Merge pull request #2 from noaa-ocs-modeling/develop

workflow updates and link fixes

.github/workflows/build.yml

@@ -7,12 +7,12 @@ on:
 
 jobs:
   build_wheels:
-    name: build wheel on ${{ matrix.os }}
+    name: Python ${{ matrix.python-version }} wheel on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ 3.8 ]
+        python-version: [ 3.9 ]
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
@@ -24,8 +24,8 @@ jobs:
         uses: actions/cache@v2
         with:
           path: ~/.cache/pip
-          key: ${{ matrix.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('setup.py') }}
-          restore-keys: ${{ matrix.os }}-pip-${{ matrix.python-version }}-
+          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('setup.py') }}
+          restore-keys: ${{ runner.os }}-pip-${{ matrix.python-version }}-
       - name: Install dependencies
         run: pip install --upgrade pip setuptools wheel
       - name: Build wheel
@@ -42,25 +42,23 @@ jobs:
         uses: actions/checkout@v2
       - name: Install Python
         uses: actions/setup-python@v2
-        with:
-          python-version: '3.8'
       - name: Package source
         run: python setup.py sdist
       - name: Save source package
         uses: actions/upload-artifact@v2
         with:
           path: ./dist/*.tar.gz
   upload_pypi:
-    name: publish wheel to PyPI
+    name: publish to PyPI
     needs: [ build_wheels, build_sdist ]
     runs-on: ubuntu-latest
     steps:
-      - name: Retrieve wheel
+      - name: Retrieve wheel(s) and source
         uses: actions/download-artifact@v2
         with:
           name: artifact
           path: dist
-      - name: Upload wheel
+      - name: Upload wheel(s) and source
         uses: pypa/gh-action-pypi-publish@master
         with:
           user: __token__

.github/workflows/tests.yml

@@ -4,12 +4,12 @@ on: [ push ]
 
 jobs:
   tests:
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ ubuntu-latest, windows-latest ]
-        python-version: [ 3.8 ]
-    name: test in Python ${{ matrix.python-version }} on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
+        python-version: [ 3.8, 3.9 ]
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
@@ -25,10 +25,13 @@ jobs:
           restore-keys: ${{ runner.os }}-pip-${{ matrix.python-version }}-
       - name: Update pip
         run: python -m pip install --upgrade pip
+      - name: Install wheel
+        run: pip install wheel
+      - name: Run setup.py on Windows
+        if: contains(matrix.os, 'windows')
+        run: python setup.py install
       - name: Install dependencies
-        run: |
-          pip install wheel
-          pip install -e .[testing]
+        run: pip install -e .[testing]
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names

examples/descriptions_within_bounds.py

@@ -0,0 +1,17 @@
+import numpy
+
+from seabed.ngdc import NGDCSeabedDescriptions
+
+if __name__ == '__main__':
+    # define bounds
+    bounds = numpy.array([[-77, 39], [-75, 40]])
+
+    # retrieve a list of the first 5 surveys
+    first_5_surveys = NGDCSeabedDescriptions.all_surveys()[:5]
+
+    # get surveys within specific bounds
+    seabed_object = NGDCSeabedDescriptions(surveys=first_5_surveys, bounds=bounds)
+    surveys_within_bounds = seabed_object.surveys
+
+    print(f'all surveys: {first_5_surveys}')
+    print(f'surveys within transformed bounds: {surveys_within_bounds}')

examples/descriptions_within_transformed_bounds.py

@@ -0,0 +1,28 @@
+import numpy
+from pyproj import CRS, Transformer
+
+from seabed.ngdc import NGDCSeabedDescriptions
+
+if __name__ == '__main__':
+    # define bounds
+    bounds = numpy.array([[-77, 39], [-75, 40]])
+
+    # transform bounds to desired CRS
+    source_crs = CRS.from_epsg(4326)
+    transformed_crs = CRS.from_epsg(32618)
+    transformed_bounds = numpy.ravel(
+        numpy.stack(
+            Transformer.from_crs(source_crs, transformed_crs).transform(bounds[:, 0], bounds[:, 1]),
+            axis=1,
+        )
+    )
+
+    # retrieve a list of the first 5 surveys
+    first_5_surveys = NGDCSeabedDescriptions.all_surveys()[:5]
+
+    # get surveys within specific bounds
+    seabed_object = NGDCSeabedDescriptions(surveys=first_5_surveys, bounds=transformed_bounds, crs=transformed_crs)
+    surveys_within_bounds = seabed_object.surveys
+
+    print(f'all surveys: {first_5_surveys}')
+    print(f'surveys within transformed bounds: {surveys_within_bounds}')

