chore: update remaining python dependencies

.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
   # docs:
   #   runs-on: ubuntu-22.04
   #   steps:
-  #   - uses: actions/checkout@v3
+  #   - uses: actions/checkout@v4
   #   - name: Set up Python 3.11
   #     uses: actions/setup-python@v4
   #     with:
@@ -50,16 +50,16 @@ jobs:
   lint:
     runs-on: ubuntu-22.04
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Cache python dependencies
       uses: actions/cache@v3
       with:
         path: |
           ~/.cache/pip
           ~/.cache/pre-commit
-        key: pip-lint-${{ hashFiles('.pre-commit-config.yaml', 'pyproject.toml') }}
+        key: lint-${{ hashFiles('.pre-commit-config.yaml', 'pyproject.toml') }}
         restore-keys: |
-          pip-lint-
+          lint-
     - name: Set up Python 3.11
       uses: actions/setup-python@v4
       with:
@@ -71,30 +71,17 @@ jobs:
 
   tests:
     runs-on: ubuntu-22.04
-    strategy:
-      matrix:
-        python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v3
-    - name: Cache python dependencies
-      uses: actions/cache@v3
-      with:
-        path: ~/.cache/pip
-        key: pip-tests-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}
-        restore-keys: |
-          pip-tests-${{ matrix.python-version }}-
-    - name: Set up Python ${{ matrix.python-version }}
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
       uses: actions/setup-python@v4
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: '3.11'
+        cache: pip
     - name: Install python dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip install hatch
-
-    # TODO: remove, once dependencies are updated
-    - run: hatch run python -m pip list
-    - run: hatch run python -m pip list --outdated
+        python -m pip install --upgrade hatch
 
     - name: Run test suite with coverage
       run: hatch run cov

fuji_server/helper/linked_vocab_helper.py

@@ -128,7 +128,7 @@ def get_linked_vocab_by_iri(self, IRI, isnamespaceIRI=False, firstonly = True):
                                     comb_regex = reg_res.get('regex').lstrip('^').rstrip('$')
                                 else:
                                     if '?' in reg_res.get('pattern'):
-                                        reg_res['pattern']=reg_res.get('pattern').replace('?','\?')
+                                        reg_res['pattern']=reg_res.get('pattern').replace('?',r'\?')
                                     comb_regex = reg_res.get('pattern').split('$1')[0].rstrip('/#')
 
                                 if comb_regex not in tested_patterns:

pyproject.toml

@@ -16,30 +16,32 @@ classifiers = [
   "Topic :: Scientific/Engineering :: Information Analysis"
 ]
 dependencies = [
+  # dependencies with major version on zero are defined with
+  # major.minor.patch, because they can potentially introduce breaking changes
+  # in minor version updates anytime
   "beautifulsoup4~=4.12",
   "configparser~=6.0",
   "connexion[swagger-ui]~=2.14",
-  "extruct~=0.13.0",
+  "extruct~=0.16.0",
   "feedparser~=6.0",
-  "flask~=2.2.5",  # pin due to flask 2.3.0 json_encoder issue
   "flask-cors~=4.0",
-  "flask-limiter<=2.0.0",
+  "flask-limiter~=3.5",
   "hashid~=3.1.4",
   "idutils~=1.2",
   "jmespath~=1.0",
-  "levenshtein~=0.21.1",
+  "levenshtein~=0.22.0",
   "lxml~=4.9",
-  "pandas~=1.3",
+  "pandas~=2.1",
   "pyRdfa3~=3.5",
   "pyld~=2.0",
-  "pyyaml!=6.0.0,!=5.4.0,!=5.4.1",  # 6.0.1
+  "pyyaml~=6.0",
   "rapidfuzz~=3.3",
-  "rdflib~=6.1",
+  "rdflib~=7.0",
   "requests~=2.31",
-  "sparqlwrapper~=1.8",
-  "tika~=1.24",
-  "tldextract~=3.1",
-  "urlextract~=1.2",
+  "sparqlwrapper~=2.0",
+  "tika~=2.6",
+  "tldextract~=3.4",
+  "urlextract~=1.8",
   "waitress~=2.1"
 ]
 description = "FUJI (FAIRsFAIR Data Objects Assessment Service), A service to evaluate FAIR data objects based on FAIRsFAIR Metrics"
@@ -66,22 +68,21 @@ dev = [
   "fuji[testing]"
 ]
 docs = [
-  "docutils>=0.14,<0.18",
-  "myst-parser~=0.16",
-  "sphinx~=4.2",
-  "sphinx-rtd-theme~=1.0"
+  "myst-parser~=2.0",
+  "sphinx~=7.2",
+  "sphinx-rtd-theme~=1.3"
 ]
 lint = [
-  "pre-commit~=3.3"
+  "pre-commit~=3.4"
 ]
 report = [
-  "bokeh~=2.4",
+  "bokeh~=3.2",
   "jupyter~=1.0"
 ]
 testing = [
   "pytest~=7.4",
   "pytest-cov~=4.1",
-  "pytest-randomly~=3.1",
+  "pytest-randomly~=3.15",
   "pytest-recording~=0.13",
   "pytest-xdist~=3.3"
 ]
@@ -130,6 +131,15 @@ lint = "pre-commit run --all-files --color=always {args}"
 test = "pytest {args}"
 
 [tool.pytest.ini_options]
+filterwarnings = [
+  # warnings from pyrdfa
+  "ignore: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12:DeprecationWarning",
+  # warnings from feedparser
+  "ignore:'cgi' is deprecated and slated for removal in Python 3.13:DeprecationWarning",
+  # warnings from tika
+  "ignore:pkg_resources is deprecated as an API:DeprecationWarning",
+  "ignore:Deprecated call to `pkg_resources.declare_namespace:DeprecationWarning"
+]
 markers = [
   "manual",  # tests which should be triggered manual only
   "noci",  # tests which should not run on the CI