Docs: Fixing Pydantic sphinx issues on Github deployment

.github/workflows/manual-pages-deploy.yml

@@ -18,10 +18,10 @@ jobs:
 
     - name: Update docs configuration with version (tag) name
       run: |
-        sed -i "s/PACKAGE_VERSION/${{ github.ref_name }}/" setup.py
-        sed -i "s/PACKAGE_VERSION/${{ github.ref_name }}/" CHAP/__init__.py
-        sed -i "s/PACKAGE_VERSION/${{ github.ref_name }}/" docs/conf.py
-        sed -i "s/PACKAGE_VERSION/${{ github.ref_name }}/" docs/installation.md
+        sed -i "s/PACKAGE_VERSION/0.0.1/" setup.py
+        sed -i "s/PACKAGE_VERSION/0.0.1/" CHAP/__init__.py
+        sed -i "s/PACKAGE_VERSION/0.0.1/" docs/conf.py
+        sed -i "s/PACKAGE_VERSION/0.0.1/" docs/installation.md
 
     - name: Setup Miniconda
       uses: conda-incubator/setup-miniconda@v3

CHAP/__init__.py

@@ -41,9 +41,4 @@
     Module defining the base `Writer` class to derive all others from.
 """
 
-#from CHAP.models import CHAPBaseModel
-#from CHAP.reader import Reader
-#from CHAP.processor import Processor
-#from CHAP.writer import Writer
-
 version = 'PACKAGE_VERSION'

CHAP/common/__init__.py

@@ -27,75 +27,3 @@
     Module for generic Writers used in multiple experiment-specific workflows.
 """
 
-#from CHAP.common.processor import (
-##    AnimationProcessor,
-#    AsyncProcessor,
-#    BinarizeProcessor,
-#    ConvertStructuredProcessor,
-#    ExpressionProcessor,
-#    ImageProcessor,
-#    MapProcessor,
-#    MPICollectProcessor,
-#    MPIMapProcessor,
-#    MPISpawnMapProcessor,
-#    NexusToNumpyProcessor,
-##    NexusToTiffsprocessor,
-#    NexusToXarrayProcessor,
-#    NexusToZarrProcessor,
-#    NormalizeNexusProcessor,
-#    NormalizeMapProcessor,
-#    NumpyStackProcessor,
-#    NumpySumProcessor,
-#    NumpyToNXfieldProcessor,
-#    PandasToXarrayProcessor,
-#    PrintProcessor,
-#    PyfaiAzimuthalIntegrationProcessor,
-#    RawDetectorDataMapProcessor,
-#    SetupNXdataProcessor,
-#    UpdateNXvalueProcessor,
-#    UpdateNXdataProcessor,
-#    UnstructuredToStructuredProcessor,
-#    NXdataToDataPointsProcessor,
-#    XarrayToNexusProcessor,
-#    XarrayToNumpyProcessor,
-#    ZarrToNexusProcessor,
-#)
-#from CHAP.common.reader import (
-#    BinaryFileReader,
-#    ConfigReader,
-#    DetectorDataReader,
-#    FabioImageReader,
-#    H5Reader,
-#    LinkamReader,
-#    MapReader,
-#    PandasReader,
-#    NexusReader,
-#    NXdataReader,
-#    NXfieldReader,
-#    SpecReader,
-#    URLReader,
-#    YAMLReader,
-#    ZarrReader,
-#)
-#from CHAP.common.writer import (
-#    ExtractArchiveWriter,
-#    FileTreeWriter,
-#    H5Writer,
-#    ImageWriter,
-#    MatplotlibAnimationWriter,
-#    MatplotlibFigureWriter,
-#    NexusWriter,
-#    NexusValuesWriter,
-#    PyfaiResultsWriter,
-#    YAMLWriter,
-#    TXTWriter,
-#    ZarrValuesWriter,
-#    ZarrWriter,
-#)
-#from CHAP.common.map_utils import (
-#    MapSliceProcessor,
-#    SpecScanToMapConfigProcessor,
-#)
-#from CHAP.common.nexus_utils import (
-#    NexusMakeLinkProcessor,
-#)

CHAP/common/map_utils.py

@@ -11,11 +11,11 @@
 )
 
