Merge pull request #40 from NASA-PDS/python3.13

jordanpadams · web-flow · commit c2b27d0afa02 · 2025-09-02T11:08:45.000-04:00
Upgrade to Python 3.13
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -20,13 +20,15 @@ repos:
     rev: v0.910
     hooks:
     -   id: mypy
-        files: ^src/|tests/
+        files: ^src/
 
--   repo: https://github.com/python/black
-    rev: 21.7b0
-    hooks:
-    -   id: black
-        files: ^src/|tests/
+# "Black" is disabled as it's conflicting with reorder_python_imports
+#
+# -   repo: https://github.com/python/black
+#     rev: 21.7b0
+#     hooks:
+#     -   id: black
+#         files: ^src/|tests/
 
 -   repo: local
     hooks:
@@ -53,9 +55,11 @@ repos:
         args:
           - '--baseline'
           - '.secrets.baseline'
+          - '--disable-plugin'
+          - 'AbsolutePathDetectorExperimental'
           - --exclude-files '\.secrets..*'
-          - --exclude-files '\.git.*'
           - --exclude-files '\.pre-commit-config\.yaml'
+          - --exclude-files '\.git.*'
           - --exclude-files '\.mypy_cache'
           - --exclude-files '\.pytest_cache'
           - --exclude-files '\.tox'
diff --git a/.secrets.baseline b/.secrets.baseline
@@ -84,6 +84,10 @@
     {
       "path": "detect_secrets.filters.allowlist.is_line_allowlisted"
     },
+    {
+      "path": "detect_secrets.filters.common.is_baseline_file",
+      "filename": ".secrets.baseline"
+    },
     {
       "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
       "min_level": 2
@@ -133,22 +137,6 @@
     }
   ],
   "results": {
-    "data/export.ndjson": [
-      {
-        "type": "Hex High Entropy String",
-        "filename": "data/export.ndjson",
-        "hashed_secret": "15bf7bbaf9857f33dbeaef3ea59e20dd7515c7df",
-        "is_verified": false,
-        "line_number": 3
-      },
-      {
-        "type": "Hex High Entropy String",
-        "filename": "data/export.ndjson",
-        "hashed_secret": "c67d18c26d910fc1615b6818adb3ebfc60f466a7",
-        "is_verified": false,
-        "line_number": 53
-      }
-    ],
     "setup.cfg": [
       {
         "type": "Email Address",
@@ -159,5 +147,5 @@
       }
     ]
   },
-  "generated_at": "2023-11-17T21:56:18Z"
+  "generated_at": "2025-09-02T14:28:21Z"
 }
diff --git a/LICENSE.txt b/LICENSE.txt
@@ -198,4 +198,4 @@ Apache License
    distributed under the License is distributed on an "AS IS" BASIS,
    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and
-   limitations under the License.
+   limitations under the License.
diff --git a/NOTICE.txt b/NOTICE.txt
@@ -1,6 +1,6 @@
-PDS Archive Analytics (update licensing below per specific organization)
+PDS Archive Analytics
 
-Copyright 2021, California Institute of Technology ("Caltech").
+Copyright 2021–2025, California Institute of Technology ("Caltech").
 U.S. Government sponsorship acknowledged.
 
 All rights reserved.
diff --git a/README.md b/README.md
@@ -11,7 +11,7 @@ Kibana-based reporting tool for analytics of the archive
    * Click on Saved Objects
    * Once inside of "Edit Saved Objects: you can:
       * Click on Export Everything
-      * Or select each Dashboards, Searches, and Visualizations 
+      * Or select each Dashboards, Searches, and Visualizations
       * Then, click on Export Button (This will export a NDJSON file with all yout dashboard, saved searches, and, visualizations)
 
  2. Procedure for importing config
@@ -26,14 +26,14 @@ Kibana-based reporting tool for analytics of the archive
 
 ## Contribute
 
-* Issue Tracker: https://github.com/NASA-PDS/archive-analytics/issues
-* Source Code: https://github.com/NASA-PDS/archive-analytics/
-* Wiki: https://github.com/NASA-PDS/archive-analytics/wiki
+* Issue Tracker: https://github.com/NASA-PDS/registry-dashboards/issues
+* Source Code: https://github.com/NASA-PDS/registry-dashboards/
+* Wiki: https://github.com/NASA-PDS/registry-dashboards/wiki
 
 
 ## Support
 
-If you are having issues file a bug report in Github: https://github.com/NASA-PDS/archive-analytics/issues
+If you are having issues file a bug report in Github: https://github.com/NASA-PDS/registry-dashboards/issues
 
 Or you can reach us at https://pds.nasa.gov/?feedback=true
 
@@ -43,5 +43,5 @@ Or you can reach us at https://pds.nasa.gov/?feedback=true
 The project is licensed under the Apache License, version 2. See the
 LICENSE.txt file for details.
 
