Merge branch 'dev_2022' of https://github.com/Mesharou/py-eddy-tracker into dev_2022

Author: gula

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,70 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ master ]
+  schedule:
+    - cron: '41 16 * * 4'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://git.io/codeql-language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.github/workflows/python-app.yml

@@ -3,27 +3,31 @@
 
 name: Pytest & Flake8
 
-on:
-  push:
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
+on: [push, pull_request]
 
 jobs:
   build:
-
-    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, windows-latest]
+        python_version: [3.7, 3.8, 3.9, '3.10']
+    name: Run py eddy tracker build tests
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.7
+    - name: Set up Python ${{ matrix.python_version }}
       uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: ${{ matrix.python_version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest
+        pip install flake8 pytest pytest-cov
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Install package
       run: |
@@ -34,6 +38,3 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        pytest

CHANGELOG.rst

@@ -7,14 +7,78 @@ The format is based on `Keep a Changelog <https://keepachangelog.com/en>`_
 and this project adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
 
 [Unreleased]
-------------
+-------------
 Changed
 ^^^^^^^
+
+- Remove dead end method for network will move dead end to the trash and not remove observations
+
 Fixed
 ^^^^^
+
 Added
 ^^^^^
 
+
+[3.6.1] - 2022-10-14
+--------------------
+Changed
+^^^^^^^
+
+- Rewrite particle candidate to be easily parallelize
+
+Fixed
+^^^^^
+
+- Check strictly increasing coordinates for RegularGridDataset.
+- Grid mask is check to replace mask monovalue by 2D mask with fixed value
+
+Added
+^^^^^
+
+- Add method to colorize contour with a field
+- Add option to force align on to return all step for reference dataset
+- Add method and property to network to easily select segment and network
+- Add method to found same track/segment/network in dataset
+
+[3.6.0] - 2022-01-12
+--------------------
+Changed
+^^^^^^^
+
+- Now time allows second precision (instead of daily precision) in storage on uint32 from 01/01/1950 to 01/01/2086
+  New identifications are produced with this type, old files could still be loaded.
+  If you use old identifications for tracking use the `--unraw` option to unpack old times and store data with the new format.
+- Now amplitude is stored with .1 mm of precision (instead of 1 mm), same advice as for time.
+- Expose more parameters to users for bash tools build_network & divide_network
+- Add warning when loading a file created from a previous version of py-eddy-tracker.
+
+
+
+Fixed
+^^^^^
+
+- Fix bug in convolution(filter), lowest rows was replace by zeros in convolution computation.
+  Important impact for tiny kernel
+- Fix method of sampling before contour fitting
+- Fix bug when loading dataset in zarr format, not all variables were correctly loaded
+- Fix bug when zarr dataset has same size for number of observations and contour size
+- Fix bug when tracking, previous_virtual_obs was not always loaded
+
+Added
+^^^^^
+
+- Allow to replace mask by isnan method to manage nan data instead of masked data
+- Add drifter colocation example
+
+[3.5.0] - 2021-06-22
+--------------------
+
+Fixed
+^^^^^
+- GridCollection get_next_time_step & get_previous_time_step needed more files to work in the dataset list.
+  The loop needed explicitly self.dataset[i+-1] even when i==0, therefore indice went out of range
+
 [3.4.0] - 2021-03-29
 --------------------
 Changed

README.md

@@ -10,20 +10,24 @@
 
 Method was described in :
 
+[Pegliasco, C., Delepoulle, A., Morrow, R., Faugère, Y., and Dibarboure, G.: META3.1exp : A new Global Mesoscale Eddy Trajectories Atlas derived from altimetry, Earth Syst. Sci. Data Discuss.](https://doi.org/10.5194/essd-14-1087-2022)
+
 [Mason, E., A. Pascual, and J. C. McWilliams, 2014: A new sea surface height–based code for oceanic mesoscale eddy tracking.](https://doi.org/10.1175/JTECH-D-14-00019.1)
 
 ### Use case ###
 
 Method is used in :
- 
+
 [Mason, E., A. Pascual, P. Gaube, S.Ruiz, J. Pelegrí, A. Delepoulle, 2017: Subregional characterization of mesoscale eddies across the Brazil-Malvinas Confluence](https://doi.org/10.1002/2016JC012611)
 
 ### How do I get set up? ###
 
 #### Short story ####
+
 ```bash
 pip install pyeddytracker
 ```
+
 #### Long story ####
 
 To avoid problems with installation, use of the virtualenv Python virtual environment is recommended.
@@ -34,12 +38,20 @@ Then use pip to install all dependencies (numpy, scipy, matplotlib, netCDF4, ...
 pip install numpy scipy netCDF4 matplotlib opencv-python pyyaml pint polygon3
 ```
 
-Then run the following to install the eddy tracker:
+Clone :
+
+```bash
+git clone https://github.com/AntSimi/py-eddy-tracker
+```
+
+Then run the following to install the eddy tracker :
 
