Merge branch 'main' of github.com:GilesStrong/mode_muon_tomography in…

…to kuhn_scatter_model

.github/workflows/linting.yml

@@ -10,8 +10,8 @@ jobs:
   black:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
         with:
           python-version: "3.8"
       - uses: psf/black@22.1.0
@@ -21,17 +21,26 @@ jobs:
   flake8:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
         with:
           python-version: "3.8"
       - uses: py-actions/flake8@v1
-
+
+  isort:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.8"
+      - uses: isort/isort-action@master
+
   mypy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
       with:
         python-version: "3.8"
     - name: Install Dependencies

.pre-commit-config.yaml

@@ -11,12 +11,11 @@ repos:
     - id: flake8
       args: [--ignore=E741 W503 E203 E501 C901]
 
-  # - repo: https://github.com/pre-commit/mirrors-mypy
-  #   rev: v0.812
-  #   hooks:
-  #     - id: mypy
-  #       exclude: tests/|setup.py
-  #       args: [--disallow-untyped-calls, --disallow-untyped-defs, --check-untyped-defs, --ignore-missing-imports, --no-strict-optional]
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black", "--filter-files"]
 
   - repo: local
     hooks:

AUTHORS.md

@@ -2,7 +2,7 @@
 
 The TomOpt project, and its continued development and support, is the result of the combined work of many people, whose contributions are summarised below.
 
-In order to start time, the TomOpt authors/contributors are: Giles Strong, Tommaso Dorigo, Andrea Giammanco, Pietro Vischia, Jan Kieseler, Maxime Lagrange, Federico Nardi, Haitham Zaraket, Max Lamparth, Federica Fanzago, Oleg Savchenko, Nitesh Sharma, Anna Bordignon, Mariam Safieldin.
+In order to start time, the TomOpt authors/contributors are: Giles Strong, Tommaso Dorigo, Andrea Giammanco, Pietro Vischia, Jan Kieseler, Maxime Lagrange, Federico Nardi, Haitham Zaraket, Max Lamparth, Federica Fanzago, Oleg Savchenko, Nitesh Sharma, Anna Bordignon, Mariam Safieldin, Aitor Orio.
 
 ## Giles Chatham Strong (@GilesStrong)
 

docs/source/conf.py

@@ -6,13 +6,14 @@
 
 # -- Path setup --------------------------------------------------------------
 
+import datetime
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import os
 import sys
-import datetime
 
 sys.path.insert(0, os.path.abspath("../.."))
 

requirements.txt

@@ -1,6 +1,6 @@
 # User requirements
 functorch
-torch>=1.10.0
+torch>=1.10.0,<2.0.0  # pt 2 hasn't been fully tested yet
 seaborn ~= 0.11.0
 matplotlib >= 3.1
 numpy >=1.20.2
@@ -21,4 +21,5 @@ pytest
 mypy
 pytest-mock
 flaky
-pytest-lazy-fixture
+pytest-lazy-fixture
+isort

setup.cfg

@@ -4,6 +4,9 @@ license_files = LICENSE
 [bdist_wheel]
 universal=0
 
+[isort]
+profile = black
+
 [mypy]
 python_version = 3.8
 disallow_untyped_calls = False

setup.py

@@ -2,14 +2,14 @@
 # -*- coding: utf-8 -*-
 
 try:
-    from setuptools import setup, find_packages
+    from setuptools import find_packages, setup
 except ImportError:
-    from distutils.core import setup, find_packages
+    from distutils.core import find_packages, setup
 
 with open("README.md", encoding="utf-8") as fin:
     long_description = fin.read()
 
-dev_only = ["pre-commit", "black", "flake8", "mypy", "pytest", "pytest-mock", "flaky", "pytest-lazy-fixture"]
+dev_only = ["pre-commit", "black", "flake8", "mypy", "pytest", "isort", "pytest-mock", "flaky", "pytest-lazy-fixture"]
 with open("requirements.txt", encoding="utf-8") as f:
     requirements = [r for r in f.read().strip().split("\n") if r not in dev_only]
 

tests/test_callbacks.py

@@ -1,44 +1,53 @@
-import pytest
-import numpy as np
-from pytest_mock import mocker  # noqa F401
 import math
-import pandas as pd
+import os
 from functools import partial
 from glob import glob
-from fastcore.all import Path
-import matplotlib.pyplot as plt
-import h5py
-import os
 
