dkist-processing-common 10.5.4__py3-none-any.whl → 12.1.0rc1__py3-none-any.whl

dkist_processing_common-12.1.0rc1.dist-info/METADATA

@@ -0,0 +1,265 @@
+Metadata-Version: 2.4
+Name: dkist-processing-common
+Version: 12.1.0rc1
+Summary: Common task classes used by the DKIST science data processing pipelines
+Author-email: NSO / AURA <dkistdc@nso.edu>
+License: BSD-3-Clause
+Project-URL: Homepage, https://nso.edu/dkist/data-center/
+Project-URL: Repository, https://bitbucket.org/dkistdc/dkist-processing-common/
+Project-URL: Documentation, https://docs.dkist.nso.edu/projects/common
+Project-URL: Help, https://nso.atlassian.net/servicedesk/customer/portal/5
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.13
+Description-Content-Type: text/x-rst
+Requires-Dist: asdf<4.0.0,>=3.5.0
+Requires-Dist: astropy>=7.0.0
+Requires-Dist: dkist-fits-specifications<5.0,>=4.0.0
+Requires-Dist: dkist-header-validator<6.0,>=5.0.0
+Requires-Dist: dkist-processing-core==7.0.1
+Requires-Dist: dkist-processing-pac<4.0,>=3.1
+Requires-Dist: dkist-service-configuration<5.0,>=4.2.0
+Requires-Dist: dkist-spectral-lines<4.0,>=3.0.0
+Requires-Dist: solar-wavelength-calibration<3.0,>=2.0.0
+Requires-Dist: globus-sdk<5.0.0,>=4.0.0
+Requires-Dist: gqlclient[pydantic]==1.2.3
+Requires-Dist: sqids==0.5.1
+Requires-Dist: matplotlib>=3.4
+Requires-Dist: moviepy>=2.0.0
+Requires-Dist: numpy>=1.26.4
+Requires-Dist: object-clerk==1.0.0
+Requires-Dist: pandas>=1.4.2
+Requires-Dist: pillow>=10.2.0
+Requires-Dist: pydantic>=2.7.2
+Requires-Dist: redis==6.4.0
+Requires-Dist: requests>=2.23
+Requires-Dist: scipy>=1.15.1
+Requires-Dist: sunpy>=3.0.0
+Requires-Dist: talus==1.3.4
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-xdist; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-mock; extra == "test"
+Requires-Dist: hypothesis; extra == "test"
+Requires-Dist: towncrier; extra == "test"
+Requires-Dist: dkist-data-simulator>=5.2.6; extra == "test"
+Requires-Dist: dkist-processing-common[inventory]; extra == "test"
+Requires-Dist: dkist-processing-common[asdf]; extra == "test"
+Requires-Dist: dkist-processing-common[quality]; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-astropy; extra == "docs"
+Requires-Dist: sphinx-changelog; extra == "docs"
+Requires-Dist: sphinx-autoapi!=3.1.0; extra == "docs"
+Requires-Dist: pytest; extra == "docs"
+Requires-Dist: towncrier<22.12.0; extra == "docs"
+Requires-Dist: dkist-sphinx-theme; extra == "docs"
+Provides-Extra: inventory
+Requires-Dist: dkist-inventory<2.0,>=1.11.2; extra == "inventory"
+Provides-Extra: asdf
+Requires-Dist: dkist-inventory[asdf]<2.0,>=1.11.2; extra == "asdf"
+Provides-Extra: quality
+Requires-Dist: dkist-quality<3.0,>=2.0.0; extra == "quality"
+
+dkist-processing-common
+=======================
+
+|codecov|
+
+This repository works in concert with `dkist-processing-core <https://pypi.org/project/dkist-processing-core/>`_ and `dkist-processing-*instrument*` to
+form the DKIST calibration processing stack.
+
+Usage
+-----
+
+The classes in this repository should be used as the base of any DKIST processing pipeline tasks. Science tasks should subclass `ScienceTaskL0ToL1Base`.
+
+Each class is built on an abstract base class with the `run` method left for a developer to fill out with the required steps that the task should take.
+This class is then used as the callable object for the workflow and scheduling engine.
+
+Example
+-------
+
+.. code-block:: python
+
+    from dkist_processing_common.tasks.base import ScienceTaskL0ToL1Base
+
+
+    class RemoveArtifacts(ScienceTaskL0ToL1Base):
+        def run(self):
