Project dependencies may have API risk issues #43
Description
Hi, In medicaltorch, inappropriate dependency versioning constraints can cause risks.
Below are the dependencies and version constraints that the project is using
nibabel>=2.2.1
scipy>=1.0.0
numpy>=1.14.1
torch>=0.4.0
torchvision>=0.2.1
tqdm>=4.23.0
scikit-image==0.15.0
The version constraint == will introduce the risk of dependency conflicts because the scope of dependencies is too strict.
The version constraint No Upper Bound and * will introduce the risk of the missing API Error because the latest version of the dependencies may remove some APIs.
After further analysis, in this project,
The version constraint of dependency scipy can be changed to >=0.19.0,<=1.7.3.
The version constraint of dependency tqdm can be changed to >=4.36.0,<=4.64.0.
The above modification suggestions can reduce the dependency conflicts as much as possible,
and introduce the latest version as much as possible without calling Error in the projects.
The invocation of the current project includes all the following methods.
The calling methods from the scipy
scipy.spatial.distance.directed_hausdorff scipy.ndimage.filters.gaussian_filter scipy.ndimage.interpolation.map_coordinates scipy.spatial.distance.dice scipy.spatial.distance.jaccard
The calling methods from the tqdm
tqdm.tqdm.set_postfix tqdm.tqdm
The calling methods from the all methods
self.up3 self.mp3 self.conv1a f.read re.search self.branch4a_bn DownConv isinstance numpy.arange ValueError scipy.spatial.distance.directed_hausdorff self.conv3 self.dc5 torch.LongTensor numpy.any numpy.copy range numpy.allclose torch.from_numpy self.branch4a_drop self.ec2 self.mp1 index.self.handlers.get_pair_data torch.nn.BatchNorm2d numpy.sqrt self.branch5b_bn self.metadata.keys training_mean.input_data.pow.sum torch.stack torch.nn.LeakyReLU self.input_handle.header.get_zooms self.conv2_bn torchvision.transforms.functional.pad numpy.float32 input.view self.conv1b_bn numpy.zeros input_data.np.flip.copy torchvision.transforms.functional.rotate self.sample_transform type self.slice_filter_fn numpy.random.uniform len tflat.iflat.sum medicaltorch.transforms.ToTensor self.conv9 self.up_conv self.branch1a SegmentationPair2D.get_pair_slice prediction.flatten self.dc4 self.branch2a self.branch4b_bn noise.astype.astype self.result_dict.items target.index_select self.threshold.target.torch.gt.float.view f.read.splitlines mt_collate self.branch3b_bn self.branch1a_bn numpy.random.random self.branch1b_drop self.branch3a self.branch3b_drop self.input_handle.header.get_data_shape self._build_train_input_filename self.gt_handle.header.get_data_shape self.conv2a_bn PIL.Image.fromarray.resize torch.nn.functional.avg_pool2d self.ec0 sample_data.numpy self.branch3b self.amort self.conv2b_drop self.branch1a_drop error_msg.format os.path.dirname self.up1 torchvision.transforms.functional.center_crop self.input_handle.get_fdata target.index_select.view numpy.squeeze self.branch4b_drop int self.ec3 Mock nibabel.as_closest_canonical self.branch3a_bn os.path.exists self.branch1b SegmentationPair2D UpConv numpy.divide target.view self.input_handle.get_fdata.numel torch.nn.Conv2d PIL.Image.fromarray.mean self.propagate_params self.Unet.super.__init__ self.batch.items self.branch2a_bn collections.defaultdict self.input_handle.get_fdata.sum self.down_conv torch.gt sys.path.insert numeric_score input.size masking.squeeze.sum self.branch2b_drop i.self.handlers.get_pair_data self.up2 self.branch4a coord.self.handlers.get_pair_data tqdm.tqdm NotImplementedError self.indexes.append self.mp2 self.dc3 torch.nn.functional.relu indices.image.map_coordinates.reshape self.conv4 self._prepare_indexes self.get_pair_data DatasetManager self.branch2b self.branch5b torchvision.transforms.functional.to_tensor self.conv2b_bn self.dc1 SampleMetadata self.gt_handle.header.get_zooms labeled_target.view.sum self.dc8 skimage.exposure.equalize_adapthist torch.is_tensor self.UNet3D.super.__init__ torch.cat format numpy.random.randint self.transform PIL.Image.fromarray.std self.ec7 self.branch3a_drop setuptools.setup self.downconv.size setuptools.find_packages elem.dtype.name.startswith scipy.ndimage.filters.gaussian_filter torch.nn.Dropout2d masking.sum.sum self.conv1b_drop self.conv2b scipy.spatial.distance.dice numpy.isnan elem.dtype.name.__numpy_type_map self.conv2a_drop self.conv1a_bn torch.DoubleTensor numpy.reshape torch.nn.ConvTranspose3d codecs.open self.branch5a torch.nn.Conv3d torch.nn.MaxPool3d RuntimeError masking.squeeze.nonzero list self.prediction self.conv2_drop os.path.join groundtruth.flatten numpy.meshgrid self.amort_bn numpy.random.rand torchvision.transforms.functional.affine numpy.round input.index_select self.dc2 self.sample_augment.append self.dc0 scipy.ndimage.interpolation.map_coordinates masking.nonzero.squeeze self.conv2a self.ec5 map TypeError tqdm.tqdm.set_postfix self.sample_augment self.branch1b_bn self.transform.undo_transform self._load_filenames torch.nn.Sequential self.label_augment self.get_params input.index_select.view scipy.spatial.distance.jaccard self.conv1a_drop self.DownConv.super.__init__ round self.handlers.append self.UpConv.super.__init__ self.dc9 SegmentationPair2D.get_pair_shapes numpy.transpose self.downconv os.path.abspath numpy.percentile self.gt_handle.get_fdata numpy.array self.conv2 self.pool0 numpy.flip self.conv1_drop self.ec1 self.filename_pairs.append torchvision.transforms.functional.normalize self.branch5a_bn self.branch5b_drop self.ec4 self.elastic_transform numpy.sum self.branch2b_bn super.__init__ self.concat_bn torch.sigmoid diff_conf.mean self.ec6 global_pool.expand.expand t.undo_transform self.threshold.target.torch.gt.float self.branch2a_drop numpy.random.normal self.branch4b labeled_input.view.sum self.conv1 self.get_pair_shapes self.dc6 PIL.Image.fromarray self.branch5a_drop self.amort_drop nibabel.load numpy.sqrt.item self.conv1_bn torch.nn.MaxPool2d sample.update self.dc7 self.pool2 self.concat_drop training_mean.input_data.pow metric_fn self.conv1b self.pool1 training_mean.item zip unittest.mock.MagicMock super numpy.asarray masking.squeeze.squeeze gt_data.np.flip.copy
@developer
Could please help me check this issue?
May I pull a request to fix it?
Thank you very much.