Minor changes and refinements

.github/workflows/python-app.yml

@@ -26,10 +26,9 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
+        python -m pip install flake8 pytest build
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip install poetry
-        poetry build
+        python -m build
         pip install dist/*.whl
     - name: Lint with flake8
       run: |
@@ -39,4 +38,4 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        poetry run pytest
+        pytest

.github/workflows/python-package.yml

@@ -27,10 +27,9 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
+        python -m pip install flake8 pytest build
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip install poetry
-        poetry build
+        python -m build
         pip install dist/*.whl
     - name: Lint with flake8
       run: |

.gitignore

@@ -169,6 +169,9 @@ cython_debug/
 .qodo
 /tests/test_data/RD139_Narrow_UPS1_0_1fmol_inj1.mzML
 
+# macOS metadata files
+.DS_Store
+
 # DIA-NN config file generated by tests
 diann_config.cfg
 

pyproject.toml

@@ -1,13 +1,13 @@
-[tool.poetry]
+[project]
 name = "quantms-utils"
+dynamic = ["version"]
 description = "Python scripts and helpers for the quantMS workflow"
 readme = "README.md"
 license = "MIT"
-version = "0.0.28"
 authors = [
-    "Yasset Perez-Riverol <ypriverol@gmail.com>",
-    "Dai Chengxin <chengxin2024@126.com>",
-    "Julianus Pfeuffer <jule.pf@gmail.com>"
+    { name = "Yasset Perez-Riverol", email = "ypriverol@gmail.com" },
+    { name = "Dai Chengxin", email = "chengxin2024@126.com" },
+    { name = "Julianus Pfeuffer", email = "jule.pf@gmail.com" }
 ]
 keywords = [
     "quantms",
@@ -24,26 +24,22 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Development Status :: 5 - Production/Stable"
 ]
-packages = [
-    { include = "quantmsutils" }
+dependencies = [
+    "click",
+    "sdrf-pipelines>=0.1.2",
+    "pyopenms>=3.3.0",
+    "pandas",
+    "pyarrow>=16.1.0",
+    "scipy",
 ]
 
-[tool.poetry.dependencies]
-python = "*"
-click = "*"
-sdrf-pipelines = ">=0.1.2"
-pyopenms = ">=3.3.0"
-pandas = "*"
-pyarrow = ">=16.1.0"
-scipy = "*"
-
-[tool.poetry.urls]
+[project.urls]
 GitHub = "https://github.com/bigbio/quantms-utils"
 PyPi = "https://pypi.org/project/quantms-utils/"
 Quantms = "https://quantms.org"
 LICENSE = "https://github.com/bigbio/quantms-utils/blob/main/LICENSE"
 
-[tool.poetry.scripts]
+[project.scripts]
 quantmsutilsc = "quantmsutils.quantmsutilsc:main"
 
 [tool.isort]
@@ -54,5 +50,14 @@ line-length = 99
 target-version = ["py39"]
 
 [build-system]
-requires = ["poetry-core>=1.2.0"]
-build-backend = "poetry.core.masonry.api"
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.version.raw-options]
+local_scheme = "no-local-version"
+
+[tool.hatch.build.targets.wheel]
+packages = ["quantmsutils"]