Merge pull request #90 from umr-lops/replace-datatree-xarray

first attempt to replace xarray-datatree by xarray native DataTrees

Author: agrouaze

.github/workflows/ci.yaml

@@ -0,0 +1,84 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  detect-skip-ci-trigger:
+    name: "Detect CI Trigger: [skip-ci]"
+    if: |
+      github.repository == 'umr-lops/utils_xsarslc_l1b'
+      && (
+          github.event_name == 'push' || github.event_name == 'pull_request'
+      )
+    runs-on: ubuntu-latest
+    outputs:
+      triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 2
+      - uses: xarray-contrib/ci-trigger@v1
+        id: detect-trigger
+        with:
+          keyword: "[skip-ci]"
+
+  ci:
+    name: ${{ matrix.os }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    needs: detect-skip-ci-trigger
+
+    if: needs.detect-skip-ci-trigger.outputs.triggered == 'false'
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+
+    steps:
+      - name: Checkout the repository
+        uses: actions/checkout@v4
+        with:
+          # need to fetch all tags to get a correct version
+          fetch-depth: 0 # fetch all branches and tags
+
+      - name: Setup environment variables
+        run: |
+          echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
+
+          echo "CONDA_ENV_FILE=ci/requirements/environment.yaml" >> $GITHUB_ENV
+
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: ${{ env.CONDA_ENV_FILE }}
+          environment-name: slcl1butils-tests
+          cache-environment: true
+          cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{matrix.python-version}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
+          create-args: >-
+            python=${{matrix.python-version}}
+
+      - name: Install slcl1butils
+        run: |
+          python -m pip install --no-deps -e .
+
+      - name: Import slcl1butils
+        run: |
+          python -c "import slcl1butils"
+
+      - name: Run tests
+        run: |
+          python -m pytest --cov=slcl1butils

ci/requirements/environment.yaml

@@ -2,7 +2,7 @@ name: slcl1butils-tests
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python
   # development
   - ipython
   - pre-commit
@@ -14,6 +14,7 @@ dependencies:
   # testing
   - pytest
   - pytest-reportlog
+  - pytest-cov
   - hypothesis
   - coverage
   # I/O
@@ -23,7 +24,6 @@ dependencies:
   - fsspec
   # data
   - xarray
-  - xarray-datatree
   - dask
   - numpy
   - pandas

docs/conf.py

@@ -60,7 +60,6 @@
     "numpy": ("https://numpy.org/doc/stable", None),
     "xarray": ("https://docs.xarray.dev/en/latest/", None),
     "rasterio": ("https://rasterio.readthedocs.io/en/latest/", None),
-    "datatree": ("https://xarray-datatree.readthedocs.io/en/latest/", None),
     'geoviews': ('https://geoviews.org/index.html', None)
 }
 

docs/examples/display_a_IW_L1B_xspectra.ipynb

@@ -27,7 +27,7 @@
    "source": [
     "import glob\n",
     "import os\n",
-    "import datatree\n",
+    "import xarray as xr\n",
     "from slcl1butils.utils import get_test_file\n",
     "#l1bncfile_pattern = os.path.abspath('../../assests/*iw*nc')\n",
     "one_safe_l1b = get_test_file('S1B_IW_XSP__1SDV_20210328T055258_20210328T055325_026211_0320D4_DC31_A13.SAFE')\n",
@@ -47,7 +47,7 @@
    },
    "outputs": [],
    "source": [
-    "dt = datatree.open_datatree(l1bncfile)\n",
+    "dt = xr.open_datatree(l1bncfile)\n",
     "dt"
    ]
   },
@@ -187,7 +187,7 @@
     "tile_line_i = 0\n",
     "tile_sample_i = 3\n",
     "fig = plt.figure()\n",
-    "slcl1butils.plotting.display_one_spectra.plot_a_single_xspec_cart_L1B_IW(ds,'VV',tile_line_i,tile_sample_i,'test display',fig,cat_xspec=cat_xspec,part='Re')"
+    "slcl1butils.plotting.display_one_spectra.plot_a_single_xspec_cart_l1b_iw(ds,'VV',tile_line_i,tile_sample_i,'test display',fig,cat_xspec=cat_xspec,part='Re')"
    ]
   }
  ],
@@ -207,7 +207,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.9.15"
   }
  },
  "nbformat": 4,

docs/examples/do_L1C_SAFE_from_L1B_SAFE_example.ipynb

@@ -108,7 +108,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.9.15"
   }
  },
  "nbformat": 4,

docs/examples/plotting_L1B_geometry_with_holoview_example.ipynb

@@ -164,7 +164,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.9.15"
   }
  },
  "nbformat": 4,

docs/index.rst

@@ -6,7 +6,7 @@ slcl1butils: functions to play with IFREMER L1B Sentinel-1 SLC SAR products
 
 Acquisition modes available in L1B IFREMER product family are IW and WV.
 
