Python client for Basepair

Python bindings for Basepair's API and command line interface (CLI).

Sentry & custom metrics (optional)

Install with Sentry support:

pip install basepair[sentry]

The library provides shared Sentry init and entity metric constants so consumer apps (Pinda, webapp, ivfapp, kmap) do not duplicate scrubbing, sampling, or metric naming.

Important: basepair-python does not read environment variables for Sentry or metrics. Each app loads its own config and passes explicit parameters.

Sentry init

from basepair.sentry import init_sentry

init_sentry(
    dsn=os.environ.get("SENTRY_DSN"),
    environment=os.environ["MODE"],
    release=os.environ["VERSION"],
    service="pinda-backend",
    traces_sample_rate=float(os.environ["SENTRY_TRACES_SAMPLE_RATE"]),
    profile_sample_rate=float(os.environ["SENTRY_PROFILE_SAMPLE_RATE"]),
    project_name=os.environ.get("PROJECT_NAME"),
    customer_app=os.environ.get("CUSTOMER_APP"),
    debug=os.environ.get("SENTRY_DEBUG") == "true",
    low_value_transactions=("/api/health", "/api/health/"),
)

Empty dsn → no-op (safe for local dev).
Required when dsn is set: environment, release, service, traces_sample_rate, profile_sample_rate.
Optional: project_name, customer_app, debug, low_value_transactions, server_name, enable_logs, enable_metrics.
enable_logs / enable_metrics are passed through to sentry_sdk.init only when set. Omit them for SDK defaults (Sentry Logs off; custom metrics on).

Django apps can use request context helpers:

from basepair.sentry.django import SentryContextMiddleware, set_request_sentry_context

Entity metrics

basepair.metrics is a safe emit helper plus shared metric name constants. The HTTP client does not auto-emit — each app records metrics in its own PIs / workflows, into its own Sentry DSN.

Webapp — METRIC_ANALYSIS_* → webapp.entity.analysis.*
Pinda — METRIC_PINDA_ANALYSIS_* → pinda.analysis.* (use from all Pinda apps / Temporal workflows for consistent names)

from basepair.metrics import (
    METRIC_ANALYSIS_BULK_START,
    METRIC_PINDA_ANALYSIS_BULK_START,
    METRIC_PINDA_ANALYSIS_TERMINAL,
    Outcome,
    emit,
)

# Webapp DSN
emit.incr(METRIC_ANALYSIS_BULK_START, tags={"outcome": Outcome.SUCCESS})

# Pinda DSN (partiseq, revvity, …)
emit.incr(METRIC_PINDA_ANALYSIS_BULK_START, tags={"outcome": Outcome.SUCCESS})
emit.incr(METRIC_PINDA_ANALYSIS_TERMINAL, tags={"terminal_status": "completed"})

Requires sentry-sdk>=2.44.0 for the metrics API. No-op when Sentry is not initialized.

Spec: Confluence — Sentry Custom Metrics

Using MFA

Note: It is advisable to use MFA for increased security and best practices

After you have been added to the list of collaborators, you can verify if MFA has been activated for you by visiting collaboration page

How to build and push to pypi:

Automated publishing of distribution

In the testing stage of the changes, it is advisable to use Test PyPI. We already have github actions to publish on both Test PyPI and PyPI.

Manual way from local

python setup.py sdist bdist_wheel # This will create two files in a newly created dist directory, a source archive and a wheel:
twine upload dist/* # To upload it to Pypi
Uploading distributions to https://upload.pypi.org/legacy/
Enter your username:
Enter your password:

Note: username must be __token__ (not your pypi username) password is the token. You may generate the token -> token creation page.

That is it!

Below is a successful execution sample:

Uploading distributions to https://upload.pypi.org/legacy/
Enter your username: __token__
Enter your password:
Uploading basepair-2.0.7-py3-none-any.whl
100% ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.0/51.0 kB • 00:00 • 36.3 MB/s
Uploading basepair-2.0.7.tar.gz
100% ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.4/37.4 kB • 00:00 • 47.2 MB/s

View at:
https://pypi.org/project/basepair/2.0.7/

Metadata

Release files for basepair 3.5.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for basepair 3.5.0
File	Size	Uploaded
basepair-3.5.0.tar.gz	83.5 kB	Sep 10, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for basepair 3.5.0
File	Interpreter	ABI	Platform	Reset
basepair-3.5.0-py3-none-any.whl 114.8 kB Sep 10, 2026	Python 3	none	any	Details

Total release size: 198.3 kB

Release files / basepair-3.5.0.tar.gz

Download URL	basepair-3.5.0.tar.gz
Size	83.5 kB
Tags	Source
SHA-256 checksum How to use checksums	`b3a3b5ff4be3012a956ae0c9911af9abf343899d60f87f0fe0b302a1791748cb`
BLAKE2b-256 checksum How to use checksums	`961e4c808fdbcb3c0a8348f10b350737cf9c944723a4f6f89eacf6edd95381b5`
Upload date	Sep 10, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.14.7`

Release files / basepair-3.5.0-py3-none-any.whl

Download URL	basepair-3.5.0-py3-none-any.whl
Size	114.8 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`366adc16a2dffb8c19b274900221d04bc25c09462790e46cb39582023dc7561d`
BLAKE2b-256 checksum How to use checksums	`08595282a6f5dd01320e739fa9c7c7ef2b8a7a1785c1ca837539bc4151460fd4`
Upload date	Sep 10, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.14.7`