dkist-processing-dlnirsp 1.6.12

Science processing code for the DLNIRSP instrument on DKIST

Overview

The dkist-processing-dlnirsp library contains the implementation of the DLNIRSP pipelines as a collection of the dkist-processing-core framework and dkist-processing-common Tasks.

The recommended project structure is to separate tasks and workflows into separate packages. Having the workflows in their own package facilitates using the build_utils to test the integrity of those workflows in the unit test.

Environment Variables

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.’
PIP_TIMEOUT	annotation=int required=False default=15 description=’Timeout for pip installs in seconds.’
PIP_RETRIES	annotation=int required=False default=5 description=’Number of retries for pip installs.’
IS_NOTEBOOK_EXECUTION_ENVIRONMENT	annotation=bool required=False default=False description=’Indication of whether the code is running in a notebook execution environment.’ examples=[True, False]
NOTEBOOK_SAVE_WAIT_ATTEMPTS	annotation=int required=False default=120 description=’Number of attempts to check for a saved notebook before raising an error.’
NOTEBOOK_SAVE_WAIT_DELAY	annotation=int required=False default=1 description=’Number of seconds to wait between notebook save checks.’
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.’
FTS_ATLAS_DATA_DIR	annotation=Union[str, NoneType] required=False default=None description=’Common cached directory for downloaded FTS Atlas.’

Development

git clone [e-mail]:dkistdc/dkist-processing-dlnirsp.git
cd dkist-processing-dlnirsp
pre-commit install
pip install -e .[test]
pytest -v --cov dkist_processing_nirsp

Build

Artifacts are built through Bitbucket Pipelines.

The pipeline can be used in other repos with a modification of the package and artifact locations to use the names relevant to the target repo.

e.g. dkist-processing-test -> dkist-processing-vbi and dkist_processing_test -> dkist_processing_vbi

Deployment

Deployment is done with turtlebot and follows the process detailed in dkist-processing-core

Additionally, when a new release is ready to be built the following steps need to be taken:

1. Freezing Dependencies

A new “frozen” extra is generated by the dkist-dev-tools package. If you don’t have dkist-dev-tools installed please follow the directions from that repo.

To freeze dependencies run

ddt freeze vX.Y.Z[rcK]

Where “vX.Y.Z[rcK]” is the version about to be released.

2. 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 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 in 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:

# 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

Science Changelog

Whenever a release involves changes to the scientific quality of L1 data, additional changelog fragment(s) should be created. These fragments are intended to be as verbose as is needed to accurately capture the scope of the change(s), so feel free to use all the fancy RST you want. Science fragments are placed in the same changelog/ directory as other fragments, but are always called:

<PR NUMBER | +>.science[.<COUNTER>].rst

In the case that a single pull request encapsulates the entirety of the scientific change then the first field should be that PR number (same as the normal CHANGELOG). If, however, there is not a simple mapping from a single PR to a scienctific change then use the character “+” instead; this will create a changelog entry with no associated PR. For example:

$ ls changelog/
99.bugfix.rst    # This is a normal changelog fragment associated with a bugfix in PR 99
99.science.rst   # Apparently that bugfix also changed the scientific results, so that PR also gets a science fragment
+.science.rst    # This fragment is not associated with a PR

When it comes time to build the SCIENCE_CHANGELOG, use the science_towncrier.sh script in this repo to do so. This script accepts all the same arguments as the default towncrier. For exmaple:

./science_towncrier.sh build --version vx.y.z

This will update the SCIENCE_CHANGELOG and remove any science fragments from the changelog directory.

3. Tag and Push

Once all commits are in place add a git tag that will define the released version, then push the tags up to Bitbucket:

git tag vX.Y.Z[rcK]
git push --tags origin BRANCH

In the case of an rc, BRANCH will likely be your development branch. For full releases BRANCH should be “main”.