From 052d104a6176421fffd10ba35fcab8bb5dca6731 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fl=C3=A1vio=20Code=C3=A7o=20Coelho?= <fccoelho@gmail.com>
Date: Tue, 26 Nov 2024 19:19:41 -0300
Subject: [PATCH 01/11] started migrating to uv for package management

---
 poetry.lock                 | 1025 -----------------------------------
 pyproject.toml              |  100 ++--
 pyreaddbc/_build_readdbc.py |    2 +-
 pyreaddbc/_readdbc.c        |    4 +
 pyreaddbc/readdbc.py        |    3 +-
 5 files changed, 57 insertions(+), 1077 deletions(-)
 delete mode 100644 poetry.lock

diff --git a/poetry.lock b/poetry.lock
deleted file mode 100644
index 5831745..0000000
--- a/poetry.lock
+++ /dev/null
@@ -1,1025 +0,0 @@
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diff --git a/pyproject.toml b/pyproject.toml
index 5bfad0a..d1254d2 100644
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-[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"
 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"}
+#include = [
+#    {path = "pyreaddbc/_readdbc.so"}
+#]
+[tool.setuptools]
+py-modules = ["pyreaddbc"]
+ext-modules = [
+    {name = "pyreaddbc._readdbc",  sources = ["pyreaddbc/_readdbc.c"],     include-dirs = ["pyreaddbc"],    libraries = ["readdbc"],    library-dirs = ["pyreaddbc"]},
 ]
 
-packages = [
-    { include = "pyreaddbc" },
-]
+[tool.setuptools.cmdclass]
+build_py = "pyreaddbc._build_readdbc"
 
-[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"
+
diff --git a/pyreaddbc/_build_readdbc.py b/pyreaddbc/_build_readdbc.py
index 9d3cc98..f6d7c2a 100644
--- a/pyreaddbc/_build_readdbc.py
+++ b/pyreaddbc/_build_readdbc.py
@@ -1,4 +1,4 @@
-u"""
+"""
 Created on 16/08/16
 by fccoelho
 license: GPL V3 or Later
diff --git a/pyreaddbc/_readdbc.c b/pyreaddbc/_readdbc.c
index 270ab46..cfde2b1 100644
--- a/pyreaddbc/_readdbc.c
+++ b/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__
diff --git a/pyreaddbc/readdbc.py b/pyreaddbc/readdbc.py
index 8cd1b05..c7a5002 100644
--- a/pyreaddbc/readdbc.py
+++ b/pyreaddbc/readdbc.py
@@ -8,7 +8,8 @@
 try:
     from pyreaddbc._readdbc import ffi, lib
 except (ImportError, ModuleNotFoundError):
-    from ._readdbc import ffi, lib
+    pass
+    # from ._readdbc import ffi, lib
 
 
 def dbc2dbf(infile, outfile):

From c388e3c56df6839ecb0781fa6f3d7d28fdec51ce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fl=C3=A1vio=20Code=C3=A7o=20Coelho?= <fccoelho@gmail.com>
Date: Fri, 29 Nov 2024 13:58:02 -0300
Subject: [PATCH 02/11] modified building script

---
 pyreaddbc/__init__.py       | 2 +-
 pyreaddbc/_build_readdbc.py | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/pyreaddbc/__init__.py b/pyreaddbc/__init__.py
index c8f9569..c8cf0e5 100644
--- a/pyreaddbc/__init__.py
+++ b/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
 
 
diff --git a/pyreaddbc/_build_readdbc.py b/pyreaddbc/_build_readdbc.py
index f6d7c2a..fa571ef 100644
--- a/pyreaddbc/_build_readdbc.py
+++ b/pyreaddbc/_build_readdbc.py
@@ -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)
 
 

From a6f0c3085a2c1f1b511da31b9e3eb7472b788e09 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fl=C3=A1vio=20Code=C3=A7o=20Coelho?= <fccoelho@gmail.com>
Date: Fri, 29 Nov 2024 14:51:34 -0300
Subject: [PATCH 03/11] bumped version to 1.2.0

---
 pyproject.toml        | 10 ++--------
 pyreaddbc/__init__.py |  2 +-
 2 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index d1254d2..2264f21 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,7 +13,7 @@ dependencies = [
     "setuptools>=75.6.0",
 ]
 name = "pyreaddbc"
-version = "1.1.0"
+version = "1.2.0"
 description = "pyreaddbc package"
 readme = "README.md"
 classifiers = [
@@ -28,18 +28,12 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
 ]
 
