DM-41811: Add pre-commit and update doc build

.pre-commit-config.yaml

@@ -0,0 +1,31 @@
+default_language_version:
+  python: python3
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 23.3.0
+    hooks:
+      - id: black
+        # It is recommended to specify the latest version of Python
+        # supported by your project here, or alternatively use
+        # pre-commit's default_language_version, see
+        # https://pre-commit.com/#top_level-default_language_version
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        name: isort (python)
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.1.8
+    hooks:
+      - id: ruff
+  - repo: https://github.com/numpy/numpydoc
+    rev: "v1.6.0"
+    hooks:
+      - id: numpydoc-validation

doc/lsst.meas.extensions.multiprofit/index.rst

@@ -14,8 +14,15 @@ lsst.meas.extensions.multiprofit
 .. Using lsst.meas.extensions.multiprofit
 .. ======================================
 
-There is currently one master task, which is a subtask of a generic multiband
-fitting ``lsst.pipe.tasks.PipelineTask`` (``lsst.pipe.tasks.fit_multiband.MultibandFitTask``); future tasks will likely follow this pattern.
+``lsst.meas.extensions.multiprofit`` implements separate tasks for PSF and source model fitting
+using ``lsst.multiprofit``. The tasks depend on more generic ``lsst.pipe.tasks.PipelineTask``
+classes defined in ``lsst.pipe.tasks.fit_coadd_psf`` and ``lsst.pipe.tasks.fit_coadd_multiband``.
+Note that as implied by the names, the PSF fitting task is single-band only.
+
+Because these tasks produce patch-based Arrow/Astropy tables, a generic task to consolidate
+the results into a single multiband tract-based table is also provided. It is anticipated that
+this functionality will be folded into the tasks producing objectTable_tract instances in
+``lsst.pipe.tasks.postprocess``.
 
 .. toctree linking to topics related to using the module's APIs.
 
@@ -28,7 +35,7 @@ Contributing
 ============
 
 ``lsst.meas.extensions.multiprofit`` is developed at https://github.com/lsst-dm/meas_extensions_multiprofit.
-You can find Jira issues for this module under the `meas_extensions_multiprofit <https://jira.lsstcorp.org/issues/?jql=project%20%3D%20DM%20AND%20component%20%3D%20meas_extensions_multiprofit>`_ component.
+You can find Jira issues for multiprofit through `search <https://jira.lsstcorp.org/issues/?jql=text%20~%20%22multiprofit%22>`_.
 
 .. If there are topics related to developing this module (rather than using it), link to this from a toctree placed here.
 
@@ -89,6 +96,11 @@ Configurations
 Python API reference
 ====================
 
-.. automodapi:: lsst.meas.extensions.multiprofit
-   :no-main-docstr:
+.. automodapi:: lsst.meas.extensions.multiprofit.consolidate_astropy_table
+   :no-inheritance-diagram:
+
+.. automodapi:: lsst.meas.extensions.multiprofit.fit_coadd_multiband
+   :no-inheritance-diagram:
+
+.. automodapi:: lsst.meas.extensions.multiprofit.fit_coadd_psf
    :no-inheritance-diagram:

pyproject.toml

@@ -97,3 +97,18 @@ max-doc-length = 79
 
 [tool.ruff.pydocstyle]
 convention = "numpy"
+
+[tool.numpydoc_validation]
+checks = [
+    "all",  # All except the rules listed below.
+    "ES01",  # No extended summary required.
+    "EX01",  # Example section.
+    "GL01",  # Summary text can start on same line as """
+    "GL08",  # Do not require docstring.
+    "PR04",  # numpydoc parameter types are redundant with type hints
+    "RT01",  # Unfortunately our @property trigger this.
+    "RT02",  # Does not want named return value. DM style says we do.
+    "SA01",  # See Also section.
+    "SS05",  # pydocstyle is better at finding infinitive verb.
+    "SS06",  # Summary can go into second line.
+]

python/lsst/meas/extensions/multiprofit/consolidate_astropy_table.py

@@ -19,14 +19,14 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
+from collections import defaultdict
+
+import astropy.table as apTab
 import lsst.pex.config as pexConfig
-from lsst.pex.config.configurableActions import ConfigurableAction, ConfigurableActionField
 import lsst.pipe.base as pipeBase
 import lsst.pipe.base.connectionTypes as connectionTypes
-
-import astropy.table as apTab
-from collections import defaultdict
 import numpy as np
+from lsst.pex.config.configurableActions import ConfigurableAction, ConfigurableActionField
 
 
 class CatalogAction(ConfigurableAction):
@@ -90,7 +90,7 @@ def __call__(self, data, **kwargs):
 
 
 class InputConfig(pexConfig.Config):
-    """Config for inputs to ConsolidateAstropyTableTask"""
+    """Config for inputs to ConsolidateAstropyTableTask."""
 
     doc = pexConfig.Field[str](doc="Doc for connection", optional=False)
     action = ConfigurableActionField[CatalogAction](
@@ -107,7 +107,7 @@ class InputConfig(pexConfig.Config):
 
 
 class ConsolidateAstropyTableConfigBase(pexConfig.Config):
-    """Config for ConsolidateAstropyTableTask"""
+    """Config for ConsolidateAstropyTableTask."""
 
     inputs = pexConfig.ConfigDictField(
         doc="Mapping of input dataset type config by name",
@@ -117,8 +117,12 @@ class ConsolidateAstropyTableConfigBase(pexConfig.Config):
     )
 