+import h5py
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+import pytest
 import torch
-from torch import Tensor
 import torch.nn.functional as F
+from fastcore.all import Path
+from pytest_mock import mocker  # noqa F401
+from torch import Tensor
 
-from tomopt.optimisation.callbacks.callback import Callback
-from tomopt.optimisation.callbacks.eval_metric import EvalMetric
+from tomopt.muon import MuonBatch, MuonGenerator2016
 from tomopt.optimisation.callbacks import (
-    NoMoreNaNs,
-    PredHandler,
+    CostCoefWarmup,
+    HeatMapGif,
+    HitRecord,
     MetricLogger,
+    MuonResampler,
+    NoMoreNaNs,
+    OneCycle,
     PanelMetricLogger,
-    ScatterRecord,
-    HitRecord,
-    CostCoefWarmup,
     PanelOptConfig,
-    MuonResampler,
-    HeatMapGif,
-    VolumeTargetPredHandler,
-    Save2HDF5PredHandler,
-    WarmupCallback,
+    PanelUpdateLimiter,
     PostWarmupCallback,
+    PredHandler,
+    Save2HDF5PredHandler,
+    ScatterRecord,
     SigmoidPanelSmoothnessSchedule,
-    PanelUpdateLimiter,
-    OneCycle,
+    VolumeTargetPredHandler,
+    WarmupCallback,
 )
+from tomopt.optimisation.callbacks.callback import Callback
+from tomopt.optimisation.callbacks.eval_metric import EvalMetric
 from tomopt.optimisation.loss import VoxelX0Loss
-from tomopt.optimisation.wrapper.volume_wrapper import AbsVolumeWrapper, FitParams, PanelVolumeWrapper
-from tomopt.volume import PanelDetectorLayer, DetectorPanel, DetectorHeatMap, SigmoidDetectorPanel
-from tomopt.muon import MuonBatch, MuonGenerator2016
+from tomopt.optimisation.wrapper.volume_wrapper import (
+    AbsVolumeWrapper,
+    FitParams,
+    PanelVolumeWrapper,
+)
+from tomopt.volume import (
+    DetectorHeatMap,
+    DetectorPanel,
+    PanelDetectorLayer,
+    SigmoidDetectorPanel,
+)
 
 LW = Tensor([1, 1])
 SZ = 0.1

tests/test_forwards_backwards.py

@@ -1,16 +1,23 @@
 from collections import defaultdict
-import pytest
-from pytest_lazyfixture import lazy_fixture
 
+import pytest
 import torch
-from torch import nn, Tensor
 import torch.nn.functional as F
+from pytest_lazyfixture import lazy_fixture
+from torch import Tensor, nn
 
 from tomopt.core import X0
-from tomopt.volume import Volume, PassiveLayer, PanelDetectorLayer, DetectorPanel, DetectorHeatMap, SigmoidDetectorPanel
+from tomopt.inference import PanelX0Inferrer, ScatterBatch
 from tomopt.muon import MuonBatch, MuonGenerator2016
-from tomopt.inference import ScatterBatch, PanelX0Inferrer
-from tomopt.optimisation import VoxelX0Loss, MuonResampler
+from tomopt.optimisation import MuonResampler, VoxelX0Loss
+from tomopt.volume import (
+    DetectorHeatMap,
+    DetectorPanel,
+    PanelDetectorLayer,
+    PassiveLayer,
+    SigmoidDetectorPanel,
+    Volume,
+)
 
 LW = Tensor([1, 1])
 SZ = 0.1

tests/test_heatmap.py

@@ -1,20 +1,19 @@
-import pytest
-from pytest_mock import mocker  # noqa F401
-from unittest.mock import patch
-import numpy as np
-from fastcore.all import Path
 import os
+from unittest.mock import patch
 
+import numpy as np
+import pytest
 import torch
+from fastcore.all import Path
+from pytest_mock import mocker  # noqa F401
 from torch import Tensor, nn
 
-from tomopt.volume import PassiveLayer, PanelDetectorLayer, DetectorHeatMap, Volume
-from tomopt.volume.heatmap import GMM
-from tomopt.optimisation import MuonResampler
-from tomopt.muon import MuonBatch, MuonGenerator2016
 from tomopt.core import X0
+from tomopt.muon import MuonBatch, MuonGenerator2016
+from tomopt.optimisation import MuonResampler
 from tomopt.utils import jacobian
-
+from tomopt.volume import DetectorHeatMap, PanelDetectorLayer, PassiveLayer, Volume
+from tomopt.volume.heatmap import GMM
 
