Merge pull request #76 from munterfi/bugfix/ci-poetry-install

Bugfix/ci poetry install

.github/workflows/gdal-stable-test.yml

@@ -25,8 +25,8 @@ jobs:
 
     - name: Install poetry
       run: |
-        curl -sSL \
-          "https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py" | python
+        curl -sSL https://install.python-poetry.org | python3 -
+        echo "${HOME}/.local/bin" >> $GITHUB_PATH
 
     - name: Set up cache
       uses: actions/cache@v1
@@ -36,7 +36,6 @@ jobs:
 
     - name: Install dependencies
       run: |
-        source "$HOME/.poetry/env"
         poetry config virtualenvs.in-project true
 
         # Pip install without GDAL

.github/workflows/gdal-unstable-test.yml

@@ -24,8 +24,8 @@ jobs:
 
     - name: Install poetry
       run: |
-        curl -sSL \
-          "https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py" | python
+        curl -sSL https://install.python-poetry.org | python3 -
+        echo "${HOME}/.local/bin" >> $GITHUB_PATH
 
     - name: Set up cache
       uses: actions/cache@v1
@@ -35,7 +35,6 @@ jobs:
 
     - name: Install dependencies
       run: |
-        source "$HOME/.poetry/env"
         poetry config virtualenvs.in-project true
 
         # Pip install without GDAL

.github/workflows/package-check.yml

@@ -22,8 +22,8 @@ jobs:
 
     - name: Install poetry
       run: |
-        curl -sSL \
-          "https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py" | python
+        curl -sSL https://install.python-poetry.org | python3 -
+        echo "${HOME}/.local/bin" >> $GITHUB_PATH
 
     - name: Set up cache
       uses: actions/cache@v1
@@ -33,21 +33,16 @@ jobs:
 
     - name: Install dependencies
       run: |
-        source "$HOME/.poetry/env"
         poetry config virtualenvs.in-project true
-
-        # Install
         poetry install
 
     - name: Run checks
       run: |
-        source "$HOME/.poetry/env"
         poetry run flake8 glacier_flow_model tests --count
         poetry run mypy .
         poetry run pytest --cov=glacier_flow_model
         cd docs && poetry run make html && cd ..
 
     - name: Upload coverage reports to Codecov
       run: |
-        source "$HOME/.poetry/env"
         poetry run codecov

.github/workflows/package-publish.yml

@@ -24,18 +24,16 @@ jobs:
 
     - name: Install poetry
       run: |
-        curl -sSL \
-          "https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py" | python
+        curl -sSL https://install.python-poetry.org | python3 -
+        echo "${HOME}/.local/bin" >> $GITHUB_PATH
 
     - name: Install dependencies
       run: |
-        source "$HOME/.poetry/env"
         poetry config virtualenvs.in-project true
         poetry install
 
     - name: Run checks
       run: |
-        source "$HOME/.poetry/env"
         poetry run flake8 glacier_flow_model tests --count
         poetry run mypy .
         poetry run pytest --cov=glacier_flow_model
@@ -46,7 +44,6 @@ jobs:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        source "$HOME/.poetry/env"
         poetry build
         python3 -m pip install --upgrade twine
         python3 -m twine upload dist/*

CHANGELOG.rst

@@ -3,6 +3,15 @@ Changelog
 
 This packages uses `semantic versioning <https://semver.org/>`_.
 
+Version 0.3.0
+-------------
+
+- Features:
+    - Remove the direct dependency on GDAL via the :code:`osgeo` package and
+      use the :code:`rasterio` package to read and write raster files instead.
+- Bugfixes:
+    - Fix failing CI due to an defunct poetry installation instruction.
+
 Version 0.2.0
 -------------
 

docs/environment.yml

@@ -4,6 +4,7 @@ channels:
 dependencies:
 - scipy
 - numpy
+- rasterio
 - gdal
 - libgdal
 - matplotlib

glacier_flow_model/data/access.py

@@ -2,8 +2,8 @@
 import importlib.resources as resources
 from logging import getLogger
 
-from osgeo.gdal import Dataset
-from osgeo.gdal import Open
+from rasterio import open
+from rasterio import DatasetReader
 
 LOG = getLogger(__name__)
 
@@ -39,7 +39,7 @@ def locate_dem() -> str:
             return str(file_path)
 
     @staticmethod
-    def load_dem() -> Dataset:
+    def load_dem() -> DatasetReader:
         """
         Loads the file 'dem.tif' on the current system.
 
@@ -51,5 +51,5 @@ def load_dem() -> Dataset:
         """
         file_path = PkgDataAccess.locate_dem()
         LOG.info("Reading DEM from '%s' ...", file_path)
-        dem = Open(file_path)
+        dem = open(file_path)
         return dem

glacier_flow_model/model.py

@@ -7,9 +7,7 @@
 import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
-from osgeo.gdal import GDT_Float32
-from osgeo.gdal import GetDriverByName
-from osgeo.gdal import Open
+from rasterio import open
 from scipy.ndimage import gaussian_filter
 from scipy.ndimage import uniform_filter
 
@@ -120,9 +118,8 @@ def __init__(
         """
 
         # Load DEM ------------------------------------------------------------
-        dem = Open(dem_path)
-        band = dem.GetRasterBand(1)
-        ele = band.ReadAsArray().astype(np.float32)
+        dem = open(dem_path)
+        ele = dem.read(1).astype(np.float32)
 
         # Instance variables --------------------------------------------------
         self.model_name = Path(dem_path).stem if model_name is None else model_name
@@ -138,15 +135,11 @@ def __init__(
         self._setup_ndarrays()  # Variable arrays (ele, h, u ,hs)
 
         # Coordinate reference system and dem resolution
-        self._geo_trans = dem.GetGeoTransform()
-        self._geo_proj = dem.GetProjection()
-        self.res = self._geo_trans[1]
+        self._dem_meta = dem.meta
+        self.res = dem.res[0]
 
         # Geographical extent of the dem
-        nrows, ncols = ele.shape
-        x0, dx, dxdy, y0, dydx, dy = self._geo_trans
-        x1 = x0 + dx * ncols
-        y1 = y0 + dy * nrows
+        x0, y0, x1, y1 = dem.bounds
         self.extent = (x0, x1, y1, y0)
 
         # Setup statistics
@@ -591,16 +584,11 @@ def _export_tif(self, file_path: Path) -> None:
             self.h.shape[1],
             file_path,
         )
-        driver = GetDriverByName("GTiff")
-        data_set = driver.Create(
-            str(file_path), self.h.shape[1], self.h.shape[0], 3, GDT_Float32
-        )
-        data_set.GetRasterBand(1).WriteArray(self.store.mean("h"))
-        data_set.GetRasterBand(2).WriteArray(self.store.mean("u"))
-        data_set.GetRasterBand(3).WriteArray(self.store.diff("h"))
-        data_set.SetGeoTransform(self._geo_trans)
-        data_set.SetProjection(self._geo_proj)
-        data_set.FlushCache()
+        self._dem_meta.update(count=3)
+        with open(file_path, 'w', **self._dem_meta) as dst:
+            dst.write_band(1, self.store.mean("h"))
+            dst.write_band(2, self.store.mean("u"))
+            dst.write_band(3, self.store.diff("h"))
 
     # Visualization -----------------------------------------------------------
     @staticmethod