drop python 3.8 support #339

.github/workflows/pydna_test_and_coverage_workflow.yml

@@ -15,13 +15,11 @@ jobs:
       fail-fast: false
       matrix:
         os: ["macos-latest", "windows-latest"]
-        python-version: ["3.12", "3.11", "3.10", "3.9", "3.8"]
+        python-version: ["3.12", "3.11", "3.10", "3.9"]
         include:
-          - os: ubuntu-latest
-            python-version: "3.8"
-            codecov: true
           - os: ubuntu-latest
             python-version: "3.9"
+            codecov: true
           - os: ubuntu-latest
             python-version: "3.10"
           - os: ubuntu-latest
@@ -51,7 +49,6 @@ jobs:
         uses: snok/install-poetry@v1
         with:
           virtualenvs.prefer-active-python: true
-          version: ${{ matrix.python-version == '3.8' && '1.8.2' || 'latest' }}
       - name: 🔩 list Poetry settings
         run: poetry config --list
 

.pre-commit-config.yaml

@@ -7,6 +7,8 @@ repos:
     args: [--branch, master]
   # Format yaml files
   - id: check-yaml
+  # Ignore conda build meta.yaml files
+    exclude: ^scripts/conda-build/meta.*\.yaml$
   # Fix end-of-file issues
   - id: end-of-file-fixer
   # Fix trailing whitespace

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 authors = [
-    {name = "Björn F. Johansson", email = "[email protected]"},
-    {name = "Manuel Lera-Ramirez", email = "[email protected]"}
+  { name = "Björn F. Johansson", email = "[email protected]" },
+  { name = "Manuel Lera-Ramirez", email = "[email protected]" },
 ]
 classifiers = [
   "Development Status :: 4 - Beta",
@@ -11,7 +11,6 @@ classifiers = [
   "Intended Audience :: Science/Research",
   "License :: OSI Approved :: BSD License",
   "Operating System :: OS Independent",
-  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
@@ -27,7 +26,10 @@ readme = "README.md"
 Changelog = "https://github.com/pydna-group/pydna/blob/master/docs/CHANGELOG.md#changelog"
 [tool.poetry]
 description = "Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules."
-authors = ["Björn F. Johansson <[email protected]>", "Manuel Lera-Ramirez <[email protected]>"]
+authors = [
+  "Björn F. Johansson <[email protected]>",
+  "Manuel Lera-Ramirez <[email protected]>",
+]
 documentation = "https://pydna-group.github.io/pydna"
 homepage = "https://github.com/pydna-group/pydna#-pydna"
 license = "BSD"
@@ -41,17 +43,14 @@ biopython = ">=1.80,<1.85"
 cai2 = { version = ">=1.0.5", optional = true }
 matplotlib = { version = ">=3.4.3", optional = true }
 networkx = ">=2.8.8"
-numpy = [
-  { version = ">1.26", python = ">=3.9" },
-  { version = "<1.24", python = "<3.9" },
-]
+numpy = ">1.26"
 pillow = { version = ">=8.4.0", optional = true }
 prettytable = ">=3.5.0"
 pydivsufsort = ">=0.0.14"
 pyfiglet = "0.8.post1"
 pyparsing = { version = ">=2.4.7", optional = true }
 pyperclip = { version = ">=1.8.2", optional = true }
-python = ">=3.8,<4.0"
+python = ">=3.9,<4.0"
 requests = { version = ">=2.26.0", optional = true }
 scipy = [
   { version = ">=1.11.3", python = ">=3.12", optional = true },
@@ -88,19 +87,16 @@ sphinx-autobuild = "^2021.3.14"
 sphinx-rtd-theme = ">=1.3,<4.0"
 nbconvert = "^7.16.4"
 myst-parser = [
-  { version = ">3.0.0", python = "<3.10"},
-  { version = ">=4.0.0", python = ">=3.10"},
+  { version = ">3.0.0", python = "<3.10" },
+  { version = ">=4.0.0", python = ">=3.10" },
 ]
 
 [tool.poetry.group.dev.dependencies]
 autopep8 = "^2.1.0"
 black = "^24.4.2"
-flake8-bugbear = [{ version = ">=24.4.21", python = ">=3.8.1" }]
-pre-commit = [
-  { version = ">3.6", python = ">=3.9" },
-  { version = "<3.6", python = "<3.9" },
-]
+pre-commit = ">3.6"
 nbstripout = "^0.7.1"
+flake8-bugbear = "^24.12.12"
 
 [tool.pytest.ini_options]
 minversion = "6.0.2"

scripts/conda-build/meta (copy).yaml

@@ -10,7 +10,7 @@ source:
   path: .
 requirements:
     host:
-    - python>=3.8,<4.0
+    - python>=3.9,<4.0
     - pip
     - poetry-core
     - poetry-dynamic-versioning

scripts/conda-build/meta (copy2).yaml

@@ -11,7 +11,7 @@ source:
   path: .
 requirements:
     host:
-    - python >=3.8
+    - python >=3.9
     - pip
     - poetry
     - poetry-dynamic-versioning

scripts/conda-build/meta2.yaml

@@ -10,7 +10,7 @@ source:
   path: .
 requirements:
     host:
-    - python>=3.8,<4.0
+    - python>=3.9,<4.0
     - pip
     - poetry-core
     - poetry-dynamic-versioning

scripts/conda-build/myenvironment.yaml

@@ -9,7 +9,7 @@
 ###############################################################################
 name: some-name-env
 dependencies:
-  - python>=3.8,<4.0
+  - python>=3.9,<4.0
   - conda-forge::appdirs>=1.4.4,<2.0.0
   - conda-forge::biopython>=1.80,<2.0
   - conda-forge::networkx>=2.8.8,<3.0.0