Merge branch 'main' of https://github.com/johntruckenbrodt/pyroSAR in…

…to feature/coherence_gamma

.github/workflows/python-package-conda.yml

@@ -0,0 +1,56 @@
+name: conda build
+
+on: [ push ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    services:
+      postgres:
+        image: postgis/postgis:16-3.4
+        env:
+          POSTGRES_PASSWORD: Password12!
+        ports:
+          - 5432:5432
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: '3.10'
+      - name: install ESA SNAP
+        run: |
+          wget -nv https://download.esa.int/step/snap/10_0/installers/esa-snap_sentinel_linux-10.0.0.sh
+          bash esa-snap_sentinel_linux-10.0.0.sh -q -dir $GITHUB_ACTION_PATH/esa-snap
+      - name: Set paths and variables
+        run: |
+          echo "$CONDA/bin" >> $GITHUB_PATH
+          echo "$GITHUB_ACTION_PATH/esa-snap/bin" >> $GITHUB_PATH
+          echo "PROJ_DATA=$CONDA/share/proj" >> $GITHUB_ENV
+      - name: Install dependencies
+        run: |
+          : # https://github.com/conda/conda/issues/13560#issuecomment-1992720842
+          conda install -y python=3.10
+          conda env update --file environment.yml --name base
+      - name: Lint with flake8
+        run: |
+          conda install flake8
+          # stop the build if there are Python syntax errors or undefined names
+          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: Install package
+        run: |
+          pip install .
+      - name: Test with pytest
+        run: |
+          conda install pytest coverage
+          coverage run -m pytest
+        env:
+          PGUSER: postgres
+          PGPASSWORD: Password12!
+      - name: Publish to coveralls.io
+        uses: coverallsapp/github-action@v2
+        with:
+          github-token: ${{ github.token }}

.github/workflows/python-publish.yml

@@ -0,0 +1,39 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [ published ]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.travis.yml

@@ -12,7 +12,7 @@ env:
     - TESTDATA_DIR=$HOME/testdata
     - PGUSER=travis
     - PGPASSWORD=Password12!
-    - SNAP_VERSION=9
+    - SNAP_VERSION=10
 
 addons:
   postgresql: '14'
@@ -31,11 +31,11 @@ services:
   - postgresql
 
 python:
-  - '3.7'
+  - '3.10'
 
 before_install:
-  - export SNAP_INSTALLER=esa-snap_sentinel_unix_"$SNAP_VERSION"_0_0.sh
-  - wget -O $SNAP_INSTALLER https://download.esa.int/step/snap/"$SNAP_VERSION".0/installers/"$SNAP_INSTALLER"
+  - export SNAP_INSTALLER=esa-snap_sentinel_linux-"$SNAP_VERSION".0.0.sh
+  - wget -O $SNAP_INSTALLER https://download.esa.int/step/snap/"$SNAP_VERSION"_0/installers/"$SNAP_INSTALLER"
   - bash $SNAP_INSTALLER -q
   - export PATH=$PATH:/opt/snap/bin
 
@@ -60,6 +60,3 @@ script:
 
 after_success:
   - coveralls
-
-notifications:
-  slack: pyrosar:bs03zodEkRSYr8MN5HrgfSeB

LICENSE.txt

@@ -1,4 +1,4 @@
-# Copyright (c) 2014-2023, the pyroSAR Developers.
+# Copyright (c) 2014-2024, the pyroSAR Developers.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
 documentation files (the "Software"), to deal in the Software without restriction, including without limitation the

README.md

@@ -5,12 +5,10 @@
 <h3 align="center">A Python Framework for Large-Scale SAR Satellite Data Processing</h3>
 
