feat(package): Migrating to uv

.github/workflows/build.yaml

@@ -8,7 +8,7 @@ jobs:
     timeout-minutes: 60
     strategy:
       matrix:
-        python-version: ["3.11"]
+        python-version: ["3.11", "3.12"]
     concurrency:
       group: ci-${{ github.ref }}
       cancel-in-progress: true
@@ -18,9 +18,9 @@ jobs:
         shell: bash -l {0}
 
     steps:
-    - uses: actions/checkout@v2
-    
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: actions/checkout@v4
+
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniconda-version: "latest"
         mamba-version: "*"
@@ -29,13 +29,22 @@ jobs:
         activate-environment: pyreaddbc
         use-mamba: true
         miniforge-variant: Mambaforge
-
-    - name: Install dependencies
-      run: |
-        # poetry config experimental.new-installer false
-        poetry config virtualenvs.create false
-        poetry build
-        poetry install
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+
+    - name: Set up Python
+      run: uv python install
+
+    - name: Install the project
+      run: uv sync --all-extras --dev
+
+    - name: Run tests
+      # For example, using `pytest`
+      run: uv run pytest tests
+
+    - name: Build wheel
+      run: uv build --wheel
 
     - name: Lint with flake8
       run: |
@@ -44,6 +53,3 @@ jobs:
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
-    - name: Test with pytest
-      run: |
-        poetry run pytest -vv -k "ZIKABR21 or STPI2206 or sids" tests/

conda/dev.yaml

@@ -6,4 +6,5 @@ dependencies:
   - cffi
   - gcc
   - pip
+  - uv
   - poetry

pyproject.toml

@@ -1,64 +1,58 @@
-[build-system]
-requires = [
-    "poetry-core>=1.0.0", "setuptools>=41.0.0", "wheel", "cffi"]
-build-backend = "poetry.core.masonry.api"
-
-[tool.poetry.build]
-script = "pyreaddbc/_build_readdbc.py"
-generate-setup-file = false
-
-[tool.poetry.group.dev.dependencies]
-pandas = "^2.1.0"
-
-[tool.poetry]
+[project]
+authors = [
+    { name = "Flavio Codeco Coelho", email = "fccoelho@gmail.com" },
+    { name = "Sandro Loch", email = "es.loch@gmail.com" },
+]
+license = { text = "AGPL-3.0" }
+requires-python = "<4,>=3.9"
+dependencies = [
+    "dbfread<3,>=2.0.7",
+    "tqdm<5,>=4.64.0",
+    "cffi<2,>=1.15.1",
+    "pyyaml>=6",
+    "setuptools>=75.6.0",
+]
 name = "pyreaddbc"
-version = "1.1.0"  # changed by semantic-release
+version = "1.1.0"   # changed by semantic-release
 description = "pyreaddbc package"
 readme = "README.md"
-authors = ["Flavio Codeco Coelho <fccoelho@gmail.com>", "Sandro Loch <es.loch@gmail.com>"]
-license = "AGPL-3.0"
-repository = "https://github.com/osl-incubator/pyreaddbc"
-homepage = "https://github.com/osl-incubator/pyreaddbc"
-
-# Pypi classifiers: https://pypi.org/classifiers/
-classifiers = [  #! Update me
-  "Development Status :: 3 - Alpha",
-  "Intended Audience :: Developers",
-  "Operating System :: OS Independent",
-  "Topic :: Software Development :: Libraries :: Python Modules",
-  "License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
-  "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.9",
-  "Programming Language :: Python :: 3.10",
-  "Programming Language :: Python :: 3.11",
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "Operating System :: OS Independent",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
 ]
 
-include = [
-    {path = "pyreaddbc/_readdbc.so"}
+[tool.setuptools]
+py-modules = ["pyreaddbc"]
+ext-modules = [
+    {name = "pyreaddbc._readdbc",  sources = ["pyreaddbc/_readdbc.c", "pyreaddbc/c-src/blast.c"],     include-dirs = ["pyreaddbc", "pyreaddbc/c-src"]}#,    libraries = ["readdbc"],    library-dirs = ["pyreaddbc"]},
 ]
 
-packages = [
-    { include = "pyreaddbc" },
-]
-
-[tool.poetry.dependencies]
-python = ">=3.9,<4"
-dbfread = ">=2.0.7,<3"
-tqdm = ">=4.64.0,<5"
-cffi = ">=1.15.1,<2"
-pyyaml = ">=6"
+[build-system]
+requires = ["setuptools>=61", "cffi"]
+build-backend = "setuptools.build_meta"
 
-[tool.poetry.dev-dependencies]
-black = ">=22.6.0"
-isort = ">=5.10.1"
-flake8 = ">=5.0.4"
-pre-commit = ">=2.20.0"
-pytest = ">=7.1.2"
-commitizen = ">=2.32.2"
-chardet = ">=5.2.0"
+[build]
+default = ["python", "-m", "./pyreaddbc/_build_readdbc.py"]
 
 [tool.black]
 line-length = 79
 skip-string-normalization = true
-target-version = ["py39", "py310", "py311"]
+target-version = ["py39", "py310", "py311", "py312"]
 exclude = "docs/"
+
+[project.optional-dependencies]
+dev = [
+    "pytest<9.0.0,>=8.1.1",
+    "pandas<3.0.0,>=2.1.0",
+]
+
+[project.urls]
+Repository = "https://github.com/AlertaDengue/pyreaddbc"
+

pyreaddbc/__init__.py

@@ -1,6 +1,6 @@
 """pyreaddbc Python package"""
 from importlib import metadata as importlib_metadata
-
+# import ._build_readdbc
 from .readdbc import *  # noqa F403
 
 

pyreaddbc/_build_readdbc.py

@@ -1,4 +1,4 @@
-u"""
+"""
 Created on 16/08/16
 by fccoelho
 license: GPL V3 or Later
@@ -20,8 +20,8 @@
         source=f.read(),
         source_extension=".c",
         libraries=["c"],
-        sources=[str(PACKAGE_REL_PATH / "c-src" / "blast.c")],
-        include_dirs=[str(PACKAGE_REL_PATH / "c-src")],
+        sources=[str(PACKAGE_ABS_PATH /"c-src"/ "blast.c")],
+        include_dirs=[str(PACKAGE_ABS_PATH / "c-src"), str(PACKAGE_ABS_PATH), str(PACKAGE_REL_PATH)],
     )
 ffibuilder.cdef(
     """
@@ -31,7 +31,7 @@
     """
 )
 
-with open(PACKAGE_ABS_PATH / "c-src" / "blast.h") as f:
+with open(PACKAGE_ABS_PATH / "c-src" / "blast.h", "r") as f:
     ffibuilder.cdef(f.read(), override=True)
 
 

pyreaddbc/_readdbc.c

@@ -281,11 +281,15 @@ static int search_in_struct_unions(const struct _cffi_type_context_s *ctx,
     typedef unsigned char _Bool;
 #  endif
 # endif
+# define _cffi_float_complex_t   _Fcomplex    /* include <complex.h> for it */
+# define _cffi_double_complex_t  _Dcomplex    /* include <complex.h> for it */
 #else
 # include <stdint.h>
 # if (defined (__SVR4) && defined (__sun)) || defined(_AIX) || defined(__hpux)
 #  include <alloca.h>
 # endif
+# define _cffi_float_complex_t   float _Complex
+# define _cffi_double_complex_t  double _Complex
 #endif
 
 #ifdef __GNUC__