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build: fix python 3.11 installation #634

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build: fix python 3.11 installation #634

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4de52a2
add py 3.11 build
gcroci2 Jul 31, 2024
adc3a4a
add defaults channel
gcroci2 Jul 31, 2024
3fd3434
change required python versions range
gcroci2 Jul 31, 2024
3142a3c
reupload pre-trained files
gcroci2 Jul 31, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/build-repo.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ jobs:
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.10"] # ["3.10", "3.11"]
python-version: ["3.10", "3.11"]

# https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
defaults:
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2 changes: 1 addition & 1 deletion .gitignore
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Expand Up @@ -21,7 +21,7 @@ dist/*

# hdf5 and tar
*.hdf5
*.tar
# *.tar

# test
htmlcov
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2 changes: 1 addition & 1 deletion env/deeprank2.yml
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Expand Up @@ -7,7 +7,7 @@ channels:
- conda-forge
- sbl
dependencies:
- python=3.10
- python>=3.10,<3.12
- pip>=23.3
- sbl::libcifpp=5.1.0
- sbl::dssp=4.2.2.1
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Binary file added tests/data/pretrained/testing_graph_model2.pth.tar
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Binary file added tests/data/pretrained/testing_grid_model2.pth.tar
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12 changes: 6 additions & 6 deletions tests/test_dataset.py
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Expand Up @@ -277,7 +277,7 @@ def test_inherit_info_dataset_train_griddataset(self) -> None:

def test_inherit_info_pretrained_model_griddataset(self) -> None:
# Test the inheritance not giving in any parameters
pretrained_model = "tests/data/pretrained/testing_grid_model.pth.tar"
pretrained_model = "tests/data/pretrained/testing_grid_model2.pth.tar"
dataset_test = GridDataset(
hdf5_path=self.hdf5_path,
train_source=pretrained_model,
Expand Down Expand Up @@ -309,7 +309,7 @@ def test_inherit_info_pretrained_model_griddataset(self) -> None:
def test_no_target_dataset_griddataset(self) -> None:
hdf5_no_target = "tests/data/hdf5/test_no_target.hdf5"
hdf5_target = "tests/data/hdf5/1ATN_ppi.hdf5"
pretrained_model = "tests/data/pretrained/testing_grid_model.pth.tar"
pretrained_model = "tests/data/pretrained/testing_grid_model2.pth.tar"

dataset = GridDataset(
hdf5_path=hdf5_no_target,
Expand Down Expand Up @@ -1190,7 +1190,7 @@ def test_inherit_info_dataset_train_graphdataset(self) -> None:

def test_inherit_info_pretrained_model_graphdataset(self) -> None:
hdf5_path = "tests/data/hdf5/test.hdf5"
pretrained_model = "tests/data/pretrained/testing_graph_model.pth.tar"
pretrained_model = "tests/data/pretrained/testing_graph_model2.pth.tar"
dataset_test = GraphDataset(
hdf5_path=hdf5_path,
train_source=pretrained_model,
Expand Down Expand Up @@ -1238,7 +1238,7 @@ def test_inherit_info_pretrained_model_graphdataset(self) -> None:
def test_no_target_dataset_graphdataset(self) -> None:
hdf5_no_target = "tests/data/hdf5/test_no_target.hdf5"
hdf5_target = "tests/data/hdf5/test.hdf5"
pretrained_model = "tests/data/pretrained/testing_graph_model.pth.tar"
pretrained_model = "tests/data/pretrained/testing_graph_model2.pth.tar"

dataset = GraphDataset(
hdf5_path=hdf5_no_target,
Expand Down Expand Up @@ -1290,15 +1290,15 @@ def test_invalid_pretrained_model_path(self) -> None:

