move from setuptools setup.py -> project.toml

.github/workflows/python-app.yml

@@ -26,8 +26,10 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python -m pip install flake8 pytest
+        pip install poetry
+        poetry build
+        pip install dist/*.whl
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

.github/workflows/python-package.yml

@@ -19,8 +19,10 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python -m pip install flake8 pytest
+        pip install poetry
+        poetry build
+        pip install dist/*.whl
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

.github/workflows/python-publish.yml

@@ -21,7 +21,10 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install build
+        python -m pip install flake8 pytest
+        pip install poetry
+        poetry build
+        pip install dist/*.whl
     - name: Build package
       run: python -m build
     - name: Publish package

README.md

@@ -31,7 +31,7 @@ Install with setup.py:
 ```bash
 $ git clone https://github.com/PRIDE-Archive/pridepy
 $ cd pridepy
-$ python setup.py sdist bdist_wheel 
+$ poetry build
 $ pip install dist/pridepy-{version}.tar.gz
 ```
 

pyproject.toml

@@ -0,0 +1,109 @@
+[tool.poetry]
+name = "pridepy"
+version = "0.0.7"
+description = "Python Client library for PRIDE Rest API"
+authors = [
+    "PRIDE Team <[email protected]>",
+]
+maintainers = [
+    "PRIDE Team <[email protected]>",
+]
+readme = "README.md"
+license = "Apache-2.0"
+keywords = [
+    "PRIDE",
+    "proteomics",
+    "mass-spectrometry",
+    "API",
+    "big data",
+    "bioinformatics",
+    "data science",
+]
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Development Status :: 5 - Production/Stable"
+]
+packages = [
+    { include = "pridepy" }
+]
+include = [
+    "LICENSE",
+    "README.md",
+    "**/*.txt",
+    "**/*.md",
+    "aspera/**/*"
+]
+
+[tool.poetry.dependencies]
+python = "^3.7"
+requests = "^2.31.0"
+ratelimit = "^2.2.1"
+click = "^8.1.7"
+plotly = "^5.18.0"
+tqdm = "^4.66.1"
+boto3 = "^1.34.0"
+botocore = "^1.34.0"
+httpx = "^0.27.0"
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^8.0.0"
+black = "^24.1.0"
+isort = "^5.13.0"
+pytest-cov = "^4.1.0"
+mypy = "^1.8.0"
+
+[tool.poetry.urls]
+PyPI = "https://pypi.org/project/pridepy/"
+PRIDE = "https://www.ebi.ac.uk/pride/archive/"
+Documentation = "https://github.com/PRIDE-Archive/pridepy#readme"
+Repository = "https://github.com/PRIDE-Archive/pridepy"
+License = "https://github.com/PRIDE-Archive/pridepy/LICENSE"
+
+[tool.poetry.scripts]
+pridepy = "pridepy:main"
+
+[tool.black]
+line-length = 99
+target-version = ["py39"]
+include = '\.pyi?$'
+extend-exclude = '''
+# A regex preceded with ^/ will apply only to files and directories
+# in the root of the project.
+^/tests/
+'''
+
+[tool.isort]
+profile = "black"
+multi_line_output = 3
+line_length = 99
+include_trailing_comma = true
+force_grid_wrap = 0
+use_parentheses = true
+ensure_newline_before_comments = true
+
+[tool.mypy]
+python_version = "3.9"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = true
+disallow_incomplete_defs = true
+check_untyped_defs = true
+disallow_untyped_decorators = false
+no_implicit_optional = true
+warn_redundant_casts = true
+warn_unused_ignores = true
+warn_no_return = true
+warn_unreachable = true
+
+[build-system]
+requires = ["poetry-core>=1.2.0"]
+build-backend = "poetry.core.masonry.api"

recipe/meta.yaml

@@ -19,7 +19,7 @@ requirements:
   host:
     - python >=3.9
     - pip
-    - setuptools
+    - poetry-core >=1.2.0
   run:
     - requests~=2.31.0
     - ratelimit~=2.2.1