Merge pull request #309 from RadioAstronomySoftwareGroup/reorganize_t…

…ests Reorganize tests
RadioAstronomySoftwareGroup · Jul 20, 2020 · 2409930 · 2409930
2 parents a39e3c1 + f12bcde
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,8 +1,9 @@
 # Changelog
 
-## [Unreleased]
+## [1.2.0] - 2020-7-20
 
 ### Added
+- Diffuse models in mock catalogs, via the analytic_diffuse module.
 - quantity_shared_bcast function to allow objects derived from astropy.units.Quantity to use shared memory broadcasting.
 - SkyModelData class to replace recarray conversion in pyradiosky.
 - quiet keyword for run_uvsim, to suppress stdout printing.
@@ -12,14 +13,22 @@
 - Benchmarking tools.
 
 ### Changed
+- Switch to a new definition for the Counter class, without threading.
+- Cleaned up unit tests
 - Use `at_frequencies` method to enable support for all pyradiosky spectral types.
 - Only do coherency calculation when the time changes
 - Only do beam eval when time, freq, or beam type changes.
 - The definition of the Airy beam now uses the exact value of c, not 3e8.
 
 ### Fixed
+- Keep a UVBeam with more than two frequencies for tests, so the (default) cubic interpolation works.
+- Use pytest hooks to ensure the profiler tests run last.
+- Switched to using a remote-memory-access based counter class. Appears to have fixed bug in the Counter test.
 - Ensure that source positions, coherency matrices, and Jones matrices are updated at the right times.
-- Error early if the task list is too long for gather
+- Error early if the task list is too long for gather.
+
+### Deprecated
+- Support for pyradiosky versions <0.1.0.
 
 ## [1.1.2] - 2020-2-14
 

diff --git a/ci/tests.yaml b/ci/tests.yaml
@@ -19,5 +19,6 @@ dependencies:
   - scipy
   - setuptools_scm
   - pip:
-    - pyradiosky
+    - pyradiosky>=0.1.0
     - lunarsky
+    - git+git://github.com/aelanman/analytic_diffuse
diff --git a/docs/parameter_files.rst b/docs/parameter_files.rst
@@ -149,8 +149,9 @@ Telescope Configuration
     This yaml file provides the telescope name, location in latitude/longitude/altitude
     in degrees/degrees/meters (respectively), and the `beam dictionary`.
     In this case, beam_id == 0 is the UVBeam file hera.uvbeam, beam_id == 1
-    is an Airy disk with diameter 14 m, beam_id == 2 is a Gaussian beam with
-    sigma 0.03, and beam_id == 3 is another Airy beam. When specifying a shape
+    is an Airy disk with diameter 16 m, beam_id == 2 is a Gaussian beam with
+    sigma 0.03, beam_id == 3 is another Airy beam with diameter 12 m, 4 is a Gaussian
+    with diameter 14 m, and 5 is a Gaussian with with diameter 12 m. When specifying a shape
     parameter for a specific beam_id, the beam type needs to be specified using
     the type keyword (rather than on the same line as the beam_id) and then
     the shape keyword can be specified in the next line at the same indent level.

diff --git a/environment.yml b/environment.yml
@@ -22,5 +22,6 @@ dependencies:
   - sphinx
   - pip:
     - pre-commit
-    - pyradiosky
+    - pyradiosky>=0.1.0
     - lunarsky
+    - git+git://github.com/aelanman/analytic_diffuse
diff --git a/pyuvsim/antenna.py b/pyuvsim/antenna.py
@@ -103,6 +103,7 @@ def get_beam_jones(self, array, source_alt_az, frequency, reuse_spline=True,
         # interp_data has shape:
         #   (Naxes_vec, Nspws, Nfeeds, 1 (freq),  Ncomponents (source positions))
         jones_matrix = np.zeros((2, 2, Ncomponents), dtype=np.complex)
+
         # first axis is feed, second axis is theta, phi (opposite order of beam!)
         jones_matrix[0, 0] = interp_data[1, 0, 0, 0, :]
         jones_matrix[1, 1] = interp_data[0, 0, 1, 0, :]