seabed/base.py

@@ -1,8 +1,10 @@
 from abc import ABC, abstractmethod
-import os
 from os import PathLike
+from pathlib import Path
+from typing import Union
 
 from geopandas import GeoDataFrame
+import numpy
 from pyproj import CRS
 
 from .utilities import get_logger
@@ -22,8 +24,29 @@ def __init__(
         crs: CRS = None,
     ):
         self.bounds = bounds
-        self.__surveys = surveys
-        self.crs = CRS.from_user_input(crs) if crs is not None else None
+        self.surveys = surveys
+        self.crs = crs
+
+    @property
+    def bounds(self) -> (float, float, float, float):
+        return self.__bounds
+
+    @bounds.setter
+    def bounds(self, bounds: (float, float, float, float)):
+        if isinstance(bounds, numpy.ndarray):
+            if len(bounds.shape) > 1:
+                bounds = bounds.ravel()
+        else:
+            bounds = numpy.asarray(bounds)
+        self.__bounds = bounds
+
+    @property
+    def crs(self) -> CRS:
+        return self.__crs
+
+    @crs.setter
+    def crs(self, crs: Union[CRS, str]):
+        self.__crs = CRS.from_user_input(crs) if crs is not None else None
 
     @classmethod
     @abstractmethod
@@ -32,10 +55,12 @@ def all_surveys(cls) -> [str]:
 
     @property
     def surveys(self) -> [str]:
-        if self.__surveys is None:
-            self.__surveys = self.__class__.all_surveys()
         return self.__surveys
 
+    @surveys.setter
+    def surveys(self, surveys: [str]):
+        self.__surveys = surveys if surveys is not None else self.__class__.all_surveys()
+
     def __getitem__(self, survey: str) -> GeoDataFrame:
         raise NotImplementedError
 
@@ -64,7 +89,9 @@ def write(self, filename: PathLike, **kwargs):
             '.xml': 'GML',
         }
 
-        extension = os.path.splitext(filename)[-1]
-        kwargs['driver'] = drivers[extension]
+        if not isinstance(filename, Path):
+            filename = Path(filename)
+
+        kwargs['driver'] = drivers[filename.suffix]
 
         self.data.to_file(str(filename), **kwargs)

seabed/ngdc.py

@@ -33,7 +33,6 @@ def __init__(
     @classmethod
     def all_surveys(cls) -> [str]:
         response = requests.get(URL)
-        print(response.status_code)
         if response.status_code != 200:
             raise ConnectionError(
                 f'abnormal status "{response.status_code}" when connecting to {URL}'

setup.py

@@ -1,21 +1,72 @@
 #!/usr/bin/env python
+import importlib
+import logging
+import os
+from pathlib import Path
+import subprocess
+import sys
 
