add a coverage rc, workflow test, pragmas

Author: basaks

.coveragerc

@@ -0,0 +1,55 @@
+# .coveragerc to control coverage.py
+[run]
+branch = True
+source = pyrate
+#omit =
+    # omit everything in
+    # pyrate/tasks/*
+    # omit these files
+#    pyrate/pyratelog.py
+#    pyrate/scripts/main.py
+#    pyrate/pyaps.py
+#    pyrate/compat.py
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    def __str__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+    raise ValueError
+    raise RuntimeError
+    raise IOError
+    except OSError
+    except ValueError
+    except IndexError
+    raise ImportError
+    except ImportError
+    raise ConfigException
+    raise ReferencePhaseError
+    raise RefPixelError
+    raise RoipacException
+    raise GeotiffException
+    raise RasterException
+    raise IfgException
+    raise GammaException
+    raise PreprocessError
+    raise TimeSeriesError
+    raise OrbitalError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:
+
+ignore_errors = True
+
+[html]
+directory = coverage_html_report

.travis.yml

@@ -60,7 +60,7 @@ install:
 script:
   #  - python scripts/update_placeholder_paths.py
   - mpirun -n 3 pytest tests/test_mpi.py
-  - pytest --cov-report term-missing:skip-covered --cov=pyrate tests/
+  - pytest --cov-config=.coveragerc --cov-report term-missing:skip-covered --cov=pyrate tests/
 
 
 after_success:

pyrate/configuration.py

@@ -130,7 +130,7 @@ def __init__(self, config_file_path):
                                      PYRATE_DEFAULT_CONFIGRATION[parameter_name]["PossibleValues"])
 
         # bespoke parameter validation
-        if self.refchipsize % 2 != 1:
+        if self.refchipsize % 2 != 1:  # pragma: no cover
             if self.refchipsize - 1 > 1:
                 # Configuration parameters refchipsize must be odd
                 # values too large (>101) will slow down the process without significant gains in results.

pyrate/core/prepifg_helper.py

@@ -27,7 +27,7 @@
 from numbers import Number
 from subprocess import check_call
 from tempfile import mkstemp
-
+from decimal import Decimal
 
 from numpy import array, where, nan, isnan, nanmean, float32, zeros, \
     sum as nsum
@@ -348,7 +348,7 @@ def _max_bounds(ifgs):
     ymin = min([i.y_last for i in ifgs])
     return xmin, ymin, xmax, ymax
 
-from decimal import Decimal
+
 def _get_same_bounds(ifgs):
     """
     Check and return bounding box for ALREADY_SAME_SIZE option.

pyrate/main.py

@@ -116,6 +116,9 @@ def main():
         prepifg.main(params)
 
         log.info("***********PROCESS**************")
+
+        # reset params as prepifg modifies params
+        params = _params_from_conf(args.config_file)
         process.main(params)
 
         log.info("***********MERGE**************")

tests/conftest.py

@@ -103,9 +103,11 @@ def roipac_or_gamma_conf(request):
     return request.param
 
 
-@pytest.fixture(params=[TEST_CONF_GAMMA], scope='session')
+@pytest.fixture(params=[TEST_CONF_GAMMA])
 def gamma_conf(request):
-    return request.param
+    params = Configuration(TEST_CONF_GAMMA).__dict__
+    yield request.param
+    shutil.rmtree(params[cf.OUT_DIR])
 
 
 @pytest.fixture

tests/test_system.py

@@ -14,9 +14,10 @@
 #   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
+
 """
-This Python module contains tests for mpi operations in PyRate.
-Tun this module as 'mpirun -n 4 pytest tests/test_mpi.py'
+pyrate basic workflow for all supported input datasets
+
 """
 from subprocess import check_call
 from pathlib import Path
@@ -37,3 +38,14 @@ def test_workflow(system_conf):
         log_file_name = 'pyrate.log.' + stage
         files = list(Path(params[cf.OUT_DIR]).glob(log_file_name + '.*'))
         assert len(files) == 1
+
+
+def test_single_workflow(gamma_conf):
+
+    check_call(f"pyrate workflow -f {gamma_conf}", shell=True)
+
+    params = Configuration(gamma_conf).__dict__
+
+    log_file_name = 'pyrate.log.' + 'workflow'
+    files = list(Path(params[cf.OUT_DIR]).glob(log_file_name + '.*'))
+    assert len(files) == 1