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Refactor the code #27

Merged
merged 10 commits into from
Nov 21, 2024
Merged

Refactor the code #27

merged 10 commits into from
Nov 21, 2024

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pawel-czyz
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@pawel-czyz pawel-czyz commented Nov 19, 2024

This PR refactors the code in the following ways:

  • Resolve issue Use consistent shapes of the observed proportions #24, using consistent shape (n_timepoints, n_variants).
  • Define the public API.
  • Add more type annotations and documentation.
  • Refactor the notebook, using more informative variable names and auxiliary utilities to simplify it.

@pawel-czyz pawel-czyz added the refactor Changes refactoring the code label Nov 19, 2024
@pawel-czyz pawel-czyz linked an issue Nov 19, 2024 that may be closed by this pull request
@pawel-czyz pawel-czyz marked this pull request as ready for review November 20, 2024 12:08
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This was referenced Nov 20, 2024
@dr-david dr-david merged commit f739fea into main Nov 21, 2024
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@dr-david dr-david deleted the issue-24 branch November 21, 2024 13:49
dr-david added a commit that referenced this pull request Nov 21, 2024
dr-david added a commit that referenced this pull request Nov 22, 2024
* evaluation workflow

* fixed data expands

* solve lineage overcounting

* Save current changes for testing older version

* compatibility with refactor #27

* added fitted plots (in progress)
dr-david added a commit that referenced this pull request Nov 27, 2024
* evaluation workflow

* fixed data expands

* solve lineage overcounting

* Save current changes for testing older version

* compatibility with refactor #27

* added fitted plots (in progress)

* numerically stable logit predictions

* Generalize the function

---------

Co-authored-by: Paweł Czyż <[email protected]>
dr-david added a commit that referenced this pull request Nov 28, 2024
* evaluation workflow

* fixed data expands

* solve lineage overcounting

* Save current changes for testing older version

* compatibility with refactor #27

* added fitted plots (in progress)

* numerically stable logit predictions

* Generalize the function

---------

Co-authored-by: Paweł Czyż <[email protected]>
pawel-czyz pushed a commit that referenced this pull request Jan 16, 2025
* evaluation workflow

* fixed data expands

* solve lineage overcounting

* Save current changes for testing older version

* compatibility with refactor #27

* added fitted plots (in progress)

* numerically stable logit predictions

* Generalize the function
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Use consistent shapes of the observed proportions
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