From 9ea306ecdb85648b7774fdbc175518e40574313b Mon Sep 17 00:00:00 2001 From: Miles Smith Date: Sun, 28 Apr 2024 00:08:52 -0500 Subject: [PATCH 1/2] switch from poetry to pdm --- .gitignore | 1 + CHANGELOG.md | 6 +++ pyproject.toml | 106 +++++++++++++++++++++++++------------------------ 3 files changed, 62 insertions(+), 51 deletions(-) diff --git a/.gitignore b/.gitignore index afc91b0..6654b0d 100644 --- a/.gitignore +++ b/.gitignore @@ -122,3 +122,4 @@ cython_debug/ *.pickle test.py +.pdm-python diff --git a/CHANGELOG.md b/CHANGELOG.md index 3337ed7..f0560e5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,11 @@ Changelog +# [0.41.0] + +## Changed + +- Replaced use of poetry as package manager with pdm + # [0.40.0] ## Changed diff --git a/pyproject.toml b/pyproject.toml index 66c7992..3b679ed 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,61 +1,65 @@ -[tool.poetry] +[build-system] +requires = ["pdm-backend"] +build-backend = "pdm.backend" + +[project] name = "velocyto" -version = "0.31.0" +version = "0.41.0" +authors = [ + {name = "Linnarsson Lab", email = "sten.linnarsson@ki.se"}, +] description = "RNA velocity analysis for single cell RNA-seq data" -authors = ["Linnarsson Lab "] -license = "BSD-2-Clause" readme = "README.md" -homepage = "https://github.com/velocyto-team/velocyto.py" -repository = "https://github.com/velocyto-team/velocyto.py" -documentation = "http://velocyto.org/velocyto.py/index.html" -keywords = ["RNAseq", "singlecell", "bioinformatics", "transcriptomics"] -include = [ - # C extensions must be included in the wheel distributions - { path = "src/velocyto/*.so", format = "wheel" }, - { path = "src/velocyto/*.csv", format = "wheel" }, - { path = "src/velocyto/*.pyx", format = "wheel" }, - { path = "src/velocyto/*.c", format = "wheel" }, - { path = "barcodes/*.gz", format = ["sdist", "wheel"] } +keywords = [ + "RNAseq", + "singlecell", + "bioinformatics", + "transcriptomics", +] +license = {text = "BSD-2-Clause"} +requires-python = "<3.11,>=3.10" +dependencies = [ + "numba>=0.57.1", + "numpy<1.25,>=1.21", + "scipy>=1.13", + "cython>=3.0", + "matplotlib<4.0,>=3.8", + "h5py<4.0.0,>=3.10.0", + "loompy<4.0.0,>=3.0.7", + "pysam<1.0.0,>=0.21.0", + "pandas>=2.0.3", + "scikit-learn<2.0.0,>=1.3.0", + "rpy2<4.0.0,>=3.5.13", + "typer<1.0.0,>=0.9.0", + "loguru<1.0.0,>=0.7.0", + "rich<14.0.0,>=13.5.2", + "tqdm<5.0.0,>=4.65.0", + "anndata<1.0.0,>=0.9.2", ] -[tool.poetry.dependencies] -python = ">=3.10,<3.11" -numba = "^0.57.1" -numpy = ">=1.21,<1.25" -scipy = ">=1.12" -cython = "^3.0" -matplotlib = "^3.8" -h5py = "^3.10.0" -loompy = "^3.0.7" -pysam = "^0.21.0" -pandas = "^2.0.3" -scikit-learn = "^1.3.0" -rpy2 = "^3.5.13" -typer = "^0.9.0" -loguru = "^0.7.0" -rich = "^13.5.2" -tqdm = "^4.65.0" -anndata = "^0.9.2" - -[tool.poetry.extras] +[project.optional-dependencies] R = ["rpy2"] -[tool.poetry.group.dev.dependencies] -mypy = "^1.4.1" -ipython = "^8.14.0" -nox = "^2023.4.22" -nox-poetry = "^1.0.3" -memray = "^1.9.1" -memory-profiler = "^0.61.0" -ruff = "^0.3.5" - -[build-system] -requires = ["poetry-core>=1.0.0", "cython", "numpy", "toml", "setuptools"] -build-backend = "poetry.core.masonry.api" +[project.urls] +homepage = "https://github.com/velocyto-team/velocyto.py" +repository = "https://github.com/velocyto-team/velocyto.py" +documentation = "http://velocyto.org/velocyto.py/index.html" -[tool.poetry.scripts] +[project.scripts] velocyto = "velocyto.commands.cli:velocyto" -[tool.poetry.build] -generate-setup-file = false -script = "build.py" + +[tool.pdm] +[tool.pdm.dev-dependencies] +dev = [ + "mypy<2.0.0,>=1.4.1", + "ipython<9.0.0,>=8.14.0", + "nox<2024.0.0,>=2023.4.22", + "nox-poetry<2.0.0,>=1.0.3", + "memray<2.0.0,>=1.9.1", + "memory-profiler<1.0.0,>=0.61.0", + "ruff<1.0.0,>=0.3.5", +] + +[tool.pdm.build] +includes = ["src/velocyto/*.so", "src/velocyto/*.csv", "src/velocyto/*.pyx", "src/velocyto/*.c"] From 674e02bef4b360fc29890a85bb04b3cb5fb9d600 Mon Sep 17 00:00:00 2001 From: Miles Smith 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