diff --git a/pyuvsim/data/28m_triangle_10time_10chan.uvfits b/pyuvsim/data/28m_triangle_10time_10chan.uvfits
diff --git a/pyuvsim/data/5km_triangle_10time_1chan.yaml b/pyuvsim/data/5km_triangle_10time_1chan.yaml
diff --git a/pyuvsim/data/5km_triangle_1time_1chan.yaml b/pyuvsim/data/5km_triangle_1time_1chan.yaml
diff --git a/pyuvsim/data/5km_triangle_1time_1chan_6ant.yaml b/pyuvsim/data/5km_triangle_1time_1chan_6ant.yaml
diff --git a/pyuvsim/data/5km_triangle_2time_1chan.yaml b/pyuvsim/data/5km_triangle_2time_1chan.yaml
diff --git a/pyuvsim/data/HERA65_layout.csv b/pyuvsim/data/HERA65_layout.csv
diff --git a/pyuvsim/data/HERA_NicCST.uvbeam b/pyuvsim/data/HERA_NicCST.uvbeam
diff --git a/pyuvsim/data/bl_lite_mixed.yaml b/pyuvsim/data/bl_lite_mixed.yaml
@@ -7,6 +7,10 @@ beam_paths:
     type: gaussian
     sigma: 0.03
   3: airy
+  4:
+    type: gaussian
+    diameter: 14
+  5: gaussian
 diameter: 12
 spline_interp_opts:
         kx: 4

diff --git a/pyuvsim/data/laptop_size_sim.yaml b/pyuvsim/data/laptop_size_sim.yaml
diff --git a/pyuvsim/data/letter_R_12pt_2458098.27471265.txt b/pyuvsim/data/letter_R_12pt_2458098.27471265.txt
diff --git a/pyuvsim/data/mock_catalog_heratext.npz b/pyuvsim/data/mock_catalog_heratext.npz
diff --git a/pyuvsim/data/nocore_mwa_herasky.yaml b/pyuvsim/data/nocore_mwa_herasky.yaml
diff --git a/pyuvsim/data/single_off_zenith_healpix.hdf5 b/pyuvsim/data/single_off_zenith_healpix.hdf5
diff --git a/pyuvsim/data/test_config/28m_triangle_10time_10chan.yaml b/pyuvsim/data/test_config/28m_triangle_10time_10chan.yaml
@@ -1,9 +1,10 @@
 beam_paths:
   0: HERA_NicCST.uvbeam
   1: 'uniform'
-  2: 'gaussian'
+  2:
+    type: 'gaussian'
+    sigma: 0.02
   3: 'airy'
-sigma: 0.02
 diameter: 14.6
 telescope_location: (-30.721527777777847, 21.428305555555557, 1073.0000000046566)
 telescope_name: HERA
diff --git a/pyuvsim/data/test_config/28m_triangle_10time_10chan_nosigma.yaml b/pyuvsim/data/test_config/28m_triangle_10time_10chan_nosigma.yaml
diff --git a/pyuvsim/data/test_config/28m_triangle_10time_10chan_sigmaonly.yaml b/pyuvsim/data/test_config/28m_triangle_10time_10chan_sigmaonly.yaml
diff --git a/pyuvsim/data/test_config/obsparam_diffuse_sky.yaml b/pyuvsim/data/test_config/obsparam_diffuse_sky.yaml
@@ -0,0 +1,20 @@
+filing:
+  outdir: '.'
+  outfile_name: 'sim_results.uvfits'
+freq:
+  Nfreqs: 1
+  bandwidth: 800000.0
+  start_freq: 100000000.0
+sources:
+  catalog: 'mock'
+  time: 2457458.1738949567
+  mock_arrangement: 'diffuse'
+  diffuse_model: 'monopole'
+  map_nside: 128
+telescope:
+  telescope_config_name: 'hera_uniform.yaml'
+  array_layout: 'triangle_bl_layout.csv'
+time:
+  Ntimes: 1
+  integration_time: 11.0
+  start_time: 2457458.1738949567
diff --git a/pyuvsim/data/test_config/param_10time_10chan_1.yaml b/pyuvsim/data/test_config/param_10time_10chan_1.yaml
diff --git a/pyuvsim/data/test_config/param_10time_10chan_2.yaml b/pyuvsim/data/test_config/param_10time_10chan_2.yaml
diff --git a/pyuvsim/data/test_config/param_10time_10chan_3.yaml b/pyuvsim/data/test_config/param_10time_10chan_3.yaml