Merge pull request #3049 from nabobalis/0.9

[0.9] Backports and CI update

.circleci/config.yml

@@ -58,7 +58,7 @@ jobs:
           command: pip install -U pip
       - run:
           name: Install dependencies
-          command: pip install --progress-bar off -e .[all]
+          command: pip install --progress-bar off .[all]
       - run:
           name: Run tests
           command: python setup.py test
@@ -82,7 +82,7 @@ jobs:
           command: pip install -U pip
       - run:
           name: Install dependencies
-          command: pip install --progress-bar off -e .[all]
+          command: pip install --progress-bar off .[all]
       - run:
           name: Run tests
           command: python setup.py test
@@ -108,10 +108,10 @@ jobs:
           command: /opt/python/cp36-cp36m/bin/pip install --progress-bar off numpy==1.15.3 scipy astropy matplotlib==1.5.3
       - run:
           name: Install dependencies two
-          command: /opt/python/cp36-cp36m/bin/pip install --progress-bar off sqlalchemy scikit-image==0.13.1 glymur drms suds-jurko beautifulsoup4 requests python-dateutil pytest pytest-cov pytest-mock pytest-xdist mock hypothesis pytest-astropy pytest-rerunfailures
+          command: /opt/python/cp36-cp36m/bin/pip install --progress-bar off sqlalchemy scikit-image==0.13.1 glymur drms suds-jurko beautifulsoup4 requests python-dateutil pytest pytest-cov pytest-mock mock hypothesis pytest-astropy pytest-rerunfailures
       - run:
           name: Run tests
-          command: PYTHONHASHSEED=42 /opt/python/cp36-cp36m/bin/pytest -n=4
+          command: PYTHONHASHSEED=42 /opt/python/cp36-cp36m/bin/pytest
     environment:
           MPLBACKEND: agg
           COLUMNS: 180

.travis.yml

@@ -37,8 +37,8 @@ env:
         - MAIN_CMD='python setup.py'
         - SETUP_CMD='test --coverage'
         - CONDA_CHANNELS='sunpy'
-        - CONDA_DEPENDENCIES='openjpeg Cython jinja2 scipy matplotlib mock requests beautifulsoup4 sqlalchemy scikit-image pytest-mock lxml pyyaml pandas pytest-astropy suds-jurko glymur pytest-xdist dask drms sphinx-astropy pytest-cov hypothesis'
-        - PIP_DEPENDENCIES='pytest-sugar pytest-xdist'
+        - CONDA_DEPENDENCIES='openjpeg Cython jinja2 scipy matplotlib mock requests beautifulsoup4 sqlalchemy scikit-image pytest-mock lxml pyyaml pandas pytest-astropy suds-jurko glymur dask drms sphinx-astropy pytest-cov hypothesis'
+        - PIP_DEPENDENCIES='pytest-sugar'
         - EVENT_TYPE='push pull_request cron'
         - MPLBACKEND='agg'
         - JOB='test'

CHANGELOG.rst

@@ -1,3 +1,14 @@
+Sunpy 0.9.7 (2019-05-01)
+========================
+
+Bug Fixes
+---------
+
+- If Carrington longitude ("crln_obs") is found in the FITS header, `~sunpy.map.Map` converts this to the correct Heliographic longitude. (`#2946 <https://github.com/sunpy/sunpy/pull/2946>`__)
+- Fix HGS <> HCRS test due to Ecliptic frame changes in astropy 3.2 (`#3075 <https://github.com/sunpy/sunpy/pull/3075>`__)
+- Fixes bug when creating a timeseries from a URL and bug when creating a TimeSeries from  older GOES/XRS fits files. (`#3081 <https://github.com/sunpy/sunpy/pull/3081>`__)
+
+
 Sunpy 0.9.6 (2019-01-28)
 ========================
 

azure-pipelines.yml

@@ -10,15 +10,18 @@ jobs:
     name: Linux_37_online
     os: linux
     tox: py37-online -- -n=4
+    python: '3.7'
 
 - template: azure-templates.yml
   parameters:
     name: Windows_27_offline
     os: windows
-    tox: py27-offline
+    tox: py27-offline --
+    python: '2.7'
 
