Merge pull request #111 from climate-processes/dev

Version 1.3 release candidate

.github/workflows/check_formatting.yml

@@ -0,0 +1,14 @@
+name: check_formatting
+on: [push, pull_request]
+jobs:
+  formatting_job:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.8'
+      - run: pip install .
+      - run: pip install black
+      - run: black tobac --check
+

.github/workflows/docker-image.yml

@@ -1,10 +1,6 @@
 name: Docker Image CI
 
-on:
-  push:
-    branches: [ master, dev, v2.0-dev ]
-  pull_request:
-    branches: [ master, dev, v2.0-dev ]
+on: [push, pull_request]
 
 jobs:
 

.gitignore

@@ -0,0 +1,5 @@
+*.pyc
+__pycache__
+.vscode
+htmlcov
+.coverage

.pre-commit-config.yaml

@@ -0,0 +1,5 @@
+repos:
+-   repo: https://github.com/psf/black
+    rev: 21.12b0
+    hooks:
+    -   id: black

CHANGELOG.md

@@ -0,0 +1,29 @@
+### Tobac Changelog
+
+_**Version 1.3:**_
+
+**Enhancements**
+
+- Significant performance improvements for tracking [#89](https://github.com/climate-processes/tobac/pull/89)
+- Significant performance improvements for feature detection and segmentation [#90](https://github.com/climate-processes/tobac/pull/90)
+- Performance improvement for `calculate_area` [#93](https://github.com/climate-processes/tobac/issues/93)
+- Added ability to set a user defined stub cell value instead of `np.nan`. Default value is `-1` and stub cell values are now integers instead of floats by default [#74](https://github.com/climate-processes/tobac/issues/93)
+- Added deprecation warnings for parameters `min_num` in feature detection and `d_min` in tracking, and added exceptions when multiple, incompatible parameters are given (e.g. `d_max` and `v_max`) [#107](https://github.com/climate-processes/tobac/pull/107)
+
+**Bug fixes**
+
+- Fixed level parameter in segmentation, as this previously had no effect [#92](https://github.com/climate-processes/tobac/pull/92)
+- Remove `is` comparisons for string literals [#99](https://github.com/climate-processes/tobac/pull/99)
+- Added missing `raise` for exception in `get_spacings` [#105](https://github.com/climate-processes/tobac/pull/105)
+- Remove automatic setting of matplotlib backend to `agg` on import [#100](https://github.com/climate-processes/tobac/pull/100)
+- Fix deprecation warnings for changed import paths in dependencies [#110](https://github.com/climate-processes/tobac/pull/110)
+
+**Documentation**
+
+- Added recommended python style [#72](https://github.com/climate-processes/tobac/issues/72)
+- Updated author list and email addresses [#109](https://github.com/climate-processes/tobac/pull/109)
+
+**Repository enhancements**
+
+- Black formatting of all python code and formatting check in actions [#78](https://github.com/climate-processes/tobac/pull/78)
+- Pre-commit hook for black formatting [#96](https://github.com/climate-processes/tobac/pull/96)

CONTRIBUTING.md

@@ -36,8 +36,9 @@ Please create a new issue on [GitHub](https://github.com/climate-processes/tobac
 * If it is a larger change or an newly added feature or workflow, please place an example of use in the [tobac-tutorials](https://github.com/climate-processes/tobac-tutorials) repository or adapt the existing examples there.
 * If necessary add a folder or modify a file.
 * The code should be PEP 8 compliant, as this facilitates our collaboration. Please use the latest version of [black](https://black.readthedocs.io/en/stable/) to format your code. When you submit a pull request, all files are checked for formatting.
+* The tobac repository is set up with pre-commit hooks to automatically format your code when commiting changes. Please run the command "pre-commit install" in the root directory of tobac to set up pre-commit formatting.
 
-We hope that we can respond within two weeks.
+We aim to respond to all new issues/pull requests as soon as possible, however at times this is not possible due to work commitments.
 