-The products are *netCDF* files containing `datatree`_ object.
+The products are *netCDF* files containing `xarray.datatree` object.
 
 
 
@@ -104,5 +104,4 @@ Last documentation build: |today|
    basic_api
 
 .. _on github: https://github.com/umr-lops/utils_xsarslc_l1b
-.. _datatree: https://github.com/xarray-contrib/datatree
 .. _xarray: http://xarray.pydata.org

docs/installing.rst

@@ -4,8 +4,8 @@
 Installation
 ************
 
-L1B SAR SLC IFREMER products are netCDF (.nc) files containing groups.
-To read netCDF files with groups, a possible python library is `xarray-datatree`.
+Level-1B SAR SLC IFREMER products are netCDF (.nc) files containing groups.
+To read netCDF files with groups, a possible python library is `xarray`.
 Installation in a conda_ environment is recommended.
 
 

environment.yml

@@ -6,7 +6,6 @@ dependencies:
   - geoviews
   - fsspec
   - numpy
-  - xarray-datatree
   - xarray
   - rasterio
   - rioxarray

get_polygons_from_l1b.py

@@ -1,15 +1,10 @@
 # +
-import datatree
 import numpy as np
-from glob import glob
-import os
-import matplotlib.pyplot as plt
 from shapely import geometry
 from shapely import wkt
-import time
+
 import xarray as xr
 
-# from xsarslc.tools import xndindex
 
 # +
 def get_swath_tiles_polygons_from_l1bgroup(l1b_ds, swath_only=False, variable_names = [None],ik=0,burst_type=None):
@@ -176,66 +171,3 @@ def get_swath_tiles_polygons_from_l1bfiles(l1b_files, variable_names = [None], i
         return polygons,coordinates,variables
     else:
         return polygons,coordinates
-
-
-# def get_polygons_from_l1b(files, varnames = None):
-
-#     pts_tiles_intra = []; pts_tiles_inter = []; pts_swath = []
-#     t0 = time.time()
-
-#     pts_tiles = {}
-#     burst_type = ['intraburst','interburst']
-#     variables = {}
-#     for brst in burst_type:
-#         variables[brst] = {}
-#         pts_tiles[brst] = []
-#         if (varnames is not None):
-#             for varname in varnames:
-#                 variables[brst][varname] = []
-
-#     for cpt,_file in enumerate(files):
-
-#         dt = datatree.open_datatree(_file)
-
-#         polyswath = wkt.loads(dt['intraburst'].ds.attrs['footprint'])
-#         lon,lat = polyswath.exterior.xy
-#         _pts_swath = [(x,y) for x,y in zip(lon,lat)]
-#         pts_swath.append(_pts_swath)
-        
-        
-#         for brst in burst_type:
-
-#             lon_corners = dt[brst]['corner_longitude'].squeeze()
-#             lat_corners = dt[brst]['corner_latitude'].squeeze()
-#             Nt = dt[brst].ds.sizes['tile_sample']
-#             bursts = dt[brst]['burst'].values        
-#             for ib in bursts:
-#                 for it in np.arange(Nt):
-
-#                     # Get corner list
-#                     _lon1 = lon_corners.sel(burst=ib).isel(tile_sample=it,c_line=0)
-#                     _lon2 = lon_corners.sel(burst=ib).isel(tile_sample=it,c_line=1)
-#                     _lat1 = lat_corners.sel(burst=ib).isel(tile_sample=it,c_line=0)
-#                     _lat2 = lat_corners.sel(burst=ib).isel(tile_sample=it,c_line=1)
-#                     lon = list(_lon1.values) + list(_lon2.values[::-1])
-#                     lat = list(_lat1.values) + list(_lat2.values[::-1])
-#                     _pts_tiles = [ (x,y) for x,y in zip(lon,lat)]
-#                     pts_tiles[brst].append(_pts_tiles)
-
-#                     # Get variables
-#                     if (varnames is not None):
-#                         for varname in varnames:
-#                                 variables[brst][varname].append(dt[brst][varname].sel(burst=ib).isel(tile_sample=it).values[0])
-                        
-                    
-                                                            
-                    
-#     t1 = time.time()
-#     print(t1-t0)
-#     if (varnames is not None):
-#         return pts_swath, pts_tiles, variables
-#     else:
-#         return pts_swath, pts_tiles
-# -
-
-