Merge branch 'main' into i466

Author: jordanpadams

.github/workflows/branch-cicd.yaml

@@ -43,7 +43,7 @@ jobs:
                 name: Set up Python 3
                 uses: actions/setup-python@v5
                 with:
-                    python-version: '3.9'
+                    python-version: '3.13'
             -
                 name: 💵 Python Cache
                 uses: actions/cache@v4

.github/workflows/codeql-analysis.yml

@@ -40,10 +40,10 @@ jobs:
     - name: Checkout repository
       uses: actions/checkout@v4
 
-    - name: Setup python 3.9
+    - name: Setup python 3.13
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.13
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL

.github/workflows/secrets-detection.yaml

@@ -47,7 +47,7 @@ jobs:
                     detect-secrets scan --disable-plugin AbsolutePathDetectorExperimental --baseline .secrets.new \
                         --exclude-files '\.secrets..*' \
                         --exclude-files '\.git.*' \
-                        --exclude-files '\.pre-commit-config.yaml' \
+                        --exclude-files '\.pre-commit-config\.yaml' \
                         --exclude-files '\.mypy_cache' \
                         --exclude-files '\.pytest_cache' \
                         --exclude-files '\.tox' \

.pre-commit-config.yaml

@@ -18,7 +18,8 @@ repos:
     -   id: reorder-python-imports
         files: ^src/|tests/
 
-# Disabling "black" because it's conflicting with "reorder_python_imports"
+# Disabling "black" for now as it's conflicting with reorder_python_imports
+# (They keep fighting over whether to have a blank line before imports)
 #
 # -   repo: local
 #     hooks:
@@ -52,10 +53,13 @@ repos:
     hooks:
       - id: detect-secrets
         args:
+          - '--disable-plugin'
+          - 'AbsolutePathDetectorExperimental'
           - '--baseline'
           - '.secrets.baseline'
           - --exclude-files '\.secrets..*'
           - --exclude-files '\.git.*'
+          - --exclude-files '\.pre-commit-config\.yaml'
           - --exclude-files '\.mypy_cache'
           - --exclude-files '\.pytest_cache'
           - --exclude-files '\.tox'

README.md

@@ -7,7 +7,7 @@ The Planetary Data System (PDS) Digital Object Identifier (DOI) Service provides
 
 ## Prerequisites
 
-- Python 3.9 or above
+- Python 3.13 or above
 - A login to the DOI Service Provider endpoint server (currently DataCite)
 
 
@@ -38,7 +38,7 @@ If you get an error like
 
     src/types.h:36:2: error: You need a compatible libgit2 version (1.1.x)
 
-then you're probably using [brew.sh](https://brew.sh)'s Python 3.10. Use their Python 3.9 instead.
+then you're probably using [brew.sh](https://brew.sh)'s Python 3.10. Use their Python 3.13 instead.
 
 Update your local configuration to access the DOI service provider's test server.
 

docs/source/conf.py

@@ -34,13 +34,9 @@
     "sphinx.ext.githubpages",
     "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
-    "sphinx_rtd_theme",
     "sphinxarg.ext",
 ]
 
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ["_templates"]
-
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
@@ -63,8 +59,6 @@
 
 html_theme_options = {
     "canonical_url": "",
-    "logo_only": False,
-    "display_version": True,
     "prev_next_buttons_location": "bottom",
     "style_external_links": False,
     # Toc options
@@ -77,8 +71,6 @@
 
 html_logo = "_static/images/PDS_Planets.png"
 
-html_context = {
-    "css_files": [
-        "_static/theme_overrides.css",  # override wide tables in RTD theme
-    ],
-}
+html_css_files = [
+    'theme_overrides.css',
+]

docs/source/installation/index.rst

@@ -9,7 +9,7 @@ Requirements
 Prior to installing this software, ensure your system meets the following
 requirements:
 
-•  Python_ 3.9 or above. Python 2 will absolutely *not* work.
+•  Python_ 3.13 or above. Python 2 will absolutely *not* work.
 •  ``libxml2`` version 2.9.2; later 2.9 versions are fine.  Run ``xml2-config
    --version`` to find out.
 •  ``libxslt`` version 1.1.28; later 1.1 versions are OK too. Run ``xslt-config`` to see.