-Copyright © 2019–2021 California Institute of Technology ("Caltech").
+Copyright © 2019–2025 California Institute of Technology ("Caltech").
 ALL RIGHTS RESERVED. U.S. Government sponsorship acknowledged.
diff --git a/SECURITY.md b/SECURITY.md
@@ -14,4 +14,4 @@ Use this section to tell people about which versions of your project are current
 
 ## Reporting a Vulnerability
 
-To report a vulnerability in this package, please [submit a new isssue using the Vulnerability Issue template](https://github.com/NASA-PDS-Incubator/validate/issues/new?assignees=jordanpadams&labels=triage-needed%2C+security&template=vulnerability-issue.md&title=%5BSECURITY%5D+Title+Here).
+To report a vulnerability in this package, please [submit a new isssue using the Vulnerability Issue template](https://github.com/NASA-PDS/registry-dashboards/issues/new?template=-vulnerability-issue.yml).
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -18,7 +18,7 @@
 # -- Project information -----------------------------------------------------
 
 project = 'PDS Archive Analytics'
-copyright = '2021 California Institute of Technology'
+copyright = '2021–2025 California Institute of Technology'
 author = 'NASA Planetary Data System'
 release = '0.0'
 version = '0.0'
@@ -36,12 +36,8 @@
     'sphinx.ext.viewcode',
     'sphinx.ext.githubpages',
     'sphinx.ext.autosummary',
-    'sphinx_rtd_theme'
 ]
 
-# 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.
@@ -65,7 +61,24 @@
 html_logo = '_static/images/PDS_Planets.png'
 
 html_context = {
-    'css_files': [
-        '_static/theme_overrides.css',  # override wide tables in RTD theme
-    ],
+    'display_github': True,
+    'github_user': 'nasa-pds',
+    'github_repo': 'registry-dashboards',
+    'github_version': 'main/docs/source/',
+}
+
+html_css_files = [
+    'theme_overrides.css',
+]
+
+html_theme_options = {
+    'canonical_url': '',
+    'prev_next_buttons_location': 'bottom',
+    'style_external_links': False,
+    # Toc options
+    'collapse_navigation': True,
+    'sticky_navigation': True,
+    'navigation_depth': 4,
+    'includehidden': True,
+    'titles_only': False
 }
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -15,5 +15,3 @@ Sitemap
     :caption: Support
 
     /support/*
-
-
diff --git a/docs/source/support/contribute.rst b/docs/source/support/contribute.rst
@@ -19,5 +19,3 @@ Report a Bug
 ============
 
 To report a bug found in either a software tool or services, report in the individual repo for the project, or in our `Engineering Node Operations repo <https://github.com/NASA-PDS/pdsen-operations/issues>`_ and we will triage it appropriately.
-
-
diff --git a/docs/source/support/forum.rst b/docs/source/support/forum.rst
@@ -1,4 +1,4 @@
 OpenPlanetary Forum
 ===================
 
-We also have a user forum on the OpenPlanetary Forum (TBD link to forum) and a `#pds4 OpenPlanetary Slack channel <https://openplanetary.slack.com/archives/C61NEHW7L>`_ (note: you must become an `OpenPlanetary Member <https://www.openplanetary.org/join>`_ to join the Slack Org).
+We also have a user forum on the OpenPlanetary Forum (TBD link to forum) and a `#pds4 OpenPlanetary Slack channel <https://openplanetary.slack.com/archives/C61NEHW7L>`_ (note: you must become an `OpenPlanetary Member <https://www.openplanetary.org/join>`_ to join the Slack Org).
diff --git a/docs/source/support/help.rst b/docs/source/support/help.rst
@@ -1,4 +1,4 @@
 Help
 ====
 
-TBD
+TBD
diff --git a/setup.cfg b/setup.cfg
@@ -8,47 +8,43 @@ long_description = file: README.md
 long_description_content_type = text/markdown
 license = apache-2.0
 keywords = pds, planetary data, kibana, analytics, analysis, archive, big data, huge data, data, yuge
-url = https://github.com/NASA-PDS/archive-analytics
-download_url = https://github.com/NASA-PDS/archive-analytics/releases/
+url = https://github.com/NASA-PDS/registry-dashboards
+download_url = https://github.com/NASA-PDS/registry-dashboards/releases/
 classifiers =
     Development Status :: 3 - Alpha
     Intended Audience :: Science/Research
-    License :: OSI Approved :: Apache Software License
     Operating System :: OS Independent
     Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.13
     Topic :: Scientific/Engineering
 
 
 [options]
 install_requires =
 zip_safe = True
 include_package_data = True
-namespace_packages = pds
 package_dir =
     = src
 packages = find:
-python_requires = >= 3.9
+python_requires = >= 3.13
 