 <p align="center">
-  <a href='https://app.travis-ci.com/johntruckenbrodt/pyroSAR'>
-    <img src='https://app.travis-ci.com/johntruckenbrodt/pyroSAR.svg?branch=master' alt='Travis Status'></a>
-  <a href='https://ci.appveyor.com/project/johntruckenbrodt/pyrosar'>
-    <img src='https://ci.appveyor.com/api/projects/status/won0layps8mkss9h/branch/master?svg=true' alt='AppVeyor Status' /></a>
-  <a href='https://coveralls.io/github/johntruckenbrodt/pyroSAR?branch=master'>
-    <img src='https://coveralls.io/repos/github/johntruckenbrodt/pyroSAR/badge.svg?branch=master' alt='Coveralls Status' /></a>
+  <a href='https://github.com/johntruckenbrodt/pyroSAR/actions/workflows/python-package-conda.yml'>
+    <img src='https://github.com/johntruckenbrodt/pyroSAR/actions/workflows/python-package-conda.yml/badge.svg' alt='Travis Status'></a>
+  <a href='https://coveralls.io/github/johntruckenbrodt/pyroSAR?branch=main'>
+    <img src='https://coveralls.io/repos/github/johntruckenbrodt/pyroSAR/badge.svg?branch=main' alt='Coveralls Status' /></a>
   <a href='https://pyrosar.readthedocs.io/en/latest/?badge=latest'>
     <img src='https://readthedocs.org/projects/pyrosar/badge/?version=latest' alt='Documentation Status' /></a>
   <a href='https://badge.fury.io/py/pyroSAR'>

appveyor.yml

@@ -9,8 +9,8 @@ environment:
       SNAP_INSTALL: C:\projects\snap
       PGUSER: postgres
       PGPASSWORD: Password12!
-      SNAP_VERSION: 9
-      SNAP_INSTALLER: esa-snap_sentinel_windows-x64_%SNAP_VERSION%_0_0.exe
+      SNAP_VERSION: 10
+      SNAP_INSTALLER: esa-snap_sentinel_windows-%SNAP_VERSION%.0.0.exe
 
 platform:
   - x64
@@ -48,7 +48,7 @@ install:
   - conda config --add channels conda-forge
 
   # install ESA SNAP
-  - appveyor DownloadFile https://download.esa.int/step/snap/%SNAP_VERSION%.0/installers/%SNAP_INSTALLER%
+  - appveyor DownloadFile https://download.esa.int/step/snap/%SNAP_VERSION%_0/installers/%SNAP_INSTALLER%
   - start %SNAP_INSTALLER% -q -dir %SNAP_INSTALL%
 
   - set PATH=%PATH%;%SNAP_INSTALL%\bin

docs/source/about/changelog.rst

@@ -1014,3 +1014,45 @@ Drivers
 Auxiliary Data Handling
 -----------------------
 - method :meth:`pyroSAR.S1.OSV.catch`: fixed bug in finding files starting in previous month
+
+0.25.0 | 2024-04-16
+===================
+
+Drivers
+-------
+- class :class:`pyroSAR.drivers.Archive`:
+
+  + replaced column `bbox` with `geometry`; requires database migration
+  + method :meth:`~pyroSAR.drivers.Archive.export2shp`: improved column name laundering
+
+SNAP API
+--------
+- function :func:`pyroSAR.snap.auxil.gpt`: fixed bug that occurred during removal of BNR node
+
+Ancillary Tools
+---------------
+- new classes :class:`pyroSAR.ancillary.Lock` and :class:`pyroSAR.ancillary.LockCollection`
+  for custom file/folder locking
+
+Auxiliary Data Handling
+-----------------------
+
+changes to Sentinel-1 OSV data handling:
+
+- function :meth:`pyroSAR.auxdata.dem_create`:
+
+  + make use of new classes :class:`~pyroSAR.ancillary.Lock` and :class:`~pyroSAR.ancillary.LockCollection`
+    for DEM download and mosaic creation (new argument `lock_timeout`)
+  + check whether all VRT source files exist
+
+0.26.0 | 2024-05-15
+===================
+
+SNAP API
+--------
+- compatibility with SNAP 10.
+- completely revised configuration mechanisms. See
+
+  + :doc:`/general/configuration`
+  + :class:`pyroSAR.examine.ExamineSnap`
+  + :class:`pyroSAR.examine.SnapProperties`

