0.15

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.14.0
+current_version = 0.15.0
 commit = True
 tag = True
 message = version: {current_version} → {new_version}

.github/workflows/docs.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - main
+      - dev
 
 jobs:
   docs:
@@ -14,6 +15,6 @@ jobs:
       - uses: actions/setup-python@v5
       - run: |
           pip install uv
-          uv sync --only-group docs
+          uv sync --group=docs
       - run: |
           uv run mkdocs gh-deploy --force

.github/workflows/pypi.yml

@@ -13,8 +13,9 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
       - run: |
-          pip install build
-          python -m build
+          pip install uv
+      - run: |
+          uv build
       - uses: pypa/gh-action-pypi-publish@release/v1
         with:
           skip-existing: true

.github/workflows/test.yml

@@ -10,14 +10,29 @@
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest] # macos-latest
-        python-version: [3.9, 3.13]
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
       - run: |
-          pip install tox
+          pip install uv
+          uv sync --group=test
       - run: |
-          tox
+          uv run tox
+
+  codecov:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - run: |
+          pip install uv
+          uv sync --group=test
+      - run: |
+          uv run pytest --cov=datatools --cov-report=term-missing --cov-report=xml:coverage.xml
+      - uses: codecov/codecov-action@v4
+        with:
+          files: coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true

.gitignore

@@ -14,4 +14,9 @@ build
 site
 _archive
 __pycache__
-*.lock
+.pytest_cache
+coverage.xml
+.coverage
+htmlcov
+.snakemake
+.ruff_cache

.pre-commit-config.yaml

@@ -1,25 +1,24 @@
-exclude: ^.*(.min.js|.min.css)$
+exclude: ^$
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
-      - id: check-yaml
+      - id: check-case-conflict # checks for files that would conflict in case-insensitive filesystems.
+      - id: check-merge-conflict # checks for files that contain merge conflict strings.
+      - id: check-yaml # checks yaml files for parseable syntax.
         args: ["--unsafe"] # because of tags in mkdocs.yml
-      - id: end-of-file-fixer
-      - id: trailing-whitespace
-  - repo: https://github.com/psf/black
-    rev: 25.1.0
+      - id: detect-private-key # detects the presence of private keys.
+      - id: end-of-file-fixer # ensures that a file is either empty, or ends with one newline.
+      - id: fix-byte-order-marker # removes utf-8 byte order marker.
+      - id: mixed-line-ending # replaces or checks mixed line ending.
+      - id: requirements-txt-fixer # sorts entries in requirements.txt.
+      - id: trailing-whitespace # trims trailing whitespace.
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.9
     hooks:
-      - id: black
-  - repo: https://github.com/pycqa/isort
-    rev: 6.0.1
-    hooks:
-      - id: isort
-        args: ["--profile", "black", "--filter-files"]
-  - repo: https://github.com/pycqa/flake8
-    rev: 7.3.0
-    hooks:
-      - id: flake8
-        additional_dependencies:
-          - flake8-black>=0.1.1
-        args: ["--max-line-length=88", "--ignore=E20,W503,E704"] # black compatible
+      # Run the linter.
+      - id: ruff-check
+        args: [--fix]
+      # Run the formatter.
+      - id: ruff-format

.ruff.toml

@@ -0,0 +1,51 @@
+
+line-length = 88
+exclude = ["**/migrations/*.py"]
+
+[format]
+quote-style = "double"
+indent-style = "space"
+skip-magic-trailing-comma = false
+line-ending = "auto"
+
+
+[lint]
+select = [
+  "E",   # pycodestyle
+  "F",   # Pyflakes
+  "UP",  # pyupgrade
+  "B",   # flake8-bugbear: opinionated bug & design warnings
+  "SIM", # flake8-simplify
+  "I",   # isort: imports
+  "S",   # flake8-bandit: Security issues
+  "A",   # flake8-builtins
+  "C4",  # flake8-comprehensions
+  "D",   # pydocstyle
+]
+ignore = [
+  "B017", # assert-raises-exception
+  "D105", # Missing docstring in magic method
+  "D107", # undocumented-public-init
+  "D202", # blank-line-after-function
+  "D203", # incorrect-blank-line-before-class
+  "D211", # blank-line-before-class
+  "D213", # multi-line-summary-second-line
+  "D400", # First line should end with a period
+  "D401", # non-imperative-mood
+  "D403", # first-word-uncapitalized
+  "D415", # missing-terminal-punctuation
+  "D412", # otherwise docstring tests will be badly formatted - we need empty line
+  #"S101", # assert
+  "S113", # request-without-timeout
+  "S310", # suspicious-url-open-usage
+  "S603", # subprocess-without-shell-equals-true
+  #"S608", # hardcoded-sql-expression
+]
+
+
+[lint.isort]
+combine-as-imports = true
+force-sort-within-sections = true
+
+[lint.pydocstyle]
+ignore-decorators = ["abc.abstractmethod"]

