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Add generic observation processes which combine the convolution with the noise model. - #644

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cdc-mitzimorris merged 80 commits into
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mem_generic_observations
Jan 29, 2026
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cdc-mitzimorris merged 80 commits into
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mem_generic_observations

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This PR adds work that was done in https://github.com/cdcent/cfa-pyrenew-hierarchical/pull/4 to PyRenew.

It adds the base observation process class, concrete implementations for Count processes and the abstract base class for Measurement processes, together with unit tests and two new tutorials for count and measurement observation processes respectively.

Once this PR and the work done in https://github.com/cdcent/cfa-pyrenew-hierarchical/pull/5 have been added to PyRenew, subsequent PRs will deprecate unused features and harmonize the documentation and tutorials.

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codecov Bot commented Dec 23, 2025 •

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Codecov Report

❌ Patch coverage is 97.81421% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 97.18%. Comparing base (02446c5) to head (df9f76e).
⚠️ Report is 5 commits behind head on main.

Files with missing lines Patch % Lines
pyrenew/observation/count_observations.py 94.91% 3 Missing ⚠️
pyrenew/observation/noise.py 98.38% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #644      +/-   ##
==========================================
+ Coverage   96.98%   97.18%   +0.19%     
==========================================
  Files          42       47       +5     
  Lines        1094     1277     +183     
==========================================
+ Hits         1061     1241     +180     
- Misses         33       36       +3     
Flag Coverage Δ
unittests 97.18% <97.81%> (+0.19%) ⬆️

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Thank you for your contribution @cdc-mitzimorris 🚀! Your github-pages is ready for download 👉 here 👈!
(The artifact expires on 2026-02-05T13:10:20Z. You can re-generate it by re-running the workflow here.)

Comment thread docs/tutorials/observation_processes_counts.qmd Outdated
Comment thread docs/tutorials/observation_processes_counts.qmd Outdated
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Comment thread docs/tutorials/observation_processes_counts.qmd Outdated
Comment thread test/test_observation_counts.py
Comment thread test/test_observation_counts.py
Comment thread test/test_observation_measurements.py

@dylanhmorris dylanhmorris left a comment

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Thanks @cdc-mitzimorris. Final fix needed for NaN-padding question, all other changes can be deferred to future PRs.

cdc-mitzimorris and others added 9 commits January 28, 2026 15:48
Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>
Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>
Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>
Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>
Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>
Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>
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@dylanhmorris - all requested changes made.

Comment thread docs/tutorials/observation_processes_counts.qmd Outdated
Comment thread docs/tutorials/observation_processes_counts.qmd Outdated
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Thanks @cdc-mitzimorris! Left suggestions that should fix the tutorial rendering. Apologies for failing to make those along with the test changes in my last review. Please merge when ready!

cdc-mitzimorris and others added 4 commits January 29, 2026 08:04
Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>
Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>
Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>
Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>
@cdc-mitzimorris
cdc-mitzimorris merged commit 9b4643e into main Jan 29, 2026
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cdc-mitzimorris deleted the mem_generic_observations branch January 29, 2026 13:48
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3 participants