Python310 upgrade

.github/workflows/cd.yml

@@ -0,0 +1,42 @@
+name: CD Workflow
+
+on:
+  push:
+    branches:
+      - "main"
+
+permissions:
+  contents: read
+  id-token: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: '3.10'
+          auto-activate-base: false
+
+      - name: Build package
+        shell: bash -l {0}
+        run: |
+          conda create -n deploy_env python=3.10 libgdal=3.5.2 build -c conda-forge -y
+          conda activate deploy_env
+          python -m build -C--global-option=bdist_wheel -C--global-option=--build-number=0 --wheel
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          verbose: true
+          password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/ci.yml

@@ -0,0 +1,53 @@
+name: CI Workflow
+
+on:
+  pull_request:
+    branches:
+      - "main"
+permissions:
+  contents: read
+
+jobs:
+  quality:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+      - name: Create test env
+        shell: bash -l {0}
+        run: |
+          pip install pylint mccabe
+      - name: code quality
+        shell: bash -l {0}
+        run: |
+          pylint --disable=all --fail-under=10 --enable=too-many-statements src/eolab/georastertools/
+          pylint --disable=all --fail-under=10 --enable=too-many-nested-blocks src/eolab/georastertools/
+          ./continuous_integration/scripts/check_mccabe_complexity.sh 25 src/eolab/georastertools
+  test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Setup Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Setup Miniconda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: '3.10'
+        auto-activate-base: false
+    - name: Create test env
+      shell: bash -l {0}
+      run: |
+        conda create -n test_env python=3.10 libgdal=3.5.2 -c conda-forge -c defaults -y
+        conda activate test_env
+        PIP_NO_BINARY=rasterio pip install .
+        pip install pylint mccabe
+    - name: test
+      shell: bash -l {0}
+      run: |
+        conda activate test_env
+        pytest --cov-fail-under=65 --compare --durations=0

.gitignore

@@ -5,7 +5,6 @@
 # Distribution / packaging 
 .Python build/ 
 develop-eggs/ 
-dist/ 
 downloads/ 
 eggs/ 
 .eggs/ 
@@ -15,10 +14,11 @@ parts/
 sdist/ 
 var/ 
 wheels/ 
-*.whl
+dist/
 *.egg-info/ 
 .installed.cfg 
 *.egg 
+*.whl
 *.manifest 
 *.spec 
 

README.rst

@@ -2,15 +2,17 @@
 Raster tools
 ============
 
-This project provides a command line named **rastertools** that enables various calculation tools:
+This project provides a command line named **georastertools** that enables various calculation tools:
 
 
 - the calculation of radiometric indices on satellite images
+- the calculation of the Compute the Sky View Factor (SVF) of a Digital Elevation Model (DHM).
+- the calculation of the hillshades of a Digital Elevation / Surface / Height Model
 - the calculation of the speed of evolution of radiometry from images between two dates
 - the calculation of zonal statistics of the bands of a raster, that is to say statistics such as min, max, average, etc.
   on subareas (defined by a vector file) of the area of interest.
 
-The **rastertools** project also aims to make the handling of the following image products transparent:
+The **georastertools** project also aims to make the handling of the following image products transparent:
 
 - Sentinel-2 L1C PEPS (https://peps.cnes.fr/rocket/#/search)
 - Sentinel-2 L2A PEPS (https://peps.cnes.fr/rocket/#/search)
@@ -21,7 +23,7 @@ The **rastertools** project also aims to make the handling of the following imag
 It is thus possible to input files in the command line in any of the formats above. 
 It is also possible to specify your own product types by providing a JSON file as a parameter of the command line (cf. docs/usage.rst)
 
-Finally, **rastertools** offers an API for calling these different tools in Python and for extending its capabilities, for example by defining new radiometric indices.
+Finally, **georastertools** offers an API for calling these different tools in Python and for extending its capabilities, for example by defining new radiometric indices.
 
 Installation
 ============
@@ -30,100 +32,94 @@ Create a conda environment by typing the following:
 
 .. code-block:: bash
 
-  conda env create -f environment.yml
-  conda env update -f env_update.yml
-
-The following dependencies will be installed in the ``rastertools`` environment:
-
-- pyscaffold
-- geopandas
-- scipy
-- gdal
-- rasterio
-- tqdm
-
-Install ``rastertools`` in the conda environment by typing the following:
-
-.. code-block:: bash
-
-  conda activate rastertools
-  pip install -e .
-
-.. note::
-
-  Note: Installing in a *virtualenv* does not work properly for this project. For unexplained reasons, 
-  the VRTs that are created in memory by rastertools to handle image products are not properly managed 
-  with an installation in a virtualenv.
-
-For more details, including installation as a Docker or Singularity image, please refer to the documentation. : `Installation <docs/install.rst>`_
+  conda env create -n georastertools
+  conda activate
+  conda install python=3.10 libgdal=3.5.2
+  pip install georastertools --no-binary rasterio
 
+For more details, including installation as a Docker or Singularity image, please refer to the documentation. : docs/install.rst
 
 Usage
 =====
 
-rastertools
-^^^^^^^^^^^
-The rastertools command line is the high-level command for activating the various tools.
+georastertools
+^^^^^^^^^^^^^^
+The georastertools command line is the high-level command for activating the various tools.
 
