Merge branch 'develop' into issue_147

.github/workflows/pydna_pypi_build_workflow.yml

@@ -4,6 +4,7 @@ on:
     types: [published]
     branches:
       - master
+      - dev_bjorn
 jobs:
   build:
     name: Build
@@ -53,13 +54,9 @@ jobs:
         shell: bash -l {0}
         run: git describe --tags
 
-      - name: 🔩 Build pypi wheel package
-        shell: bash -l {0}
-        run: poetry build
-
-      - name: 🔼 Publish a Python distribution to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+      - name: Build and publish to pypi
+        uses: JRubics/[email protected]
         with:
-          user: __token__
-          password: ${{ secrets.PYDNA_PYPI_TOKEN }}
-          skip_existing: true
+          pypi_token: ${{ secrets.PYPI_TOKEN }}
+          repository_name: "testpypi"
+          repository_url: "https://test.pypi.org/legacy/"

.github/workflows/pydna_test_and_coverage_workflow.yml

@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ 'macos-latest', 'windows-latest' ]
-        python-version: ["3.11", "3.10", "3.9", "3.8"]
+        python-version: ["3.12", "3.11", "3.10", "3.9", "3.8"]
         include:
         - os: ubuntu-latest
           python-version: "3.8"
@@ -25,6 +25,8 @@ jobs:
           python-version: "3.10"
         - os: ubuntu-latest
           python-version: "3.11"
+        - os: ubuntu-latest
+          python-version: "3.12"
 
     runs-on: ${{ matrix.os }}
     steps:

pyproject.toml

@@ -11,35 +11,35 @@ classifiers=["Development Status :: 4 - Beta",
              "Intended Audience :: Science/Research",
              "License :: OSI Approved :: BSD License",
              "Operating System :: OS Independent",
-             "Programming Language :: Python :: 3.7",
              "Programming Language :: Python :: 3.8",
              "Programming Language :: Python :: 3.9",
              "Programming Language :: Python :: 3.10",
              "Programming Language :: Python :: 3.11",
+             "Programming Language :: Python :: 3.12",
              "Topic :: Education",
              "Topic :: Scientific/Engineering :: Bio-Informatics", ]
-[project.urls]
-homepage = "https://github.com/BjornFJohansson/pydna#-pydna"
-documentation = "https://pydna.readthedocs.io/?badge=latest"
-repository = "https://github.com/BjornFJohansson/pydna/tree/dev_bjorn"
-changelog = "https://github.com/BjornFJohansson/pydna/blob/master/docs/CHANGELOG.md#changelog"
+[tool.poetry.urls]
+Changelog = "https://github.com/BjornFJohansson/pydna/blob/master/docs/CHANGELOG.md#changelog"
 [tool.poetry]
 name = "pydna"
 version = "5.2.0-a.15"
 description = "Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules."
 authors = ["BjornFJohansson <[email protected]>"]
 license = "BSD"
 readme = "README.md"
+homepage = "https://github.com/BjornFJohansson/pydna#-pydna"
+documentation = "https://pydna.readthedocs.io/?badge=latest"
+repository = "https://github.com/BjornFJohansson/pydna/tree/dev_bjorn"
 [tool.poetry.dependencies]
 python = ">=3.8"
 appdirs = ">=1.4.4"
 biopython = ">=1.80"
 networkx = ">=2.8.8"
 pydivsufsort = ">=0.0.11"
 prettytable = ">=3.5.0"
-pyfiglet = ">=0.8.post1"
+pyfiglet = "0.8.post1"
 pyperclip = { version = ">=1.8.2", optional = true }
-scipy = { version = ">=1.8.0", optional = true }
+scipy = { version = ">=1.9.3", optional = true }
 matplotlib = { version = ">=3.4.3", optional = true }
 pillow = { version = ">=8.4.0", optional = true }
 pyparsing = { version = ">=2.4.7", optional = true }

src/pydna/dseq.py

@@ -1313,8 +1313,7 @@ def twice_cutters(self, batch: _RestrictionBatch = None):
         return self.n_cutters(n=2, batch=batch)
 
     def n_cutters(self, n=3, batch: _RestrictionBatch = None):
-        """Returns the enzymes in a RestrictionBatch that cut the sequence
-        n times."""
+        """Enzymes in a RestrictionBatch cutting n times."""
         if not batch:
             batch = CommOnly
         ana = batch.search(self)