docs/source/api/ancillary.rst

@@ -17,3 +17,5 @@ Ancillary Functions
         multilook_factors
         parse_datasetname
         seconds
+        Lock
+        LockCollection

docs/source/general/configuration.rst

@@ -0,0 +1,23 @@
+#############
+Configuration
+#############
+
+pyroSAR stores configuration under `$HOME/.pyrosar`.
+It contains a file `config.ini` which stores installation paths of SNAP and GAMMA.
+The installations are first identified by running the respective `Examine*` class (e.g. :class:`~pyroSAR.examine.ExamineSnap`):
+
+.. code-block:: python
+
+    from pyroSAR.examine import ExamineSnap
+    config = ExamineSnap()
+
+SNAP configuration can also be modified with this class, either by the object properties `userpath` and `auxdatapath` or by the underlying :class:`~pyroSAR.examine.SnapProperties` object:
+
+.. code-block:: python
+
+    config.userpath = '/path/to/snap/data'
+    config.snap_properties['snap.userdir'] = '/path/to/snap/data'
+
+The values are directly written to either `snap.auxdata.properties` or `snap.properties` under `$HOME/.snap/etc`.
+The content of these files will override that in the files found under `etc` in the SNAP installation folder.
+Setting a parameter to `None` will comment out the value in the respective file.

docs/source/index.rst

@@ -10,6 +10,7 @@ General Topics
 
     general/installation
     general/filenaming
+    general/configuration
     general/OSV
     general/DEM
     general/snap

environment-dev.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python>=3.6
+  - python>=3.8,<3.11
   - progressbar2
   - numpy
   - spatialist>=0.12.1
@@ -17,6 +17,7 @@ dependencies:
   - pillow
   - lxml
   - packaging
+  - libspatialite>=5.1.0
   - coveralls
   - coverage
   - pytest

environment-doc.yml

@@ -3,6 +3,7 @@ channels:
   - conda-forge
   - defaults
 dependencies:
+  - python>=3.8,<3.11
   - matplotlib
   - numpy
   - sphinx<7.0  # https://github.com/readthedocs/sphinx_rtd_theme/issues/1463

environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python>=3.6
+  - python>=3.8,<3.11  # https://github.com/kvesteri/sqlalchemy-utils/issues/716
   - progressbar2
   - numpy
   - spatialist>=0.12.1
@@ -17,3 +17,4 @@ dependencies:
   - pillow
   - lxml
   - packaging
+  - libspatialite>=5.1.0

pyproject.toml

@@ -4,7 +4,7 @@ requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2", "wheel"]
 [project]
 name = "pyroSAR"
 description = "a framework for large-scale SAR satellite data processing"
-requires-python = ">=3.6"
+requires-python = ">=3.8,<3.11"
 license = { file = "LICENSE.txt" }
 maintainers = [
     { name = "John Truckenbrodt", email = "[email protected]" }

pyroSAR/S1/polysimplify.py

@@ -300,7 +300,7 @@ def __init__(self, geom, precision=None, return_GDAL=True):
                 name = geom.geom_type.upper()
                 self.Geometry = lambda w: fromstr(w)
                 self.pts = np.array(geom.tuple)
-            elif isinstance(geom, unicode) or isinstance(geom, str):
+            elif isinstance(geom, str) or isinstance(geom, bytes):
                 # assume wkt
                 # for WKT
                 def str2tuple(q):

pyroSAR/__init__.py

@@ -1,18 +1,10 @@
 from .drivers import *
-import sys
 from . import ancillary, drivers
 
-if sys.version_info >= (3, 8):
-    from importlib.metadata import version, PackageNotFoundError
-    try:
-        __version__ = version(__name__)
-    except PackageNotFoundError:
-        # package is not installed
-        pass
-else:
-    from pkg_resources import get_distribution, DistributionNotFound
-    try:
-        __version__ = get_distribution(__name__).version
-    except DistributionNotFound:
-        # package is not installed
-        pass
+from importlib.metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version(__name__)
+except PackageNotFoundError:
+    # package is not installed
+    pass