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.github/workflows/python-app.yml

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# This workflow will install Python dependencies, run tests and lint with a single version of Python
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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name: Python application
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name: Pytest & Flake8
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on:
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push:

.readthedocs.yml

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version: 2
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conda:
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environment: doc/environment.yml
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python:
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install:
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- method: setuptools
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path: .

CHANGELOG.rst

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Changelog
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=========
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All notable changes to this project will be documented in this file.
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The format is based on `Keep a Changelog <https://keepachangelog.com/en>`_
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and this project adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
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[Unreleased]
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------------
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Changed
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^^^^^^^
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Fixed
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^^^^^
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Added
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^^^^^
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[3.4.0] - 2021-03-29
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--------------------
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Changed
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^^^^^^^
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- `TrackEddiesObservations.filled_by_interpolation` method stop to normalize longitude, to continue to have same
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beahviour you must call before `TrackEddiesObservations.normalize_longitude`
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Fixed
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^^^^^
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- Use `safe_load` for yaml load
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- repr of EddiesObservation when the collection is empty (time attribute empty array)
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- display_timeline and event_timeline can now use colors according to 'y' values.
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- event_timeline now plot all merging event in one plot, instead of one plot per merging. Same for splitting. (avoid bad legend)
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Added
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^^^^^
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- Identification file could be load in memory before to be read with netcdf library to get speed up in case of slow disk
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- Add a filter option in EddyId to be able to remove fine scale (like noise) with same filter order than high scale
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filter
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- Add **EddyQuickCompare** to have few figures about several datasets in comparison based on match function
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- Color and text field for contour in **EddyAnim** could be choose
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- Save EddyAnim in mp4
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- Add method to get eddy contour which enclosed obs defined with (x,y) coordinates
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- Add **EddyNetworkSubSetter** to subset network which need special tool and operation after subset
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- Network:
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- Add method to find relatives segments
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- Add method to get cloase network in an other atlas
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- Management of time cube data for advection
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[3.3.0] - 2020-12-03
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--------------------
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Added
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^^^^^
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- Add an implementation of visvalingam algorithm to simplify polygons with low modification
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- Add method to found close tracks in an other atlas
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- Allow to give a x reference when we display grid to be able to change xlim
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- Add option to EddyId to select data index like `--indexs time=5 depth=2`
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- Add a method to merge several indexs type for eddy obs
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- Get dataset variable like attribute, and lifetime/age are available for all observations
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- Add **EddyInfos** application to get general information about eddies dataset
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- Add method to inspect contour rejection (which are not in eddies)
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- Grid interp could be "nearest" or "bilinear"
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Changed
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^^^^^^^
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- Now to have object informations in plot label used python ```format``` style, several key are available :
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- "t0"
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- "t1"
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- "nb_obs"
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- "nb_tracks" (only for tracked eddies)
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[3.2.0] - 2020-09-16
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--------------------
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[3.1.0] - 2020-06-25
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--------------------

README.md

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[![Documentation Status](https://readthedocs.org/projects/py-eddy-tracker/badge/?version=stable)](https://py-eddy-tracker.readthedocs.io/en/stable/?badge=stable)
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[![Gitter](https://badges.gitter.im/py-eddy-tracker/community.svg)](https://gitter.im/py-eddy-tracker/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
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[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/AntSimi/py-eddy-tracker/master?urlpath=lab/tree/notebooks/python_module/)
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[![pytest](https://github.com/AntSimi/py-eddy-tracker/actions/workflows/python-app.yml/badge.svg)](https://github.com/AntSimi/py-eddy-tracker/actions/workflows/python-app.yml)
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# README #
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### How do I get set up? ###
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#### Short story ####
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```bash
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pip install pyeddytracker
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```
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#### Long story ####
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To avoid problems with installation, use of the virtualenv Python virtual environment is recommended.
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Then use pip to install all dependencies (numpy, scipy, matplotlib, netCDF4, ...), e.g.:
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### Tools gallery ###
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Several examples based on py eddy tracker module are [here](https://py-eddy-tracker.readthedocs.io/en/latest/python_module/index.html).
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![](https://py-eddy-tracker.readthedocs.io/en/latest/_static/logo.png)
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[![](https://py-eddy-tracker.readthedocs.io/en/latest/_static/logo.png)](https://py-eddy-tracker.readthedocs.io/en/latest/python_module/index.html)
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### Quick use ###
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apt.txt

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libgl1-mesa-glx

check.sh

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isort src tests examples
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black src tests examples
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blackdoc src tests examples
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flake8 tests examples src --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 tests examples src --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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pytest -vv --cov py_eddy_tracker --cov-report html

doc/api.rst

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py_eddy_tracker.observations.network
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py_eddy_tracker.observations.observation
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py_eddy_tracker.observations.tracking
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py_eddy_tracker.observations.groups
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py_eddy_tracker.eddy_feature
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py_eddy_tracker.generic
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py_eddy_tracker.gui

doc/changelog.rst

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.. include:: ../CHANGELOG.rst

doc/conf.py

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sphinx_gallery_conf = {
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"examples_dirs": "../examples", # path to your example scripts
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"gallery_dirs": "python_module",
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"capture_repr": ("_repr_html_",),
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"capture_repr": ("_repr_html_", "__repr__"),
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"backreferences_dir": "gen_modules/backreferences",
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"doc_module": ("py_eddy_tracker",),
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"reference_url": {
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"py_eddy_tracker": None,
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"matplotlib": "https://matplotlib.org/",
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"numpy": "https://docs.scipy.org/doc/numpy/",
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},
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"line_numbers": False,
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"filename_pattern": "/pet",
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"repo": "py-eddy-tracker",
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"branch": "master",
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"binderhub_url": "https://mybinder.org",
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"dependencies": ["../requirements.txt"],
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"dependencies": ["environment.yml"],
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# Optional keys
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"use_jupyter_lab": True,
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},

doc/custom_tracking.rst

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Code my own tracking
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********************
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To use your own tracking method, you just need to create a class which inherit
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To use your own tracking method, you just need to create a class which inherits
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from :meth:`py_eddy_tracker.observations.observation.EddiesObservations` and set this class in yaml file like
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we see in the previous topic.
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