+            # task code here
+            total = 2 + 5
+
+Deployment
+----------
+
+dkist-processing-common is deployed to `PyPI <https://pypi.org/project/dkist-processing-common/>`_
+
+Environment Variables
+---------------------
+
+.. list-table::
+   :widths: 10 90
+   :header-rows: 1
+
+   * - Variable
+     - Field Info
+   * - LOGURU_LEVEL
+     - annotation=str required=False default='INFO' alias_priority=2 validation_alias='LOGURU_LEVEL' description='Log level for the application'
+   * - MESH_CONFIG
+     - annotation=dict[str, MeshService] required=False default_factory=dict alias_priority=2 validation_alias='MESH_CONFIG' description='Service mesh configuration' examples=[{'upstream_service_name': {'mesh_address': 'localhost', 'mesh_port': 6742}}]
+   * - RETRY_CONFIG
+     - annotation=RetryConfig required=False default_factory=RetryConfig description='Retry configuration for the service'
+   * - OTEL_SERVICE_NAME
+     - annotation=str required=False default='unknown-service-name' alias_priority=2 validation_alias='OTEL_SERVICE_NAME' description='Service name for OpenTelemetry'
+   * - DKIST_SERVICE_VERSION
+     - annotation=str required=False default='unknown-service-version' alias_priority=2 validation_alias='DKIST_SERVICE_VERSION' description='Service version for OpenTelemetry'
+   * - NOMAD_ALLOC_ID
+     - annotation=str required=False default='unknown-allocation-id' alias_priority=2 validation_alias='NOMAD_ALLOC_ID' description='Nomad allocation ID for OpenTelemetry'
+   * - NOMAD_ALLOC_NAME
+     - annotation=str required=False default='unknown-allocation-name' alias='NOMAD_ALLOC_NAME' alias_priority=2 description='Allocation name for the deployed container the task is running on.'
+   * - NOMAD_GROUP_NAME
+     - annotation=str required=False default='unknown-allocation-group' alias='NOMAD_GROUP_NAME' alias_priority=2 description='Allocation group for the deployed container the task is running on'
+   * - OTEL_EXPORTER_OTLP_TRACES_INSECURE
+     - annotation=bool required=False default=True description='Use insecure connection for OTLP traces'
+   * - OTEL_EXPORTER_OTLP_METRICS_INSECURE
+     - annotation=bool required=False default=True description='Use insecure connection for OTLP metrics'
+   * - OTEL_EXPORTER_OTLP_TRACES_ENDPOINT
+     - annotation=Union[str, NoneType] required=False default=None description='OTLP traces endpoint. Overrides mesh configuration' examples=['localhost:4317']
+   * - OTEL_EXPORTER_OTLP_METRICS_ENDPOINT
+     - annotation=Union[str, NoneType] required=False default=None description='OTLP metrics endpoint. Overrides mesh configuration' examples=['localhost:4317']
+   * - OTEL_PYTHON_DISABLED_INSTRUMENTATIONS
+     - annotation=list[str] required=False default_factory=list description='List of instrumentations to disable. https://opentelemetry.io/docs/zero-code/python/configuration/' examples=[['pika', 'requests']]
+   * - OTEL_PYTHON_FASTAPI_EXCLUDED_URLS
+     - annotation=str required=False default='health' description='Comma separated list of URLs to exclude from OpenTelemetry instrumentation in FastAPI.' examples=['client/.*/info,healthcheck']
+   * - SYSTEM_METRIC_INSTRUMENTATION_CONFIG
+     - annotation=Union[dict[str, bool], NoneType] required=False default=None description='Configuration for system metric instrumentation. https://opentelemetry-python-contrib.readthedocs.io/en/latest/instrumentation/system_metrics/system_metrics.html' examples=[{'system.memory.usage': ['used', 'free', 'cached'], 'system.cpu.time': ['idle', 'user', 'system', 'irq'], 'system.network.io': ['transmit', 'receive'], 'process.runtime.memory': ['rss', 'vms'], 'process.runtime.cpu.time': ['user', 'system'], 'process.runtime.context_switches': ['involuntary', 'voluntary']}]