 
-class ConsolidateAstropyTableConnections(pipeBase.PipelineTaskConnections, dimensions=("tract", "skymap")):
-    """Connections for ConsolidateAstropyTableTask"""
+class ConsolidateAstropyTableConnections(
+    # Ignore the undocumented inherited config arg in __init__
+    pipeBase.PipelineTaskConnections,
+    dimensions=("tract", "skymap"),  # numpydoc ignore=PR01
+):
+    """Connections for ConsolidateAstropyTableTask."""
 
     cat_output = connectionTypes.Output(
         doc="Per-tract horizontal concatenation of the input AstropyTables",
@@ -154,7 +158,7 @@ class ConsolidateAstropyTableConfig(
     ConsolidateAstropyTableConfigBase,
     pipelineConnections=ConsolidateAstropyTableConnections,
 ):
-    """PipelineTaskConfig for ConsolidateAstropyTableTask"""
+    """PipelineTaskConfig for ConsolidateAstropyTableTask."""
 
 
 class ConsolidateAstropyTableTask(pipeBase.PipelineTask):

python/lsst/meas/extensions/multiprofit/fit_coadd_multiband.py

@@ -20,21 +20,18 @@
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 import math
-import numpy as np
-import pydantic
-from pydantic.dataclasses import dataclass
-from typing import Any, Mapping, Sequence
+from typing import Any, Mapping, Sequence, Type
 
 import gauss2d as g2
 import gauss2d.fit as g2f
-
-from lsst.daf.butler.formatters.parquet import astropy_to_arrow
 import lsst.geom as geom
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
 import lsst.pipe.tasks.fit_coadd_multiband as fitMB
 import lsst.utils.timer as utilsTimer
-
+import numpy as np
+import pydantic
+from lsst.daf.butler.formatters.parquet import astropy_to_arrow
 from lsst.multiprofit.config import set_config_from_dict
 from lsst.multiprofit.fit_psf import CatalogPsfFitterConfig, PsfRebuildFitFlagError
 from lsst.multiprofit.fit_source import (
@@ -43,19 +40,18 @@
     CatalogSourceFitterConfig,
 )
 from lsst.multiprofit.utils import get_params_uniq
-
-from typing import Type
+from pydantic.dataclasses import dataclass
 
 from .utils import get_spanned_image
 
 
 class NotPrimaryError(RuntimeError):
-    """RuntimeError for sources that are not primary and shouldn't be fit"""
+    """RuntimeError for sources that are not primary and shouldn't be fit."""
 
 
 @dataclass(frozen=True, kw_only=True, config=fitMB.CatalogExposureConfig)
 class CatalogExposurePsfs(fitMB.CatalogExposureInputs, CatalogExposureSourcesABC):
-    """Input data from lsst pipelines, parsed for MultiProFit"""
+    """Input data from lsst pipelines, parsed for MultiProFit."""
 
     channel: g2f.Channel = pydantic.Field(title="Channel for the image's band")
     config_fit: CatalogSourceFitterConfig = pydantic.Field(title="Channel for the image's band")
@@ -141,6 +137,11 @@ class MultiProFitSourceTask(CatalogSourceFitterABC, fitMB.CoaddMultibandFitSubTa
     prior measurements from single- or merged multiband catalogs for
     initialization.
 
+    Parameters
+    ----------
+    **kwargs
+        Keyword arguments to pass to CoaddMultibandFitSubTask.__init__.
+
     Notes
     -----
     See https://github.com/lsst-dm/multiprofit for more MultiProFit info.
@@ -149,7 +150,7 @@ class MultiProFitSourceTask(CatalogSourceFitterABC, fitMB.CoaddMultibandFitSubTa
     ConfigClass = MultiProFitSourceConfig
     _DefaultName = "multiProFitSource"
 
-    def __init__(self, **kwargs):
+    def __init__(self, **kwargs: Any):
         errors_expected = {} if "errors_expected" not in kwargs else kwargs.pop("errors_expected")
         if NotPrimaryError not in errors_expected:
             errors_expected[NotPrimaryError] = "not_primary_flag"
@@ -172,6 +173,8 @@ def _init_component(
             The component to initialize.
         values_init
             Initial values to set per parameter type.
+        limits_init
+            Initial limits to set per parameter type.
         """
         # These aren't necessarily all free - should set cen_x, y
         # even if they're fixed, for example

python/lsst/meas/extensions/multiprofit/fit_coadd_psf.py

@@ -19,16 +19,14 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
-from pydantic.dataclasses import dataclass
-
-from lsst.daf.butler.formatters.parquet import astropy_to_arrow
 import lsst.pex.config as pexConfig
-from lsst.pex.exceptions import InvalidParameterError
 import lsst.pipe.base as pipeBase
 import lsst.pipe.tasks.fit_coadd_psf as fitCP
 import lsst.utils.timer as utilsTimer
-
+from lsst.daf.butler.formatters.parquet import astropy_to_arrow
 from lsst.multiprofit.fit_psf import CatalogExposurePsfABC, CatalogPsfFitter, CatalogPsfFitterConfig
+from lsst.pex.exceptions import InvalidParameterError
+from pydantic.dataclasses import dataclass
 
 
 @dataclass(frozen=True, kw_only=True, config=fitCP.CatalogExposureConfig)
@@ -53,6 +51,11 @@ class MultiProFitPsfTask(CatalogPsfFitter, fitCP.CoaddPsfFitSubTask):
     evaluated at the centroid of each source in the corresponding
     catalog.
 
+    Parameters
+    ----------
+    **kwargs
+        Keyword arguments to pass to CoaddPsfFitSubTask.__init__.
+
     Notes
     -----
     See https://github.com/lsst-dm/multiprofit for more MultiProFit info.