def test_invalid_pretrained_model_data_type(self) -> None:
hdf5_graph = "tests/data/hdf5/test.hdf5"
pretrained_grid_model = "tests/data/pretrained/testing_grid_model.pth.tar"
pretrained_grid_model = "tests/data/pretrained/testing_grid_model2.pth.tar"
with pytest.raises(TypeError):
GraphDataset(
hdf5_path=hdf5_graph,
train_source=pretrained_grid_model,
)

hdf5_grid = "tests/data/hdf5/1ATN_ppi.hdf5"
pretrained_graph_model = "tests/data/pretrained/testing_graph_model.pth.tar"
pretrained_graph_model = "tests/data/pretrained/testing_graph_model2.pth.tar"
with pytest.raises(TypeError):
GridDataset(
hdf5_path=hdf5_grid,
Expand Down
12 changes: 6 additions & 6 deletions tests/test_trainer.py
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Expand Up @@ -658,7 +658,7 @@ def test_invalid_no_cuda_available(self) -> None:
def test_train_method_no_train(self) -> None:
# Graphs data
test_data_graph = "tests/data/hdf5/test.hdf5"
pretrained_model_graph = "tests/data/pretrained/testing_graph_model.pth.tar"
pretrained_model_graph = "tests/data/pretrained/testing_graph_model2.pth.tar"

dataset_test = GraphDataset(hdf5_path=test_data_graph, train_source=pretrained_model_graph)
trainer = Trainer(
Expand All @@ -672,7 +672,7 @@ def test_train_method_no_train(self) -> None:

# Grids data
test_data_grid = "tests/data/hdf5/1ATN_ppi.hdf5"
pretrained_model_grid = "tests/data/pretrained/testing_grid_model.pth.tar"
pretrained_model_grid = "tests/data/pretrained/testing_grid_model2.pth.tar"

dataset_test = GridDataset(hdf5_path=test_data_grid, train_source=pretrained_model_grid)
trainer = Trainer(
Expand All @@ -687,7 +687,7 @@ def test_train_method_no_train(self) -> None:
def test_test_method_pretrained_model_on_dataset_with_target(self) -> None:
# Graphs data
test_data_graph = "tests/data/hdf5/test.hdf5"
pretrained_model_graph = "tests/data/pretrained/testing_graph_model.pth.tar"
pretrained_model_graph = "tests/data/pretrained/testing_graph_model2.pth.tar"

dataset_test = GraphDataset(hdf5_path=test_data_graph, train_source=pretrained_model_graph)

Expand All @@ -705,7 +705,7 @@ def test_test_method_pretrained_model_on_dataset_with_target(self) -> None:

# Grids data
test_data_grid = "tests/data/hdf5/1ATN_ppi.hdf5"
pretrained_model_grid = "tests/data/pretrained/testing_grid_model.pth.tar"
pretrained_model_grid = "tests/data/pretrained/testing_grid_model2.pth.tar"

dataset_test = GridDataset(hdf5_path=test_data_grid, train_source=pretrained_model_grid)

Expand All @@ -724,7 +724,7 @@ def test_test_method_pretrained_model_on_dataset_with_target(self) -> None:
def test_test_method_pretrained_model_on_dataset_without_target(self) -> None:
# Graphs data
test_data_graph = "tests/data/hdf5/test_no_target.hdf5"
pretrained_model_graph = "tests/data/pretrained/testing_graph_model.pth.tar"
pretrained_model_graph = "tests/data/pretrained/testing_graph_model2.pth.tar"

dataset_test = GraphDataset(hdf5_path=test_data_graph, train_source=pretrained_model_graph)

Expand All @@ -744,7 +744,7 @@ def test_test_method_pretrained_model_on_dataset_without_target(self) -> None:

# Grids data
test_data_grid = "tests/data/hdf5/test_no_target.hdf5"
pretrained_model_grid = "tests/data/pretrained/testing_grid_model.pth.tar"
pretrained_model_grid = "tests/data/pretrained/testing_grid_model2.pth.tar"

dataset_test = GridDataset(hdf5_path=test_data_grid, train_source=pretrained_model_grid)

Expand Down
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