Nuad

Release notes

BREAKING CHANGE: `Result.value` is a float

If you write your own constraints, the field `Result.value` is now just an optional float, and it cannot be a `str` or a `pint.Quantity`. We have removed pint as a dependency and just manually track units such as kcal/mol as strings in the `Result` objects (with an optional field `Result.unit`). This speeds up gathering results after evaluating a constraint.

Commits
- 31922c7: bumped version (Dave Doty) [246](https://github.com/UC-Davis-molecular-computing/nuad/pull/246)
- c64b22f: newline changes? (David Doty) [246](https://github.com/UC-Davis-molecular-computing/nuad/pull/246)
- 1e1f9dc: Update constraints.py (Dave Doty) [246](https://github.com/UC-Davis-molecular-computing/nuad/pull/246)
- 80ecf81: added type annotation to new function (Dave Doty) [246](https://github.com/UC-Davis-molecular-computing/nuad/pull/246)
- a55bc03: fixed mypy and PYCharm warnings (Dave Doty) [246](https://github.com/UC-Davis-molecular-computing/nuad/pull/246)
- 2db538f: Update constraints.py (David Doty) [246](https://github.com/UC-Davis-molecular-computing/nuad/pull/246)
- f3fe507: Update constraints.py (David Doty) [246](https://github.com/UC-Davis-molecular-computing/nuad/pull/246)
- 9966ccf: Update constraints.py (David Doty) [246](https://github.com/UC-Davis-molecular-computing/nuad/pull/246)
- 25a259d: updated notebooks (David Doty) [246](https://github.com/UC-Davis-molecular-computing/nuad/pull/246)
- 5a96158: Update many_strands_no_common_domains.py (David Doty) [246](https://github.com/UC-Davis-molecular-computing/nuad/pull/246)
- ab96c3b: Update many_strands_no_common_domains.py (David Doty) [246](https://github.com/UC-Davis-molecular-computing/nuad/pull/246)
- af26906: Update many_strands_no_common_domains.py (David Doty) [246](https://github.com/UC-Davis-molecular-computing/nuad/pull/246)
- d6734bd: Update many_strands_no_common_domains.py (David Doty) [246](https://github.com/UC-Davis-molecular-computing/nuad/pull/246)
- 212a4d8: minor (David Doty) [246](https://github.com/UC-Davis-molecular-computing/nuad/pull/246)
- 483b9a4: minor (David Doty) [246](https://github.com/UC-Davis-molecular-computing/nuad/pull/246)
- 563a4a7: Update vienna_nupack.py (David Doty) [246](https://github.com/UC-Davis-molecular-computing/nuad/pull/246)
- 876cbc6: closes 233: minimize time spent creating `pint.Quantity` objects (David Doty) [245](https://github.com/UC-Davis-molecular-computing/nuad/pull/245)
- 1809e60: Update search.py (David Doty) [245](https://github.com/UC-Davis-molecular-computing/nuad/pull/245)
- dcb353d: Update requirements.txt (David Doty) [245](https://github.com/UC-Davis-molecular-computing/nuad/pull/245)
- 35dee5f: Merge branch 'dev' into 233-for-speed-minimize-time-spent-creating-pintquantity-objects (David Doty) [245](https://github.com/UC-Davis-molecular-computing/nuad/pull/245)
- b1dd679: Update result-allocate-time-trials.ipynb (David Doty) [245](https://github.com/UC-Davis-molecular-computing/nuad/pull/245)
- c76e7f0: Update constraints.py (David Doty) [245](https://github.com/UC-Davis-molecular-computing/nuad/pull/245)

Implemented non-orthogonal domain constraints as in 240, useful for ideas such as in these papers:

https://drops.dagstuhl.de/opus/volltexte/2023/18787/pdf/LIPIcs-DNA-29-4.pdf
https://www.nature.com/articles/s41557-022-01111-y

