Merge pull request #846 from HERA-Team/lstbin-improvements

Lstbin improvements
HERA-Team · Jun 23, 2023 · e68775a · e68775a
2 parents c7fdf56 + bf4d418
commit e68775a
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Showing 28 changed files with 5,895 additions and 12,604 deletions.
diff --git a/...bit/0001_3a0f8a44c3a469bd3e3d27009467f90515500b11_20230510_220806_uncommited-changes.json b/...bit/0001_3a0f8a44c3a469bd3e3d27009467f90515500b11_20230510_220806_uncommited-changes.json
diff --git a/...bit/0002_3a0f8a44c3a469bd3e3d27009467f90515500b11_20230510_220918_uncommited-changes.json b/...bit/0002_3a0f8a44c3a469bd3e3d27009467f90515500b11_20230510_220918_uncommited-changes.json
diff --git a/...bit/0003_3a0f8a44c3a469bd3e3d27009467f90515500b11_20230510_221820_uncommited-changes.json b/...bit/0003_3a0f8a44c3a469bd3e3d27009467f90515500b11_20230510_221820_uncommited-changes.json
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -33,6 +33,7 @@ jobs:
 
       - name: Install
         run: |
+          pip install --upgrade pip
           pip install .[dev]
 
       - name: Run Tests

diff --git a/.gitignore b/.gitignore
@@ -30,3 +30,8 @@ hera_cal/data/zen.*.sum.bda.downsampled.redcal_meta.hdf5
 
 htmlcov/
 cache_temp/
+
+# Scalene profiling output
+profile.json
+profile.html
+.benchmarks/*
diff --git a/ci/hera_cal_tests.yml b/ci/hera_cal_tests.yml
@@ -24,10 +24,8 @@ dependencies:
   - jaxlib
   - optax
   - line_profiler
-
+  - pyuvdata>=2.3.3
   - pip:
-    - git+https://github.com/RadioAstronomySoftwareGroup/pyuvdata
-    # - git+https://github.com/HERA-Team/aipy
     - git+https://github.com/HERA-Team/hera_filters
     - git+https://github.com/HERA-Team/linsolve
     - git+https://github.com/HERA-Team/hera_qm

diff --git a/hera_cal/_cli_tools.py b/hera_cal/_cli_tools.py
@@ -109,7 +109,6 @@ def run_script(**kwargs):
 Then, any logging statements in hera_cal code (or your own code in the interactive
 session) will have the desired logging behavior.
 
-
 """
 from __future__ import annotations
 
@@ -583,4 +582,4 @@ def filter_kwargs(kwargs: dict) -> dict:
             not k.startswith("profile_") and 
             not k.startswith("log_")
         )
-    }
+    }
diff --git a/hera_cal/abscal.py b/hera_cal/abscal.py
@@ -2450,7 +2450,6 @@ def match_times(datafile, modelfiles, filetype='uvh5', atol=1e-5):
 
     return match
 
-
 def cut_bls(datacontainer, bls=None, min_bl_cut=None, max_bl_cut=None, inplace=False):
     """
     Cut visibility data based on min and max baseline length.
@@ -4322,6 +4321,7 @@ def run_model_based_calibration(data_file, model_file, output_filename, auto_fil
                                    ref_antenna_name=refant_init, sky_catalog=f'{model_file}',
                                    metadata_only=False, sky_field=field_str, cal_type='gain',
                                    future_array_shapes=True)
+
     hc = io.to_HERACal(hc)
     hc.update(flags=data_ant_flags)
     # generate cal object from model to hold model flags.
@@ -4422,7 +4422,6 @@ def run_model_based_calibration(data_file, model_file, output_filename, auto_fil
 
     # update the calibration array.
     hc.update(gains=abscal_gains)
-
     hc.write(output_filename, clobber=clobber, spoof_missing_channels=spoof_missing_channels)