-#include = [
-#    {path = "pyreaddbc/_readdbc.so"}
-#]
 [tool.setuptools]
 py-modules = ["pyreaddbc"]
 ext-modules = [
-    {name = "pyreaddbc._readdbc",  sources = ["pyreaddbc/_readdbc.c"],     include-dirs = ["pyreaddbc"],    libraries = ["readdbc"],    library-dirs = ["pyreaddbc"]},
+    {name = "pyreaddbc._readdbc",  sources = ["pyreaddbc/_readdbc.c"],     include-dirs = ["pyreaddbc"]}#,    libraries = ["readdbc"],    library-dirs = ["pyreaddbc"]},
 ]
 
-[tool.setuptools.cmdclass]
-build_py = "pyreaddbc._build_readdbc"
-
 [build-system]
 requires = ["setuptools>=61", "cffi"]
 build-backend = "setuptools.build_meta"
diff --git a/pyreaddbc/__init__.py b/pyreaddbc/__init__.py
index c8cf0e5..2f1a1d3 100644
--- a/pyreaddbc/__init__.py
+++ b/pyreaddbc/__init__.py
@@ -1,6 +1,6 @@
 """pyreaddbc Python package"""
 from importlib import metadata as importlib_metadata
-import _build_readdbc
+# import ._build_readdbc
 from .readdbc import *  # noqa F403
 
 

From e6651ecd50a333078b8e36b185cc438801f16ece Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fl=C3=A1vio=20Code=C3=A7o=20Coelho?= <fccoelho@gmail.com>
Date: Fri, 29 Nov 2024 15:18:34 -0300
Subject: [PATCH 04/11] passing tests and updated pyproject to complete
 compilation of sources.

---
 .github/workflows/build.yaml | 27 ++++++++++++++++++---------
 pyproject.toml               |  2 +-
 pyreaddbc/readdbc.py         |  3 +--
 3 files changed, 20 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index 32d7475..18dacd8 100644
--- a/.github/workflows/build.yaml
+++ b/.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
@@ -18,7 +18,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     
     - uses: conda-incubator/setup-miniconda@v2
       with:
@@ -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: |
diff --git a/pyproject.toml b/pyproject.toml
index 2264f21..b4f718b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,7 +31,7 @@ classifiers = [
 [tool.setuptools]
 py-modules = ["pyreaddbc"]
 ext-modules = [
-    {name = "pyreaddbc._readdbc",  sources = ["pyreaddbc/_readdbc.c"],     include-dirs = ["pyreaddbc"]}#,    libraries = ["readdbc"],    library-dirs = ["pyreaddbc"]},
+    {name = "pyreaddbc._readdbc",  sources = ["pyreaddbc/_readdbc.c", "pyreaddbc/c-src/blast.c"],     include-dirs = ["pyreaddbc", "pyreaddbc/c-src"]}#,    libraries = ["readdbc"],    library-dirs = ["pyreaddbc"]},
 ]
 
 [build-system]
diff --git a/pyreaddbc/readdbc.py b/pyreaddbc/readdbc.py
index c7a5002..8cd1b05 100644
--- a/pyreaddbc/readdbc.py
+++ b/pyreaddbc/readdbc.py
@@ -8,8 +8,7 @@
 try:
     from pyreaddbc._readdbc import ffi, lib
 except (ImportError, ModuleNotFoundError):
-    pass
-    # from ._readdbc import ffi, lib
+    from ._readdbc import ffi, lib
 
 
 def dbc2dbf(infile, outfile):

From 3f8d560e6ec0c13d8e1cada6eacaea56b63a2bcf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fl=C3=A1vio=20Code=C3=A7o=20Coelho?= <fccoelho@gmail.com>
Date: Fri, 29 Nov 2024 15:22:37 -0300
Subject: [PATCH 05/11] removed last reference of poetry from build.yaml

---
 .github/workflows/build.yaml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index 18dacd8..e21bdcc 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -53,6 +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/

From 440e62cfd6a684ed7fb477ce121f7b4babe1de00 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Flavio=20Code=C3=A7o=20Coelho?= <fccoelho@gmail.com>
Date: Mon, 2 Dec 2024 10:42:12 -0300
Subject: [PATCH 06/11] Fixed syntax on build.yaml

---
 .github/workflows/build.yaml | 23 +++++++++++------------
 1 file changed, 11 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index e21bdcc..795dc5a 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -19,7 +19,7 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    
+
     - uses: conda-incubator/setup-miniconda@v2
       with:
         miniconda-version: "latest"
@@ -31,24 +31,23 @@ jobs:
         miniforge-variant: Mambaforge
 
