Add Python 3.11-3.13 support, drop 3.6-3.8 support

.github/workflows/ci.yml

@@ -4,37 +4,33 @@ on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
   schedule:
     - cron: "7 18 * * 0"
 
 jobs:
   build:
-
+    name: unit-test py${{ matrix.python-version }}
     runs-on: ubuntu-latest
 
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+    - name: "Set up Python ${{ matrix.python-version }}"
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-
+    
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip install -e .[test]
+        pip install .[test]
 
     - name: Test with pytest
-      run: |
-        pytest tests
+      run: pytest

CONTRIBUTING.rst

@@ -66,13 +66,7 @@ Ready to contribute? Here's how to set up `seabird` for local development.
 
    a. Using Conda (assuming you already have it installed)
 
-        I. Python 2::
-
-            $ conda create --name seabird python=2
-
-        II. Or, Python 3::
-
-            $ conda create --name seabird python=3
+            $ conda create --name seabird python=3.10
 
         Activate your conda environment, and take advantage of conda::
 

docs/source/install.rst

@@ -1,21 +1,3 @@
-************
-Installation
-************
-
-Requirements
-============
-
-- `Python <http://www.python.org/>`_ 2.7 or 3.X (recommended >=3.5)
-
-- `Numpy <http://www.numpy.org>`_ (>=1.1)
-
-Optional requirement
---------------------
-
-- `netCDF4 <https://pypi.python.org/pypi/netCDF4>`_, if you want to be able to export the data into netCDF files.
-
-- `CoTeDe <http://cotede.castelao.net>`_, if you want to quality control your data with custom or pre-set group of checks.
-
 Installing Seabird
 ==================
 

pyproject.toml

@@ -12,20 +12,21 @@ name="seabird"
 dynamic = ["version"]
 description="Parser for Sea-Bird's CTD and TSG"
 readme = "README.rst"
-requires-python = ">=3.6"
+requires-python = ">=3.9"
 keywords = ["oceanography", "ocean data", "CTD", "TSG", "SeaBird", "hydrography", "parser"]
+license = {file = "LICENSE.rst"}
 classifiers=[
   "Development Status :: 5 - Production/Stable",
   "Natural Language :: English",
   "Intended Audience :: Science/Research",
   "License :: OSI Approved :: BSD License",
   "Operating System :: OS Independent",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.6",
-  "Programming Language :: Python :: 3.7",
-  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
   "Topic :: Scientific/Engineering"
 ]
 dependencies = [
@@ -51,6 +52,8 @@ QC = ["cotede>=0.20.2"]
 
 [project.urls]
 repository = "https://github.com/castelao/seabird"
+documentation = "https://seabird.readthedocs.io"
+
 [project.scripts]
 "seabird" = "seabird.cli:cli"
 
@@ -60,3 +63,10 @@ line-length = 88
 [tool.setuptools_scm]
 write_to = "seabird/version.py"
 git_describe_command = "git describe --dirty --tags --long --match 'v*' --first-parent"
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+testpaths = [
+  "tests",
+]
+filterwarnings = ["error"]

seabird/__init__.py

@@ -3,15 +3,13 @@
 
 from .cnv import CNV, fCNV
 from .exceptions import CNVError
+import importlib.metadata
 
 # __all__ = ['CNV', 'fCNV']
 
-
-from pkg_resources import get_distribution, DistributionNotFound
-
 try:
-    __version__ = get_distribution(__name__).version
-except DistributionNotFound:
+    __version__ = importlib.metadata.version(__name__)
+except Exception:
     try:
         from .version import version as __version__
     except ImportError:

seabird/cnv.py

@@ -1,20 +1,13 @@
 from datetime import datetime, timedelta
 import re
-import pkg_resources
+import importlib.resources
 import os
 import logging
 import struct
 import json
+from . import rules
+import hashlib
 
-try:
-    import hashlib
-
-    md5 = hashlib.md5
-except ImportError:
-    # for Python << 2.5
-    import md5
-
-    md5 = md5.new
 
