8000 Apply code style rules to stpipe by emolter · Pull Request #9150 · spacetelescope/jwst · GitHub
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Merged
merged 4 commits into from
Feb 6, 2025
Merged

Apply code style rules to stpipe #9150

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8f1718b
Apply code style rules to stpipe
emolter Feb 6, 2025
f9d082c
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Feb 6, 2025
2852e68
remove unused function from testing init
emolter Feb 6, 2025
a86a74e
Merge branch 'main' into JP-3860-stpipe
melanieclarke Feb 6, 2025
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1 change: 0 additions & 1 deletion .pre-commit-config.yaml
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Expand Up @@ -83,7 +83,6 @@ repos:
jwst/skymatch/.* |
jwst/spectral_leak/.* |
jwst/srctype/.* |
jwst/stpipe/.* |
jwst/straylight/.* |
jwst/superbias/.* |
jwst/tests/.* |
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4 changes: 2 additions & 2 deletions .ruff.toml
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Expand Up @@ -79,7 +79,7 @@ exclude = [
# "jwst/source_catalog/**.py",
"jwst/spectral_leak/**.py",
"jwst/srctype/**.py",
"jwst/stpipe/**.py",
# "jwst/stpipe/**.py",
"jwst/straylight/**.py",
"jwst/superbias/**.py",
"jwst/tests/**.py",
Expand Down Expand Up @@ -209,7 +209,7 @@ ignore-fully-untyped = true # Turn of annotation checking for fully untyped cod
# "jwst/source_catalog/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
"jwst/spectral_leak/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
"jwst/srctype/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
"jwst/stpipe/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
# "jwst/stpipe/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
"jwst/straylight/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
"jwst/superbias/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
"jwst/tests/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
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4 changes: 3 additions & 1 deletion jwst/stpipe/__init__.py
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@@ -1,5 +1,7 @@
"""JWST implementation of steps and pipelines."""

from .core import JwstStep as Step, JwstPipeline as Pipeline
from .utilities import record_step_status, query_step_status


__all__ = ['Step', 'Pipeline', 'record_step_status', 'query_step_status']
__all__ = ["Step", "Pipeline", "record_step_status", "query_step_status"]
98 changes: 79 additions & 19 deletions jwst/stpipe/core.py
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@@ -1,6 +1,5 @@
"""
JWST-specific Step and Pipeline base classes.
"""
"""JWST-specific Step and Pipeline base classes."""

from functools import wraps
import logging
import warnings
Expand All @@ -20,18 +19,19 @@


class JwstStep(Step):
"""A JWST pipeline step."""

spec = """
output_ext = string(default='.fits') # Output file type
""" # noqa: E501
""" # noqa: E501

@classmethod
def _datamodels_open(cls, init, **kwargs):
return datamodels.open(init, **kwargs)


def load_as_level2_asn(self, obj):
"""Load object as an association
"""
Load object as an association.

Loads the specified object into a Level2 association.
If necessary, prepend `Step.input_dir` to all members.
Expand All @@ -51,11 +51,12 @@ def load_as_level2_asn(self, obj):
from ..associations.lib.update_path import update_key_value

asn = LoadAsLevel2Asn.load(obj, basename=self.output_file)
update_key_value(asn, 'expname', (), mod_func=self.make_input_path)
update_key_value(asn, "expname", (), mod_func=self.make_input_path)
return asn

def load_as_level3_asn(self, obj):
"""Load object as an association
"""
Load object as an association.

Loads the specified object into a Level3 association.
If necessary, prepend `Step.input_dir` to all members.
Expand All @@ -75,52 +76,111 @@ def load_as_level3_asn(self, obj):
from ..associations.lib.update_path import update_key_value

asn = LoadAsAssociation.load(obj)
update_key_value(asn, 'expname', (), mod_func=self.make_input_path)
update_key_value(asn, "expname", (), mod_func=self.make_input_path)
return asn

def finalize_result(self, result, reference_files_used):
"""
Update the result with the software version and reference files used.

