Remove named tensors

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,26 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+A clear and concise description on how to reproduce the problem.
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Environment**
+dlup version:
+How installed:
+Python version:
+Operating System:
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.pre-commit-config.yaml

@@ -34,15 +34,22 @@ repos:
     - id: isort
       name: isort (pyi)
       types: [pyi]
--   repo: https://github.com/pycqa/pylint
-    rev: v2.8.2
-    hooks:
-    -   id: pylint
 -   repo: https://github.com/psf/black
-    rev: 21.5b0
+    rev: 21.6b0
     hooks:
     -   id: black
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.812
+    rev: v0.902
     hooks:
     - id: mypy
+      additional_dependencies: [types-requests, types-docutils]
+-   repo: local
+    hooks:
+    -   id: pylint
+        name: pylint
+        entry: pylint
+        language: system
+        types: [python]
+        args:
+            - dlup
+            - --errors-only

README.md

@@ -1,5 +1,5 @@
-[![tox](https://github.com/directgroup/direct/actions/workflows/tox.yml/badge.svg)](https://github.com/directgroup/direct/actions/workflows/tox.yml) 
-[![pylint](https://github.com/directgroup/direct/actions/workflows/pylint.yml/badge.svg)](https://github.com/directgroup/direct/actions/workflows/pylint.yml) 
+[![tox](https://github.com/directgroup/direct/actions/workflows/tox.yml/badge.svg)](https://github.com/directgroup/direct/actions/workflows/tox.yml)
+[![pylint](https://github.com/directgroup/direct/actions/workflows/pylint.yml/badge.svg)](https://github.com/directgroup/direct/actions/workflows/pylint.yml)
 [![black](https://github.com/directgroup/direct/actions/workflows/black.yml/badge.svg)](https://github.com/directgroup/direct/actions/workflows/black.yml)
 
 # DIRECT

direct/checkpointer.py

@@ -1,5 +1,6 @@
 # coding=utf-8
 # Copyright (c) DIRECT Contributors
+"""Checkpointer module. Handles all logic related to checkpointing."""
 import datetime
 import logging
 import pathlib
@@ -25,6 +26,8 @@
 
 
 class Checkpointer:
+    """Main Checkpointer module. Handles writing and restoring from checkpoints of modules and submodels."""
+
     def __init__(
         self,
         save_directory: pathlib.Path,
@@ -180,8 +183,12 @@ def _load_checkpoint(self, checkpoint_path: PathOrString) -> Dict:
         try:
             checkpoint = torch.load(checkpoint_path, map_location=torch.device("cpu"))
 
-        except UnpicklingError as e:
-            self.logger.exception(f"Tried to load {checkpoint_path}, but was unable to unpickle: {e}.")
+        except UnpicklingError as exc:
+            self.logger.exception(
+                "Tried to load {checkpoint_path}, but was unable to unpickle: {exc}.",
+                checkpoint_path=checkpoint_path,
+                exc=exc,
+            )
             raise
 
         return checkpoint

direct/common/subsample.py

@@ -102,7 +102,7 @@ def __call__(self, data, seed=None, return_acs=False):
         ndarray
         """
         self.rng.seed(seed)
-        mask = self.mask_func(data, return_acs=return_acs)
+        mask = self.mask_func(data, return_acs=return_acs)  # pylint: disable = E1123
         return mask
 
 

direct/data/bbox.py

@@ -1,5 +1,6 @@
 # coding=utf-8
 # Copyright (c) DIRECT Contributors
+"""Utilities to handle images with respect to bounding boxes."""
 from typing import List, Union
 
 import numpy as np
@@ -59,10 +60,8 @@ def crop_to_bbox(
         patch = pad_value * np.ones(bbox_size, dtype=data.dtype)
 
     patch_idx = [slice(i, j) for i, j in zip(l_offset, bbox_size - r_offset)]
-    patch_names = patch.names
 
-    patch.rename(None)[tuple(patch_idx)] = out.rename(None)
-    patch = patch.refine_names(*patch_names)
+    patch[tuple(patch_idx)] = out
 
     return patch