Commits
- f33833e: bumped version (David Doty) [243](https://github.com/UC-Davis-molecular-computing/nuad/pull/243)
- d64cdad: added `_normalize_domains_pairs_disjoint_parameters` (David Doty) [243](https://github.com/UC-Davis-molecular-computing/nuad/pull/243)
- 85536d3: added `rna_plex_domain_pairs_nonorthogonal_constraint` and cleaned up docstrings (David Doty) [242](https://github.com/UC-Davis-molecular-computing/nuad/pull/242)
- 3f19333: Update constraints.py (David Doty) [242](https://github.com/UC-Davis-molecular-computing/nuad/pull/242)
- 6136766: Update constraints.py (David Doty) [242](https://github.com/UC-Davis-molecular-computing/nuad/pull/242)
- 69972f8: closes 240: constraint to specify NUPACK/ViennaRNA non-complementary domain binding affinities (David Doty) [242](https://github.com/UC-Davis-molecular-computing/nuad/pull/242)
- 52718c6: fixed docstring (David Doty) [242](https://github.com/UC-Davis-molecular-computing/nuad/pull/242)
- a89ff57: modified docstrings (Dave Doty) [242](https://github.com/UC-Davis-molecular-computing/nuad/pull/242)
- c36b4ee: Update many_strands_no_common_domains.py (Dave Doty) [243](https://github.com/UC-Davis-molecular-computing/nuad/pull/243)

Hmm, not sure what happened to version 0.4.3, but here we are.

Commits
- bf51917: bumped version (David Doty) [239](https://github.com/UC-Davis-molecular-computing/nuad/pull/239)
- 0710859: closes 237: add Constraint using RNAplex (David Doty) [238](https://github.com/UC-Davis-molecular-computing/nuad/pull/238)
- fae8189: updated actions checkout and python-setup v2 to v3 (David Doty) [238](https://github.com/UC-Davis-molecular-computing/nuad/pull/238)
- c2346a5: Update docs-check.yml (David Doty) [238](https://github.com/UC-Davis-molecular-computing/nuad/pull/238)
- 57e23fc: changed `IDTFields` to `VendorFields` and changed associated names; also removed xlrd and replaced with openpyxl in testing code (David Doty) [238](https://github.com/UC-Davis-molecular-computing/nuad/pull/238)
- 94efee0: fixes 236: add unit test actions for Python 3.10 and 3.11 (David Doty) [238](https://github.com/UC-Davis-molecular-computing/nuad/pull/238)
- a3be2b1: fixed docstring (David Doty) [238](https://github.com/UC-Davis-molecular-computing/nuad/pull/238)
- ba44897: unfixes 236 (David Doty) [238](https://github.com/UC-Davis-molecular-computing/nuad/pull/238)
- dfe5387: minor whitespace change to trigger re-running github actions (David Doty) [238](https://github.com/UC-Davis-molecular-computing/nuad/pull/238)

Commits
- 84a0940: bumped version (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- 10a5d81: changed default score transfer function to cubic (instead of quadratice) (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- fb73ed7: added longest complementary subsequence constraint (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- a6ff4a3: replaced types `np.bool` and `np.int` with Python types `bool` and `int` as suggested in update to numpy 1.24 (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- a8746b4: added longest common subsequence constraint (calculated fast using numpy as a heuristic for pairwise interaction of strands) (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- c00d799: Update constraints.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- 194ce38: Update constraints.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- 74cdea9: changed `Result.summary` to getter/setter property to calculate automatically from value if missing (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- a0d8213: Update constraints.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- 6bfec58: moved pathos import in vienna_nupack module so that lack of pathos does not cause error; still imported unconditionally in search.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- 673fccd: added noqa to suppress PyCharm warning (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- e3f78d6: added faster version of seqs2arr (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- 2ba4ca6: made check for equal sequence lengths in `seqs2arr` slightly faster with numpy code (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- d1c1d37: Update np.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- 70ff9c2: Update np.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- bc1f36a: Update np.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- 60ff09e: Update np.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- eb5868c: Update np.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- 574a6fd: Update np.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- 8aca96a: Update np.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- 39f9a5f: Update np.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- a153ced: Update README.md (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- b1c8228: Update README.md (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- 07b8a91: Update search.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- 387a053: Update search.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- 0fe3a32: added p8634 variant of M13 (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- 7346987: Update constraints.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- e13f69a: Update CONTRIBUTING.md (Dave Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- d3c7d21: fixed type of `DNASeqList` `seqs` constructor parameter to be optional `None` (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- f8efb7c: Update np.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)
- 307d098: Update np.py (David Doty) [234](https://github.com/UC-Davis-molecular-computing/nuad/pull/234)