Parameters
----------
result : `~jwst.datamodels.DataModel`
The output data model to be updated.
reference_files_used : list of tuple
The names and file paths of reference files used.
"""
if isinstance(result, JwstDataModel):
result.meta.calibration_software_revision = __version_commit__ or 'RELEASE'
result.meta.calibration_software_revision = __version_commit__ or "RELEASE"
result.meta.calibration_software_version = __version__

if len(reference_files_used) > 0:
for ref_name, filename in reference_files_used:
if hasattr(result.meta.ref_file, ref_name):
getattr(result.meta.ref_file, ref_name).name = filename
result.meta.ref_file.crds.sw_version = crds_client.get_svn_version()
result.meta.ref_file.crds.context_used = crds_client.get_context_used(result.crds_observatory)
result.meta.ref_file.crds.context_used = crds_client.get_context_used(
result.crds_observatory
)
if self.parent is None:
log.info(f"Results used CRDS context: {result.meta.ref_file.crds.context_used}")


def remove_suffix(self, name):
"""
Remove the suffix if a known suffix is already in name.

Parameters
----------
name : str
The name to remove the suffix from.

Returns
-------
name : str
The name with the suffix removed.
"""
return remove_suffix(name)

@wraps(Step.run)
def run(self, *args, **kwargs):
"""
Run the step.

Parameters
----------
*args
Arguments passed to `stpipe.Step.run`.
**kwargs
Keyword arguments passed to `stpipe.Step.run`.

Returns
-------
result : Any
The step output
"""
result = super().run(*args, **kwargs)
if not self.parent:
log.info(f"Results used jwst version: {__version__}")
return result

@wraps(Step.__call__)
def __call__(self, *args, **kwargs):
def __call__(self, *args, **kwargs): # numpydoc ignore=RT01
"""Deprecated method. Use `run` instead.""" # noqa: D401
if not self.parent:
warnings.warn(
"Step.__call__ is deprecated. It is equivalent to Step.run "
"and is not recommended. See "
"https://jwst-pipeline.readthedocs.io/en/latest/jwst/"
"user_documentation/running_pipeline_python.html"
"#advanced-use-pipeline-run-vs-pipeline-call for more details.",
UserWarning
UserWarning,
stacklevel=2,
)
return super().__call__(*args, **kwargs)


# JwstPipeline needs to inherit from Pipeline, but also
# be a subclass of JwstStep so that it will pass checks
# when constructing a pipeline using JwstStep class methods.
class JwstPipeline(Pipeline, JwstStep):
def finalize_result(self, result, reference_files_used):
"""
A JWST pipeline.

JwstPipeline needs to inherit from Pipeline, but also
be a subclass of JwstStep so that it will pass checks
when constructing a pipeline using JwstStep class methods.
"""

def finalize_result(self, result, _reference_files_used):
"""
Update the result with the software version and reference files used.

Parameters
----------
result : `~jwst.datamodels.DataModel`
The output data model to be updated.
_reference_files_used : list of tuple
The names and file paths of reference files used.
"""
if isinstance(result, JwstDataModel):
log.info(f"Results used CRDS context: {crds_client.get_context_used(result.crds_observatory)}")
log.info(
"Results used CRDS context: "
f"{crds_client.get_context_used(result.crds_observatory)}"
)
155 changes: 77 additions & 78 deletions jwst/stpipe/integration.py
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@@ -1,12 +1,11 @@
"""
Entry point implementations.
"""
"""Entry point implementations."""


def get_steps():
"""
Return tuples describing the stpipe.Step subclasses provided
by this package. This method is registered with the stpipe.steps
Return tuples describing the stpipe.Step subclasses provided by this package.

This method is registered with the stpipe.steps
entry point.