LICENSE

@@ -0,0 +1,121 @@
+Creative Commons Legal Code
+
+CC0 1.0 Universal
+
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+    LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN
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+    REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS
+    PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM
+    THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED
+    HEREUNDER.
+
+Statement of Purpose
+
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README.md

@@ -1,5 +1,13 @@
 # README
 
+[![github](https://img.shields.io/badge/GitHub-181717?style=flat&logo=github&logoColor=white)](https://github.com/wingechr/datatools)
+[![docs](https://img.shields.io/badge/docs-GitHub%20Pages-blue?style=?style=flat&logo=readthedocs&logoColor=white)](https://wingechr.github.io/datatools/)
+[![pypi](https://img.shields.io/pypi/v/wingechr-datatools.svg?style=flat&logo=python&logoColor=white)](https://pypi.org/project/wingechr-datatools)
+[![test](https://github.com/wingechr/datatools/actions/workflows/test.yml/badge.svg)](https://github.com/wingechr/datatools/actions/workflows/test.yml)
+[![snyk](https://snyk.io/test/github/wingechr/datatools/badge.svg)](https://snyk.io/test/github/wingechr/datatools)
+[![codecov](https://codecov.io/gh/wingechr/datatools/branch/dev/graph/badge.svg)](https://codecov.io/gh/wingechr/datatools)
+[![license](https://img.shields.io/badge/License-CC0%201.0-lightgrey?style=flat&logo=creativecommons&logoColor=white)](https://github.com/wingechr/datatools/blob/dev/LICENSE)
+
 ## Installation
 
 `pip install wingechr-datatools`

datatools/__init__.py

@@ -1,15 +1,6 @@
-__version__ = "0.14.0"
+"""data processing tools."""
 
-from datatools import utils
-from datatools.converter import Converter
-from datatools.process import Function
-from datatools.storage import Metadata, Resource, Storage
+__version__ = "0.15.0"
+__all__ = ["FileDataStorage"]
 
-__all__ = [
-    "Storage",
-    "Resource",
-    "Metadata",
-    "Function",
-    "Converter",
-    "utils",
-]
+from datatools.storage.file import FileDataStorage

datatools/__main__.py

@@ -0,0 +1,42 @@
+"""datatools cmd entry point."""
+
+import logging
+
+import click
+import coloredlogs
+
+from datatools import __version__
+from datatools.storage.__main__ import main as storage_main
+from datatools.utils import wrap_exception
+
+LOGLEVELS_COLORS = {
+    "debug": "blue",
+    "info": "green",
+    "warning": "yellow",
+    "error": "red",
+}
+
+
+@click.group()
+# @click.pass_context
+@click.version_option(version=__version__)
+@click.option(
+    "--loglevel", "-l", type=click.Choice(LOGLEVELS_COLORS.keys()), default="info"
+)
+def main(loglevel: str) -> None:
+    """TODO"""
+    coloredlogs.install(
+        level=getattr(logging, loglevel.upper()),
+        fmt="[%(asctime)s %(levelname)7s] %(message)s",
+        datefmt="%Y-%m-%d %H:%M:%S",
+        field_styles={k: {"color": "white"} for k in ["asctime", "levelname"]},
+        level_styles={k: {"color": v} for k, v in LOGLEVELS_COLORS.items()},
+    )
+    logging.debug("loglevel: %s", loglevel)
+
+
+main.add_command(storage_main, name="storage")
+
+
+if __name__ == "__main__":
+    wrap_exception(main)