 from setuptools import config, find_packages, setup
 
+BUILT_PACKAGES = {'fiona': ['gdal'], 'geopandas': ['gdal', 'fiona'], 'numpy': [], 'pyproj': ['proj']}
+is_conda = (Path(sys.prefix) / 'conda-meta').exists()
+
+if is_conda:
+    conda_packages = []
+    for conda_package in BUILT_PACKAGES:
+        try:
+            importlib.import_module(conda_package)
+        except:
+            conda_packages.append(conda_package)
+    if len(conda_packages) > 0:
+        subprocess.check_call(['conda', 'install', '-y', *conda_packages])
+
+if os.name == 'nt':
+    for required_package, pipwin_dependencies in BUILT_PACKAGES.items():
+        try:
+            importlib.import_module(required_package)
+        except:
+            try:
+                import pipwin
+            except:
+                subprocess.check_call([sys.executable, '-m', 'pip', 'install', 'pipwin'])
+
+            failed_pipwin_packages = []
+            for pipwin_package in pipwin_dependencies + [required_package]:
+                try:
+                    subprocess.check_call([sys.executable, '-m', 'pipwin', 'install', pipwin_package.lower()])
+                except subprocess.CalledProcessError:
+                    failed_pipwin_packages.append(pipwin_package)
+
+            if len(failed_pipwin_packages) > 0:
+                raise RuntimeError(
+                    f'failed to download or install non-conda Windows build(s) of {" and ".join(failed_pipwin_packages)}; you can either\n'
+                    '1) install within an Anaconda environment, or\n'
+                    f'2) `pip install <file>.whl`, with `<file>.whl` downloaded from {" and ".join("https://www.lfd.uci.edu/~gohlke/pythonlibs/#" + value.lower() for value in failed_pipwin_packages)} for your Python version'
+                )
+
 try:
-    from dunamai import Version
-except ImportError:
-    import sys
-    import subprocess
+    try:
+        from dunamai import Version
+    except:
+        import sys
+        import subprocess
+
+        subprocess.check_call([sys.executable, '-m', 'pip', 'install', 'dunamai'])
+        from dunamai import Version
+
+    version = Version.from_any_vcs().serialize()
+except RuntimeError as error:
+    logging.exception(error)
+    version = '0.0.0'
 
-    subprocess.check_call([sys.executable, '-m', 'pip', 'install', 'dunamai'])
-    from dunamai import Version
+logging.info(f'using version {version}')
 
 metadata = config.read_configuration('setup.cfg')['metadata']
 
 setup(
     name=metadata['name'],
-    version=Version.from_any_vcs().serialize(),
+    version=version,
     author=metadata['author'],
     author_email=metadata['author_email'],
     description=metadata['description'],

tests/test_seabed.py

@@ -3,20 +3,35 @@
 
 from seabed.ngdc import NGDCSeabedDescriptions
 
-CRS = CRS.from_epsg(32618)
 
-BOUNDS = numpy.array([[-77, 39], [-75, 40]])
-BOUNDS = numpy.ravel(
-    numpy.stack(
-        Transformer.from_crs(CRS.from_epsg(4326), CRS).transform(BOUNDS[:, 0], BOUNDS[:, 1]),
-        axis=1,
-    )
-)
+def test_surveys():
+    surveys = NGDCSeabedDescriptions.all_surveys()
+
+    assert len(surveys) > 0
+
+
+def test_seabed_descriptions_within_bounds():
+    bounds = numpy.array([[-77, 39], [-75, 40]])
+    first_5_surveys = NGDCSeabedDescriptions.all_surveys()[:5]
+    seabed = NGDCSeabedDescriptions(surveys=first_5_surveys, bounds=bounds)
+
+    assert seabed.data.shape[0] > 0
+    assert seabed.data.shape[1] == 14
+    assert len(seabed.descriptions) > 0
+    assert any(seabed.data['Survey'].isin(['492']))
 
 
-def test_seabed_descriptions():
-    surveys = NGDCSeabedDescriptions.all_surveys()[:5]
-    seabed = NGDCSeabedDescriptions(bounds=BOUNDS, surveys=surveys, crs=CRS)
+def test_seabed_descriptions_within_transformed_bounds():
+    bounds = numpy.array([[-77, 39], [-75, 40]])
+    transformed_crs = CRS.from_epsg(32618)
+    transformed_bounds = numpy.ravel(
+        numpy.stack(
+            Transformer.from_crs(CRS.from_epsg(4326), transformed_crs).transform(bounds[:, 0], bounds[:, 1]),
+            axis=1,
+        )
+    )
+    first_5_surveys = NGDCSeabedDescriptions.all_surveys()[:5]
+    seabed = NGDCSeabedDescriptions(surveys=first_5_surveys, bounds=transformed_bounds, crs=transformed_crs)
 
     assert seabed.data.shape[0] > 0
     assert seabed.data.shape[1] == 14