setup.cfg

@@ -15,7 +15,6 @@ classifiers =
     Environment :: Web Environment
     Framework :: Flask
     Intended Audience :: Science/Research
-    License :: OSI Approved :: Apache Software License
     Operating System :: OS Independent
     Programming Language :: Python :: 3
     Topic :: Scientific/Engineering
@@ -39,12 +38,12 @@ install_requires =
     itsdangerous==2.0.1
     jinja2==3.1.4
     jsonschema~=3.0.0
-    lxml==5.3.0
+    lxml==6.0.0
     nltk==3.5
-    numpy==1.21.2
+    numpy==2.2.3
     openapi-schema-validator~=0.1.4
-    openpyxl~=3.0.7
-    pandas==1.3.4
+    openpyxl~=3.1.0
+    pandas==2.3.0
     python-dateutil~=2.9.0.post0
     python-jose[cryptography]
     pytz==2020.1
@@ -64,16 +63,16 @@ include_package_data = True
 package_dir =
     = src
 packages = find:
-python_requires = >= 3.9
+python_requires = >= 3.13
 test_suite = pds_doi_service.test.suite
 
 
 [options.extras_require]
 dev =
+    aiosmtpd~=1.4.6
     build~=1.2.2
-    black~=24.8.0
-    flake8~=7.1.1
-    flake8-bugbear~=24.8.19
+    flake8~=7.3.0
+    flake8-bugbear~=24.12.12
     flake8-docstrings~=1.7.0
     pep8-naming~=0.14.1
     pydocstyle~=6.3.0
@@ -83,18 +82,18 @@ dev =
     pytest-watch~=4.2.0
     pytest-xdist~=3.6.1
     pre-commit~=3.3.3
-    sphinx~=5.0.0
-    sphinx-rtd-theme~=0.5.0
+    sphinx~=8.2.3
+    sphinx-rtd-theme~=3.0.2
     types-setuptools~=68.1.0.0
     sphinxcontrib-napoleon~=0.7
     tox>=3.28,<4.24
     flask_testing~=0.8.0
-    sphinx-rtd-theme>=0.5,<3.1
+    sphinx-rtd-theme~=3.0.2
     sphinx-argparse~=0.2.5
     behave~=1.2.6
     allure-behave~=2.8.13
     behave-testrail-reporter~=0.4.0
-    pygit2~=1.9.2
+    pygit2~=1.18.2
     lxml-stubs~=0.5.1
     pandas-stubs~=2.0.1.230501
     types-flask~=1.1.6

src/pds_doi_service/__init__.py

@@ -1,5 +1,5 @@
 # encoding: utf-8
 """Planetary Data System's Digital Object Identifier service"""
-import pkg_resources
+import importlib.resources
 
-__version__ = VERSION = pkg_resources.resource_string(__name__, "VERSION.txt").decode("utf-8").strip()
+__version__ = VERSION = importlib.resources.files(__name__).joinpath("VERSION.txt").read_text().strip()

src/pds_doi_service/api/test/test_dois_controller.py

@@ -5,6 +5,7 @@
 import os
 import unittest
 from datetime import datetime
+from importlib import resources
 from os.path import abspath
 from os.path import exists
 from os.path import join
@@ -24,7 +25,6 @@
 from pds_doi_service.core.outputs.service import DOIServiceFactory
 from pds_doi_service.core.outputs.service import SERVICE_TYPE_DATACITE
 from pds_doi_service.core.util.config_parser import DOIConfigUtil
-from pkg_resources import resource_filename
 
 from ._base import BaseTestCase
 
@@ -47,7 +47,7 @@ class TestDoisController(BaseTestCase):
 
     @classmethod
     def setUpClass(cls):
-        cls.test_dir = resource_filename(__name__, "")
+        cls.test_dir = str(resources.files(__name__))
         cls.test_data_dir = join(cls.test_dir, "data")
         cls.input_dir = abspath(join(cls.test_dir, os.pardir, os.pardir, os.pardir, os.pardir, "input"))
         cls.service_type = DOIServiceFactory.get_service_type()