 LW = Tensor([1, 1])
 SZ = 0.1

tests/test_inference.py

@@ -1,27 +1,33 @@
-import pytest
-from pytest_mock import mocker  # noqa F401
-import numpy as np
-from unittest.mock import patch
-from typing import Tuple
 import math
-from pytest_lazyfixture import lazy_fixture
+from typing import Tuple
+from unittest.mock import patch
 
+import numpy as np
+import pytest
 import torch
-from torch import Tensor, nn
 import torch.nn.functional as F
+from pytest_lazyfixture import lazy_fixture
+from pytest_mock import mocker  # noqa F401
+from torch import Tensor, nn
 
-from tomopt.volume import PassiveLayer, Volume, PanelDetectorLayer, DetectorPanel, SigmoidDetectorPanel
-from tomopt.muon import MuonBatch, MuonGenerator2016
 from tomopt.core import X0
 from tomopt.inference import (
+    DenseBlockClassifierFromX0s,
+    GenScatterBatch,
     PanelX0Inferrer,
     ScatterBatch,
-    GenScatterBatch,
-    DenseBlockClassifierFromX0s,
 )
 from tomopt.inference.volume import AbsIntClassifierFromX0
+from tomopt.muon import MuonBatch, MuonGenerator2016
 from tomopt.optimisation import MuonResampler
 from tomopt.utils import jacobian
+from tomopt.volume import (
+    DetectorPanel,
+    PanelDetectorLayer,
+    PassiveLayer,
+    SigmoidDetectorPanel,
+    Volume,
+)
 
 LW = Tensor([1, 1])
 SZ = 0.1

tests/test_loss.py

@@ -1,11 +1,16 @@
-from pytest_mock import mocker  # noqa F401
 import numpy as np
-
 import torch
-from torch import nn, Tensor
 import torch.nn.functional as F
-
-from tomopt.optimisation import VoxelX0Loss, VoxelClassLoss, VolumeClassLoss, VolumeIntClassLoss, integer_class_loss
+from pytest_mock import mocker  # noqa F401
+from torch import Tensor, nn
+
+from tomopt.optimisation import (
+    VolumeClassLoss,
+    VolumeIntClassLoss,
+    VoxelClassLoss,
+    VoxelX0Loss,
+    integer_class_loss,
+)
 from tomopt.optimisation.loss.loss import AbsDetectorLoss
 from tomopt.volume import Volume
 

tests/test_muon.py

@@ -1,13 +1,12 @@
-import pytest
-from pytest_mock import mocker  # noqa F401
 import numpy as np
-
+import pytest
 import torch
+from pytest_mock import mocker  # noqa F401
 from torch import Tensor, nn
 
-from tomopt.muon import MuonGenerator2016, MuonGenerator2015, MuonBatch
-from tomopt.volume import PassiveLayer, Volume, PanelDetectorLayer, DetectorPanel
 from tomopt.core import X0
+from tomopt.muon import MuonBatch, MuonGenerator2015, MuonGenerator2016
+from tomopt.volume import DetectorPanel, PanelDetectorLayer, PassiveLayer, Volume
 
 N = 3
 LW = Tensor([1, 1])
@@ -307,6 +306,7 @@ def test_muon_batch_scatter_dtheta_dphi():
     assert (batch.xy == start.xy).all()
 
 
+@pytest.mark.flaky(max_runs=3, min_passes=1)
 def test_muon_batch_angle_consistency():
     volume = Volume(get_panel_layers())
     mg = MuonGenerator2016.from_volume(volume)

tests/test_passives.py

@@ -1,18 +1,17 @@
 import pytest
-
 import torch
-from torch import nn, Tensor
 import torch.nn.functional as F
+from torch import Tensor, nn
 
 from tomopt.core import X0
 from tomopt.optimisation.data.passives import (
+    AbsPassiveGenerator,
+    BlockPresentPassiveGenerator,
     PassiveYielder,
-    VoxelPassiveGenerator,
     RandomBlockPassiveGenerator,
-    BlockPresentPassiveGenerator,
-    AbsPassiveGenerator,
+    VoxelPassiveGenerator,
 )
-from tomopt.volume import Volume, PassiveLayer, PanelDetectorLayer, DetectorPanel
+from tomopt.volume import DetectorPanel, PanelDetectorLayer, PassiveLayer, Volume
 
 LW = Tensor([1, 1])
 SZ = 0.1