Merge branch 'master' into v03_with_new_fields

.github/workflows/tests.yml

@@ -0,0 +1,36 @@
+name: Tests
+
+on:
+  pull_request:
+  push:
+    branches: [master,main]
+
+jobs:
+  run:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        os: [windows-latest, ubuntu-latest, macos-latest]
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Setup Micromamba
+      uses: mamba-org/provision-with-micromamba@main
+      with:
+        environment-file: false
+
+    - name: Python ${{ matrix.python-version }}
+      shell: bash -l {0}
+      run: |
+        micromamba create --name TEST python=${{ matrix.python-version }} --file requirements.txt --file requirements-dev.txt --channel conda-forge
+        micromamba activate TEST
+        python -m pip install -e . --no-deps --force-reinstall
+
+    - name: Tests
+      shell: bash -l {0}
+      run: |
+        micromamba activate TEST
+        python -m pytest -rxs tests

LICENSE.txt

@@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
-

README.rst

@@ -36,7 +36,7 @@ roms.yaml
         title: "USGS-CMG-COAWST Model: CBLAST2007 Ripples with SWAN-40m res"
 
         summary: "Simulation of hydrodynamics and bottom stress south of Marthas Vineyard, MA using the COAWST modeling system.  These results are from the 40m inner nest of a four-level nested simulation."
-        
+
         project:
             - CMG_Portal
             - Sandy_Portal
@@ -85,9 +85,9 @@ roms.yaml
         pattern: .*test_nc4_[0-9]{4}\.nc$
 
 
-Notes on the YAML file: 
+Notes on the YAML file:
 
-1. The aggregation `dir:` is the directory where the data (e.g. NetCDF files) are located, relative to the directory where the NcML will be.  In the above example, the NetCDF files are located in a subdirectory called "Output".  If the NetCDF files will be in the same directory as the NcML file, specify `dir: '.'`. 
+1. The aggregation `dir:` is the directory where the data (e.g. NetCDF files) are located, relative to the directory where the NcML will be.  In the above example, the NetCDF files are located in a subdirectory called "Output".  If the NetCDF files will be in the same directory as the NcML file, specify `dir: '.'`.
 
 2. Specify that all variables should appear in the aggregation (none excluded) like this:
 

requirements.txt

@@ -1,4 +1,3 @@
 docopt
 netCDF4
 ruamel.yaml
-six

setup.py

@@ -1,29 +1,31 @@
 import os
 import sys
+
 from setuptools import setup
 from setuptools.command.test import test as TestCommand
 
 
 class PyTest(TestCommand):
     def finalize_options(self):
         TestCommand.finalize_options(self)
-        self.test_args = ['--verbose']
+        self.test_args = ["--verbose"]
         self.test_suite = True
 
     def run_tests(self):
         import pytest
+
         errno = pytest.main(self.test_args)
         sys.exit(errno)
 
 
 def extract_version():
     version = None
     fdir = os.path.dirname(__file__)
-    fnme = os.path.join(fdir, 'yaml2ncml', '__init__.py')
+    fnme = os.path.join(fdir, "yaml2ncml", "__init__.py")
     with open(fnme) as fd:
         for line in fd:
-            if (line.startswith('__version__')):
-                _, version = line.split('=')
+            if line.startswith("__version__"):
+                _, version = line.split("=")
                 version = version.strip()[1:-1]
                 break
     return version
@@ -33,35 +35,37 @@ def extract_version():
 
 
 def read(*parts):
-    return open(os.path.join(rootpath, *parts), 'r').read()
+    return open(os.path.join(rootpath, *parts)).read()
 
 
-long_description = '{}\n{}'.format(read('README.rst'), read('CHANGES.txt'))
-LICENSE = read('LICENSE.txt')
+long_description = "{}\n{}".format(read("README.rst"), read("CHANGES.txt"))
+LICENSE = read("LICENSE.txt")
 
-with open('requirements.txt') as f:
+with open("requirements.txt") as f:
     require = f.readlines()
 install_requires = [r.strip() for r in require]
 
-setup(name='yaml2ncml',
-      version=extract_version(),
-      packages=['yaml2ncml'],
-      license=LICENSE,
-      description='ncML aggregation from YAML specifications',
-      long_description=long_description,
-      author='Rich Signell',
-      author_email='rsignell@usgs.gov',
-      install_requires=install_requires,
-      entry_points=dict(console_scripts=[
-          'yaml2ncml = yaml2ncml.yaml2ncml:main']
-          ),
-      url='https://github.com/rsignell-usgs/yaml2ncml',
-      keywords=['YAML', 'ncml'],
-      classifiers=['Development Status :: 4 - Beta',
-                   'Programming Language :: Python :: 2.7',
-                   'Programming Language :: Python :: 3.4',
-                   'Programming Language :: Python :: 3.5',
-                   'License :: OSI Approved :: MIT License'],
-      tests_require=['pytest'],
-      cmdclass=dict(test=PyTest),
-      zip_safe=False)
+setup(
+    name="yaml2ncml",
+    version=extract_version(),
+    packages=["yaml2ncml"],
+    license=LICENSE,
+    description="ncML aggregation from YAML specifications",
+    long_description=long_description,
+    author="Rich Signell",
+    author_email="rsignell@usgs.gov",
+    install_requires=install_requires,
+    entry_points=dict(console_scripts=["yaml2ncml = yaml2ncml.yaml2ncml:main"]),
+    url="https://github.com/rsignell-usgs/yaml2ncml",
+    keywords=["YAML", "ncml"],
+    classifiers=[
+        "Development Status :: 4 - Beta",
+        "Programming Language :: Python :: 2.7",
+        "Programming Language :: Python :: 3.4",
+        "Programming Language :: Python :: 3.5",
+        "License :: OSI Approved :: MIT License",
+    ],
+    tests_require=["pytest"],
+    cmdclass=dict(test=PyTest),
+    zip_safe=False,
+)