 ```bash
 python setup.py install
 ```
+
 ### Tools gallery ###
+
 Several examples based on py eddy tracker module are [here](https://py-eddy-tracker.readthedocs.io/en/latest/python_module/index.html).
 
 [![](https://py-eddy-tracker.readthedocs.io/en/latest/_static/logo.png)](https://py-eddy-tracker.readthedocs.io/en/latest/python_module/index.html)

check.sh

@@ -1,7 +1,5 @@
-isort src tests examples
-black src tests examples
-blackdoc src tests examples
-flake8 tests examples src --count --select=E9,F63,F7,F82 --show-source --statistics
-# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-flake8 tests examples src --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-pytest -vv --cov py_eddy_tracker --cov-report html
+isort .
+black .
+blackdoc .
+flake8 .
+python -m pytest -vv --cov py_eddy_tracker --cov-report html

doc/conf.py

@@ -96,9 +96,9 @@
 master_doc = "index"
 
 # General information about the project.
-project = u"py-eddy-tracker"
-copyright = u"2019, A. Delepoulle & E. Mason"
-author = u"A. Delepoulle & E. Mason"
+project = "py-eddy-tracker"
+copyright = "2019, A. Delepoulle & E. Mason"
+author = "A. Delepoulle & E. Mason"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -272,8 +272,8 @@
     (
         master_doc,
         "py-eddy-tracker.tex",
-        u"py-eddy-tracker Documentation",
-        u"A. Delepoulle \\& E. Mason",
+        "py-eddy-tracker Documentation",
+        "A. Delepoulle \\& E. Mason",
         "manual",
     ),
 ]
@@ -304,7 +304,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, "py-eddy-tracker", u"py-eddy-tracker Documentation", [author], 1)
+    (master_doc, "py-eddy-tracker", "py-eddy-tracker Documentation", [author], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -320,7 +320,7 @@
     (
         master_doc,
         "py-eddy-tracker",
-        u"py-eddy-tracker Documentation",
+        "py-eddy-tracker Documentation",
         author,
         "py-eddy-tracker",
         "One line description of project.",

doc/environment.yml

@@ -2,7 +2,7 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python=3.7
+  - python=3.10
   - ffmpeg
   - pip:
     - sphinx-gallery

doc/grid_identification.rst

@@ -47,38 +47,42 @@ Activate verbose
 .. code-block:: python
 
     from py_eddy_tracker import start_logger
-    start_logger().setLevel('DEBUG') # Available options: ERROR, WARNING, INFO, DEBUG
+
+    start_logger().setLevel("DEBUG")  # Available options: ERROR, WARNING, INFO, DEBUG
 
 Run identification
 
 .. code-block:: python
 
     from datetime import datetime
+
     h = RegularGridDataset(grid_name, lon_name, lat_name)
-    h.bessel_high_filter('adt', 500, order=3)
+    h.bessel_high_filter("adt", 500, order=3)
     date = datetime(2019, 2, 23)
     a, c = h.eddy_identification(
-        'adt', 'ugos', 'vgos', # Variables used for identification
-        date, # Date of identification
-        0.002, # step between two isolines of detection (m)
-        pixel_limit=(5, 2000), # Min and max pixel count for valid contour
-        shape_error=55, # Error max (%) between ratio of circle fit and contour
-        )
+        "adt",
+        "ugos",
+        "vgos",  # Variables used for identification
+        date,  # Date of identification
+        0.002,  # step between two isolines of detection (m)
+        pixel_limit=(5, 2000),  # Min and max pixel count for valid contour
+        shape_error=55,  # Error max (%) between ratio of circle fit and contour
+    )
 
 Plot the resulting identification
 
 .. code-block:: python
 
-    fig = plt.figure(figsize=(15,7))
-    ax = fig.add_axes([.03,.03,.94,.94])
-    ax.set_title('Eddies detected -- Cyclonic(red) and Anticyclonic(blue)')
-    ax.set_ylim(-75,75)
-    ax.set_xlim(0,360)
-    ax.set_aspect('equal')
-    a.display(ax, color='b', linewidth=.5)
-    c.display(ax, color='r', linewidth=.5)
+    fig = plt.figure(figsize=(15, 7))
+    ax = fig.add_axes([0.03, 0.03, 0.94, 0.94])
+    ax.set_title("Eddies detected -- Cyclonic(red) and Anticyclonic(blue)")
+    ax.set_ylim(-75, 75)
+    ax.set_xlim(0, 360)
+    ax.set_aspect("equal")
+    a.display(ax, color="b", linewidth=0.5)
+    c.display(ax, color="r", linewidth=0.5)
     ax.grid()
-    fig.savefig('share/png/eddies.png')
+    fig.savefig("share/png/eddies.png")
 
 .. image:: ../share/png/eddies.png
 
@@ -87,7 +91,8 @@ Save identification data
 .. code-block:: python
 
     from netCDF import Dataset
-    with Dataset(date.strftime('share/Anticyclonic_%Y%m%d.nc'), 'w') as h:
+
+    with Dataset(date.strftime("share/Anticyclonic_%Y%m%d.nc"), "w") as h:
         a.to_netcdf(h)
-    with Dataset(date.strftime('share/Cyclonic_%Y%m%d.nc'), 'w') as h:
+    with Dataset(date.strftime("share/Cyclonic_%Y%m%d.nc"), "w") as h:
         c.to_netcdf(h)