 - template: azure-templates.yml
   parameters:
     name: Windows_36_offline
     os: windows
-    tox: py36-offline
+    tox: py36-offline --
+    python: '3.6'

azure-templates.yml

@@ -9,18 +9,47 @@ jobs:
       vmImage: Ubuntu 16.04
 
   steps:
-  - task: CondaEnvironment@1
-    displayName: 'Create conda environment'
+
+  - ${{ if eq(parameters.os, 'linux') }}:
+    - script: |
+        sudo apt-get install -y libopenjpeg5
+      displayName: apt install openjpeg
+
+  - ${{ if eq(parameters.os, 'macos') }}:
+    - script: |
+        brew install openjpeg
+      displayName: brew install openjpeg
+
+  - task: UsePythonVersion@0
     inputs:
-      createCustomEnvironment: True
-      environmentName: "test"
-      createOptions: python="3.6"
+      versionSpec: ${{ parameters.python }}
 
   - script: pip install --upgrade tox
     displayName: install tox
 
-  - script: pip install --upgrade tox-conda
-    displayName: install tox-conda
+  - ${{ if contains(parameters.tox, 'conda') }}:
+    - script: pip install --upgrade tox-conda
+      displayName: install tox-conda
+
+  - script: tox -e ${{ parameters.tox }} -vvv --junitxml=junit/test-results.xml --cov-report=xml --cov-report=html
+    displayName: run tox
+
+  - script: |
+      pip install --upgrade codecov
+      codecov --name ${{ format(parameters.name) }}
+    displayName: run codecov
+    condition: succeededOrFailed()
+
+  - task: PublishTestResults@2
+    condition: succeededOrFailed()
+    inputs:
+      testResultsFiles: '**/test-*.xml'
+      testRunTitle: 'Publish test results for ${{ format(parameters.name) }}'
 
-  - script: tox -e ${{ parameters.tox }}
-    displayName: run tox-conda
+  - ${{ if contains(parameters.tox, 'online') }}:
+    - task: PublishCodeCoverageResults@1
+      condition: succeededOrFailed()
+      inputs:
+        codeCoverageTool: Cobertura
+        summaryFileLocation: '$(System.DefaultWorkingDirectory)/**/coverage.xml'
+        reportDirectory: '$(System.DefaultWorkingDirectory)/**/htmlcov'

setup.cfg

@@ -15,7 +15,7 @@ database_requires = sqlalchemy
 image_requires = scikit-image
 jpeg2000_requires = glymur
 net_requires = drms, suds-jurko, beautifulsoup4, python-dateutil
-tests_requires = pytest<3.7, pytest-cov, pytest-mock, pytest-xdist, mock, hypothesis, pytest-astropy
+tests_requires = pytest<3.7, pytest-cov, pytest-mock, mock, hypothesis, pytest-astropy
 docs_requires = ruamel.yaml, sphinx, sunpy-sphinx-theme, sphinx-gallery, sphinx-astropy, towncrier
 # version should be PEP386 compatible (http://www.python.org/dev/peps/pep-0386)
 version = 0.9.7

sunpy/coordinates/tests/test_transformations.py

@@ -8,8 +8,13 @@
 
 import astropy.units as u
 from astropy.tests.helper import quantity_allclose, assert_quantity_allclose
-from astropy.coordinates import (SkyCoord, get_body_barycentric, HeliocentricTrueEcliptic, Angle,
+from astropy.coordinates import (SkyCoord, get_body_barycentric, Angle,
                                  ConvertError)
+try:
+    from astropy.coordinates import HeliocentricMeanEcliptic
+except ImportError:
+    from astropy.coordinates import HeliocentricTrueEcliptic as HeliocentricMeanEcliptic
+
 from astropy.time import Time
 
 from sunpy.coordinates import (Helioprojective, HeliographicStonyhurst,
@@ -132,22 +137,22 @@ def test_hcrs_hgs_array_obstime():
 
 def test_hgs_hcrs():
     # This test checks the HGS->HCRS transformation by transforming from HGS to
-    # HeliocentricTrueEcliptic (HTE).  It will fail if there are errors in Astropy's
-    # HCRS->ICRS or ICRS->HTE transformations.
+    # HeliocentricMeanEcliptic (HME).  It will fail if there are errors in Astropy's
+    # HCRS->ICRS or ICRS->HME transformations.
 