 ### Numpydoc Example <a name='docstringExample'>
 ```python

README.md

@@ -52,7 +52,9 @@ pip install tobac/
 
 Contributing
 ------------
-The current development branch is v2.0-dev.
+The current development branch for minor updates to tobac v1 is dev.
+
+Preliminary development of the future major update to tobac is v2.0-dev.
 
 For more details on contributing, please see https://github.com/climate-processes/tobac/blob/v2.0-dev/CONTRIBUTING.md
 

conda-requirements.txt

@@ -4,9 +4,10 @@ scipy
 scikit-image
 pandas
 pytables
-matplotlib 
+matplotlib
 iris
-cf-units 
-xarray 
+cf-units
+xarray
 cartopy
 trackpy
+pre-commit

examples/Example_OLR_Tracking_model/Example_OLR_Tracking_model.ipynb

@@ -165,7 +165,7 @@
     "parameters_features={}\n",
     "parameters_features['position_threshold']='weighted_diff'\n",
     "parameters_features['sigma_threshold']=0.5\n",
-    "parameters_features['min_num']=4\n",
+    "parameters_features['n_min_threshold']=4\n",
     "parameters_features['target']='minimum'\n",
     "parameters_features['threshold']=[250,225,200,175,150]"
    ]
@@ -409,7 +409,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -423,7 +423,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,

examples/Example_OLR_Tracking_satellite/Example_OLR_Tracking_satellite.ipynb

@@ -296,7 +296,7 @@
     "parameters_features={}\n",
     "parameters_features['position_threshold']='weighted_diff'\n",
     "parameters_features['sigma_threshold']=0.5\n",
-    "parameters_features['min_num']=4\n",
+    "parameters_features['n_min_threshold']=4\n",
     "parameters_features['target']='minimum'\n",
     "parameters_features['threshold']=[250,225,200,175,150]"
    ]
@@ -538,7 +538,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -552,7 +552,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,

examples/Example_Precip_Tracking/Example_Precip_Tracking.ipynb

@@ -324,7 +324,6 @@
     "parameters_features={}\n",
     "parameters_features['position_threshold']='weighted_diff'\n",
     "parameters_features['sigma_threshold']=0.5\n",
-    "parameters_features['min_num']=3\n",
     "parameters_features['min_distance']=0\n",
     "parameters_features['sigma_threshold']=1\n",
     "parameters_features['threshold']=[1,2,3,4,5,10,15] #mm/h\n",
@@ -438,8 +437,7 @@
     "parameters_linking['memory']=0\n",
     "parameters_linking['time_cell_min']=5*60\n",
     "parameters_linking['method_linking']='predict'\n",
-    "parameters_linking['v_max']=10\n",
-    "parameters_linking['d_min']=2000\n"
+    "parameters_linking['v_max']=10\n"
    ]
   },
   {
@@ -589,7 +587,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -603,7 +601,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,

examples/Example_Updraft_Tracking/Example_Updraft_Tracking.ipynb

@@ -559,7 +559,6 @@
     "parameters_features={}\n",
     "parameters_features['position_threshold']='weighted_diff'\n",
     "parameters_features['sigma_threshold']=0.5\n",
-    "parameters_features['min_num']=3\n",
     "parameters_features['min_distance']=0\n",
     "parameters_features['sigma_threshold']=1\n",
     "parameters_features['threshold']=[3,5,10] #m/s\n",
@@ -658,8 +657,7 @@
     "parameters_linking['memory']=0\n",
     "parameters_linking['time_cell_min']=5*60\n",
     "parameters_linking['method_linking']='predict'\n",
-    "parameters_linking['v_max']=10\n",
-    "parameters_linking['d_min']=2000\n"
+    "parameters_linking['v_max']=10\n"
    ]
   },
   {
@@ -763,7 +761,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -777,7 +775,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,

setup.py

@@ -1,12 +1,28 @@
 from setuptools import setup
 
-setup(name='tobac',
-      version='1.2',
-      description='Tracking and object-based analysis of clouds',
-      url='http://github.com/climate-processes/tobac',
-      author='Max Heikenfeld',
-      author_email='max.heikenfeld@physics.ox.ac.uk',
