merge changes from dev_bjorn

.github/workflows/pydna_test_and_coverage_workflow.yml

@@ -27,43 +27,38 @@ jobs:
           python-version: "3.11"
         - os: ubuntu-latest
           python-version: "3.12"
-
+    defaults:
+      run:
+        shell: bash
     runs-on: ${{ matrix.os }}
     steps:
-
       - name: 🛑 Cancel Previous Runs
         uses: styfle/cancel-workflow-action@0.11.0
 
       - name: ⬇️ Checkout
         uses: actions/checkout@v3
 
-      - name: 🌍 Install conda environment from pydna_test_environment.yml
-        uses: mamba-org/setup-micromamba@v1
+      - name: 🔩 Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
         with:
-          environment-file: pydna_test_environment.yml
-          create-args: python=${{ matrix.python-version }}
-          cache-downloads: true
-          cache-environment: true
+          python-version: ${{ matrix.python-version }}
 
-      - name: 🐍 micromamba info
-        shell: bash -l {0}
-        run: micromamba info
+      - name: 🐍 Display Python version
+        run: python -c "import sys; print(sys.version)"
 
-      - name: 🐍 micromamba list
-        shell: bash -l {0}
-        run: micromamba list
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+           virtualenvs.prefer-active-python: true
 
-      - name: 🔩 Set version
-        shell: bash -l {0}
-        run: poetry dynamic-versioning
+      - name: 🔩 list Poetry settings
+        run: poetry config --list
 
-      - name: 🔩 Install from source
-        shell: bash -l {0}
-        run: pip install --editable . --no-deps
+      - name: 🔩 Install with Poetry
+        run: poetry install --all-extras --with test
 
-      - name: 🔎 python run_test.py
-        shell: bash -l {0}
-        run: python run_test.py
+      - name: 🔎 poetry run python run_test.py
+        run: poetry run python run_test.py
 
       - name: 🔼 Upload coverage to Codecov
         if: (matrix.codecov)

pyproject.toml

@@ -45,12 +45,10 @@ pillow = { version = ">=8.4.0", optional = true }
 pyparsing = { version = ">=2.4.7", optional = true }
 requests = { version = ">=2.26.0", optional = true }
 cai2 = { version = ">=1.0.5", optional = true }
-pyqt5 = { version = ">=5.15.0", optional = true }
 [tool.poetry.extras]
 clipboard = ["pyperclip"]
 gel = ["scipy", "matplotlib", "pillow"]
 download = ["pyparsing", "requests"]
-gui = ["pyqt5"]
 express = ["cai2"]
 [build-system]
 requires = ["poetry-core",

run_test.py

@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+
 import sys
 import os
 import logging
 import tempfile
-import pytest
 import pathlib
-
+import pytest
 
 pathlib.Path("coverage.xml").unlink(missing_ok=True)
 pathlib.Path(".coverage").unlink(missing_ok=True)

src/pydna/dseq.py

@@ -492,7 +492,6 @@ def from_full_sequence_and_overhangs(cls, full_sequence: str, crick_ovhg: int, w
 
         return Dseq(watson, crick=crick, ovhg=crick_ovhg)
 
-
     # @property
     # def ovhg(self):
     #     """The ovhg property. This cannot be set directly, but is a

tests/test_module_dseq.py

@@ -770,9 +770,10 @@ def test_translate():
 
 def test_from_full_sequence_and_overhangs():
     from pydna.dseq import Dseq
+
     test_cases = [
         (2, 2, "AAAA", "TTTT"),
-        (-2, 2, "AAAAAA", "TT" ),
+        (-2, 2, "AAAAAA", "TT"),
         (2, -2, "AA", "TTTTTT"),
         (-2, -2, "AAAA", "TTTT"),
         (0, 0, "AAAAAA", "TTTTTT"),