     # Use published HGS coordinates in the Astronomical Almanac (2013), pages C6-C7
     obstime = Time('2013-01-28')
     earth_hgs = SkyCoord(0*u.deg, -5.73*u.deg, 0.9848139*u.AU, frame=HeliographicStonyhurst,
                          obstime=obstime)
 
-    # Transform to HTE at observation-time equinox
-    earth_hte = earth_hgs.transform_to(HeliocentricTrueEcliptic(equinox=obstime))
+    # Transform to HME at observation-time equinox
+    earth_hme = earth_hgs.transform_to(HeliocentricMeanEcliptic(equinox=obstime))
 
     # Validate against published values from the Astronomical Almanac (2013), page C6 per page E2
     # The dominant source of inaccuracy is the limited precision of the published B0 used above
-    assert quantity_allclose(earth_hte.lon, Angle('308d13m30.51s') - 180*u.deg, atol=5*u.arcsec)
-    assert quantity_allclose(earth_hte.lat, -Angle('-0.27s'), atol=10*u.arcsec)
-    assert quantity_allclose(earth_hte.distance, 0.9848139*u.AU, atol=5e-7*u.AU)
+    assert quantity_allclose(earth_hme.lon, Angle('308d13m30.51s') - 180*u.deg, atol=5*u.arcsec)
+    assert quantity_allclose(earth_hme.lat, -Angle('-0.27s'), atol=10*u.arcsec)
+    assert quantity_allclose(earth_hme.distance, 0.9848139*u.AU, atol=5e-7*u.AU)
 
 
 def test_hgs_hgc_roundtrip():

sunpy/database/tests/test_tables.py

@@ -442,8 +442,8 @@ def test_entry_from_query_results_with_none_wave(qr_with_none_waves):
 def test_entry_from_query_results_with_none_wave_and_default_unit(
         qr_with_none_waves):
     entries = list(entries_from_query_result(qr_with_none_waves, 'nm'))
-    assert len(entries) == 4
-    assert entries == [
+    assert len(entries) == 10
+    expected = [
         DatabaseEntry(
             source='SOHO', provider='SDAC', physobs='intensity',
             fileid='/archive/soho/private/data/processed/virgo/level1/1212/HK/121222_1.H01',
@@ -471,8 +471,39 @@ def test_entry_from_query_results_with_none_wave_and_default_unit(
             observation_time_start=datetime(2012, 12, 24, 0, 1, 58),
             observation_time_end=datetime(2012, 12, 25, 0, 1, 57),
             instrument='VIRGO', size=14.0, wavemin=None,
+            wavemax=None),
+        DatabaseEntry(
+            source='SOHO', provider='SDAC', physobs='intensity',
+            fileid='/archive/soho/private/data/processed/virgo/sph/VIRGO_D4.2_SPH_960411_120914.tar.gz',
+            observation_time_start=datetime(1996, 4, 11, 0, 0),
+            observation_time_end=datetime(2012, 9, 14, 0, 0),
+            instrument='VIRGO', size=512000.0, wavemin=None,
+            wavemax=None),
+        DatabaseEntry(
+            source='SOHO', provider='SDAC', physobs='intensity',
+            fileid='/archive/soho/private/data/processed/virgo/spm/SPM_blue_intensity_series.tar.gz',
+            observation_time_start=datetime(1996, 4, 11, 0, 0),
+            observation_time_end=datetime(2014, 3, 30, 23, 59),
+            instrument='VIRGO', size=32652.0, wavemin=None,
+            wavemax=None),
+        DatabaseEntry(
+            source='SOHO', provider='SDAC', physobs='intensity',
+            fileid='/archive/soho/private/data/processed/virgo/spm/SPM_green_intensity_series.tar.gz',
+            observation_time_start=datetime(1996, 4, 11, 0, 0),
+            observation_time_end=datetime(2014, 3, 30, 23, 59),
+            instrument='VIRGO', size=32652.0, wavemin=None,
+            wavemax=None),
+        DatabaseEntry(
+            source='SOHO', provider='SDAC', physobs='intensity',
+            fileid='/archive/soho/private/data/processed/virgo/spm/SPM_red_intensity_series.tar.gz',
+            observation_time_start=datetime(1996, 4, 11, 0, 0),
+            observation_time_end=datetime(2014, 3, 30, 23, 59),
+            instrument='VIRGO', size=32652.0, wavemin=None,
             wavemax=None)]
 
+    for e in expected:
+        assert e in entries
+
 
 def test_create_display_table_missing_entries():
     with pytest.raises(TypeError):

sunpy/map/map_factory.py

@@ -260,18 +260,20 @@ def __call__(self, *args, **kwargs):
 
         Parameters
         ----------
-
         composite : boolean, optional
-            Indicates if collection of maps should be returned as a CompositeMap
+            Indicates if collection of maps should be returned as a CompositeMap.
+            Default is ``False``.
 
         cube : boolean, optional
             Indicates if collection of maps should be returned as a MapCube
 
         sequence : boolean, optional
-            Indicates if collection of maps should be returned as a MapSequence
+            Indicates if collection of maps should be returned as a MapSequence.
+            Default is ``False``.
 
         silence_errors : boolean, optional
             If set, ignore data-header pairs which cause an exception.
+            Default is ``False``.
 
