Merge pull request #110 from LCOGT/fix/logging-adapter

Fix/logging adapter

.github/workflows/ci_tests.yml

@@ -29,10 +29,10 @@ jobs:
             python: 3.8
             toxenv: codestyle
 
-          - name: Python 3.7 with minimal dependencies
+          - name: Python 3.8 with minimal dependencies
             os: ubuntu-latest
-            python: 3.7
-            toxenv: py37-test
+            python: 3.8
+            toxenv: py38-test
 
           - name: Python 3.8 with all optional dependencies and coverage checking
             os: ubuntu-latest

CHANGES.md

@@ -1,3 +1,7 @@
+1.1.3 (2023-11-17)
+------------------
+- Fixes to use BANZAI LoggingAdapter
+
 1.1.2 (2023-07-25)
 ------------------
 - Update NRES Frame Factory to handle UNKNOWN as a valid empty coordinate

Dockerfile

@@ -1,10 +1,10 @@
-FROM docker.lco.global/banzai:1.9.8
+FROM ghcr.io/lcogt/banzai:1.13.1
 
 USER root
 
-RUN conda install -y coveralls sphinx statsmodels docutils=0.15
+RUN conda install -y coveralls sphinx statsmodels docutils
 
-RUN pip install astropy==4.2
+RUN pip install astropy==5.3.4
 
 COPY --chown=10087:10000 . /lco/banzai-nres
 

banzai_nres/__init__.py

@@ -1,8 +1,3 @@
 # ----------------------------------------------------------------------------
 from ._astropy_init import *   # noqa
 # ----------------------------------------------------------------------------
-
-import logging
-from banzai.logs import BanzaiLogger
-
-logging.setLoggerClass(BanzaiLogger)

banzai_nres/classify.py

@@ -1,6 +1,7 @@
 from banzai.stages import Stage
 from banzai_nres.frames import NRESObservationFrame
 from banzai_nres import dbs
+from banzai.logs import get_logger
 import warnings
 from astropy import units
 from astropy.time import Time
@@ -10,11 +11,10 @@
 from banzai_nres import phoenix
 import numpy as np
 from banzai.utils import import_utils
-import logging
 import astroquery.exceptions
 
 
-logger = logging.getLogger('banzai')
+logger = get_logger()
 
 
 def find_object_in_catalog(image, db_address, gaia_class, simbad_class):

banzai_nres/dbs.py

@@ -2,16 +2,16 @@
 from sqlalchemy import Column, String, Integer, Float, Index, ForeignKey
 import boto3
 import banzai.dbs
+from banzai.logs import get_logger
 import os
 from glob import glob
-import logging
 from sqlalchemy import func, desc
 from sqlalchemy.ext.hybrid import hybrid_method
 import numpy as np
 
 from banzai_nres.utils.phoenix_utils import parse_phoenix_header
 
-logger = logging.getLogger('banzai')
+logger = get_logger()
 
 
 class PhoenixModel(Base):

banzai_nres/extract.py

@@ -3,11 +3,11 @@
 from banzai.stages import Stage
 from banzai_nres.frames import Spectrum1D, NRESObservationFrame
 from banzai_nres.utils.trace_utils import get_trace_region
-import logging
 from banzai.data import ArrayData
+from banzai.logs import get_logger
 
 
-logger = logging.getLogger('banzai')
+logger = get_logger()
 
 
 class WeightedExtract(Stage):

banzai_nres/frames.py

@@ -2,10 +2,10 @@
 from banzai.lco import LCOFrameFactory, LCOObservationFrame, LCOCalibrationFrame
 from banzai.frames import ObservationFrame
 from banzai.data import DataProduct, ArrayData, HeaderOnly, DataTable
+from banzai.logs import get_logger
 from matplotlib.backends.backend_pdf import PdfPages
 from matplotlib import pyplot
 from io import BytesIO
-import logging
 from typing import Optional
 import numpy as np
 from astropy.table import Table
@@ -15,7 +15,7 @@
 from banzai.utils import fits_utils
 
 
-logger = logging.getLogger('banzai')
+logger = get_logger()
 
 
 class Spectrum1D:

banzai_nres/main.py

@@ -23,11 +23,10 @@
 import numpy as np
 import multiprocessing
 
-import logging
 import argparse
 import requests
 
-logger = logging.getLogger(__name__)
+logger = logs.get_logger()
 
 
 def nres_run_realtime_pipeline():

banzai_nres/pdf.py

@@ -4,11 +4,11 @@
 from astropy import units
 
 from banzai.stages import Stage
+from banzai.logs import get_logger
 from banzai_nres import phoenix
-import logging
 from banzai_nres.qc.qc_science import get_snr
 
-logger = logging.getLogger('banzai')
+logger = get_logger()
 
 
 class MakePDFSummary(Stage):

banzai_nres/phoenix.py

@@ -10,10 +10,9 @@
 from scipy import interpolate
 from banzai_nres.continuum import ContinuumNormalizer
 from banzai_nres.utils import phoenix_utils
-import logging
+from banzai.logs import get_logger
 
-
-logger = logging.getLogger('banzai')
+logger = get_logger()
 
 
 class PhoenixModelLoader:

banzai_nres/qc/qc_science.py

@@ -1,8 +1,8 @@
 import numpy as np
 from banzai.stages import Stage
-import logging
+from banzai.logs import get_logger
 
