Merge pull request #11 from SteveGrehl/dev

Add Python 3.12 and Python 3.13 to build

.github/workflows/python-package-conda.yml

@@ -13,19 +13,19 @@ jobs:
     runs-on:  ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-latest, ubuntu-latest, windows-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        os: [macos-12, ubuntu-latest, windows-latest]
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
         architecture: ['x64']
 
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
         architecture: ${{ matrix.architecture }}
     - name: setup-conda
-      uses: s-weigand/setup-conda@v1.1.1
+      uses: s-weigand/setup-conda@v1
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory

conda_build_config.yaml

@@ -1,6 +1,10 @@
+---
+# Status of Python versions: https://devguide.python.org/versions/
+# Also change github workflow in python-package-conda.yml
 python_version:
-  - 3.7
   - 3.8
   - 3.9
   - 3.10
-  - 3.11
+  - 3.11
+  - 3.12
+  - 3.13

ruff.toml

@@ -0,0 +1,80 @@
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".ipynb_checkpoints",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pyenv",
+    ".pytest_cache",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    ".vscode",
+    "__pypackages__",
+    "__pycache__",
+    "_build",
+    "assets",
+    "buck-out",
+    "build",
+    "dist",
+    "docs",
+    "node_modules",
+    "site-packages",
+    "venv",
+]
+
+# Same as Black.
+line-length = 88
+indent-width = 4
+
+# Assume Python 3.9
+target-version = "py39"
+
+[lint]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
+# McCabe complexity (`C901`) by default.
+select = ["E4", "E7", "E9", "F"]
+ignore = []
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+# Enable auto-formatting of code examples in docstrings. Markdown,
+# reStructuredText code/literal blocks and doctests are all supported.
+#
+# This is currently disabled by default, but it is planned for this
+# to be opt-out in the future.
+docstring-code-format = false
+
+# Set the line length limit used when formatting code snippets in
+# docstrings.
+#
+# This only has an effect when the `docstring-code-format` setting is
+# enabled.
+docstring-code-line-length = "dynamic"

scripts/example2.py

@@ -1,16 +1,14 @@
 import xlum
 
 try:
-    import matplotlib
     from matplotlib import pyplot as plt
 except ModuleNotFoundError:
     import pip
     pip.main(["install", "--user", "matplotlib"])
 finally:
-    import matplotlib
     from matplotlib import pyplot as plt
 try:
-    import tkinter
+    from tkinter.filedialog import askopenfilename
 except ModuleNotFoundError:
     import pip
     pip.main(["install", "--user", "tkinter"])

src/xlum/__init__.py

@@ -1,4 +1,6 @@
 __version__ = "0.0.8"
 
 # make from_xlum available in package namespace
-from .importer import from_xlum
+# re-export avoids code scaning tools to mark it as unused
+# see: https://docs.astral.sh/ruff/rules/unused-import/
+from .importer import from_xlum as from_xlum

src/xlum/data/classes.py

@@ -1,14 +1,15 @@
 import base64
-from dataclasses import dataclass, asdict
+import logging
+import re
+from dataclasses import asdict, dataclass, field
 from datetime import datetime
+from functools import cached_property
 from typing import Dict, List
-import re
-from lxml import etree
+
 import pandas as pd
-from functools import cached_property
-import logging
+from lxml import etree
 
-from xlum.data.enumerations import CurveType, RecordType, State, SampleCondition
+from xlum.data.enumerations import CurveType, RecordType, SampleCondition, State
 
 
 class Xlum_DataFrame_Support(object):
@@ -110,25 +111,26 @@ def from_attributes(cls, dct: Dict) -> "XLum_Meta":
             else:
                 attr["state"] = State[dct["state"].upper()]
         except KeyError as ex:
-            logging.warning(f"KeyError: got {ex} expected one of {[s.name for s in State]}, using {State.UNKNOWN.name}")
+            logging.warning(
+                f"KeyError: got {ex} expected one of {[s.name for s in State]}, using {State.UNKNOWN.name}"
+            )
             attr["state"] = State.UNKNOWN.name
 
         return XLum_Meta(**attr)
 