Breaking change: `NumpyFilter` and `SequenceFilter`
The classes representing "hard" constraints (and their subclasses) `NumpyConstraint` and `SequenceConstraint` have been renamed to `NumpyFilter` and `SequenceFilter` to avoid confusion with the subclasses of the "soft" constraints class `Constraint`.

Commits
- 985ea5e: Update conf.py (David Doty) [232](https://github.com/UC-Davis-molecular-computing/nuad/pull/232)
- 03f123b: handle empty starred domain indices properly (David Doty) [232](https://github.com/UC-Davis-molecular-computing/nuad/pull/232)
- 56f8985: fixed bug where subdomain check was ruling out checking a domain against itself (David Doty) [232](https://github.com/UC-Davis-molecular-computing/nuad/pull/232)
- 5f53347: fixed rna_duplex domain pairs constraint to group sequence pairs from same pair of domains (David Doty) [232](https://github.com/UC-Davis-molecular-computing/nuad/pull/232)
- c7aa82a: added parameter `ignore_missing_thresholds` to strand pairs constraints generator based on number of complementary domains (David Doty) [232](https://github.com/UC-Davis-molecular-computing/nuad/pull/232)
- a13587a: minor (David Doty) [232](https://github.com/UC-Davis-molecular-computing/nuad/pull/232)
- c7d0508: bumped version (David Doty) [232](https://github.com/UC-Davis-molecular-computing/nuad/pull/232)

Breaking change: implemented issue 227: rename "hard" constraints `NumpyConstraint` and `SequenceConstraint` to `NumpyFilter` and `SequenceFilter`, as well as existing subclasses of `NumpyFilter`.

Commits
- 7a489d8: swapped `filename` and `directory` parameter order in idt export methods (David Doty) [230](https://github.com/UC-Davis-molecular-computing/nuad/pull/230)
- 7965355: fixed idt fields bug (David Doty) [230](https://github.com/UC-Davis-molecular-computing/nuad/pull/230)
- 40abd39: Update constraints.py (David Doty) [230](https://github.com/UC-Davis-molecular-computing/nuad/pull/230)
- ea2ac4c: closes 227: rename "hard" constraints `NumpyConstraint` and `SequenceConstraint` to `NumpyFilter` and `SequenceFilter` (David Doty) [229](https://github.com/UC-Davis-molecular-computing/nuad/pull/229)
- 5827335: updated docs for `NumpyFilter` (David Doty) [229](https://github.com/UC-Davis-molecular-computing/nuad/pull/229)
- 98ed5af: Update constraints.py (David Doty) [229](https://github.com/UC-Davis-molecular-computing/nuad/pull/229)
- 758e34e: minor renaming (David Doty) [229](https://github.com/UC-Davis-molecular-computing/nuad/pull/229)
- b0429a0: changed ubuntu image to 20.04 to deal with issue https://github.com/actions/runner-images/issues/6647 (David Doty) [#229](https://github.com/UC-Davis-molecular-computing/nuad/pull/229)
- 142d43a: bumped version (David Doty) [230](https://github.com/UC-Davis-molecular-computing/nuad/pull/230)
- f664fd2: bumped minor version to reflect breaking change of changing names of hard constraints from Constraint to Filter (David Doty) [230](https://github.com/UC-Davis-molecular-computing/nuad/pull/230)