Merge branch 'master' into velocity_hourly

Author: mhidas

.travis.yml

@@ -4,12 +4,12 @@ python:
   - "3.6"
 
 install:
-  - pip install -r requirements.txt
-  - pip install coverage
+  - pip install -r test_requirements.txt
+  - pip install pytest-cov
   - pip install codecov
 
 script:
-  - coverage run setup.py test
+  - pytest --cov=./
 
 after_success:
 - codecov

Dockerfile

@@ -7,6 +7,7 @@ ENV LANG C.UTF-8
 ENV PATH /home/builder/.local/bin:$PATH
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential \
     ca-certificates \
     git \
     libxml2-dev \
@@ -26,6 +27,7 @@ RUN wget -q https://bootstrap.pypa.io/get-pip.py \
 
 RUN pip install \
     Cython==0.29 \
+    numpy>=1.13.0 \
     bump2version==0.5.10
 
 RUN useradd --create-home --no-log-init --shell /bin/bash --uid $BUILDER_UID builder

Jenkinsfile

@@ -34,7 +34,8 @@ pipeline {
                 }
                 stage('test') {
                     steps {
-                        sh 'python setup.py test'
+                        sh 'pip install --user -r test_requirements.txt'
+                        sh 'pytest'
                     }
                 }
                 stage('package') {

aodntools/timeseries_products/aggregated_timeseries.py

@@ -310,6 +310,7 @@ def main_aggregator(files_to_agg, var_to_agg, site_code, input_dir='', output_di
     obs_int_template = {'datatype': np.int16, 'zlib': True, 'dimensions': ('OBSERVATION',)}
     inst_S256_template = {'datatype': 'S1', 'dimensions': ('INSTRUMENT', "strlen")}
     inst_float_template = {'datatype': np.float32, 'dimensions': ('INSTRUMENT',), "fill_value": 99999.0}
+    inst_double_template = {'datatype': np.float64, 'dimensions': ('INSTRUMENT',), "fill_value": 99999.0}
 
     agg_variable = ds.createVariable(varname=var_to_agg, **obs_float_template)
     agg_variable_qc = ds.createVariable(varname=var_to_agg + '_quality_control', **obs_byte_template)
@@ -325,8 +326,8 @@ def main_aggregator(files_to_agg, var_to_agg, site_code, input_dir='', output_di
 
     source_file = ds.createVariable(varname='source_file', **inst_S256_template)
     instrument_id = ds.createVariable(varname='instrument_id', **inst_S256_template)
-    LATITUDE = ds.createVariable(varname='LATITUDE', **obs_double_template)
-    LONGITUDE = ds.createVariable(varname='LONGITUDE', **obs_double_template)
+    LATITUDE = ds.createVariable(varname='LATITUDE', **inst_double_template)
+    LONGITUDE = ds.createVariable(varname='LONGITUDE', **inst_double_template)
     NOMINAL_DEPTH = ds.createVariable(varname='NOMINAL_DEPTH', **inst_float_template)
 
     ## main loop

setup.py

@@ -4,10 +4,18 @@
     'jsonschema>=2.6.0,<3.0.0',
     'numpy>=1.13.0',
     'netCDF4>=1.5.3',
-    'pandas>=0.24.2',
-    'xarray>=0.11.3'
+    'pandas>=0.24.2,<0.25.0',
+    'xarray>=0.11.3,<0.14.0'
 ]
 
+TESTS_REQUIRE = [
+    'pytest'
+]
+
+EXTRAS_REQUIRE = {
+    'testing': TESTS_REQUIRE
+}
+
 PACKAGE_DATA = {
     'aodntools.ncwriter': ['*.json'],
     'aodntools.timeseries_products': ['*.json']
@@ -29,6 +37,8 @@
     zip_safe=False,
     python_requires='>=3.5',
     install_requires=INSTALL_REQUIRES,
+    tests_require=TESTS_REQUIRE,
+    extras_require=EXTRAS_REQUIRE,
     test_suite='test_aodntools',
     classifiers=[
         'Development Status :: 5 - Production/Stable',

test_aodntools/timeseries_products/test_aggregated_timeseries.py

@@ -44,6 +44,14 @@ def test_main_aggregator(self):
         for var in obs_vars:
             self.assertEqual(dataset.variables[var].dimensions, ('OBSERVATION',))
 
+        inst_vars = {'LATITUDE', 'LONGITUDE', 'NOMINAL_DEPTH'}
+        for var in inst_vars:
+            self.assertEqual(dataset.variables[var].dimensions, ('INSTRUMENT',))
+
+        string_vars = {'source_file', 'instrument_id'}
+        for var in string_vars:
+            self.assertEqual(dataset.variables[var].dimensions, ('INSTRUMENT', 'strlen'))
+
         for f in chartostring(dataset['source_file'][:]):
             self.assertIn(f, INPUT_FILES)
 

test_requirements.txt

@@ -0,0 +1,3 @@
+--index-url https://pypi.python.org/simple/
+-r requirements.txt
+-e .[testing]