 .. code-block:: console
 
-  $ rastertools --help
-  usage: rastertools [-h] [-t RASTERTYPE] [--version] [-v] [-vv]
-                     {filter,fi,radioindice,ri,speed,sp,svf,hillshade,hs,zonalstats,zs,tiling,ti}
-                     ...
-
-  Collection of tools on raster data
-
-  optional arguments:
-    -h, --help            show this help message and exit
-    -t RASTERTYPE, --rastertype RASTERTYPE
-                          JSON file defining additional raster types of input
-                          files
-    --version             show program's version number and exit
-    -v, --verbose         set loglevel to INFO
-    -vv, --very-verbose   set loglevel to DEBUG
-
-  Commands:
-    {filter,fi,radioindice,ri,speed,sp,svf,hillshade,hs,zonalstats,zs,tiling,ti}
-      filter (fi)         Apply a filter to a set of images
-      radioindice (ri)    Compute radiometric indices
-      speed (sp)          Compute speed of rasters
-      svf                 Compute Sky View Factor of a Digital Height Model
-      hillshade (hs)      Compute hillshades of a Digital Height Model
-      zonalstats (zs)     Compute zonal statistics
-      tiling (ti)         Generate image tiles
-
-Calling rastertools returns the following exit codes:
+  $ rio georastertools --help
+  Usage: rio georastertools [OPTIONS] COMMAND [ARGS]...
+
+  Main entry point for the `georastertools` Command Line Interface.
+
+  The `georastertools` CLI provides tools for raster processing and analysis
+  and allows configurable data handling, parallel processing, and debugging
+  support.
+
+  Logging:
+
+      - INFO level (`-v`) gives detailed step information.
+
+      - DEBUG level (`-vv`) offers full debug-level tracing.
+
+  Environment Variables:
+
+      - `RASTERTOOLS_NOTQDM`: If the log level is above INFO, sets this to
+      disable progress bars.
+
+      - `RASTERTOOLS_MAXWORKERS`: If `max_workers` is set, it defines the max
+      workers for georastertools.
+
+    Options:
+      -t, --rastertype PATH  JSON file defining additional raster types of input
+                             files
+      --max_workers INTEGER  Maximum number of workers for parallel processing. If
+                             not given, it will default to the number of
+                             processors on the machine. When all processors are
+                             not allocated to run georastertools, it is thus
+                             recommended to set this option.
+      --debug                Store to disk the intermediate VRT images that are
+                             generated when handling the input files which can be
+                             complex raster product composed of several band
+                             files.
+      -v, --verbose          set loglevel to INFO
+      -vv, --very-verbose    set loglevel to DEBUG
+      --version              Show the version and exit.
+      -h, --help             Show this message and exit.
+
+    Commands:
+      fi           Apply a filter to a set of images.
+      filter       Apply a filter to a set of images.
+      hillshade    Execute the hillshade subcommand on a Digital Elevation Model...
+      hs           Execute the hillshade subcommand on a Digital Elevation Model...
+      radioindice  Compute the requested radio indices on raster data.
+      ri           Compute the requested radio indices on raster data.
+      sp           Compute the speed of radiometric values for multiple...
+      speed        Compute the speed of radiometric values for multiple...
+      svf          Compute the Sky View Factor (SVF) of a Digital Elevation...
+      ti           Generate tiles of an input raster image following the...
+      tiling       Generate tiles of an input raster image following the...
+      timeseries   Generate a timeseries of images (without gaps) from a set...
+      ts           Generate a timeseries of images (without gaps) from a set...
+      zonalstats   Compute zonal statistics of a raster image.
+      zs           Compute zonal statistics of a raster image.
+
+Calling georastertools returns the following exit codes:
 
 .. code-block:: console
 
     0: everything went well
     1: processing error
     2: incorrect invocation parameters
 
-Details of the various subcommands are presented in the documentation : `Usage <docs/cli.rst>`_
-
-
-Tests & documentation
-=====================
-
-To run tests and generate documentation, the following dependencies must be installed in the conda environment. :
-
-- py.test et pytest-cov (tests execution)
-- sphinx (documentation generation)
-
-Pour cela, exécuter la commande suivante :
-
-.. code-block:: console
-
-  conda env update -f env_test.yml
-
+Details of the various subcommands are presented in the documentation : docs/cli.rst
 
 Tests
 ^^^^^
 
 The project comes with a suite of unit and functional tests. To run them, 
-launch the command ``pytest tests``. To run specific tests, execute ``pytest tests -k "<nom_du_test>"``.
+launch the command ``pytest tests``. To run specific tests, execute ``pytest tests -k "<test_name>"``.
 
 The tests may perform comparisons between generated files and reference files. 
 In this case, the tests depend on the numerical precision of the platforms. 

continuous_integration/scripts/check_mccabe_complexity.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+
+if [ -z "$1" ] || [ -z "$2" ]; then
+    echo "Error: You must specify a McCabe threshold and a directory to analyze."
+    echo "Usage: $0 <threshold> <directory>"
+    exit 1
+fi
+
+threshold=$1
+directory=$2
+
+if [ ! -d "$directory" ]; then
+    echo "Error: The directory '$directory' does not exist."
+    exit 1
+fi
+
+all_files_ok=true
+for file in $(find "$directory" -name "*.py"); do
+    echo "Analyzing $file ..."
+    output=$(python -m mccabe --min "$threshold" "$file")
+
+    if [ -n "$output" ]; then
+        echo "Error: McCabe complexity too high in $file"
+        echo "$output"
+        all_files_ok=false
+    fi
+done
+
+if $all_files_ok; then
+    echo "✅ All files have McCabe scores less than or equal to $threshold. ✅"
+else
+    echo "❌ Some files have a complexity higher than $threshold ❌"
+    exit 1
+fi
+
+exit 0