+   * - ISB_USERNAME
+     - annotation=str required=False default='guest' description='Username for the interservice-bus.'
+   * - ISB_PASSWORD
+     - annotation=str required=False default='guest' description='Password for the interservice-bus.'
+   * - ISB_EXCHANGE
+     - annotation=str required=False default='master.direct.x' description='Exchange for the interservice-bus.'
+   * - ISB_QUEUE_TYPE
+     - annotation=str required=False default='classic' description='Queue type for the interservice-bus.' examples=['quorum', 'classic']
+   * - BUILD_VERSION
+     - annotation=str required=False default='dev' description='Fallback build version for workflow tasks.'
+   * - MAX_FILE_DESCRIPTORS
+     - annotation=int required=False default=1024 description='Maximum number of file descriptors to allow the process.'
+   * - GQL_AUTH_TOKEN
+     - annotation=Union[str, NoneType] required=False default='dev' description='The auth token for the metadata-store-api.'
+   * - OBJECT_STORE_ACCESS_KEY
+     - annotation=Union[str, NoneType] required=False default=None description='The access key for the object store.'
+   * - OBJECT_STORE_SECRET_KEY
+     - annotation=Union[str, NoneType] required=False default=None description='The secret key for the object store.'
+   * - OBJECT_STORE_USE_SSL
+     - annotation=bool required=False default=False description='Whether to use SSL for the object store connection.'
+   * - MULTIPART_THRESHOLD
+     - annotation=Union[int, NoneType] required=False default=None description='Multipart threshold for the object store.'
+   * - S3_CLIENT_CONFIG
+     - annotation=Union[dict, NoneType] required=False default=None description='S3 client configuration for the object store.'
+   * - S3_UPLOAD_CONFIG
+     - annotation=Union[dict, NoneType] required=False default=None description='S3 upload configuration for the object store.'
+   * - S3_DOWNLOAD_CONFIG
+     - annotation=Union[dict, NoneType] required=False default=None description='S3 download configuration for the object store.'
+   * - GLOBUS_MAX_RETRIES
+     - annotation=int required=False default=5 description='Max retries for transient errors on calls to the globus api.'
+   * - GLOBUS_INBOUND_CLIENT_CREDENTIALS
+     - annotation=list[GlobusClientCredential] required=False default_factory=list description='Globus client credentials for inbound transfers.' examples=[[{'client_id': 'id1', 'client_secret': 'secret1'}, {'client_id': 'id2', 'client_secret': 'secret2'}]]
+   * - GLOBUS_OUTBOUND_CLIENT_CREDENTIALS
+     - annotation=list[GlobusClientCredential] required=False default_factory=list description='Globus client credentials for outbound transfers.' examples=[[{'client_id': 'id3', 'client_secret': 'secret3'}, {'client_id': 'id4', 'client_secret': 'secret4'}]]
+   * - OBJECT_STORE_ENDPOINT
+     - annotation=Union[str, NoneType] required=False default=None description='Object store Globus Endpoint ID.'
+   * - SCRATCH_ENDPOINT
+     - annotation=Union[str, NoneType] required=False default=None description='Scratch Globus Endpoint ID.'
+   * - SCRATCH_BASE_PATH
+     - annotation=str required=False default='scratch/' description='Base path for scratch storage.'
+   * - SCRATCH_INVENTORY_DB_COUNT
+     - annotation=int required=False default=16 description='Number of databases in the scratch inventory (redis).'
+   * - DOCS_BASE_URL
+     - annotation=str required=False default='my_test_url' description='Base URL for the documentation site.'
