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Serapieum-of-alex · Dec 8, 2024 · 6835787 · 6835787
2 parents c868e78 + e840920
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diff --git a/.flake8 b/.flake8
diff --git a/.github/workflows/conda-deployment.yml b/.github/workflows/conda-deployment.yml
@@ -13,23 +13,23 @@ jobs:
       OS: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           mamba-version: "*"
-          #use-mamba: true
+          use-mamba: true
           auto-update-conda: false
-          environment-file: environment.yml
           auto-activate-base: false
+          environment-file: environment.yml
           activate-environment: test
           python-version: ${{ matrix.python-version }}
-          channels: conda-forge,defaults
+          channels: conda-forge
           channel-priority: true
           show-channel-urls: true
 
       - name: Install dev-dependencies
         run: |
-            python -m pip install -r requirements-dev.txt
+            pip install .[dev]
 
       - name: Generate coverage report
         shell: bash -el {0}
@@ -38,6 +38,7 @@ jobs:
           conda list
           conda config --show-sources
           conda config --show
+          pip install .
           pytest -sv -m "not plot"
 
   Optional-packages:
@@ -50,23 +51,23 @@ jobs:
       OS: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           mamba-version: "*"
-          #use-mamba: true
+          use-mamba: true
           auto-update-conda: false
-          environment-file: environment-optional-packages.yml
           auto-activate-base: false
+          environment-file: environment-optional-packages.yml
           activate-environment: test
           python-version: ${{ matrix.python-version }}
-          channels: conda-forge,defaults
+          channels: conda-forge
           channel-priority: true
           show-channel-urls: true
 
       - name: Install dev-dependencies
         run: |
-            python -m pip install -r requirements-dev.txt
+            pip install .[dev]
 
       - name: Generate coverage report
         shell: bash -el {0}
@@ -76,11 +77,12 @@ jobs:
           conda list
           conda config --show-sources
           conda config --show
+          pip install .
           pytest -sv
 
       - name: test Jupyter notebook
         shell: bash -el {0}
         run: |
           conda activate test
-          pip install -e .
+          pip install .
           pytest --nbval -k ".ipynb"
diff --git a/.github/workflows/pypi-deployment.yml b/.github/workflows/pypi-deployment.yml
@@ -24,7 +24,7 @@ jobs:
         run: |
             python -m pip install --upgrade pip
             pip install --no-cache-dir Cython
-            pip install --find-links=https://girder.github.io/large_image_wheels --no-cache GDAL==3.9.0
+            pip install --find-links=https://girder.github.io/large_image_wheels --no-cache GDAL==3.10.0
 
       - name: Test GDAL installation
         run: |
@@ -33,8 +33,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-            pip install -r requirements.txt -r requirements-dev.txt
-            python setup.py install
+            pip install .[dev]
 
       - name: Generate coverage report
         run: |
@@ -64,7 +63,7 @@ jobs:
         run: |
             python -m pip install --upgrade pip
             pip install --no-cache-dir Cython
-            pip install --find-links=https://girder.github.io/large_image_wheels --no-cache GDAL==3.9.0
+            pip install --find-links=https://girder.github.io/large_image_wheels --no-cache GDAL==3.10.0
 
       - name: Test GDAL installation
         run: |
@@ -73,12 +72,12 @@ jobs:
 
       - name: Install dependencies
         run: |
-            pip install -r requirements-optional-packages.txt -r requirements-dev.txt
-            python setup.py install
+            pip install .[dev,viz]
 
-      - name: Generate coverage report
+      - name: Run Tests
         run: |
           python -m pytest -v --cov=pyramids --cov-report=xml
 
       - name: Upload coverage reports to Codecov with GitHub Action
         uses: codecov/codecov-action@v3
+
diff --git a/.github/workflows/pypi-release.yml b/.github/workflows/pypi-release.yml
@@ -27,5 +27,6 @@ jobs:
                   TWINE_USERNAME: ${{ secrets.PYPI_USERS }}
                   TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
               run: |
-                  python setup.py sdist bdist_wheel
+                  pip install build
+                  python -m build
                   twine upload dist/*
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 fail_fast: true
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: end-of-file-fixer
         name: "[py -  check] validate yaml"
@@ -58,19 +58,19 @@ repos:
         files: ^pyramids/
 
   - repo: https://github.com/pycqa/flake8
-    rev: 7.1.0
+    rev: 7.1.1
     hooks:
       - id: flake8
+        additional_dependencies: [Flake8-pyproject]
         name: "[py   - check] flake8"
-#        language_version: python3.9
         exclude: ^(examples/|tests/)
 