 # import codecs
 import numpy as np
@@ -53,7 +46,7 @@ def __init__(self, raw_text, defaults=None):
         module_logger.debug("Initializing CNV class")
 
         # Clean empty lines first
-        self.raw_text = re.sub("\n\s*(?=\n)", "", raw_text)
+        self.raw_text = re.sub(r"\n\s*(?=\n)", "", raw_text)
         self.defaults = defaults
         self.attrs = {}
         # ----
@@ -150,9 +143,9 @@ def get_attrs(self):
         # ----
         # Temporary solution. Failsafe MD5
         try:
-            self.attrs["md5"] = md5(self.raw_text.encode("utf-8")).hexdigest()
+            self.attrs["md5"] = hashlib.md5(self.raw_text.encode("utf-8")).hexdigest()
         except:
-            self.attrs["md5"] = md5(
+            self.attrs["md5"] = hashlib.md5(
                 self.raw_text.decode("latin1", "replace").encode("utf-8")
             ).hexdigest()
 
@@ -162,9 +155,10 @@ def prepare_data(self):
         self.data = []
         self.ids = []
         # ----
-        rule_file = "rules/refnames.json"
-        text = pkg_resources.resource_string(__name__, rule_file)
-        refnames = json.loads(text.decode("utf-8"))
+
+        with importlib.resources.open_text(rules, "refnames.json") as file:
+            text = file.read()
+        refnames = json.loads(text)
         # ---- Parse fields
 
         if ("attributes" in self.rule) and (

seabird/utils.py

@@ -1,13 +1,13 @@
 import os
 import re
 import logging
-import pkg_resources
+import importlib.resources
 import json
 
-# import codecs
-
+from seabird import rules
 from seabird.exceptions import CNVError
 
+
 module_logger = logging.getLogger("seabird.utils")
 
 
@@ -74,14 +74,12 @@ def load_rule(raw_text):
     It should try all available rules, one by one, and use the one
       which fits.
     """
-    rules_dir = "rules"
-    rule_files = pkg_resources.resource_listdir(__name__, rules_dir)
+    rule_files = [entry.name for entry in importlib.resources.files(rules).iterdir() if entry.is_file()]
     rule_files = [f for f in rule_files if re.match(r"^cnv.*\.json$", f)]
     for rule_file in rule_files:
-        text = pkg_resources.resource_string(
-            __name__, os.path.join(rules_dir, rule_file)
-        )
-        rule = json.loads(text.decode("utf-8"))
+        with importlib.resources.files(rules).joinpath(rule_file).open('r') as file:
+            text = file.read()
+        rule = json.loads(text)
         # Should I load using codec, for UTF8?? Do I need it?
         # f = codecs.open(rule_file, 'r', 'utf-8')
         # rule = yaml.load(f.read())

tests/test_rules.py

@@ -3,26 +3,24 @@
 """ Check the rules
 """
 
-import os
-import pkg_resources
+import importlib.resources
 import json
 import re
-import seabird
+from seabird import rules
 
 
 def test_load_available_rules():
     """Try to read all available rules
 
     https://github.com/castelao/seabird/issues/7
     """
-    rules_dir = "rules"
-    rule_files = pkg_resources.resource_listdir(seabird.__name__, rules_dir)
+    rules_dir_path = importlib.resources.files(rules)
+    rule_files = [entry.name for entry in rules_dir_path.iterdir() if entry.is_file()]
     rule_files = [f for f in rule_files if re.match("^(?!refnames).*json$", f)]
     for rule_file in rule_files:
         print("loading rule: %s", (rule_file))
-        text = pkg_resources.resource_string(
-            seabird.__name__, os.path.join(rules_dir, rule_file)
-        )
-        rule = json.loads(text.decode("utf-8"))
+        with importlib.resources.files(rules).joinpath(rule_file).open('r') as file:
+            text = file.read()
+        rule = json.loads(text)
         assert type(rule) == dict
         assert len(rule.keys()) > 0