         Notes
         -----

sunpy/map/mapbase.py

@@ -651,14 +651,16 @@ def heliographic_longitude(self):
         heliographic_longitude = self.meta.get('hgln_obs', None)
 
         if heliographic_longitude is None:
-            if self._default_heliographic_longitude is None:
-                warnings.warn_explicit(
-                    "Missing metadata for heliographic longitude: "
-                    "assuming longitude of 0 degrees",
-                    Warning, __file__,
-                    inspect.currentframe().f_back.f_lineno)
-                self._default_heliographic_longitude = 0
-            heliographic_longitude = self._default_heliographic_longitude
+            if self.meta.get('crln_obs', None) is not None:
+                heliographic_longitude = self.meta['crln_obs'] * u.deg - get_sun_L0(self.date)
+            else:
+                if self._default_heliographic_longitude is None:
+                    warnings.warn_explicit("Missing metadata for heliographic longitude: "
+                                           "assuming longitude of 0 degrees",
+                                           Warning, __file__,
+                                           inspect.currentframe().f_back.f_lineno)
+                    self._default_heliographic_longitude = 0
+                heliographic_longitude = self._default_heliographic_longitude
 
         if isinstance(heliographic_longitude, six.string_types):
             heliographic_longitude = float(heliographic_longitude)

sunpy/map/tests/test_mapbase.py

@@ -31,6 +31,9 @@
 
 testpath = sunpy.data.test.rootdir
 
+@pytest.fixture
+def hmi_test_map():
+    return sunpy.map.Map(os.path.join(testpath, "resampled_hmi.fits"))
 
 @pytest.fixture
 def aia171_test_map():
@@ -198,7 +201,9 @@ def test_coordinate_frame(aia171_test_map):
     assert frame.observer.lon == aia171_test_map.observer_coordinate.frame.lon
     assert frame.observer.radius == aia171_test_map.observer_coordinate.frame.radius
     assert frame.obstime == aia171_test_map.date
-
+
+def test_heliographic_longitude_crln(hmi_test_map):
+    assert hmi_test_map.heliographic_longitude == hmi_test_map.carrington_longitude - sunpy.coordinates.get_sun_L0(hmi_test_map.date)
 
 # ==============================================================================
 # Test Rotation WCS conversion

sunpy/timeseries/sources/goes.py

@@ -111,8 +111,8 @@ def peek(self, title="GOES Xray Flux"):
         figure.show()
 
     # ToDo: is this part of the DL pipeline? If so delete.
-    @classmethod
-    def _get_goes_sat_num(self, start, end):
+    @staticmethod
+    def _get_goes_sat_num(start, end):
         """Parses the query time to determine which GOES satellite to use."""
 
         goes_operational = {
@@ -131,10 +131,8 @@ def _get_goes_sat_num(self, start, end):
 
         sat_list = []
         for sat_num in goes_operational:
-            if ((start >= goes_operational[sat_num].start and
-                 start <= goes_operational[sat_num].end and
-                (end >= goes_operational[sat_num].start and
-                 end <= goes_operational[sat_num].end))):
+            if (goes_operational[sat_num].start <= start <= goes_operational[sat_num].end and
+                    goes_operational[sat_num].start <= end <= goes_operational[sat_num].end):
                 # if true then the satellite with sat_num is available
                 sat_list.append(sat_num)
 
@@ -166,7 +164,7 @@ def _parse_hdus(cls, hdulist):
             xrsa = hdulist[2].data['FLUX'][0][:, 1]
             seconds_from_start = hdulist[2].data['TIME'][0]
         elif 1 <= len(hdulist) <= 3:
-            start_time = parse_time(header['TIMEZERO'])
+            start_time = parse_time(header['TIMEZERO'], format='utime')
             seconds_from_start = hdulist[0].data[0]
             xrsb = hdulist[0].data[1]
             xrsa = hdulist[0].data[2]