Returns
Expand All @@ -21,77 +20,77 @@ def get_steps():
# class definitions. We need to avoid importing jwst.pipeline and
# jwst.step to keep the CLI snappy.
return [
("jwst.pipeline.Ami3Pipeline", 'calwebb_ami3', True),
("jwst.pipeline.Coron3Pipeline", 'calwebb_coron3', True),
("jwst.pipeline.DarkPipeline", 'calwebb_dark', True),
("jwst.pipeline.Detector1Pipeline", 'calwebb_detector1', True),
("jwst.pipeline.GuiderPipeline", 'calwebb_guider', True),
("jwst.pipeline.Image2Pipeline", 'calwebb_image2', True),
("jwst.pipeline.Image3Pipeline", 'calwebb_image3', True),
("jwst.pipeline.Spec2Pipeline", 'calwebb_spec2', True),
("jwst.pipeline.Spec3Pipeline", 'calwebb_spec3', True),
("jwst.pipeline.Tso3Pipeline", 'calwebb_tso3', True),
("jwst.step.AmiAnalyzeStep", 'ami_analyze', False),
("jwst.step.AmiAverageStep", 'ami_average', False),
("jwst.step.AmiNormalizeStep", 'ami_normalize', False),
("jwst.step.AssignMTWcsStep", 'assign_mtwcs', False),
("jwst.step.AssignWcsStep", 'assign_wcs', False),
("jwst.step.BackgroundStep", 'background', False),
("jwst.step.BadpixSelfcalStep", 'badpix_selfcal', False),
("jwst.step.BarShadowStep", 'barshadow', False),
("jwst.step.Combine1dStep", 'combine_1d', False),
("jwst.step.StackRefsStep", 'stack_refs', False),
("jwst.step.AlignRefsStep", 'align_refs', False),
("jwst.step.KlipStep", 'klip', False),
("jwst.step.HlspStep", 'hlsp', False),
("jwst.step.CleanFlickerNoiseStep", 'clean_flicker_noise', False),
("jwst.step.CubeBuildStep", 'cube_build', False),
("jwst.step.CubeSkyMatchStep", 'cube_skymatch', False),
("jwst.step.DarkCurrentStep", 'dark_current', False),
("jwst.step.DQInitStep", 'dq_init', False),
("jwst.step.EmiCorrStep", 'emicorr', False),
("jwst.step.Extract1dStep", 'extract_1d', False),
("jwst.step.Extract2dStep", 'extract_2d', False),
("jwst.step.FirstFrameStep", 'firstframe', False),
("jwst.step.FlatFieldStep", 'flat_field', False),
("jwst.step.FringeStep", 'fringe', False),
("jwst.step.GainScaleStep", 'gain_scale', False),
("jwst.step.GroupScaleStep", 'group_scale', False),
("jwst.step.GuiderCdsStep", 'guider_cds', False),
("jwst.step.ImprintStep", 'imprint', False),
("jwst.step.IPCStep", 'ipc', False),
("jwst.step.JumpStep", 'jump', False),
("jwst.step.LastFrameStep", 'lastframe', False),
("jwst.step.LinearityStep", 'linearity', False),
("jwst.step.MasterBackgroundStep", 'master_background', False),
("jwst.step.MasterBackgroundMosStep", 'master_background_mos', False),
("jwst.step.MRSIMatchStep", 'mrs_imatch', False),
("jwst.step.MSAFlagOpenStep", 'msa_flagging', False),
("jwst.step.NSCleanStep", 'nsclean', False),
("jwst.step.OutlierDetectionStep", 'outlier_detection', False),
("jwst.step.PathLossStep", 'pathloss', False),
("jwst.step.PersistenceStep", 'persistence', False),
("jwst.step.PhotomStep", 'photom', False),
("jwst.step.PixelReplaceStep", 'pixel_replace', False),
("jwst.step.RampFitStep", 'ramp_fit', False),
("jwst.step.RefPixStep", 'refpix', False),
("jwst.step.ResampleStep", 'resample', False),
("jwst.step.ResampleSpecStep", 'resample_spec', False),
("jwst.step.ResetStep", 'reset', False),
("jwst.step.ResidualFringeStep", 'residual_fringe', False),
("jwst.step.RscdStep", 'rscd', False),
("jwst.step.SaturationStep", 'saturation', False),
("jwst.step.SkyMatchStep", 'skymatch', False),
("jwst.step.SourceCatalogStep", 'source_catalog', False),
("jwst.step.SourceTypeStep", 'srctype', False),
("jwst.step.SpectralLeakStep", 'spectral_leak', False),
("jwst.step.StraylightStep", 'straylight', False),
("jwst.step.SuperBiasStep", 'superbias', False),
("jwst.step.TSOPhotometryStep", 'tso_photometry', False),
("jwst.step.TweakRegStep", 'tweakreg', False),
("jwst.step.ChargeMigrationStep", 'charge_migration', False),
("jwst.step.WavecorrStep", 'wavecorr', False),
("jwst.step.WfsCombineStep", 'calwebb_wfs-image3', False),
("jwst.step.WfssContamStep", 'wfss_contam', False),
("jwst.step.WhiteLightStep", 'white_light', False),
("jwst.pipeline.Ami3Pipeline", "calwebb_ami3", True),
("jwst.pipeline.Coron3Pipeline", "calwebb_coron3", True),
