Bump minimum numpyro to >=0.21.0 and remove epsilon padding for zero-mean Poisson/NegBinomial

[Copilot]

NumPyro >=0.21.0 natively supports zero-mean Poisson and Negative Binomial distributions, eliminating the need for the 1e-10 epsilon workaround previously required to avoid numerical instability.

Changes

• pyproject.toml: Bumps numpyro>=0.19.0 → numpyro>=0.21.0
• pyrenew/observation/noise.py: Removes _EPSILON = 1e-10 constant; PoissonNoise and NegativeBinomialNoise now pass predicted directly to their distributions
• pyrenew/observation/negativebinomial.py: Removes eps parameter from NegativeBinomialObservation.__init__; sample passes mu directly
• pyrenew/datasets/datagen_he_CA_126.py: Removes mu = np.maximum(mu, 1e-10) clamp in sample_negbinom; updates docstring to reflect non-negative (rather than strictly positive) mu

Before:

# noise.py
_EPSILON = 1e-10
dist.Poisson(rate=predicted + _EPSILON)
dist.NegativeBinomial2(mean=predicted + _EPSILON, concentration=concentration)

# negativebinomial.py
NegativeBinomialObservation(name, concentration_rv, eps=1e-10)
dist.NegativeBinomial2(mean=mu + self.eps, concentration=concentration)

After:

dist.Poisson(rate=predicted)
dist.NegativeBinomial2(mean=predicted, concentration=concentration)

NegativeBinomialObservation(name, concentration_rv)
dist.NegativeBinomial2(mean=mu, concentration=concentration)

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• astral.sh
  • Triggering command: /usr/bin/curl curl -LsSf REDACTED (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

[dylanhmorris]

@cdc-mitzimorris and/or @damonbayer I think this can be merged pending your review.

[github-actions]

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.49%. Comparing base (f829dcc) to head (2314c81).
⚠️ Report is 4 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #806      +/-   ##
==========================================
- Coverage   98.49%   98.49%   -0.01%     
==========================================
  Files          51       51              
  Lines        1866     1863       -3     
==========================================
- Hits         1838     1835       -3     
  Misses         28       28              

Flag	Coverage Δ
unittests	98.49% <ø> (-0.01%)	⬇️

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[damonbayer]

@copilot update the uv.lock.

[dylanhmorris]

@copilot update uv.lock.

[Copilot]

@copilot update the uv.lock.

Done — updated uv.lock in commit 4ae4326 (numpyro v0.20.1 → v0.21.0).

@copilot update uv.lock.

Done — updated uv.lock in commit 4ae4326 (numpyro v0.20.1 → v0.21.0).

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• releases.astral.sh
  • Triggering command: /home/REDACTED/.local/bin/uv uv lock (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

[damonbayer]

I just bumped everything in uv lock while we're here, so we can close a bunch of other PRs.