-      license='GNU',
-      packages=['tobac'],
-      install_requires=[],
-      zip_safe=False)
+setup(
+    name="tobac",
+    version="1.3",
+    description="Tracking and object-based analysis of clouds",
+    url="http://github.com/climate-processes/tobac",
+    author=[
+        "Max Heikenfeld",
+        "William Jones",
+        "Fabian Senf",
+        "Sean Freeman",
+        "Julia Kukulies",
+        "Peter Marinescu",
+    ],
+    author_email=[
+        "max.heikenfeld@physics.ox.ac.uk",
+        "william.jones@physics.ox.ac.uk",
+        "senf@tropos.de",
+        "sean.freeman@colostate.edu",
+        "julia.kukulies@gu.se",
+        "peter.marinescu@colostate.edu",
+    ],
+    license="BSD-3-Clause License",
+    packages=["tobac"],
+    install_requires=[],
+    zip_safe=False,
+)

tobac/__init__.py

@@ -1,23 +1,63 @@
-#from .tracking import maketrack
-from .segmentation import segmentation_3D, segmentation_2D,watershedding_3D,watershedding_2D
-from .centerofgravity import calculate_cog,calculate_cog_untracked,calculate_cog_domain
-from .plotting import plot_tracks_mask_field,plot_tracks_mask_field_loop,plot_mask_cell_track_follow,plot_mask_cell_track_static,plot_mask_cell_track_static_timeseries
-from .plotting import plot_lifetime_histogram,plot_lifetime_histogram_bar,plot_histogram_cellwise,plot_histogram_featurewise
-from .plotting import plot_mask_cell_track_3Dstatic,plot_mask_cell_track_2D3Dstatic
-from .plotting import plot_mask_cell_individual_static,plot_mask_cell_individual_3Dstatic
+# from .tracking import maketrack
+from .segmentation import (
+    segmentation_3D,
+    segmentation_2D,
+    watershedding_3D,
+    watershedding_2D,
+)
+from .centerofgravity import (
+    calculate_cog,
+    calculate_cog_untracked,
+    calculate_cog_domain,
+)
+from .plotting import (
+    plot_tracks_mask_field,
+    plot_tracks_mask_field_loop,
+    plot_mask_cell_track_follow,
+    plot_mask_cell_track_static,
+    plot_mask_cell_track_static_timeseries,
+)
+from .plotting import (
+    plot_lifetime_histogram,
+    plot_lifetime_histogram_bar,
+    plot_histogram_cellwise,
+    plot_histogram_featurewise,
+)
+from .plotting import plot_mask_cell_track_3Dstatic, plot_mask_cell_track_2D3Dstatic
+from .plotting import (
+    plot_mask_cell_individual_static,
+    plot_mask_cell_individual_3Dstatic,
+)
 from .plotting import animation_mask_field
 from .plotting import make_map, map_tracks
-from .analysis import cell_statistics,cog_cell,lifetime_histogram,histogram_featurewise,histogram_cellwise
-from .analysis import calculate_velocity,calculate_distance,calculate_area
+from .analysis import (
+    cell_statistics,
+    cog_cell,
+    lifetime_histogram,
+    histogram_featurewise,
+    histogram_cellwise,
+)
+from .analysis import calculate_velocity, calculate_distance, calculate_area
 from .analysis import calculate_nearestneighbordistance
-from .analysis import velocity_histogram,nearestneighbordistance_histogram,area_histogram
+from .analysis import (
+    velocity_histogram,
+    nearestneighbordistance_histogram,
+    area_histogram,
+)
 from .analysis import calculate_overlap
-from .utils import mask_cell,mask_cell_surface,mask_cube_cell,mask_cube_untracked,mask_cube,column_mask_from2D,get_bounding_box
-from .utils import mask_features,mask_features_surface,mask_cube_features
+from .utils import (
+    mask_cell,
+    mask_cell_surface,
+    mask_cube_cell,
+    mask_cube_untracked,
+    mask_cube,
+    column_mask_from2D,
+    get_bounding_box,
+)
+from .utils import mask_features, mask_features_surface, mask_cube_features
 
-from .utils import add_coordinates,get_spacings
+from .utils import add_coordinates, get_spacings
 from .feature_detection import feature_detection_multithreshold
 from .tracking import linking_trackpy
 from .wrapper import maketrack
 from .wrapper import tracking_wrapper
-