+
+Development
+-----------
+
+There are two prerequisites for test execution on a local machine:
+
+
+* Redis.  A running instance of redis on the local machine is required. The tests will use the default host ip of localhost and port of 6379 to connect to the database.
+
+* RabbitMQ.  A running instance of rabbitmq on the local machine is required.  The tests will use the default host of localhost and a port of 5672 to connect to the interservice bus.
+
+
+To run the tests locally, clone the repository and install the package in editable mode with the test extras.
+
+
+.. code-block:: bash
+
+    git clone git@bitbucket.org:dkistdc/dkist-processing-common.git
+    cd dkist-processing-common
+    pre-commit install
+    pip install -e .[test]
+    # Redis must be running
+    pytest -v --cov dkist_processing_common
+
+Changelog
+#########
+
+When you make **any** change to this repository it **MUST** be accompanied by a changelog file.
+The changelog for this repository uses the `towncrier <https://github.com/twisted/towncrier>`__ package.
+Entries in the changelog for the next release are added as individual files (one per change) to the ``changelog/`` directory.
+
+Writing a Changelog Entry
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+A changelog entry accompanying a change should be added to the ``changelog/`` directory.
+The name of a file in this directory follows a specific template::
+
+  <PULL REQUEST NUMBER>.<TYPE>[.<COUNTER>].rst
+
+The fields have the following meanings:
+
+* ``<PULL REQUEST NUMBER>``: This is the number of the pull request, so people can jump from the changelog entry to the diff on BitBucket.
+* ``<TYPE>``: This is the type of the change and must be one of the values described below.
+* ``<COUNTER>``: This is an optional field, if you make more than one change of the same type you can append a counter to the subsequent changes, i.e. ``100.bugfix.rst`` and ``100.bugfix.1.rst`` for two bugfix changes in the same PR.
+
+The list of possible types is defined the the towncrier section of ``pyproject.toml``, the types are:
+
+* ``feature``: This change is a new code feature.
+* ``bugfix``: This is a change which fixes a bug.
+* ``doc``: A documentation change.
+* ``removal``: A deprecation or removal of public API.
+* ``misc``: Any small change which doesn't fit anywhere else, such as a change to the package infrastructure.
+
+
+Rendering the Changelog at Release Time
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+When you are about to tag a release first you must run ``towncrier`` to render the changelog.
+The steps for this are as follows:
+
+* Run `towncrier build --version vx.y.z` using the version number you want to tag.
+* Agree to have towncrier remove the fragments.
+* Add and commit your changes.
+* Tag the release.
+
+**NOTE:** If you forget to add a Changelog entry to a tagged release (either manually or automatically with ``towncrier``)
+then the Bitbucket pipeline will fail. To be able to use the same tag you must delete it locally and on the remote branch:
+
+.. code-block:: bash
+
+    # First, actually update the CHANGELOG and commit the update
+    git commit
+
+    # Delete tags
+    git tag -d vWHATEVER.THE.VERSION
+    git push --delete origin vWHATEVER.THE.VERSION
+
+    # Re-tag with the same version
+    git tag vWHATEVER.THE.VERSION
+    git push --tags origin main
+
+.. |codecov| image:: https://codecov.io/bb/dkistdc/dkist-processing-common/graph/badge.svg?token=3QSLGSEF3O
+ :target: https://codecov.io/bb/dkistdc/dkist-processing-common