 # Local modules
-from CHAP import Processor
 from CHAP.common.models.map import (
     Detector,
     MapConfig,
 )
+from CHAP.processor import Processor
 
 def get_axes(nxdata, skip_axes=None):
     """Get the axes of a NeXus style

CHAP/common/models/__init__.py

@@ -12,8 +12,13 @@
     Map related Pydantic model configuration classes.
 """
 
-from CHAP.common.models.common import (
-    BinarizeConfig,
-    ImageProcessorConfig,
-    UnstructuredToStructuredConfig,
-)
+# System modules
+import typing
+
+# Local modules
+from CHAP.common.models.map import DetectorConfig
+
+# Avoid Pydantic "Class not fully defined" in sphinx autodoc as a
+# result of lazy importing by using DetectorConfig within a default
+# value of a pydantic instance variable
+DetectorConfig.model_rebuild(_types_namespace=vars(typing))

CHAP/common/models/integration.py

@@ -26,8 +26,8 @@
 from pyFAI.integrator.azimuthal import AzimuthalIntegrator
 
 # Local modules
-from CHAP import CHAPBaseModel
 from CHAP.common.models.map import Detector
+from CHAP.models import CHAPBaseModel
 
 
 class AzimuthalIntegratorConfig(Detector, CHAPBaseModel):
@@ -196,7 +196,7 @@ def validate_ais(cls, ais):
         return ais
 
 
-class IntegrateConfig(CHAPBaseModel):
+class _IntegrateConfig(CHAPBaseModel):
     """Class with the input parameters to perform various integrations
     with `pyFAI <https://pyfai.readthedocs.io/en/stable/>`__.
 
@@ -219,7 +219,7 @@ class IntegrateConfig(CHAPBaseModel):
     attrs: Optional[dict] = {}
 
 
-class Integrate1dConfig(IntegrateConfig):
+class Integrate1dConfig(_IntegrateConfig):
     """Class with the input parameters to perform 1D azimuthal
     integration with
     `pyFAI <https://pyfai.readthedocs.io/en/stable/>`__.
@@ -242,7 +242,7 @@ class Integrate1dConfig(IntegrateConfig):
     npt: Optional[conint(gt=0)] = 1800
 
 
-class Integrate2dConfig(IntegrateConfig):
+class Integrate2dConfig(_IntegrateConfig):
     """Class with the input parameters to perform 2D azimuthal (cake)
     integration with
     `pyFAI <https://pyfai.readthedocs.io/en/stable/>`__.
@@ -264,7 +264,7 @@ class Integrate2dConfig(IntegrateConfig):
     npt_rad: Optional[conint(gt=0)] = 1800
 
 
-class IntegrateRadialConfig(IntegrateConfig, MultiGeometryConfig):
+class IntegrateRadialConfig(_IntegrateConfig, MultiGeometryConfig):
     """Class with the input parameters to perform radial integration
     with `pyFAI <https://pyfai.readthedocs.io/en/stable/>`__.
 

CHAP/common/nexus_utils.py

@@ -5,7 +5,7 @@
 """
 
 # Local modules
-from CHAP import Processor
+from CHAP.processor import Processor
 
 
 class NexusMakeLinkProcessor(Processor):

CHAP/common/processor.py

@@ -20,13 +20,13 @@
 )
 
 # Local modules
-from CHAP import Processor
 from CHAP.common.models.common import ImageProcessorConfig
 from CHAP.common.models.map import (
     DetectorConfig,
     MapConfig,
 )
 from CHAP.pipeline import PipelineData
+from CHAP.processor import Processor
 
 
 class AsyncProcessor(Processor):

CHAP/common/reader.py

@@ -22,14 +22,14 @@
 )
 
 # Local modules
-from CHAP.reader import (
-    Reader,
-    validate_reader_model,
-)
 from CHAP.common.models.map import (
     DetectorConfig,
     SpecConfig,
 )
+from CHAP.reader import (
+    Reader,
+    validate_reader_model,
+)
 
 def validate_model(model):
     """Validate the `model` configuration.

