Fix security vulnerabilities in Python dependencies

darshan-util/pydarshan/darshan/examples/requirements-examples.txt

@@ -1,12 +1,12 @@
-jupyter
-notebook
+jupyter>=1.0.0
+notebook>=7.2.2
 
 
 # altair (has svg well exposed)
-altair
+altair>=5.0.0
 
 
 # for bokeh + svg export
 # but bokeh is almost as verbose to use as matplotlib
-bokeh
-selenium
+bokeh>=3.0.0
+selenium>=4.14.0

darshan-util/pydarshan/pyproject.toml

@@ -8,26 +8,25 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "darshan"
 dynamic = ["version"]
-requires-python = ">=3.7"
+requires-python = ">=3.8"
 description = "Python tools to interact with Darshan log records of HPC applications."
 readme = 'README.rst'
 dependencies = [
-    "cffi",
-    "numpy",
-    "pandas",
-    "matplotlib",
-    "seaborn",
-    "mako",
-    "humanize",
-    "rich"
+    "cffi>=1.15.0",
+    "numpy>=1.22.0",
+    "pandas>=2.0.0",
+    "matplotlib>=3.5.0",
+    "seaborn>=0.12.0",
+    "mako>=1.2.4",
+    "humanize>=4.0.0",
+    "rich>=13.0.0"
 ]
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Developers",
     "Intended Audience :: Science/Research",
     "Natural Language :: English",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
@@ -41,15 +40,15 @@ repository = 'https://github.com/darshan-hpc/darshan'
 
 [project.optional-dependencies]
 test = [
-    "packaging",
-    "pytest",
-    "lxml",
-    "importlib_resources;python_version<'3.9'",
+    "packaging>=21.0",
+    "pytest>=7.0.0",
+    "lxml>=4.9.1",
+    "importlib_resources>=5.0.0;python_version<'3.9'",
 ]
 dev = [
-    "sphinx",
-    "sphinx_rtd_theme",
-    "pipx"
+    "sphinx>=7.0.0",
+    "sphinx_rtd_theme>=2.0.0",
+    "pipx>=1.0.0"
 ]
 
 [tool.setuptools.packages.find]
@@ -76,12 +75,12 @@ skip = [
     "*_s390x"
 ]
 test-requires = [
-    "packaging",
-    "pytest",
-    "lxml",
-    "matplotlib",
-    "importlib_resources;python_version<'3.9'",
-    "humanize"
+    "packaging>=21.0",
+    "pytest>=7.0.0",
+    "lxml>=4.9.1",
+    "matplotlib>=3.5.0",
+    "importlib_resources>=5.0.0;python_version<'3.9'",
+    "humanize>=4.0.0"
 ]
 before-test = "pip install -U git+https://github.com/darshan-hpc/darshan-logs.git@main"
 test-command = "pytest {package}"

darshan-util/pydarshan/requirements.txt

@@ -1,4 +1,4 @@
-cffi
-numpy
-pandas
-matplotlib
+cffi>=1.15.0
+numpy>=1.22.0
+pandas>=2.0.0
+matplotlib>=3.5.0

darshan-util/pydarshan/requirements_dev.txt

@@ -1,19 +1,19 @@
-wheel
-watchdog
-twine
+wheel>=0.38.1
+watchdog>=3.0.0
+twine>=4.0.0
 
-cffi
-numpy
-pandas
-matplotlib
-seaborn
-mako
-jupyterlab
+cffi>=1.15.0
+numpy>=1.22.0
+pandas>=2.0.0
+matplotlib>=3.5.0
+seaborn>=0.12.0
+mako>=1.2.4
+jupyterlab>=4.4.8
 
-pytest
-pytest-runner
+pytest>=7.0.0
+pytest-runner>=6.0.0
 # lxml needed implicitly for pandas read_html calls in some tests
-lxml
+lxml>=4.9.1
 
-sphinx
-sphinx_rtd_theme
+sphinx>=7.0.0
+sphinx_rtd_theme>=2.0.0

darshan-util/pydarshan/setup.py

@@ -5,8 +5,8 @@
 import sys
 import os
 
-if sys.version_info[:2] < (3, 7):
-    raise RuntimeError("Python version >= 3.7 required.")
+if sys.version_info[:2] < (3, 8):
+    raise RuntimeError("Python version >= 3.8 required.")
 
 
 

readthedocs/requirements.txt

@@ -1,6 +1,6 @@
 sphinx==8.1.3
 sphinx-rtd-theme==3.0.2
-cffi
-numpy
-pandas
-matplotlib
+cffi>=1.15.0
+numpy>=1.22.0
+pandas>=2.0.0
+matplotlib>=3.5.0