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+dkist_processing_common-12.1.0rc1.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+dkist_processing_common-12.1.0rc1.dist-info/top_level.txt,sha256=LJhd1W-Vn90K8HnQDIE4r52YDpUjjMWDnllAWHBByW0,48
+dkist_processing_common-12.1.0rc1.dist-info/RECORD,,

{dkist_processing_common-10.5.4.dist-info → dkist_processing_common-12.1.0rc1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

docs/conf.py

@@ -1,4 +1,5 @@
 """Configuration file for the Sphinx documentation builder."""
+
 # -- stdlib imports ------------------------------------------------------------
 import importlib
 import sys

docs/index.rst

@@ -1,4 +1,4 @@
-.. include:: ../README.rst
+.. include:: landing_page.rst
 
 .. toctree::
     :maxdepth: 2

docs/landing_page.rst

@@ -0,0 +1,13 @@
+Overview
+========
+
+The `dkist-processing-common` code repository is a library that works with
+`dkist-processing-core <https://docs.dkist.nso.edu/projects/core/>`_ and
+`dkist-processing-*instrument*` to form the DKIST calibration processing stack.
+
+The classes in this library are used as the base of all DKIST processing pipeline
+tasks. Task classes used in instrument pipelines are built on an abstract base class
+defined here.  Developers implement a `run` method with the required steps that the
+task should take for a particular application.  The class with its `run` method
+is then used as the callable object for the workflow and scheduling engine
+(which is managed by `dkist-processing-core <https://docs.dkist.nso.edu/projects/core/>`_).

