtype: 'long'
+ # cross-entropy loss requires target to be of type 'int64'
+ dtype: 'int64'
weight:
- name: ToTensor
expand_dims: false
@@ -99,7 +99,7 @@ loaders:
label:
- name: ToTensor
expand_dims: false
- dtype: 'long'
+ dtype: 'int64'
weight:
- name: ToTensor
expand_dims: false
\ No newline at end of file
diff --git a/tests/test_dataset.py b/tests/test_dataset.py
index e0107771..46e5d519 100644
--- a/tests/test_dataset.py
+++ b/tests/test_dataset.py
@@ -1,4 +1,5 @@
import os
+from pathlib import Path
from tempfile import NamedTemporaryFile
import h5py
@@ -75,20 +76,19 @@ def test_lazy_hdf5_dataset(self, transformer_config):
assert np.all(visit_raw)
assert np.all(visit_label)
- def test_augmentation(self, transformer_config):
+ def test_augmentation(self, transformer_config, tmpdir):
raw = np.random.rand(32, 96, 96)
# assign raw to label's channels for ease of comparison
label = np.stack([raw for _ in range(3)])
# create temporary h5 file
- tmp_file = NamedTemporaryFile()
- tmp_path = tmp_file.name
- with h5py.File(tmp_path, 'w') as f:
+ tmp_file = tmpdir / "test.h5"
+ with h5py.File(tmp_file, 'w') as f:
f.create_dataset('raw', data=raw)
f.create_dataset('label', data=label)
# set phase='train' in order to execute the train transformers
phase = 'train'
- dataset = StandardHDF5Dataset(tmp_path, phase=phase,
+ dataset = StandardHDF5Dataset(tmp_file, phase=phase,
slice_builder_config=_slice_builder_conf((16, 64, 64), (8, 32, 32)),
transformer_config=transformer_config[phase]['transformer'])
@@ -120,19 +120,19 @@ def test_traverse_file_paths(self, tmpdir):
assert expected_files == actual_files
- def test_halo(self):
+ def test_halo(self, tmpdir: Path):
halo_shape = (1, 2, 3)
# create temporary h5 file
raw = np.random.rand(32, 96, 96)
- tmp_file = NamedTemporaryFile()
- tmp_path = tmp_file.name
- with h5py.File(tmp_path, 'w') as f:
+ tmp_file = tmpdir / "test.h5"
+
+ with h5py.File(tmp_file, 'w') as f:
f.create_dataset('raw', data=raw)
# halo only implemented with test phase
phase = 'test'
- dataset = StandardHDF5Dataset(tmp_path, phase=phase,
+ dataset = StandardHDF5Dataset(tmp_file, phase=phase,
slice_builder_config=_slice_builder_conf((16, 64, 64), (8, 32, 32), halo_shape),
transformer_config=_transformer_test_conf())
data_loader = DataLoader(dataset, batch_size=1, num_workers=4, shuffle=True,
diff --git a/tests/test_transforms.py b/tests/test_transforms.py
index cc182705..3d977ca0 100644
--- a/tests/test_transforms.py
+++ b/tests/test_transforms.py
@@ -5,7 +5,7 @@
class TestTransforms:
- config = {'dtype': 'long'}
+ config = {'dtype': 'int64'}
def test_random_label_to_boundary(self):
size = 20
@@ -62,7 +62,7 @@ def test_relabel(self):
def test_BaseTransformer(self):
config = {
'raw': [{'name': 'Standardize'}, {'name': 'ToTensor', 'expand_dims': True}],
- 'label': [{'name': 'ToTensor', 'expand_dims': False, 'dtype': 'long'}],
+ 'label': [{'name': 'ToTensor', 'expand_dims': False, 'dtype': 'int64'}],
'weight': [{'name': 'ToTensor', 'expand_dims': False}]
}
base_config = {'mean': 0, 'std': 1}
@@ -73,7 +73,7 @@ def test_BaseTransformer(self):
assert raw_transforms[1].expand_dims
label_transforms = transformer.label_transform().transforms
assert not label_transforms[0].expand_dims
- assert label_transforms[0].dtype == 'long'
+ assert label_transforms[0].dtype == 'int64'
weight_transforms = transformer.weight_transform().transforms
assert not weight_transforms[0].expand_dims
@@ -89,7 +89,7 @@ def test_StandardTransformer(self):
'label': [
{'name': 'RandomFlip'},
{'name': 'RandomRotate90'},
- {'name': 'ToTensor', 'expand_dims': False, 'dtype': 'long'}
+ {'name': 'ToTensor', 'expand_dims': False, 'dtype': 'int64'}
]
}
base_config = {'mean': 0, 'std': 1}
@@ -116,7 +116,7 @@ def test_AnisotropicRotationTransformer(self):
{'name': 'RandomFlip'},
{'name': 'RandomRotate90'},
{'name': 'RandomRotate', 'angle_spectrum': 17, 'axes': [[2, 1]]},
- {'name': 'ToTensor', 'expand_dims': False, 'dtype': 'long'}
+ {'name': 'ToTensor', 'expand_dims': False, 'dtype': 'int64'}
]
}
base_config = {'mean': 0, 'std': 1}
@@ -145,7 +145,7 @@ def test_LabelToBoundaryTransformer(self):
{'name': 'RandomRotate90'},
{'name': 'RandomRotate', 'angle_spectrum': 17, 'axes': [[2, 1]], 'mode': 'reflect'},
{'name': 'LabelToAffinities', 'offsets': [2, 4, 6, 8]},
- {'name': 'ToTensor', 'expand_dims': False, 'dtype': 'long'}
+ {'name': 'ToTensor', 'expand_dims': False, 'dtype': 'int64'}
]
}
base_config = {'mean': 0, 'std': 1}
@@ -179,7 +179,7 @@ def test_RandomLabelToBoundaryTransformer(self):
{'name': 'RandomRotate90'},
{'name': 'RandomRotate', 'angle_spectrum': 17, 'axes': [[2, 1]], 'mode': 'reflect'},
{'name': 'RandomLabelToAffinities', 'max_offset': 4},
- {'name': 'ToTensor', 'expand_dims': False, 'dtype': 'long'}
+ {'name': 'ToTensor', 'expand_dims': False, 'dtype': 'int64'}
]
}
base_config = {'mean': 0, 'std': 1}