pixi: First several steps towards.

Author: wwood

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.gitignore

@@ -6,3 +6,7 @@ docker/kingfisher.yml
 site
 build
 kingfisher.egg-info
+
+# pixi environments
+.pixi
+*.egg-info

bin/kingfisher

@@ -1 +1,21 @@
-__version__ = "0.4.1"
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.4.1'
+__version_tuple__ = version_tuple = (0, 4, 1)

kingfisher/version.py

@@ -0,0 +1,38 @@
+[workspace]
+authors = ["Ben Woodcroft <[email protected]>"]
+channels = ["conda-forge","bioconda"]
+name = "kingfisher"
+platforms = ["linux-64"]
+version = "0.1.0"
+
+[tasks]
+
+[dependencies]
+pigz = ">=2.8,<3"
+extern = ">=0.4.1,<0.5"
+curl = ">=8.13.0,<9"
+sra-tools = ">=3.2.1,<4"
+pandas = ">=2.2.3,<3"
+requests = ">=2.32.3,<3"
+aria2 = ">=1.37.0,<2"
+sracat = ">=0.2,<0.3"
+bird_tool_utils_python = ">=0.4.1,<0.5"
+awscli = ">=2.27.20,<3"
+pyarrow = ">=20.0.0,<21"
+tqdm = ">=4.67.1,<5"
+
+[pypi-dependencies]
+kingfisher = {path = ".", editable = true}
+
+[feature.dev.dependencies]
+# Dev/test dependencies only
+pytest = "*"
+ipython = "*"
+pytest-timeout = "*"
+pandoc = "*"
+toml = "*"
+python-build = "*"
+setuptools-scm = "*"
+
+[environments]
+dev = ["dev"]

pixi.lock

@@ -0,0 +1,44 @@
+[build-system]
+requires = ["setuptools>=64", "wheel", "setuptools_scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "kingfisher"
+description = "Download/extract biological FASTA/Q read data and metadata"
+readme = "README.md"
+requires-python = ">=3.7"
+license = "GPL-3.0-or-later"
+authors = [{ name = "Ben Woodcroft" }]
+keywords = ["metagenomics", "bioinformatics"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Programming Language :: Python :: 3"
+]
+dynamic = ["version", "dependencies"]
+
+[project.urls]
+Homepage = "https://github.com/wwood/kingfisher"
+
+[project.scripts]
+kingfisher = "kingfisher.main:main"
+
+[tool.setuptools]
+packages = ["kingfisher"]
+include-package-data = true
+
+[tool.setuptools.package-data]
+kingfisher = ["data/asperaweb_id_dsa.openssh"]
+
+[tool.setuptools.dynamic]
+dependencies = { file = ["admin/requirements.txt"] }
+
+[tool.setuptools_scm]
+version_file = "kingfisher/version.py"
+# Otherwise the push to pypi will fail on GitHub actions, because the version is malformed.
+version_scheme = "only-version"
+local_scheme = "no-local-version"
+
+[tool.setuptools.data-files]
+"." = ["README.md", "LICENCE.txt"]