dkist_processing_common/tasks/mixin/input_dataset.py

@@ -1,166 +0,0 @@
-"""Mixin for a WorkflowDataTaskBase subclass which implements input data set access functionality."""
-import json
-from dataclasses import dataclass
-from datetime import datetime
-from itertools import chain
-from pathlib import Path
-from typing import Any
-
-from dkist_processing_common.models.tags import Tag
-from dkist_processing_common.tasks.base import tag_type_hint
-
-
-frames_part_type_hint = list[dict[str, str | list[str]]] | None
-
-
-@dataclass
-class InputDatasetParameterValue:
-    """Data structure for a de-serialized input dataset parameter value."""
-
-    parameter_value_id: int
-    parameter_value: Any = None
-    parameter_value_start_date: datetime | None = None
-
-
-@dataclass
-class InputDatasetObject:
-    """Data structure for a de-serialized input dataset frame."""
-
-    bucket: str
-    object_key: str
-
-
-class InputDatasetMixin:
-    """Mixin for WorkflowDataTaskBase that accesses downloaded input dataset part documents."""
-
-    def _input_dataset_part_document(self, tags: tag_type_hint):
-        """Get the input dataset document part and deserialize it."""
-        paths: list[Path] = list(self.read(tags=tags))
-        if not paths:
-            return
-        if len(paths) > 1:
-            raise ValueError(
-                f"There are more than one input dataset part documents to parse for {tags=}"
-            )
-        p = paths[0]
-        with p.open(mode="rb") as f:
-            return json.load(f)
-
-    @property
-    def input_dataset_observe_frames_part_document(self) -> frames_part_type_hint:
-        """Get the 'observe frames' part of the input dataset."""
-        return self._input_dataset_part_document(tags=Tag.input_dataset_observe_frames())
-
-    @property
-    def input_dataset_calibration_frames_part_document(self) -> frames_part_type_hint:
-        """Get the 'calibration frames' part of the input dataset."""
-        return self._input_dataset_part_document(tags=Tag.input_dataset_calibration_frames())
-
-    @property
-    def input_dataset_parameters_part_document(
-        self,
-    ) -> list[dict[str, str | list[dict[str, int | str]]]] | None:
-        """Get the 'parameters' part of the input dataset."""
-        return self._input_dataset_part_document(tags=Tag.input_dataset_parameters())
-
-    @property
-    def input_dataset_frames(self) -> list[InputDatasetObject]:
-        """Get the list of frames for this input dataset."""
-        result = []
-        observe_frames = self.input_dataset_observe_frames_part_document or []
-        calibration_frames = self.input_dataset_calibration_frames_part_document or []
-        for frame_set in chain(observe_frames, calibration_frames):
-            for key in frame_set.get("object_keys", list()):
-                result.append(InputDatasetObject(bucket=frame_set["bucket"], object_key=key))
-        return result
-
-    @property
-    def input_dataset_parameters(self) -> dict[str, list[InputDatasetParameterValue]]:
-        """Get the input dataset parameters."""
-        parameters = self.input_dataset_parameters_part_document or []
-        result = dict()
-        for p in parameters:
-            result.update(self._input_dataset_parse_parameter(p))
-        return result
-
-    @property
-    def input_dataset_parameter_objects(self) -> list[InputDatasetObject]:
-        """Parse the parameter object locations out of the set of all parameters."""
-        result = []
-        for value_list in self.input_dataset_parameters.values():
-            for value in value_list:
-                param_value = value.parameter_value
-                if isinstance(param_value, dict) and param_value.get("is_file", False):
-                    result.append(
-                        InputDatasetObject(
-                            bucket=param_value["bucket"], object_key=param_value["objectKey"]
-                        )
-                    )
-        return result
-
-    def _input_dataset_parse_parameter(
-        self, parameter: dict
-    ) -> dict[str, list[InputDatasetParameterValue]]:
-        name: str = parameter["parameterName"]
-        raw_values: list[dict] = parameter["parameterValues"]
-        values = self._input_dataset_parse_parameter_values(raw_values=raw_values)
-        return {name: values}
-
-    def _input_dataset_parse_parameter_values(
-        self, raw_values: list[dict[str, Any]]
-    ) -> list[InputDatasetParameterValue]:
-        values = list()
-        for v in raw_values:
-            parsed_value = InputDatasetParameterValue(parameter_value_id=v["parameterValueId"])
-            parsed_value.parameter_value = self._input_dataset_parse_parameter_value(
-                raw_parameter_value=v["parameterValue"]
-            )
-            if d := v.get("parameterValueStartDate"):
-                parsed_value.parameter_value_start_date = datetime.fromisoformat(d)
-            else:
-                parsed_value.parameter_value_start_date = datetime(1, 1, 1)
-            values.append(parsed_value)
-        return values
-
-    def _input_dataset_parse_parameter_value(self, raw_parameter_value: str) -> Any:
-        """Return the json decoding of the parameter value."""
-        return json.loads(raw_parameter_value, object_hook=self._decode_parameter_value)
-
-    def _decode_parameter_value(self, param_dict: dict):
-        """Decode a parameter value."""
-        if "__file__" in param_dict:
-            return self._convert_parameter_file_value_to_path(param_dict)
-        # Nothing to do here, so return control back to json.loads()
-        return param_dict
-
-    def _convert_parameter_file_value_to_path(self, param_dict: dict):
-        """
-        Decode a parameter file value.
-
-        Note: for parameters that are files, the string passed to json.loads() looks like this:
-        '{ "__file__":
-            {
-                "bucket": "data",
-                "objectKey": "parameters/parameter_name/uuid.dat"
-            }
-        }'
-
-        In this hook, we remove the outer __file__ dict and return the inner dict with the addition of
-        a key and value for the file path. Because the file path is dependent on the existence of a tag,
-        if no tag is found, None is returned for the path. This use case will occur when we construct
-        the list of files to be transferred and tagged by the TransferL0Data task.
-        """
-        file_dict = param_dict["__file__"]
-        object_key = file_dict["objectKey"]
-        parameter_tag = Tag.parameter(Path(object_key).name)
-        paths = list(self.read(tags=parameter_tag))
-        num_paths = len(paths)
-        if num_paths == 1:
-            param_path = paths[0]
-        elif num_paths == 0:
-            param_path = None
-        else:
-            raise ValueError(f"Found multiple paths for {parameter_tag = }.")
-        file_dict["param_path"] = param_path
-        file_dict["is_file"] = True
-        return file_dict