-logger = logging.getLogger('banzai')
+logger = get_logger()
 
 # This defines the order for which we calculate the SNR value for the header.
 # By default this is the order containing the Mg b lines.

banzai_nres/qc/qc_wavelength.py

@@ -1,14 +1,14 @@
 import numpy as np
 from banzai.stages import Stage
 from banzai.utils import qc
+from banzai.logs import get_logger
 from astropy import constants
 from astropy import units
 from xwavecal.utils.wavelength_utils import find_nearest
 from banzai.utils.stats import robust_standard_deviation
-import logging
 
 
-logger = logging.getLogger('banzai')
+logger = get_logger()
 
 
 class AssessWavelengthSolution(Stage):

banzai_nres/rv.py

@@ -1,6 +1,7 @@
 from banzai.stages import Stage
 from banzai.frames import ObservationFrame
 from banzai import dbs
+from banzai.logs import get_logger
 from banzai.data import DataTable
 import numpy as np
 from astropy.table import Table, QTable
@@ -10,10 +11,9 @@
 from astropy import units
 from banzai.utils import stats
 from astropy.stats import sigma_clip
-import logging
 from banzai_nres import phoenix
 
-logger = logging.getLogger('banzai')
+logger = get_logger()
 
 
 # wavelength regions selected by eye by Mirek on 09 16 2020 wherever there are large (H alpha like, i.e. broad wings)

banzai_nres/tests/test_e2e.py

@@ -1,6 +1,7 @@
 import pytest
 from banzai.tests.utils import FakeResponse, get_min_and_max_dates
 from banzai_nres import settings
+from banzai.logs import get_logger
 import os
 import mock
 import numpy as np
@@ -20,9 +21,7 @@
 import banzai_nres.dbs
 import json
 
-import logging
-
-logger = logging.getLogger('banzai')
+logger = get_logger()
 
 TEST_PACKAGE = 'banzai_nres.tests'
 

banzai_nres/traces.py

@@ -6,13 +6,13 @@
     G. Mirek Brandt ([email protected])
 """
 from banzai.stages import Stage
-import logging
+from banzai.logs import get_logger
 from scipy import ndimage
 import numpy as np
 from banzai_nres.fitting import fit_polynomial
 from banzai.data import ArrayData
 
-logger = logging.getLogger('banzai')
+logger = get_logger()
 
 # Minimum separation between peaks in the image that could be separate traces
 MIN_TRACE_SEPARATION = 10

banzai_nres/utils/continuum_utils.py

@@ -1,10 +1,10 @@
 import numpy as np
 from scipy.ndimage import binary_dilation, percentile_filter
 from scipy.ndimage import gaussian_filter1d
-import logging
 from banzai.utils.stats import robust_standard_deviation
+from banzai.logs import get_logger
 
-logger = logging.getLogger('banzai')
+logger = get_logger()
 
 
 def mark_features(flux, sigma=3, continuum_formal_error=None, detector_resolution=4):

banzai_nres/utils/wavelength_utils.py

@@ -2,10 +2,9 @@
 from photutils.detection import DAOStarFinder
 from astropy.table import Table
 from banzai.utils.stats import robust_standard_deviation
+from banzai.logs import get_logger
 
-import logging
-
-logger = logging.getLogger('banzai')
+logger = get_logger()
 
 
 def identify_features(data, err, mask=None, nsigma=2., fwhm=6.0, **kwargs):

banzai_nres/wavelength.py

@@ -3,6 +3,7 @@
 from banzai.stages import Stage
 from banzai.data import DataTable, ArrayData
 from banzai.calibrations import CalibrationStacker, CalibrationUser
+from banzai.logs import get_logger
 from astropy import table
 
 from banzai_nres.frames import NRESObservationFrame
@@ -13,13 +14,12 @@
 from xwavecal.fibers import IdentifyFibers
 
 import sep
-import logging
 import os
 import pkg_resources
 from astropy.table import Table
 
 
-logger = logging.getLogger('banzai')
+logger = get_logger()
 
 WAVELENGTH_SOLUTION_MODEL = {0: [0, 1, 2, 3, 4, 5],
                              1: [0, 1, 2, 3, 4, 5],

docs/banzai_nres/ExampleReduction.ipynb

@@ -28,8 +28,7 @@
     "from banzai_nres import settings\n",
     "from banzai import dbs\n",
     "from banzai.utils.stage_utils import run_pipeline_stages\n",
-    "import logging\n",
-    "from banzai.logs import set_log_level\n",
+    "from banzai.logs import set_log_level, get_logger\n",
     "from glob import glob\n",
     "\n",
     "import pkg_resources"
@@ -50,7 +49,7 @@
    "outputs": [],
    "source": [
     "set_log_level('DEBUG')\n",
-    "logger = logging.getLogger('banzai')"
+    "logger = get_logger()"
    ]
   },
   {

tox.ini

@@ -1,8 +1,8 @@
 [tox]
 envlist =
-    py{37,38}-test{,-alldeps,-devdeps}{,-cov}
-    py{37,38}-test-numpy{117,118,119,120}
-    py{37,38}-test-astropy{30,40,41,42,lts}
+    py{38,39}-test{,-alldeps,-devdeps}{,-cov}
+    py{38,39}-test-numpy{117,118,119,120}
+    py{38,39}-test-astropy{30,40,41,42,lts}
     build_docs
     linkcheck
     codestyle