   #- repo: https://github.com/psf/black
   #  rev: 22.8.0
   #  hooks:
   #    - id: black
   - repo: https://github.com/ambv/black
-    rev: 24.4.2
+    rev: 24.10.0
     hooks:
       - id: black
         name: "[py   - format] black"

diff --git a/HISTORY.rst b/HISTORY.rst
@@ -229,3 +229,17 @@ Deprecated
 *Cropping a raster using a polygon is done now directly using gdal.wrap nand the the `_crop_with_polygon_by_rasterizing`
 is deprecated.
 * rename the interpolation method `nearest neighbour` to `nearest neighbor`.
+
+0.7.1 (2024-12-07)
+------------------
+* update `cleopatra` package version to 0.5.1 and update the api to use the new version.
+* update the miniconda workflow in ci.
+* update gdal to 3.10 and update the DataSource to Dataset in the `FeatureCollection.file_name`.
+* add `libgdal-netcdf` and `libgdal-hdf4` to the conda dependencies.
+
+0.7.2 (2024-12-**)
+------------------
+
+Dev
+"""
+* replace the setup.py with pyproject.toml
diff --git a/README.md b/README.md
@@ -46,7 +46,7 @@ Installing pyramids
 Installing `pyramids` from the `conda-forge` channel can be achieved by:
 
 ```
-conda install -c conda-forge pyramids=0.7.0
+conda install -c conda-forge pyramids=0.7.1
 ```
 
 It is possible to list all the versions of `pyramids` available on your platform with:
@@ -68,7 +68,7 @@ pip install git+https://github.com/Serapieum-of-alex/pyramids
 to install the last release, you can easily use pip
 
 ```
-pip install pyramids-gis==0.7.0
+pip install pyramids-gis==0.7.1
 ```
 
 Quick start

diff --git a/docs/environment.yml b/docs/environment.yml
@@ -5,7 +5,7 @@ dependencies:
   - numpy >=2.0.0
   - numpydoc==1.1.0
   - typing-extensions==3.10.*
-  - gdal==3.9.0
+  - gdal==3.10.0
   - pip:
     - pydata_sphinx_theme>=0.15.2
     - sphinxcontrib-napoleon

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -8,9 +8,9 @@ dependencies
 Required dependencies
 =====================
 
-- Python (3.9 or later)
+- Python (3.11 or later)
 - `numpy <https://www.numpy.org/>`__ (1.21 or later)
-- `GDAL <https://gdal.org/>`__ (3.6.2 or later)
+- `GDAL <https://gdal.org/>`__ (3.9.0 or later)
 - `pandas <https://pandas.pydata.org/>`__ (2 or later)
 - `geopandas <https://geopandas.org/>`__  (0.12.2 or later)
 - `Shapely <https://shapely.readthedocs.io/>`__ (1.8.4 or later)
@@ -103,7 +103,7 @@ Once you have a copy of the source, you can install it with:
 
 .. code-block:: console
 
-    $ python setup.py install
+    $ python -m pip install .
 
 
 .. _Github repo: https://github.com/MAfarrag/pyramids

diff --git a/environment-optional-packages.yml b/environment-optional-packages.yml
@@ -1,17 +1,19 @@
 channels:
   - conda-forge
 dependencies:
-  - numpy >=2.0.0
+  - numpy >=2.1.3
   - hpc >=0.1.4
-  - pip >=24.0.0
-  - gdal ==3.9.0
-  - pandas >=2.1.0
-  - geopandas >=0.14.1
-  - Shapely >=2.0.2
-  - pyproj >=3.6.1
-  - cleopatra >=0.5.0
-  - PyYAML >=6.0.1
+  - pip >=24.3.1
+  - gdal ==3.10.0
+  - libgdal-netcdf ==3.10.0
+  - libgdal-hdf4  ==3.10.0
+  - pandas >=2.2.3
+  - geopandas >=1.0.1
+  - Shapely >=2.0.6
+  - pyproj >=3.7.0
+  - cleopatra >=0.5.1
+  - PyYAML >=6.0.2
   - loguru >=0.7.2
-  - pytest >=8.2.2
-  - pytest-cov >=5.0.0
+  - pytest >=8.3.4
+  - pytest-cov >=6.0.0
   - nbval >=0.11.0
diff --git a/environment.yml b/environment.yml
@@ -1,16 +1,18 @@
 channels:
   - conda-forge
 dependencies:
-  - numpy >=2.0.0
+  - numpy >=2.1.3
   - hpc >=0.1.4
-  - pip >=24.0.0
-  - gdal ==3.9.0
-  - pandas >=2.1.0
-  - geopandas >=0.14.1
-  - Shapely >=2.0.2
-  - pyproj >=3.6.1
-  - PyYAML >=6.0.1
+  - pip >=24.3.1
+  - gdal ==3.10.0
+  - libgdal-netcdf ==3.10.0
+  - libgdal-hdf4  ==3.10.0
+  - pandas >=2.2.3
+  - geopandas >=1.0.1
+  - Shapely >=2.0.6
+  - pyproj >=3.7.0
+  - PyYAML >=6.0.2
   - loguru >=0.7.2
-  - pytest >=8.2.2
-  - pytest-cov >=5.0.0
+  - pytest >=8.3.4
+  - pytest-cov >=6.0.0
   - nbval >=0.11.0
diff --git a/examples/data/raster_like_saved.tif b/examples/data/raster_like_saved.tif