Fixed issues with pulling file resources from packages.

.github/copilot-instructions.md

@@ -2,6 +2,8 @@
 
 This document provides guidance for GitHub Copilot when working on the Whyis project.
 
+> **Keep instructions in sync.** This file and [`CLAUDE.md`](../CLAUDE.md) (in the repository root) are companion instruction files — one for GitHub Copilot, one for Claude — and share the same project guidance. Whenever you change the guidance in this file, apply the equivalent change to `CLAUDE.md` so both assistants stay aligned. Only the tool-specific framing (title, intro, and this sync note) should differ between them.
+
 ## Project Overview
 
 Whyis is a nano-scale knowledge graph publishing, management, and analysis framework built with Python and Flask. It manages knowledge as nanopublications, which are the smallest publishable units of knowledge graphs with associated provenance and publication information.

.github/workflows/python-tests.yml

@@ -51,13 +51,14 @@ jobs:
       - name: Install Python dependencies
         timeout-minutes: 15
         run: |
-          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install --upgrade pip wheel
+          pip install "setuptools<80"
           # Install test dependencies first (lightweight)
           pip install -r requirements-test.txt
           # Install core dependencies needed for unit tests (without full whyis package)
           # Use --no-deps where possible to avoid dependency resolution loops
           pip install rdflib rdflib-jsonld Flask Flask-Security-Too Flask-Script Flask-PluginEngine
-          pip install filedepot Markdown
+          pip install filedepot Markdown pytz
           # Optional dependencies - skip if they cause issues
           pip install celery eventlet redislite nltk || true
           pip install sadi setlr sdd2rdf oxrdflib || true

setup.py

@@ -155,6 +155,12 @@ def run(self):
         'requests'
     ],
     install_requires = [
+        # Python 3.12 no longer bundles setuptools, and setuptools>=81 has
+        # removed pkg_resources. Several pinned dependencies (e.g.
+        # Flask-Security 3.0.0) still import pkg_resources, so pin to a
+        # setuptools that still ships it. Whyis's own code uses whyis._resources
+        # instead and does not need pkg_resources.
+        'setuptools<81',
         'beautifulsoup4==4.7.1',
         'bibtexparser==1.1.0',
         'celery<6.0.0',

whyis/_resources.py

@@ -0,0 +1,66 @@
+"""Dependency-free replacements for the ``pkg_resources`` resource helpers.
+
+``pkg_resources`` (shipped with setuptools) is deprecated and is no longer
+guaranteed to be importable on Python 3.12+, where setuptools is not part of a
+default environment. Whyis is always installed as a regular directory on disk
+(never as a zipped egg), so we can resolve package resources directly from the
+filesystem via :mod:`importlib`. These functions mirror the small subset of the
+``pkg_resources`` API that Whyis relies on.
+"""
+
+import importlib.util
+import os
+
+__all__ = [
+    "resource_filename",
+    "resource_listdir",
+    "resource_string",
+    "resource_exists",
+    "resource_stream",
+]
+
+
+def _base_dir(package):
+    """Return the on-disk directory associated with a package or module name.
+
+    For a package (e.g. ``"whyis"``) this is the package directory. For a
+    module (e.g. ``"whyis.fuseki.fuseki"``) it is the directory containing the
+    module file, matching ``pkg_resources`` resource-resolution semantics.
+    """
+    spec = importlib.util.find_spec(package)
+    if spec is None:
+        raise ModuleNotFoundError(f"No module named {package!r}")
+    if spec.submodule_search_locations:
+        return list(spec.submodule_search_locations)[0]
+    if spec.origin and spec.origin not in ("built-in", "frozen"):
+        return os.path.dirname(spec.origin)
+    raise ValueError(f"Cannot determine a resource directory for {package!r}")
+
+
+def resource_filename(package, resource=""):
+    """Return the filesystem path to ``resource`` within ``package``."""
+    base = _base_dir(package)
+    if not resource:
+        return base
+    return os.path.join(base, *resource.split("/"))
+
+
+def resource_listdir(package, resource):
+    """List the contents of a directory ``resource`` within ``package``."""
+    return os.listdir(resource_filename(package, resource))
+
+
+def resource_string(package, resource):
+    """Return the contents of ``resource`` within ``package`` as bytes."""
+    with open(resource_filename(package, resource), "rb") as handle:
+        return handle.read()
+
+
+def resource_exists(package, resource):
+    """Return whether ``resource`` exists within ``package``."""
+    return os.path.exists(resource_filename(package, resource))
+
+
+def resource_stream(package, resource):
+    """Open ``resource`` within ``package`` as a binary stream."""
+    return open(resource_filename(package, resource), "rb")

whyis/app.py

@@ -53,7 +53,7 @@
 from whyis.nanopub import NanopublicationManager
 from whyis.authenticator import SingleUserAuthenticator
 # from flask_login.config import EXEMPT_METHODS
-from pkg_resources import resource_filename
+from whyis._resources import resource_filename
 
 rdflib.plugin.register('sparql', Result,
         'rdflib.plugins.sparql.processor', 'SPARQLResult')

whyis/commands/configure.py

@@ -5,7 +5,7 @@
 from base64 import b64encode
 import os
 from cookiecutter.main import cookiecutter
-from pkg_resources import resource_filename, resource_listdir
+from whyis._resources import resource_filename, resource_listdir
 
 try:
     from pip._internal.operations import freeze

whyis/fuseki/fuseki.py

@@ -1,4 +1,4 @@
-from pkg_resources import resource_filename, resource_listdir, resource_string
+from whyis._resources import resource_filename, resource_listdir, resource_string
 import subprocess
 import os
 import sys

whyis/manager.py

@@ -10,7 +10,7 @@
 import sys
 import os
 from cookiecutter.main import cookiecutter
-from pkg_resources import resource_filename, resource_listdir
+from whyis._resources import resource_filename, resource_listdir
 
 from whyis.config.utils import import_config_module, UnconfiguredAppException
 import json

whyis/plugin.py

@@ -1,7 +1,7 @@
 from flask import render_template
 from flask_pluginengine import Plugin as PluginBase
 from flask_pluginengine import PluginBlueprint, current_plugin
-from pkg_resources import resource_exists, resource_stream, resource_filename
+from whyis._resources import resource_exists, resource_stream, resource_filename
 import rdflib
 
 class Listener: