Merge pull request #3 from DNA-and-Natural-Algorithms-Group/numpy2

update versions to use rust numpy 0.22, pyo3 0.22; allow numpy 2

.github/workflows/python-tests.yml

@@ -29,31 +29,31 @@ jobs:
   #          options: "--check --verbose --diff"
   #          src: "./src"
 
-  mypy:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.12"
-      - uses: actions/checkout@v3
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip setuptools_scm[toml] wheel setuptools
-          python -m pip install --upgrade attrs types-attrs
-          python -m pip install --upgrade .
-          python -m pip install flake8 tox mypy
-      - name: Mypy
-        run: |
-          mypy --cache-dir .mypy_cache --install-types --non-interactive ./src
+  # mypy:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Set up Python ${{ matrix.python-version }}
+  #       uses: actions/setup-python@v4
+  #       with:
+  #         python-version: "3.12"
+  #     - uses: actions/checkout@v3
+  #     - name: Install dependencies
+  #       run: |
+  #         python -m pip install --upgrade pip setuptools_scm[toml] wheel setuptools
+  #         python -m pip install --upgrade attrs types-attrs
+  #         python -m pip install --upgrade .
+  #         python -m pip install flake8 tox mypy
+  #     - name: Mypy
+  #       run: |
+  #         mypy --cache-dir .mypy_cache --install-types --non-interactive ./src
 
   tests:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v3

.gitignore

@@ -6,4 +6,9 @@ dist/*
 *.egg
 /target
 /Cargo.lock
-.coverage
+.coverage
+**/target
+**/Cargo.lock
+**/cov.xml
+.hypothesis
+dist/

README.md

@@ -1,7 +1,7 @@
 [![Documentation Status](https://readthedocs.org/projects/qslib/badge/?version=latest)](https://stickydesign.readthedocs.io/en/latest/?badge=latest)
-![Codecov](https://img.shields.io/codecov/c/github/DNA-and-Natural-Algorithms-Group/stickydesign)
+[![Codecov](https://img.shields.io/codecov/c/github/DNA-and-Natural-Algorithms-Group/stickydesign)](https://codecov.io/gh/DNA-and-Natural-Algorithms-Group/stickydesign)
 ![GitHub Workflow
-Status](https://img.shields.io/github/workflow/status/DNA-and-Natural-Algorithms-Group/stickydesign/Tests)
+Status](https://img.shields.io/github/actions/workflow/status/DNA-and-Natural-Algorithms-Group/stickydesign/python-tests.yml?branch=main)
 ![PyPI](https://img.shields.io/pypi/v/stickydesign)
 
 The StickyDesign Sticky End Sequence Designer

accel/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "stickydesign-accel"
-version = "0.9.1"
+version = "0.9.2"
 edition = "2021"
 
 [lib]
@@ -12,7 +12,7 @@ crate-type = ["cdylib"]
 rayon = ["ndarray/rayon"]
 
 [dependencies]
-ndarray = {version = "0.15", features = ["approx", "blas", "serde"]}
-numpy = {version = "0.21"}
-pyo3 = {version = "0.21", features = ["extension-module", "experimental-declarative-modules"]}
+ndarray = {version = "0.16", features = ["approx", "blas", "serde"]}
+numpy = {version = "0.22"}
+pyo3 = {version = "0.22", features = ["extension-module"]}
 

accel/pyproject.toml

@@ -5,8 +5,8 @@ build-backend = "maturin"
 [project]
 name = 'stickydesign-accel'
 description = "Accelerated functions in Rust for stickydesign."
-dependencies = ['numpy', 'stickydesign ~= 0.9.1']
-version = "0.9.1"
+dependencies = ['numpy', 'stickydesign ~= 0.9.2']
+version = "0.9.2"
 authors = [ {name = "Constantine Evans", email = "const@costi.net"} ]
 license = {text = "BSD 3-Clause"}
 classifiers = [

docs/changelog.rst

@@ -1,6 +1,12 @@
 Changelog
 ==========
 
+0.9.2
+-----
+
+* Update versions to support Numpy 2.
+* Numerous linting and typing fixes.
+
 0.9.1
 -----
 

pyproject.toml

@@ -22,11 +22,11 @@ testpaths = ["tests"]
 
 [project]
 name = "stickydesign"
-version = "0.9.1"
+version = "0.9.2"
 authors = [{ name = "Constantine Evans", email = "const@costi.net" }]
 description = "StickyDesign DNA Tile Sticky End Package"
 readme = "README.md"
-dependencies = ["numpy ~= 1.20", "typing_extensions~=4.0"]
+dependencies = ["numpy >= 1.20, < 3.0", "typing_extensions~=4.0"]
 