tests/base_roms_test.ncml

@@ -547,6 +547,6 @@
       <values start="-1.0" increment="-0.01"/>
     </variable>
  <aggregation dimName="ocean_time" type="joinExisting">
-<scan location="data/" regExp=".*test_nc4_[0-9]{4}\.nc$" subdirs="false"/>
+<scan location="tests/data/" regExp=".*test_nc4_[0-9]{4}\.nc$" subdirs="false"/>
 </aggregation>
 </netcdf>

tests/roms_0.yaml

@@ -50,6 +50,6 @@ variables:
 
 aggregation:
     time_var: ocean_time
-    dir: data/
+    dir: tests/data/
     sample_file: test_nc4_0001.nc
     pattern: .*test_nc4_[0-9]{4}\.nc$

tests/test_cli.py

@@ -1,7 +1,4 @@
-from __future__ import (absolute_import, division, print_function)
-
 import pytest
-from docopt import DocoptExit
 from docopt import docopt
 
 from yaml2ncml import yaml2ncml
@@ -10,18 +7,18 @@
 
 
 def test_noarg_call():
-    with pytest.raises(DocoptExit):
+    with pytest.raises(SystemExit):
         yaml2ncml.main()
 
 
 def test_mandatory_arg():
-    fin = 'roms.yaml'
+    fin = "roms.yaml"
     args = docopt(__doc__, [fin])
-    assert args['INFILE'] == fin
+    assert args["INFILE"] == fin
 
 
 def test_optional_arg():
-    fin = 'test6.ncml'
-    fout = '--output=test6.ncml'
+    fin = "test6.ncml"
+    fout = "--output=test6.ncml"
     args = docopt(__doc__, [fin, fout])
-    assert args['--output'] == fout.split('=')[1]
+    assert args["--output"] == fout.split("=")[1]

tests/test_yaml2ncml.py

@@ -1,41 +1,41 @@
-from __future__ import (absolute_import, division, print_function)
-
 import subprocess
 import tempfile
+from pathlib import Path
 
 import pytest
 import ruamel.yaml as yaml
 
 from yaml2ncml import build
 
+path = Path(__file__).parent.resolve()
+
 
 def test_call():
-    output = subprocess.check_output(['yaml2ncml', 'roms_0.yaml'])
-    with open('base_roms_test.ncml') as f:
-        expected = f.read()
-    assert output.decode() == expected
+    fname = str(path.joinpath("roms_0.yaml"))
+    output = subprocess.check_output(["yaml2ncml", fname]).decode()
+    output = [line.strip() for line in output.splitlines()]
+    with path.joinpath("base_roms_test.ncml").open() as f:
+        expected = [line.strip() for line in f.read().splitlines()]
+    assert output == expected
 
 
 def test_save_file():
-    outfile = tempfile.mktemp(suffix='.ncml')
-    subprocess.call(['yaml2ncml',
-                     'roms_0.yaml',
-                     '--output={}'.format(outfile)])
-    with open('base_roms_test.ncml') as f:
+    outfile = tempfile.mktemp(suffix=".ncml")
+    fname = str(path.joinpath("roms_0.yaml"))
+    subprocess.call(["yaml2ncml", fname, f"--output={outfile}"])
+    with path.joinpath("base_roms_test.ncml").open() as f:
         expected = f.read()
     with open(outfile) as f:
         output = f.read()
     assert output == expected
 
 
 @pytest.fixture
-def load_ymal(fname='roms_1.yaml'):
-    with open(fname, 'r') as stream:
-        yml = yaml.load(stream, Loader=yaml.RoundTripLoader)
-    return yml
+def load_ymal(fname=path.joinpath("roms_1.yaml")):
+    with open(fname) as stream:
+        yield yaml.load(stream, Loader=yaml.RoundTripLoader)
 
 
-def test_bad_yaml():
+def test_bad_yaml(load_ymal):
     with pytest.raises(ValueError):
-        yml = load_ymal(fname='roms_1.yaml')
-        build(yml)
+        build(load_ymal)

yaml2ncml/__init__.py

@@ -1,11 +1,5 @@
-from __future__ import (absolute_import, division, print_function)
+from yaml2ncml.yaml2ncml import build, main
 
-from yaml2ncml.yaml2ncml import main, build
+__version__ = "0.7.3"
 
-
-__version__ = '0.7.2'
-
-__all__ = [
-    'main',
-    'build'
-    ]
+__all__ = ["main", "build"]