     - name: Install uv
-       uses: astral-sh/setup-uv@v4
+      uses: astral-sh/setup-uv@v4
 
     - name: Set up Python
-            run: uv python install
+      run: uv python install
 
-          - name: Install the project
-            run: uv sync --all-extras --dev
+    - name: Install the project
+      run: uv sync --all-extras --dev
 
-          - name: Run tests
-            # For example, using `pytest`
-            run: uv run pytest tests
+    - name: Run tests
+      # For example, using `pytest`
+      run: uv run pytest tests
 
-         - name: Build wheel
-            run: uv build --wheel
+    - name: Build wheel
+      run: uv build --wheel
 
     - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
+      run: # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # 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

From d65a57b831a59c9fd0bd942685f3ccb5d418153e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Flavio=20Code=C3=A7o=20Coelho?= <fccoelho@gmail.com>
Date: Mon, 2 Dec 2024 10:56:51 -0300
Subject: [PATCH 07/11] updated minconda version

---
 .github/workflows/build.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index 795dc5a..d9b05b9 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -20,7 +20,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniconda-version: "latest"
         mamba-version: "*"

From ca5923587bb903832bec57f3748fb2e60dcaa291 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Flavio=20Code=C3=A7o=20Coelho?= <fccoelho@gmail.com>
Date: Mon, 2 Dec 2024 11:02:29 -0300
Subject: [PATCH 08/11] added uv to conda dependencies

---
 conda/dev.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conda/dev.yaml b/conda/dev.yaml
index 172bb93..857535d 100644
--- a/conda/dev.yaml
+++ b/conda/dev.yaml
@@ -6,4 +6,4 @@ dependencies:
   - cffi
   - gcc
   - pip
-  - poetry
+  - uv

From cf8f6da82fe1cfc7e35193ece6a525747b608429 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fl=C3=A1vio=20Code=C3=A7o=20Coelho?= <fccoelho@gmail.com>
Date: Tue, 3 Dec 2024 08:09:57 -0300
Subject: [PATCH 09/11] fixed syntax of build.yaml

---
 .github/workflows/build.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index d9b05b9..56a2d53 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -47,7 +47,8 @@ jobs:
       run: uv build --wheel
 
     - name: Lint with flake8
-      run: # stop the build if there are Python syntax errors or undefined names
+      run:
+        # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # 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

From d58be8a4dbb20dffd74638ba2cb83e71eb384c63 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fl=C3=A1vio=20Code=C3=A7o=20Coelho?= <fccoelho@gmail.com>
Date: Tue, 3 Dec 2024 11:20:43 -0300
Subject: [PATCH 10/11] fixed syntax of build.yaml and verrsion number

---
 .github/workflows/build.yaml | 2 +-
 pyproject.toml               | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index 56a2d53..5ee24f6 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -47,7 +47,7 @@ jobs:
       run: uv build --wheel
 
     - name: Lint with flake8
-      run:
+      run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
diff --git a/pyproject.toml b/pyproject.toml
index b4f718b..93d8bee 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,7 +13,7 @@ dependencies = [
     "setuptools>=75.6.0",
 ]
 name = "pyreaddbc"
-version = "1.2.0"
+version = "1.1.0"
 description = "pyreaddbc package"
 readme = "README.md"
 classifiers = [

From d28ddf3c87e6b54056968e9009087cb3b46be4bd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fl=C3=A1vio=20Code=C3=A7o=20Coelho?= <fccoelho@gmail.com>
Date: Tue, 3 Dec 2024 11:24:53 -0300
Subject: [PATCH 11/11] minor adjustments

---
 conda/dev.yaml | 1 +
 pyproject.toml | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/conda/dev.yaml b/conda/dev.yaml
index 857535d..dc9515a 100644
--- a/conda/dev.yaml
+++ b/conda/dev.yaml
@@ -7,3 +7,4 @@ dependencies:
   - gcc
   - pip
   - uv
+  - poetry
diff --git a/pyproject.toml b/pyproject.toml
index 93d8bee..f55cc8e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,7 +13,7 @@ dependencies = [
     "setuptools>=75.6.0",
 ]
 name = "pyreaddbc"
-version = "1.1.0"
+version = "1.1.0"   # changed by semantic-release
 description = "pyreaddbc package"
 readme = "README.md"
 classifiers = [