("jwst.pipeline.DarkPipeline", "calwebb_dark", True),
("jwst.pipeline.Detector1Pipeline", "calwebb_detector1", True),
("jwst.pipeline.GuiderPipeline", "calwebb_guider", True),
("jwst.pipeline.Image2Pipeline", "calwebb_image2", True),
("jwst.pipeline.Image3Pipeline", "calwebb_image3", True),
("jwst.pipeline.Spec2Pipeline", "calwebb_spec2", True),
("jwst.pipeline.Spec3Pipeline", "calwebb_spec3", True),
("jwst.pipeline.Tso3Pipeline", "calwebb_tso3", True),
("jwst.step.AmiAnalyzeStep", "ami_analyze", False),
("jwst.step.AmiAverageStep", "ami_average", False),
("jwst.step.AmiNormalizeStep", "ami_normalize", False),
("jwst.step.AssignMTWcsStep", "assign_mtwcs", False),
("jwst.step.AssignWcsStep", "assign_wcs", False),
("jwst.step.BackgroundStep", "background", False),
("jwst.step.BadpixSelfcalStep", "badpix_selfcal", False),
("jwst.step.BarShadowStep", "barshadow", False),
("jwst.step.Combine1dStep", "combine_1d", False),
("jwst.step.StackRefsStep", "stack_refs", False),
("jwst.step.AlignRefsStep", "align_refs", False),
("jwst.step.KlipStep", "klip", False),
("jwst.step.HlspStep", "hlsp", False),
("jwst.step.CleanFlickerNoiseStep", "clean_flicker_noise", False),
("jwst.step.CubeBuildStep", "cube_build", False),
("jwst.step.CubeSkyMatchStep", "cube_skymatch", False),
("jwst.step.DarkCurrentStep", "dark_current", False),
("jwst.step.DQInitStep", "dq_init", False),
("jwst.step.EmiCorrStep", "emicorr", False),
("jwst.step.Extract1dStep", "extract_1d", False),
("jwst.step.Extract2dStep", "extract_2d", False),
("jwst.step.FirstFrameStep", "firstframe", False),
("jwst.step.FlatFieldStep", "flat_field", False),
("jwst.step.FringeStep", "fringe", False),
("jwst.step.GainScaleStep", "gain_scale", False),
("jwst.step.GroupScaleStep", "group_scale", False),
("jwst.step.GuiderCdsStep", "guider_cds", False),
("jwst.step.ImprintStep", "imprint", False),
("jwst.step.IPCStep", "ipc", False),
("jwst.step.JumpStep", "jump", False),
("jwst.step.LastFrameStep", "lastframe", False),
("jwst.step.LinearityStep", "linearity", False),
("jwst.step.MasterBackgroundStep", "master_background", False),
("jwst.step.MasterBackgroundMosStep", "master_background_mos", False),
("jwst.step.MRSIMatchStep", "mrs_imatch", False),
("jwst.step.MSAFlagOpenStep", "msa_flagging", False),
("jwst.step.NSCleanStep", "nsclean", False),
("jwst.step.OutlierDetectionStep", "outlier_detection", False),
("jwst.step.PathLossStep", "pathloss", False),
("jwst.step.PersistenceStep", "persistence", False),
("jwst.step.PhotomStep", "photom", False),
("jwst.step.PixelReplaceStep", "pixel_replace", False),
("jwst.step.RampFitStep", "ramp_fit", False),
("jwst.step.RefPixStep", "refpix", False),
("jwst.step.ResampleStep", "resample", False),
("jwst.step.ResampleSpecStep", "resample_spec", False),
("jwst.step.ResetStep", "reset", False),
("jwst.step.ResidualFringeStep", "residual_fringe", False),
("jwst.step.RscdStep", "rscd", False),
("jwst.step.SaturationStep", "saturation", False),
("jwst.step.SkyMatchStep", "skymatch", False),
("jwst.step.SourceCatalogStep", "source_catalog", False),
("jwst.step.SourceTypeStep", "srctype", False),
("jwst.step.SpectralLeakStep", "spectral_leak", False),
("jwst.step.StraylightStep", "straylight", False),
("jwst.step.SuperBiasStep", "superbias", False),
("jwst.step.TSOPhotometryStep", "tso_photometry", False),
("jwst.step.TweakRegStep", "tweakreg", False),
("jwst.step.ChargeMigrationStep", "charge_migration", False),
("jwst.step.WavecorrStep", "wavecorr", False),
("jwst.step.WfsCombineStep", "calwebb_wfs-image3", False),
("jwst.step.WfssContamStep", "wfss_contam", False),
("jwst.step.WhiteLightStep", "white_light", False),
]
10 changes: 0 additions & 10 deletions jwst/stpipe/tests/__init__.py
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@@ -1,10 +0,0 @@
import io


def setup():
from jwst.stpipe import log

# Turn off default logging when running tests
buffer = io.BytesIO(b"[*]\n")

log.load_configuration(buffer)
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