 [project.urls]
 homepage = "https://dna.caltech.edu/StickyDesign"
@@ -63,7 +63,7 @@ indent-width = 4
 fixable = ["ALL"]
 select = ["E4", "E7", "E9", "F", "B", "A001", "A002", "C4", "ICN", "PIE", "PYI", "RSE",
     "RET501", "SIM", "TID", "TCH", "INT", "PTH", "PD", "PLR", "PLW", "TRY",
-    "NPY", "PERF", "FURB", "RUF", "UP", "D"]
+    "NPY", "PERF", "FURB", "RUF", "UP", "D", "NPY201"]
 
 # 2. Avoid enforcing line-length violations (`E501`)
 ignore = ["E501", "TRY003", "D1", "UP007", "D205", "D401", "UP032", "UP", "PLR0913", "PLR2004", "PLR0912"]

src/stickydesign/__init__.py

@@ -1,3 +1,5 @@
+# ruff: noqa: F401, F403
+
 from .version import __version__
 
 from .endclasses import *

src/stickydesign/endclasses.py

@@ -1,8 +1,10 @@
 import numpy as np
-from typing_extensions import TypeAlias  # noqa: UP035
-from typing import Union, Literal, List, cast, Dict, Any  # noqa: UP035
-from collections.abc import Sequence
-from abc import ABC, abstractmethod, abstractproperty
+from typing_extensions import TypeAlias
+from typing import Union, Literal, List, cast, Dict, Any, TYPE_CHECKING
+from abc import ABC, abstractmethod
+
+if TYPE_CHECKING:
+    from collections.abc import Sequence
 
 __all__ = [
     'Energetics',
@@ -17,7 +19,7 @@
     'tops',
 ]
 
-EndTypes: TypeAlias = Literal['DT', 'TD', 'S']  # noqa: UP040
+EndTypes: TypeAlias = Literal['DT', 'TD', 'S']
 
 
 class PairSeqA(np.ndarray):
@@ -28,7 +30,7 @@ def __new__(cls, array: np.ndarray):
     def revcomp(self) -> 'PairSeqA':
         return cast(PairSeqA, 4 * (3 - (self[:, ::-1] % 4)) + 3 - (self[:, ::-1] // 4))
 
-    def tolist(self) -> List[str]:  # noqa: UP006
+    def tolist(self) -> List[str]:
         st = ["a", "c", "g", "t"]
         return [
             "".join([st[x // 4] for x in y] + [st[y[-1] % 4]]) for y in self
@@ -159,7 +161,7 @@ def append(s1, s2: 'EndArray') -> 'EndArray':
     def __repr__(self):
         return f"<endarray ({len(self)}): type {self.endtype}; {self.tolist()!r}>"
 
-    def tolist(self) -> List[str]:  # noqa: UP006
+    def tolist(self) -> List[str]:
         st = ["a", "c", "g", "t"]
         return ["".join([st[x] for x in y]) for y in self]
 

src/stickydesign/energetics_basic.py

@@ -14,7 +14,7 @@
 
 def py_tightloop(ens, ltmm, rtmm, intmm, singlepair, looppenalty):
     bindmax = np.zeros(ens.shape[0])
-    for e in range(0, ens.shape[0]):
+    for e in range(ens.shape[0]):
         acc = 0
         for i in range(ens.shape[1]):
             if ens[e, i] != 0:
@@ -27,8 +27,7 @@ def py_tightloop(ens, ltmm, rtmm, intmm, singlepair, looppenalty):
                 # Update: we only want to do this if the last
                 # nnpair was bound, because otherwise, we
                 # can't have a "right" mismatch.
-                if acc + rtmm[e, i] > bindmax[e]:
-                    bindmax[e] = acc + rtmm[e, i]
+                bindmax[e] = max(acc + rtmm[e, i], bindmax[e])
                 acc += intmm[e, i]
             elif ltmm[e, i] != 0 and i < ens.shape[1] - 1:
                 # don't do this for the last pair we're mismatching on
@@ -40,9 +39,7 @@ def py_tightloop(ens, ltmm, rtmm, intmm, singlepair, looppenalty):
                 # mismatch.
                 if (not singlepair) and (ltmm[e, i] >
                                                 acc + intmm[e, i]) and (
-                                                    ens[e, i + 1] > 0):
-                    acc = ltmm[e, i]
-                elif (singlepair) and (ltmm[e, i] >
+                                                    ens[e, i + 1] > 0) or (singlepair) and (ltmm[e, i] >
                                             acc + intmm[e, i]):
                     acc = ltmm[e, i]
                 else:
@@ -54,22 +51,21 @@ def py_tightloop(ens, ltmm, rtmm, intmm, singlepair, looppenalty):
 