 
 @dataclass
 class Curve(Xlum_DataFrame_Support):
-
     lstValues: List = lambda: []  # internal list in the curve node
 
     component: str = "NA"
     startDate: datetime = datetime(2013, 1, 1, 3, 42, 42, 42)
     curveType: CurveType = CurveType.UNKNOWN
     duration: float = 0.0
     offset: float = 0.0
-    xValues: List[
-        int
-    ] = lambda: []  # see: https://stackoverflow.com/questions/52063759/passing-default-list-argument-to-dataclasses
+    xValues: List[int] = (
+        lambda: []
+    )  # see: https://stackoverflow.com/questions/52063759/passing-default-list-argument-to-dataclasses
     yValues: List[int] = lambda: []
     tValues: List[int] = lambda: []
     xLabel: str = "NA"
@@ -141,7 +143,7 @@ class Curve(Xlum_DataFrame_Support):
     vUnit: str = "NA"
     detectionWindow: str = "NA"
     filter: str = "NA"
-    _meta: XLum_Meta = XLum_Meta(comment="empty curve")
+    _meta: XLum_Meta = field(default_factory=lambda: XLum_Meta(comment="empty curve"))
 
     @classmethod
     def from_element(cls, element: etree.Element) -> "Curve":
@@ -193,7 +195,9 @@ def from_element(cls, element: etree.Element) -> "Curve":
                 attr[k] = []
         # check if values are base64 encoded
         strValues = element.text
-        b64_pattern = re.compile('^([A-Za-z0-9+/]{4})*([A-Za-z0-9+/]{3}=|[A-Za-z0-9+/]{2}==)?$')
+        b64_pattern = re.compile(
+            "^([A-Za-z0-9+/]{4})*([A-Za-z0-9+/]{3}=|[A-Za-z0-9+/]{2}==)?$"
+        )
         if re.fullmatch(b64_pattern, strValues):
             strValues = base64.b64decode(strValues)
         lstStrValues = re.findall(r"[\d]+[.,\d]+|[\d]*[.][\d]+|[\d]+", strValues)
@@ -244,14 +248,13 @@ def df(self) -> pd.DataFrame:
 
 @dataclass
 class Record(Xlum_DataFrame_Support):
-
     lstCurves: List[Curve] = lambda: []
 
     recordType: RecordType = RecordType.UNKNOWN
     sequenceStepNumber: int = 0
     sampleCondition: SampleCondition = SampleCondition.UNKNOWN
 
-    _meta: XLum_Meta = XLum_Meta(comment="empty record")
+    _meta: XLum_Meta = field(default_factory=lambda: XLum_Meta(comment="empty record"))
 
     @classmethod
     def from_element(cls, element: etree.Element) -> "Record":
@@ -294,7 +297,6 @@ def from_element(cls, element: etree.Element) -> "Record":
 
 @dataclass
 class Sequence(Xlum_DataFrame_Support):
-
     lstRecords: List[Record] = lambda: []
 
     fileName: str = "NA"
@@ -303,7 +305,7 @@ class Sequence(Xlum_DataFrame_Support):
     readerSN: str = "NA"
     readerFW: str = "NA"
 
-    _meta: XLum_Meta = XLum_Meta(comment="empty sequence")
+    _meta: XLum_Meta = field(default_factory=lambda: XLum_Meta(comment="empty sequence"))
 
     @classmethod
     def from_element(cls, element: etree.Element) -> "Sequence":
@@ -338,7 +340,6 @@ def from_element(cls, element: etree.Element) -> "Sequence":
 
 @dataclass
 class Sample(Xlum_DataFrame_Support):
-
     lstSequences: List[Sequence] = lambda: []
 
     name: str = "NA"
@@ -348,7 +349,7 @@ class Sample(Xlum_DataFrame_Support):
     altitude: float = -1000.0
     doi: str = "NA"
 
-    _meta: XLum_Meta = XLum_Meta(comment="empty sample")
+    _meta: XLum_Meta = field(default_factory=lambda: XLum_Meta(comment="empty sample"))
 
     @classmethod
     def from_element(cls, element: etree.Element) -> "Sample":
@@ -388,7 +389,6 @@ def from_element(cls, element: etree.Element) -> "Sample":
 
 @dataclass
 class XlumMeta(Xlum_DataFrame_Support):
-
     lstSamples: List[Sample] = lambda: []
 
     formatVersion: str = "NA"

src/xlum/data/enumerations.py

@@ -1,7 +1,5 @@
-from asyncio.base_futures import _FINISHED
 import enum
 
-from pkg_resources import UnknownExtra
 
 class CurveType(enum.Enum):
     NA=-2