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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,11 +1,7 @@ | ||
| repos: | ||
| - repo: https://github.com/pre-commit/pre-commit-hooks | ||
| rev: v4.2.0 | ||
| hooks: | ||
| - id: check-yaml | ||
| - id: end-of-file-fixer | ||
| - id: trailing-whitespace | ||
| - repo: https://github.com/psf/black | ||
| rev: 22.3.0 | ||
| hooks: | ||
| - id: black | ||
| - repo: https://github.com/astral-sh/ruff-pre-commit | ||
| rev: v0.4.4 | ||
| hooks: | ||
| - id: ruff | ||
| args: [ --fix ] | ||
| - id: ruff-format |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,20 +1,21 @@ | ||
| [build-system] | ||
| requires = [ | ||
| "setuptools >= 64", | ||
| "wheel >= 0.37.1", | ||
| ] | ||
| build-backend = "setuptools.build_meta" | ||
| requires = ["flit_core >=3.2,<4"] | ||
| build-backend = "flit_core.buildapi" | ||
|
|
||
| [project] | ||
| name = "primaschema" | ||
| description = "A toolkit for primer scheme defintions" | ||
| authors = [ | ||
| {name = "Bede Constantinides", email="[email protected]"}, | ||
| {name = "Peter van Heusden", email="[email protected]"} | ||
| ] | ||
| dynamic = ["version", "description"] | ||
| readme = "README.md" | ||
| requires-python = ">=3.10" | ||
| requires-python = ">=3.8" | ||
| keywords = ["genomics"] | ||
| license = {text = "MIT License"} | ||
| classifiers = [ | ||
| "Framework :: Django", | ||
| "Programming Language :: Python :: 3.10", | ||
| "Programming Language :: Python :: 3.12", | ||
| "Environment :: Console", | ||
| "Intended Audience :: Science/Research", | ||
| "License :: OSI Approved :: MIT License", | ||
|
|
@@ -23,21 +24,33 @@ classifiers = [ | |
| "Operating System :: MacOS", | ||
| ] | ||
| dependencies = [ | ||
| "biopython == 1.80", | ||
| "defopt == 6.4.0", | ||
| "pandas >= 1.5.3", | ||
| "pre-commit", | ||
| "pytest", | ||
| "altair>=5.3.0", | ||
| "biopython>=1.80", | ||
| "defopt==6.4.0", | ||
| "httpx>=0.27.0", | ||
| "jsonschema", | ||
| "pyyaml", | ||
| "linkml==1.5.2", | ||
| "linkml", | ||
| "natsort>=8.4.0", | ||
| "pandas>=1.5.3", | ||
| "platformdirs>=4.2.2", | ||
| "pydantic>=2.0.0", | ||
| "pyyaml>=6.0.2", | ||
| "vl-convert-python>=1.6.0" | ||
| ] | ||
| dynamic = ["version"] | ||
|
|
||
| [project.scripts] | ||
| primaschema = "primaschema.cli:main" | ||
|
|
||
| [tool.setuptools.dynamic] | ||
| version = {attr = "primaschema.__version__"} | ||
| [project.urls] | ||
| Home = "https://github.com/pha4ge/primaschema" | ||
|
|
||
| [project.optional-dependencies] | ||
| dev = [ | ||
| "pytest", | ||
| "pre-commit", | ||
| "flit" | ||
| ] | ||
|
|
||
| [tool.flit.external-data] | ||
| directory = "test" | ||
|
|
||
| [tool.setuptools.packages.find] | ||
| where = ["src"] | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,64 @@ | ||
| """Infrastructure for tiled amplicon PCR primer scheme definitions""" | ||
|
|
||
| import logging | ||
| import logging.config | ||
| import os | ||
|
|
||
| from pathlib import Path | ||
|
|
||
| __version__ = "0.2.0" | ||
| from platformdirs import user_data_dir | ||
|
|
||
|
|
||
| __version__ = "1.0.0a0" | ||
|
|
||
|
|
||
| SCHEMES_ARCHIVE_URL = os.environ.get( | ||
| "PRIMASCHEMA_SCHEMES_ARCHIVE_URL", | ||
| "https://github.com/pha4ge/primer-schemes/archive/refs/heads/main.tar.gz", | ||
| ) | ||
| CACHE_DIR = Path( | ||
| os.environ.get("PRIMASCHEMA_CACHE_DIR") or user_data_dir("primaschema", "PHA4GE") | ||
| ) | ||
|
|
||
| PKG_DIR = Path( | ||
| os.environ.get( | ||
| "PRIMASCHEMA_ROOT_PATH", Path(__file__).absolute().parent.parent.parent | ||
| ) | ||
| ) | ||
| SCHEMA_DIR = PKG_DIR / "src" / "primaschema" / "schema" | ||
| MANIFEST_SCHEMA_PATH = SCHEMA_DIR / "manifest.json" | ||
| MANIFEST_HEADER_PATH = SCHEMA_DIR / "manifest-header.yml" | ||
|
|
||
| logging_config = { | ||
| "version": 1, | ||
| "disable_existing_loggers": False, | ||
| "formatters": { | ||
| "default": { | ||
| "format": "%(name)s %(levelname)s: %(message)s", | ||
| }, | ||
| }, | ||
| "handlers": { | ||
| "console": { | ||
| "class": "logging.StreamHandler", | ||
| "formatter": "default", | ||
| "level": "INFO", | ||
| "stream": "ext://sys.stderr", | ||
| }, | ||
| }, | ||
| "root": { | ||
| "handlers": ["console"], | ||
| "level": "INFO", | ||
| }, | ||
| "loggers": { | ||
| "primaschema": { | ||
| "handlers": ["console"], | ||
| "level": "INFO", | ||
| "propagate": False, | ||
| }, | ||
| }, | ||
| } | ||
|
|
||
| logging.config.dictConfig(logging_config) | ||
| logger = logging.getLogger("primaschema") | ||
|
|
||
| # pkg_dir = Path(__file__) | ||
| # data_dir = pkg_dir.parent / "data" | ||
| logger.debug(f"{PKG_DIR=} {SCHEMA_DIR=}") |
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