 
 class EnergeticsBasic(Energetics):
-
     """Energy functions based on several sources, primarily SantaLucia's
-       2004 paper.  This class uses the same parameters and algorithms
-       as EnergeticsDAOE, bet does not make DX-specific assumptions.
-       Instead, it assumes that each energy should simply be that of
-       two single strands attaching/detaching, without consideration
-       of nicks, stacking, or other effects related to the
-       beginning/end of each sequence.  Dangles and tails are still
-       included in mismatched binding calculations when appropriate.
-
-       Relevant arguments:
+    2004 paper.  This class uses the same parameters and algorithms
+    as EnergeticsDAOE, bet does not make DX-specific assumptions.
+    Instead, it assumes that each energy should simply be that of
+    two single strands attaching/detaching, without consideration
+    of nicks, stacking, or other effects related to the
+    beginning/end of each sequence.  Dangles and tails are still
+    included in mismatched binding calculations when appropriate.
+
+    Relevant arguments:
        
-       singlepair (bool, default False) --- treat single base pair pairings
-       as possible.
-       temperature (float in degrees Celsius, default 37) --- temperature
-       to use for the model, in C.
+    singlepair (bool, default False) --- treat single base pair pairings
+    as possible.
+    temperature (float in degrees Celsius, default 37) --- temperature
+    to use for the model, in C.
     """
 
     def __init__(self,
@@ -98,7 +94,7 @@ def __init__(self,
         self._accel = _accel
         self._allow_shifts = _allow_shifts
     @property
-    def info(self) -> Dict[str, Any]:  # noqa: F821
+    def info(self) -> Dict[str, Any]:
         info = {'enclass': 'EnergeticsDAOE',
                 'temperature': self.temperature,
                 'coaxparams': self.coaxparaminfo,
@@ -158,9 +154,9 @@ def _setup_params(self, temperature=37):
         self.intmmdG_5335 = np.zeros(256)
 
         # Dumb setup. FIXME: do this cleverly
-        for i in range(0, 4):
-            for j in range(0, 4):
-                for k in range(0, 4):
+        for i in range(4):
+            for j in range(4):
+                for k in range(4):
                     self.ltmmdG_5335[
                         i * 64 + j * 16 + k * 4 +
                         j] = self.dangle5dG[i * 4

src/stickydesign/energetics_daoe.py

@@ -102,9 +102,9 @@ def _setup_params(self, temperature=37):
         self.intmmdG_5335 = np.zeros(256)
 
         # Dumb setup. FIXME: do this cleverly
-        for i in range(0, 4):
-            for j in range(0, 4):
-                for k in range(0, 4):
+        for i in range(4):
+            for j in range(4):
+                for k in range(4):
                     self.ltmmdG_5335[
                         i * 64 + j * 16 + k * 4 +
                         j] = self.dangle5dG[i * 4
@@ -175,7 +175,7 @@ def uniform(self, seqs1, seqs2, debug=False):
             s1.shape[0])  # store for max binding at any offset
 
