setup changes (#146)

* use `pooch` instead of `wget` * use functiosn from `gartersnake` * update workflow * remove `dunamai` from documentation requirements * update build workflow * fix syntax error
oceanmodeling · Mar 2, 2022 · 728e35f · 728e35f
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commit 728e35f
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -7,59 +7,61 @@ on:
 
 jobs:
   build_wheels:
-    name: Python ${{ matrix.python-version }} wheel on ${{ matrix.os }}
+    name: build wheel
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ ubuntu-latest, windows-latest ]
+        os: [ ubuntu-latest ]
         python-version: [ '3.x' ]
     steps:
-      - name: Checkout repository
+      - name: checkout repository
         uses: actions/checkout@v2
-      - name: Install Python
+      - name: install Python
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Restore cached dependencies
+      - name: load cached `~/.local`
         uses: actions/cache@v2
         with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('setup.py') }}
-          restore-keys: ${{ runner.os }}-pip-${{ matrix.python-version }}-
-      - name: Install dependencies
-        run: pip install --user --upgrade pip setuptools wheel
-      - name: Build wheel
-        run: python setup.py bdist_wheel
-      - name: Save wheel
+          path: ~/.local
+          key: ${{ runner.os }}-python${{ matrix.python-version }}-${{ hashFiles('pyproject.toml', 'setup.*') }}
+          restore-keys: ${{ runner.os }}-python${{ matrix.python-version }}-
+      - name: build wheel
+        run: pip wheel . -w dist --no-deps
+      - name: save wheel
         uses: actions/upload-artifact@v2
         with:
+          name: build
           path: ./dist/*.whl
   build_sdist:
     name: package source
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout repository
+      - name: checkout repository
         uses: actions/checkout@v2
-      - name: Install Python
+      - name: install Python
         uses: actions/setup-python@v2
-      - name: Package source
+      - name: install dependencies
+        run: pip install dunamai
+      - name: package source
         run: python setup.py sdist
-      - name: Save source package
+      - name: save source package
         uses: actions/upload-artifact@v2
         with:
+          name: build
           path: ./dist/*.tar.gz
   upload_pypi:
     name: publish to PyPI
     needs: [ build_wheels, build_sdist ]
     runs-on: ubuntu-latest
     steps:
-      - name: Retrieve wheel(s) and source
+      - name: retrieve wheel(s) and source
         uses: actions/download-artifact@v2
         with:
-          name: artifact
+          name: build
           path: dist
-      - name: Upload wheel(s) and source
-        uses: pypa/gh-action-pypi-publish@master
+      - name: upload wheel(s) and source
+        uses: pypa/gh-action-pypi-publish@v1.5.0
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}
diff --git a/.github/workflows/formatting.yml b/.github/workflows/formatting.yml
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -3,44 +3,58 @@ name: tests
 on: [ push ]
 
 jobs:
-  tests:
-    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
+  lint:
+    name: lint
+    runs-on: ubuntu-latest
     strategy:
-      fail-fast: false
       matrix:
-        os: [ ubuntu-latest ]
-        python-version: [ '3.6', '3.x' ]
+        python-version: [ '3.x' ]
     steps:
-      - name: Checkout repository
+      - name: clone repository
         uses: actions/checkout@v2
-      - name: Install Python
+      - name: install Python
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Restore cached dependencies
+      - name: load cached `~/.local`
         uses: actions/cache@v2
         with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('setup.py') }}
-          restore-keys: ${{ runner.os }}-pip-${{ matrix.python-version }}-
-      - name: Install netCDF4 library on Linux
-        if: contains(matrix.os, 'ubuntu')
-        run: sudo apt-get update -y && sudo apt-get install -y libnetcdf-dev libnetcdff-dev
-      - name: Install dependencies
-        run: pip install ".[testing,development]"
-      - name: Lint with flake8
+          path: ~/.local
+          key: ${{ runner.os }}-python${{ matrix.python-version }}-${{ hashFiles('pyproject.toml', 'setup.*') }}
+          restore-keys: ${{ runner.os }}-python${{ matrix.python-version }}-
+      - name: install dependencies
+        run: pip install ".[development]"
+      - name: lint with flake8
         run: |
           # 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: Run tests with coverage
-        run: pytest --numprocesses auto --cov ./ --cov-report xml:coverage.xml
-      - name: Upload coverage to Codecov
-        if: matrix.python-version == '3.x'
-        uses: codecov/[email protected]
+  test:
+    needs: lint
+    name: test
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-latest ]
+        python-version: [ '3.6', '3.x' ]
+    steps:
+      - name: clone repository
+        uses: actions/checkout@v2
+      - name: install Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: load cached `~/.local`
+        uses: actions/cache@v2
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          files: coverage.xml
-          fail_ci_if_error: true
+          path: ~/.local
+          key: ${{ runner.os }}-python${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('pyproject.toml', 'setup.*') }}
+          restore-keys: ${{ runner.os }}-python${{ matrix.python-version }}-
+      - name: install `pipwin` on Windows
+        if: contains(matrix.os, 'windows')
+        run: pip install pipwin
+      - name: install dependencies
+        run: pip install ".[testing]"
+      - name: run tests
+        run: pytest --numprocesses auto
diff --git a/adcircpy/utilities.py b/adcircpy/utilities.py
@@ -5,24 +5,32 @@
 import sys
 import tarfile
 