CHAP/edd/__init__.py

@@ -29,24 +29,19 @@
     Writers unique to the EDD workflow.
 """
 
-#from CHAP.edd.processor import (
-#    DiffractionVolumeLengthProcessor,
-#    LatticeParameterRefinementProcessor,
-#    HKLProcessor,
-#    MCAEnergyCalibrationProcessor,
-#    MCATthCalibrationProcessor,
-#    ReducedDataProcessor,
-#    StrainAnalysisProcessor,
-#)
-#from CHAP.edd.reader import (
-#    EddMapReader,
-#    EddMPIMapReader,
-#    ScanToMapReader,
-#    SetupNXdataReader,
-#    UpdateNXdataReader,
-#    NXdataSliceReader,
-#    SliceNXdataReader,
-#)
-#from CHAP.edd.writer import (
-#    StrainAnalysisUpdateWriter,
-#)
+# System modules
+import typing
+
+# Local modules
+from CHAP.edd.models import (
+    DiffractionVolumeLengthConfig,
+    MCACalibrationConfig,
+    StrainAnalysisConfig,
+)
+
+# Avoid Pydantic "Class not fully defined" in sphinx autodoc as a
+# result of lazy importing by using any of these within a default
+# value of a pydantic instance variable
+DiffractionVolumeLengthConfig.model_rebuild(_types_namespace=vars(typing))
+MCACalibrationConfig.model_rebuild(_types_namespace=vars(typing))
+StrainAnalysisConfig.model_rebuild(_types_namespace=vars(typing))

CHAP/edd/models.py

@@ -5,6 +5,7 @@
 # System modules
 from copy import deepcopy
 import os
+import typing
 from typing import (
     Literal,
     Optional,
@@ -63,7 +64,7 @@ class BaselineConfig(CHAPBaseModel):
 
 # Fit configuration class
 
-class FitConfig(CHAPBaseModel):
+class _FitConfig(CHAPBaseModel):
     """Fit parameters configuration class for peak fitting.
 
     :ivar background: Background model for peak fitting, defaults
@@ -233,7 +234,12 @@ def validate_materialconfig_after(self):
 
 # Detector configuration classes
 
-class MCADetectorCalibration(Detector, FitConfig):
+# Avoid Pydantic "Class not fully defined" in sphinx autodoc as a
+# result of lazy importing by using in an _exclude pydantic instance
+# variable
+_FitConfig.model_rebuild(_types_namespace=vars(typing))
+
+class MCADetectorCalibration(Detector, _FitConfig):
     """Class representing the configuration for a single MCA detector
     element to perform detector calibration.
 
@@ -541,7 +547,7 @@ def get_tth_map(self, map_shape):
 ]
 
 
-class MCADetectorConfig(FitConfig):
+class MCADetectorConfig(_FitConfig):
     """Class representing metadata required to configure a full MCA
     detector.
 
@@ -553,7 +559,7 @@ class MCADetectorConfig(FitConfig):
         'calibration', 'diffractionvolumelength', 'strainanalysis']
     detectors: Optional[conlist(min_length=1, item_type=MCADetector)] = []
 
-    _exclude = set(vars(FitConfig()).keys())
+    _exclude = set(vars(_FitConfig()).keys())
 
     @model_validator(mode='before')
     @classmethod
@@ -605,7 +611,7 @@ def update_detectors(self):
 
 # Processor configuration classes
 
-class DiffractionVolumeLengthConfig(FitConfig):
+class DiffractionVolumeLengthConfig(_FitConfig):
     """Configuration for the differential volume length processor
     :class:`~CHAP.edd.processor.DiffractionVolumeLengthProcessor`
     for an EDD setup using a steel-foil raster scan.
@@ -633,7 +639,7 @@ class DiffractionVolumeLengthConfig(FitConfig):
     sample_thickness: Optional[confloat(gt=0, allow_inf_nan=False)] = None
     sigma_to_dvl_factor: Optional[Literal[2.0, 3.5, 4.0]] = 3.5
 
-    _exclude = set(vars(FitConfig()).keys())
+    _exclude = set(vars(_FitConfig()).keys())
 
     @model_validator(mode='after')
     def validate_diffractionvolumelengthconfig_after(self):
@@ -648,6 +654,11 @@ def validate_diffractionvolumelengthconfig_after(self):
         return self
 
 
+# Avoid Pydantic "Class not fully defined" in sphinx autodoc as a
+# result of lazy importing by using MaterialConfig within a default
+# value of a pydantic instance variable
+MaterialConfig.model_rebuild(_types_namespace=vars(typing))
+
 class MCACalibrationConfig(CHAPBaseModel):
     """Base class configuration for energy and 2&theta calibration
     processors.