v0.4.7

Small bug fixes.

Mostly pushed the version to enable nuad to be cited on Zenodo: https://zenodo.org/records/10680482

Commits

• 938b59f: bumped version (David Doty) #253
• 7704257: Update search.py (David Doty) #253
• e526731: fix Domain.name docstring (Constantine Evans) #248
• 8ade905: Update README.md (David Doty) #253
• 7a0d043: Merge branch 'dev' of https://github.com/UC-Davis-molecular-computing/dsd into dev (David Doty) #253
• b22d039: Update test.py (David Doty) #253
• 0fe23ae: minor (David Doty) #253
• 2e6d150: re-wrote sst_canvas.py example to use rna_duplex_strand_pairs_constraints_by_number_matching_domains (David Doty) #253
• 362e682: Update sst_canvas.py (David Doty) #253
• 25388ef: Update search.py (David Doty) #253
• ff181b1: fixed some mypy errors (David Doty) #253
• b004f09: Update constraints.py (David Doty) #253
• 48df73b: fixed many tuple type errors (David Doty) #253
• 47f1c7c: fixed some numpy type errors (David Doty) #253
• d05c8b5: fixed some type errors (David Doty) #253
• 113a339: suppressed type error (David Doty) #253
• 73e9ee2: updated unit test Python and Ubuntu versions (David Doty) #253
• 2df322f: downgraded Ubuntu to try to handle error in Github actions (David Doty) #253
• fb9793c: reverted unit tests action (David Doty) #253

What's Changed

• fix Domain.name docstring by @cgevans in #248
• Dev by @dave-doty in #253

Full Changelog: v0.4.6...v0.4.7

v0.4.6

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

v0.4.5

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
• d64cdad: added _normalize_domains_pairs_disjoint_parameters (David Doty) #243
• 85536d3: added rna_plex_domain_pairs_nonorthogonal_constraint and cleaned up docstrings (David Doty) #242
• 3f19333: Update constraints.py (David Doty) #242
• 6136766: Update constraints.py (David Doty) #242
• 69972f8: closes #240: constraint to specify NUPACK/ViennaRNA non-complementary domain binding affinities (David Doty) #242
• 52718c6: fixed docstring (David Doty) #242
• a89ff57: modified docstrings (Dave Doty) #242
• c36b4ee: Update many_strands_no_common_domains.py (Dave Doty) #243

v0.4.4

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

Commits

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

0.4.2

Commits

• 84a0940: bumped version (David Doty) #234
• 10a5d81: changed default score transfer function to cubic (instead of quadratice) (David Doty) #234
• fb73ed7: added longest complementary subsequence constraint (David Doty) #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
• a8746b4: added longest common subsequence constraint (calculated fast using numpy as a heuristic for pairwise interaction of strands) (David Doty) #234
• c00d799: Update constraints.py (David Doty) #234
• 194ce38: Update constraints.py (David Doty) #234
• 74cdea9: changed Result.summary to getter/setter property to calculate automatically from value if missing (David Doty) #234
• a0d8213: Update constraints.py (David Doty) #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
• 673fccd: added noqa to suppress PyCharm warning (David Doty) #234
• e3f78d6: added faster version of seqs2arr (David Doty) #234
• 2ba4ca6: made check for equal sequence lengths in seqs2arr slightly faster with numpy code (David Doty) #234
• d1c1d37: Update np.py (David Doty) #234
• 70ff9c2: Update np.py (David Doty) #234
• bc1f36a: Update np.py (David Doty) #234
• 60ff09e: Update np.py (David Doty) #234
• eb5868c: Update np.py (David Doty) #234
• 574a6fd: Update np.py (David Doty) #234
• 8aca96a: Update np.py (David Doty) #234
• 39f9a5f: Update np.py (David Doty) #234
• a153ced: Update README.md (David Doty) #234
• b1c8228: Update README.md (David Doty) #234
• 07b8a91: Update search.py (David Doty) #234
• 387a053: Update search.py (David Doty) #234
• 0fe3a32: added p8634 variant of M13 (David Doty) #234
• 7346987: Update constraints.py (David Doty) #234
• e13f69a: Update CONTRIBUTING.md (Dave Doty) #234
• d3c7d21: fixed type of DNASeqList seqs constructor parameter to be optional None (David Doty) #234
• f8efb7c: Update np.py (David Doty) #234
• 307d098: Update np.py (David Doty) #234

v0.4.1

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
• 03f123b: handle empty starred domain indices properly (David Doty) #232
• 56f8985: fixed bug where subdomain check was ruling out checking a domain against itself (David Doty) #232
• 5f53347: fixed rna_duplex domain pairs constraint to group sequence pairs from same pair of domains (David Doty) #232
• c7aa82a: added parameter ignore_missing_thresholds to strand pairs constraints generator based on number of complementary domains (David Doty) #232
• a13587a: minor (David Doty) #232
• c7d0508: bumped version (David Doty) #232

v0.4.0

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
• 7965355: fixed idt fields bug (David Doty) #230
• 40abd39: Update constraints.py (David Doty) #230
• ea2ac4c: closes #227: rename "hard" constraints NumpyConstraint and SequenceConstraint to NumpyFilter and SequenceFilter (David Doty) #229
• 5827335: updated docs for NumpyFilter (David Doty) #229
• 98ed5af: Update constraints.py (David Doty) #229
• 758e34e: minor renaming (David Doty) #229
• b0429a0: changed ubuntu image to 20.04 to deal with issue actions/runner-images#6647 (David Doty) #229
• 142d43a: bumped version (David Doty) #230
• f664fd2: bumped minor version to reflect breaking change of changing names of hard constraints from Constraint to Filter (David Doty) #230

v0.3.5

Commits

• 0376bc6: attempt to fix broken setup.py (David Doty) #226

Also had these commits from a release I lost:

@dave-doty
Update search.py
9defd52
@dave-doty
fixed some bugs related to partially updated scadnano names not on de…
b760db2
…v/main branch yet
@dave-doty
added method for assigning strand groups from nuad design to scadnano…
11ac5e2
… design as "group" key of label
@dave-doty
[updated poorly named function nupack_strand_pair_constraint_by_numbe…](https://github.com/UC-Davis-molecular-computing/nuad/pull/225/commits/6016d8446ea7b297e6f76a8a093592d962ed894e) 6016d84 …r_matching_domains to nupack_strand_pair_constraints_by_number_matching_domains
@dave-doty
fixed docstring refs to SynthesisFields (still named IDTFields)

v0.3.2

Commits

• a8cde7d: Update requirements.txt (David Doty) #221
• 9752a83: bumped version to try to fix readthedocs error on commit to main (David Doty) #221

v0.3.1

Commits

• a253254: bumped version (David Doty) #218
• fb0ea4f: testing whether forward annotations work on Python 3.7 (David Doty) #218
• 52f6666: closes #216: use | instead of Union for union type annotations (David Doty) #218
• dc5f9b2: fixed from future import annotations error in modifications.py (David Doty) #218
• df9933c: change search_for_dna_sequences to search_for_sequences (David Doty) #220
• 60d3cd6: fixed bug in specifying unitless quantities in (David Doty) #220
• 36f2d75: fixed up display_report (David Doty) #220