-import wget
+import pooch
 
 
-def download_mesh(url: str, directory: PathLike, overwrite: bool = False):
+def download_mesh(
+    url: str, directory: PathLike, known_hash: str = None, overwrite: bool = False
+):
     if not isinstance(directory, Path):
         directory = Path(directory)
     if not directory.exists():
         directory.mkdir(parents=True, exist_ok=True)
 
     if not (directory / 'fort.14').exists() or overwrite:
         logging.info(f'downloading mesh files to {directory}')
-        extract_download(url, directory, ['fort.13', 'fort.14'])
+        extract_download(
+            url, directory, ['fort.13', 'fort.14'], known_hash=known_hash, overwrite=overwrite
+        )
 
     return directory
 
 
 def extract_download(
-    url: str, directory: PathLike, filenames: [str] = None, overwrite: bool = False
+    url: str,
+    directory: PathLike,
+    filenames: [str] = None,
+    known_hash: str = None,
+    overwrite: bool = False,
 ):
     if not isinstance(directory, Path):
         directory = Path(directory)
@@ -35,7 +43,7 @@ def extract_download(
 
     temporary_filename = directory / 'temp.tar.gz'
     logging.debug(f'downloading {url} -> {temporary_filename}')
-    wget.download(url, f'{temporary_filename}')
+    temporary_filename = pooch.retrieve(url, known_hash=known_hash, fname=temporary_filename)
     logging.debug(f'extracting {temporary_filename} -> {directory}')
     with tarfile.open(temporary_filename) as local_file:
         if len(filenames) > 0:
@@ -49,8 +57,6 @@ def extract_download(
         else:
             local_file.extractall(directory)
 
-    os.remove(temporary_filename)
-
 
 def get_logger(
     name: str,

diff --git a/examples/example_1.py b/examples/example_1.py
@@ -11,11 +11,12 @@
 INPUT_DIRECTORY = DATA_DIRECTORY / 'input' / 'shinnecock'
 OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'example_1'
 
-MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
 MESH_DIRECTORY = INPUT_DIRECTORY / 'shinnecock'
 
 download_mesh(
-    url=MESH_URL, directory=MESH_DIRECTORY,
+    url='https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1',
+    directory=MESH_DIRECTORY,
+    known_hash='99d764541983bfee60d4176af48ed803d427dea61243fa22d3f4003ebcec98f4',
 )
 
 # open mesh file

diff --git a/examples/example_2.py b/examples/example_2.py
@@ -13,11 +13,12 @@
 INPUT_DIRECTORY = DATA_DIRECTORY / 'input'
 OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'example_2'
 
-MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
 MESH_DIRECTORY = INPUT_DIRECTORY / 'shinnecock'
 
 download_mesh(
-    url=MESH_URL, directory=MESH_DIRECTORY,
+    url='https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1',
+    directory=MESH_DIRECTORY,
+    known_hash='99d764541983bfee60d4176af48ed803d427dea61243fa22d3f4003ebcec98f4',
 )
 
 # open mesh file

diff --git a/examples/example_3.py b/examples/example_3.py
@@ -10,11 +10,12 @@
 INPUT_DIRECTORY = DATA_DIRECTORY / 'input'
 OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'example_3'
 
-MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
 MESH_DIRECTORY = INPUT_DIRECTORY / 'shinnecock'
 
 download_mesh(
-    url=MESH_URL, directory=MESH_DIRECTORY,
+    url='https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1',
+    directory=MESH_DIRECTORY,
+    known_hash='99d764541983bfee60d4176af48ed803d427dea61243fa22d3f4003ebcec98f4',
 )
 
 # open mesh file

diff --git a/examples/example_4.py b/examples/example_4.py
@@ -11,11 +11,12 @@
 INPUT_DIRECTORY = DATA_DIRECTORY / 'input'
 OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'example_4'
 
-MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
 MESH_DIRECTORY = INPUT_DIRECTORY / 'shinnecock'
 
 download_mesh(
-    url=MESH_URL, directory=MESH_DIRECTORY,
+    url='https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1',
+    directory=MESH_DIRECTORY,
+    known_hash='99d764541983bfee60d4176af48ed803d427dea61243fa22d3f4003ebcec98f4',
 )
 
 # open mesh file

diff --git a/examples/make_best_track_ensemble.py b/examples/make_best_track_ensemble.py
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,6 @@
+[build-system]
+requires = [
+    "dunamai",
+    "setuptools",
+]
+build-backend = "setuptools.build_meta"