Merge branch 'master' into fix_setting_copy

Author: observingClouds

.github/workflows/pypi.yaml

@@ -13,10 +13,10 @@ jobs:
   packages:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: "3.x"
 

.github/workflows/test.yml

@@ -7,31 +7,45 @@ on:
     tags: "*"
 
 jobs:
-  test:
+  linting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
       - name: Install dependencies with pip
         run: |
           python -m pip install -e .[dev]
 
-      - run: isort --recursive --diff .
-      - run: black --check --diff .
-      - run: flake8
-      - run: mypy
-      - run: pytest --cov --cov-fail-under=50
+      - uses: pre-commit/action@v3.0.1
+  test_converter:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies with pip
+        run: |
+          python -m pip install -e .[dev]
+
+      - name: Run conversion tests
+        run: pytest
+      - name: Run coverage tests
+        run: pytest --cov --cov-fail-under=50
   test_plotting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Setup Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
       - name: Install dependencies with pip

.github/workflows/validate_metadata.yml

@@ -6,7 +6,7 @@ jobs:
   validate:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Validate JSON
         uses: walbo/validate-json@v1.1.0
         with:

.pre-commit-config.yaml

@@ -1,48 +1,30 @@
 # See https://pre-commit.com/ for usage and config
 repos:
 - repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+  rev: 5.13.2
   hooks:
   - id: isort
     name: isort
     entry: isort
     types: [python]
 - repo: https://github.com/psf/black
-  rev: 23.3.0
+  rev: 24.8.0
   hooks:
   - id: black
     name: black
     entry: black
     types: [python]
-- repo: https://github.com/PyCQA/flake8
-  rev: 6.0.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.6.4
   hooks:
-  - id: flake8
-    name: flake8
-    entry: flake8
-    types: [python]
-    exclude: setup.py
+  - id: ruff
+    args: [ --fix ]
+  - id: ruff-format
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.1.1
+  rev: v1.11.2
   hooks:
   - id: mypy
     name: mypy
     entry: mypy
     types: [python]
     require_serial: true
-- repo: local
-  hooks:
-  - id: pytest
-    name: pytest
-    language: system
-    entry: pytest
-    types: [python]
-    pass_filenames: false
-
-  - id: pytest-cov
-    name: pytest
-    language: system
-    stages: [push]
-    entry: pytest --cov --cov-fail-under=50
-    types: [python]
-    pass_filenames: false

CHANGELOG.rst

@@ -7,6 +7,7 @@ unreleased
 
 * Add zenodo release information (:pr:`24`) `Hauke Schulz`_.
 * Fix warning about seeting copy of a slice of a DataFrame (:pr:`28`) `Marius Rixen`_.
+* Update infrastructure to use pyproject.toml with pdm and ruff (:pr:`29`) `Hauke Schulz`_.
 
 
 0.0.5 (2023-10-19)

pyproject.toml

@@ -0,0 +1,90 @@
+[project]
+name = "pysonde"
+dynamic = ["version"]
+description = "Post-processing tool for atmospheric sounding data"
+authors = [
+    {name = "Hauke Schulz", email = "43613877+observingClouds@users.noreply.github.com"},
+]
+dependencies = [
+    "cartopy",
+    "coverage",
+    "bottleneck",
+    "dask",
+    "metpy",
+    "netCDF4",
+    "numpy",
+    "omegaconf",
+    "pandas",
+    "Pint",
+    "Pint-Pandas",
+    "pint-xarray",
+    "PyYAML",
+    "regex",
+    "tqdm",
+    "xarray",
+]
+requires-python = ">=3.9"
+readme = "README.md"
+license = {text = "MIT"}
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Environment :: Console",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.9",
+]
+
+[project.urls]
+Homepage = "https://github.com/observingClouds/pysonde"
+
+[project.optional-dependencies]
+dev = [
+    "black",
+    "flake8",
+    "isort",
+    "mock",
+    "mypy",
+    "pre-commit",
+    "pylint",
+    "pytest",
+    "pytest-cov",
+    "pytest-lazy-fixture",
+    "yapf",
+]
+
+[project.scripts]
+sounding_converter = "pysonde.pysonde:main"
+sounding_visualize = "pysonde.make_quicklooks_rs41:main"
+
+[build-system]
+requires = ["pdm-backend"]
+build-backend = "pdm.backend"
+
+[tool.pdm.version]
+source = "scm"
+
+[tool.pdm]
+distribution = true
+
+[tool.pdm.scripts]
+post_install = "pre-commit install"
+
+[tool.mypy]
+ignore_missing_imports = true
+
+[tool.ruff]
+line-length = 88
+
+[tool.ruff.lint.mccabe]
+max-complexity = 18
+
+[tool.isort]
+profile = "black"
+multi_line_output = 3
+include_trailing_comma = true
+force_grid_wrap = 0
+use_parentheses = true
+line_length = 88

pysonde/__init__.py

@@ -1,10 +0,0 @@
-# Create __version__ attribute from setup.py information
-
-from ._version import get_versions
-
-__import__("pkg_resources").declare_namespace(__name__)
-
-try:
-    __version__ = get_versions()["version"]
-except (ValueError, ImportError):
-    __version__ = "--"

pysonde/_dataset_creator.py

@@ -34,6 +34,7 @@
     ds = create_dataset(cfg)
 
 """
+
 import logging
 
 import _helpers as h

pysonde/_helpers.py

@@ -280,7 +280,7 @@ def set_additional_var_attributes(ds, meta_data_dict, variables):
         try:
             meta_data_var = meta_data_dict[var_in]["attrs"]
             for key, value in meta_data_var.items():
-                if key not in ["_FillValue", "dtype"] and not ("time" in var_out):
+                if key not in ["_FillValue", "dtype"] and "time" not in var_out:
                     ds[var_out].attrs[key] = value
                 elif (key not in ["_FillValue", "dtype", "units"]) and (
                     "time" in var_out

pysonde/make_skewT.py

@@ -3,6 +3,7 @@
 """
 Plot skew-T diagram of converted soundings
 """
+
 import argparse
 import logging
 

pysonde/meteorology_helpers.py

@@ -239,7 +239,7 @@ def set_additional_var_attributes(ds, meta_data_dict):
         except KeyError:
             continue
         for key, value in meta_data_var.items():
-            if key not in ["_FillValue", "dtype"] and not ("time" in var):
+            if key not in ["_FillValue", "dtype"] and "time" not in var:
                 ds[var].attrs[key] = value
             elif (key not in ["_FillValue", "dtype", "units"]) and ("time" in var):
                 ds[var].attrs[key] = value

pysonde/pysonde.py

@@ -5,6 +5,7 @@
 Script to convert sounding files from different sources
 to netCDF
 """
+
 import argparse
 import logging
 import sys

pysonde/readers/reader_helpers.py

@@ -1,5 +1,5 @@
-"""Helper functions for the different readers
-"""
+"""Helper functions for the different readers"""
+
 import glob
 import os
 import shutil

pysonde/readers/readers.py

@@ -1,5 +1,5 @@
-"""Readers for different sounding formats
-"""
+"""Readers for different sounding formats"""
+
 import datetime as dt
 import logging
 import os

pysonde/sounding.py

@@ -1,5 +1,5 @@
-"""Sounding class
-"""
+"""Sounding class"""
+
 import copy
 import logging
 import os

pysonde/thermodynamics.py

@@ -1,6 +1,7 @@
 """
 Thermodynamic functions
 """
+
 import metpy
 import metpy.calc as mpcalc
 import numpy as np