 [options.extras_require]
 dev =
-    black
-    flake8
-    flake8-bugbear
-    flake8-docstrings
-    pep8-naming
-    mypy
-    pydocstyle
-    coverage
-    pytest
-    pytest-cov
-    pytest-watch
-    pytest-xdist
-    pre-commit
-    sphinx
-    sphinx-rtd-theme
-    tox
-    types-pkg_resources
+    flake8~=7.3.0
+    flake8-bugbear~=24.12.12
+    flake8-docstrings~=1.7.0
+    pep8-naming~=0.13.3
+    mypy~=1.14.1
+    pydocstyle~=6.3.0
+    coverage~=7.3.0
+    pytest~=7.4.0
+    pytest-cov~=4.1.0
+    pytest-watch~=4.2.0
+    pytest-xdist~=3.3.1
+    pre-commit~=3.3.3
+    sphinx~=8.2.3
+    sphinx-rtd-theme~=3.0.2
+    tox~=4.11.0
 
 
 [options.entry_points]
diff --git a/src/pds/__init__.py b/src/pds/__init__.py
@@ -1,5 +1,2 @@
 # -*- coding: utf-8 -*-
-
 """🪐 PDS Namespace."""
-
-__import__("pkg_resources").declare_namespace(__name__)
diff --git a/src/pds/archive_analytics/__init__.py b/src/pds/archive_analytics/__init__.py
@@ -1,8 +1,6 @@
 # encoding: utf-8
-
 """PDS Archive Analytics."""
-
-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()
diff --git a/tests/pds/__init__.py b/tests/pds/__init__.py
diff --git a/tests/pds/archive_analytics/__init__.py b/tests/pds/archive_analytics/__init__.py
diff --git a/tests/pds/archive_analytics/test_placeholder.py b/tests/pds/archive_analytics/test_placeholder.py
@@ -0,0 +1,9 @@
+# encoding: utf-8
+
+def test_placeholder():
+    """Placeholder test.
+
+    This is to satisfy `pytest` and `tox` which otherwise would fail when finding there are no tests.
+    Well, now there is!
+    """
+    pass
diff --git a/tox.ini b/tox.ini
@@ -1,5 +1,5 @@
 [tox]
-envlist = py39, docs, lint
+envlist = py313, docs, lint
 
 
 [testenv]
@@ -11,7 +11,7 @@ commands = pytest
 [testenv:docs]
 deps = .[dev]
 whitelist_externals = python
-commands = python setup.py build_sphinx
+commands = sphinx-build -b html docs/source docs/build
 
 
 [testenv:lint]
@@ -22,6 +22,6 @@ skip_install = true
 
 
 [testenv:dev]
-basepython = python3.9
+basepython = python3.13
 usedevelop = True
 deps = .[dev]

Original file line number	Diff line number	Diff line change
`@@ -84,6 +84,10 @@`
`84`	`84`	`{`
`85`	`85`	`"path": "detect_secrets.filters.allowlist.is_line_allowlisted"`
`86`	`86`	`},`
	`87`	`+ {`
	`88`	`+ "path": "detect_secrets.filters.common.is_baseline_file",`
	`89`	`+ "filename": ".secrets.baseline"`
	`90`	`+ },`
`87`	`91`	`{`
`88`	`92`	`"path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",`
`89`	`93`	`"min_level": 2`
`@@ -133,22 +137,6 @@`
`133`	`137`	`}`
`134`	`138`	`],`
`135`	`139`	`"results": {`
`136`		`- "data/export.ndjson": [`
`137`		`- {`
`138`		`- "type": "Hex High Entropy String",`
`139`		`- "filename": "data/export.ndjson",`
`140`		`- "hashed_secret": "15bf7bbaf9857f33dbeaef3ea59e20dd7515c7df",`
`141`		`- "is_verified": false,`
`142`		`- "line_number": 3`
`143`		`- },`
`144`		`- {`
`145`		`- "type": "Hex High Entropy String",`
`146`		`- "filename": "data/export.ndjson",`
`147`		`- "hashed_secret": "c67d18c26d910fc1615b6818adb3ebfc60f466a7",`
`148`		`- "is_verified": false,`
`149`		`- "line_number": 53`
`150`		`- }`
`151`		`- ],`
`152`	`140`	`"setup.cfg": [`
`153`	`141`	`{`
`154`	`142`	`"type": "Email Address",`
`@@ -159,5 +147,5 @@`
`159`	`147`	`}`
`160`	`148`	`]`
`161`	`149`	`},`
`162`		`- "generated_at": "2023-11-17T21:56:18Z"`
	`150`	`+ "generated_at": "2025-09-02T14:28:21Z"`
`163`	`151`	`}`
Original file line number	Diff line number	Diff line change
`@@ -14,4 +14,4 @@ Use this section to tell people about which versions of your project are current`
`14`	`14`
`15`	`15`	`## Reporting a Vulnerability`
`16`	`16`
`17`		`-To report a vulnerability in this package, please [submit a new isssue using the Vulnerability Issue template](https://github.com/NASA-PDS-Incubator/validate/issues/new?assignees=jordanpadams&labels=triage-needed%2C+security&template=vulnerability-issue.md&title=%5BSECURITY%5D+Title+Here).`
	`17`	`+To report a vulnerability in this package, please [submit a new isssue using the Vulnerability Issue template](https://github.com/NASA-PDS/registry-dashboards/issues/new?template=-vulnerability-issue.yml).`