         if endtype == 'TD':
-            s1_end = s1[:, 0:-1]  #
+            s1_end = s1[:, 0:-1]
             s2_end_rc = s2r[:, 1:]
             s1l = np.hstack(((4 * (s2r[:, 0] // 4) + s1[:, 0] // 4).reshape(
                 -1, 1), s1))
@@ -254,52 +254,50 @@ def uniform(self, seqs1, seqs2, debug=False):
                 ltmm = -self.ltmmdG_5335[s1_end[:, :] * 16 + s2_end_rc[:, :]]
                 rtmm = -self.rtmmdG_5335[s1_end[:, :] * 16 + s2_end_rc[:, :]]
                 intmm = -self.intmmdG_5335[s1_end[:, :] * 16 + s2_end_rc[:, :]]
-            else:  # offset < 0
-                if endtype == 'TD':
-                    ens = (s1_end[:, -offset:] == s2_end_rc[:, :offset]) * (
-                        -self.nndG[s1_end[:, -offset:]])
-                    ens[:, 0] += (ens[:, 0] != 0) * (
-                        -self.nndG[s1[:, -1]] - p.tailcordG37 +
-                        self.dangle5dG[s1[:, -1]])  # - for positive sign
-                    ens[:, -1] += (ens[:, -1] != 0) * (
-                        -self.nndG[s2[:, -1]] - p.tailcordG37 +
-                        self.dangle5dG[s2[:, -1]])  # - for positive sign
-                    ltmm = -self.ltmmdG_5335[s1_end[:, -offset:] * 16
-                                             + s2_end_rc[:, :offset]]
-                    rtmm = -self.rtmmdG_5335[s1_end[:, -offset:] * 16
-                                             + s2_end_rc[:, :offset]]
-                    intmm = -self.intmmdG_5335[s1_end[:, -offset:] * 16
-                                               + s2_end_rc[:, :offset]]
-                elif endtype == 'DT':
-                    ens = (s1_end[:, :offset] == s2_end_rc[:, -offset:]) * (
-                        -self.nndG[s1_end[:, :offset]])
-                    ens[:, 0] += (ens[:, 0] != 0) * (
-                        -self.nndG[s1[:, 0]] - p.tailcordG37 +
-                        self.dangle3dG[s1[:, 0]])  # - for positive sign
-                    ens[:, -1] += (ens[:, -1] != 0) * (
-                        -self.nndG[s2[:, 0]] - p.tailcordG37 +
-                        self.dangle3dG[s2[:, 0]])  # - for positive sign
-                    ltmm = -self.ltmmdG_5335[s1_end[:, :offset] * 16
-                                             + s2_end_rc[:, -offset:]]
-                    rtmm = -self.rtmmdG_5335[s1_end[:, :offset] * 16
-                                             + s2_end_rc[:, -offset:]]
-                    intmm = -self.intmmdG_5335[s1_end[:, :offset] * 16
-                                               + s2_end_rc[:, -offset:]]
+            elif endtype == 'TD':
+                ens = (s1_end[:, -offset:] == s2_end_rc[:, :offset]) * (
+                    -self.nndG[s1_end[:, -offset:]])
+                ens[:, 0] += (ens[:, 0] != 0) * (
+                    -self.nndG[s1[:, -1]] - p.tailcordG37 +
+                    self.dangle5dG[s1[:, -1]])  # - for positive sign
+                ens[:, -1] += (ens[:, -1] != 0) * (
+                    -self.nndG[s2[:, -1]] - p.tailcordG37 +
+                    self.dangle5dG[s2[:, -1]])  # - for positive sign
+                ltmm = -self.ltmmdG_5335[s1_end[:, -offset:] * 16
+                                         + s2_end_rc[:, :offset]]
+                rtmm = -self.rtmmdG_5335[s1_end[:, -offset:] * 16
+                                         + s2_end_rc[:, :offset]]
+                intmm = -self.intmmdG_5335[s1_end[:, -offset:] * 16
+                                           + s2_end_rc[:, :offset]]
+            elif endtype == 'DT':
+                ens = (s1_end[:, :offset] == s2_end_rc[:, -offset:]) * (
+                    -self.nndG[s1_end[:, :offset]])
+                ens[:, 0] += (ens[:, 0] != 0) * (
+                    -self.nndG[s1[:, 0]] - p.tailcordG37 +
+                    self.dangle3dG[s1[:, 0]])  # - for positive sign
+                ens[:, -1] += (ens[:, -1] != 0) * (
+                    -self.nndG[s2[:, 0]] - p.tailcordG37 +
+                    self.dangle3dG[s2[:, 0]])  # - for positive sign
+                ltmm = -self.ltmmdG_5335[s1_end[:, :offset] * 16
+                                         + s2_end_rc[:, -offset:]]
+                rtmm = -self.rtmmdG_5335[s1_end[:, :offset] * 16
+                                         + s2_end_rc[:, -offset:]]
+                intmm = -self.intmmdG_5335[s1_end[:, :offset] * 16
+                                           + s2_end_rc[:, -offset:]]
             bindmax = np.zeros(ens.shape[0])
             if debug:
                 print(offset, ens.view(np.ndarray), ltmm, rtmm, intmm)
-            for e in range(0, ens.shape[0]):
+            for e in range(ens.shape[0]):
                 acc = 0
-                for i in range(0, ens.shape[1]):
+                for i in range(ens.shape[1]):
                     if ens[e, i] != 0:
                         # we're matching. add the pair to the accumulator
                         acc += ens[e, i]
                     elif rtmm[e, i] != 0 and i > 0 and ens[e, i-1] > 0:
                         # we're mismatching on the right: see if right-dangling
                         # is highest binding so far, and continue, adding intmm
                         # to accumulator.
-                        if acc + rtmm[e, i] > bindmax[e]:
-                            bindmax[e] = acc + rtmm[e, i]
+                        bindmax[e] = max(acc + rtmm[e, i], bindmax[e])
                         acc += intmm[e, i]
                     elif ltmm[e, i] != 0 and i < ens.shape[1] - 1:
                         # don't do this for the last pair we're mismatching on
@@ -311,9 +309,7 @@ def uniform(self, seqs1, seqs2, debug=False):
                         # mismatch.
                         if (not self.singlepair) and (ltmm[e, i] >
                                                       acc + intmm[e, i]) and (
-                                                          ens[e, i + 1] > 0):
-                            acc = ltmm[e, i]
-                        elif (self.singlepair) and (ltmm[e, i] >
+                                                          ens[e, i + 1] > 0) or (self.singlepair) and (ltmm[e, i] >
                                                     acc + intmm[e, i]):
                             acc = ltmm[e, i]
                         else: