Merge pull request #107 from yoctoyotta1024/fix-vulnerability

fix: Security vulnerability
yoctoyotta1024 · Sep 4, 2024 · 0807669 · 0807669
2 parents 75acf87 + b6210eb
commit 0807669
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Showing 12 changed files with 6 additions and 11 deletions.
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -53,7 +53,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download build artifacts (i.e. documentation)
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: html-docs
           path: docs/build/html/

diff --git a/ci_environment.yaml b/ci_environment.yaml
@@ -8,9 +8,11 @@ dependencies:
     - pip:
       - numpy
       - pytest
-      - sphinx==7.4 # TODO(CB): update sphinx allowed version for CI
+      - sphinx
       - furo
       - sphinx_copybutton
       - sphinxcontrib-bibtex
+      - sphinxcontrib-applehelp
+      - sphinxcontrib-htmlhelp
       - breathe
       - pre-commit
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -18,7 +18,6 @@
 configuration for CLEO documentation made using Sphinx
 """
 
-
 # Configuration file for the Sphinx documentation builder.
 #
 # For the full list of built-in configuration values, see the documentation:

diff --git a/examples/bubble3d/bubble3d.py b/examples/bubble3d/bubble3d.py
@@ -20,7 +20,6 @@
 piggyback ICON bubble test case
 """
 
-
 import os
 import sys
 from pathlib import Path

diff --git a/examples/bubble3d/yac_bubble_data_reader.py b/examples/bubble3d/yac_bubble_data_reader.py
@@ -20,7 +20,6 @@
 output data and CLEO (e.g. for the bubble test case)
 """
 
-
 #!/usr/bin/env python3
 
 from yac import YAC, UnstructuredGrid, Field, Location, Calendar, TimeUnit, def_calendar

diff --git a/examples/fromfile/src/gen_input_thermo.py b/examples/fromfile/src/gen_input_thermo.py
@@ -20,7 +20,6 @@
 for CLEO to run example with 3-D time-varying thermodynamics.
 """
 
-
 import sys
 import numpy as np
 

diff --git a/examples/fromfile/src/plot_output_thermo.py b/examples/fromfile/src/plot_output_thermo.py
@@ -20,7 +20,6 @@
 fromfile example.
 """
 
-
 import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib.gridspec import GridSpec

diff --git a/pySD/initsuperdropsbinary_src/__init__.py b/pySD/initsuperdropsbinary_src/__init__.py
@@ -17,7 +17,6 @@
 File Description:
 """
 
-
 __all__ = [
     "create_initsuperdrops",
     "read_initsuperdrops",

diff --git a/pySD/thermobinary_src/create_thermodynamics.py b/pySD/thermobinary_src/create_thermodynamics.py
@@ -17,7 +17,6 @@
 File Description:
 """
 
-
 import numpy as np
 from os.path import isfile
 from .. import cxx2py, readconfigfile, writebinary

diff --git a/pySD/writebinary.py b/pySD/writebinary.py
@@ -18,7 +18,6 @@
 File Description:
 """
 
-
 import numpy as np
 import struct
 

diff --git a/requirements.txt b/requirements.txt
@@ -3,6 +3,8 @@ sphinx
 furo
 sphinx_copybutton
 sphinxcontrib-bibtex
+sphinxcontrib-applehelp
+sphinxcontrib-htmlhelp
 breathe
 numpy
 scipy

diff --git a/setup.py b/setup.py
@@ -15,7 +15,6 @@
 Copyright (c) 2023 MPI-M, Clara Bayley
 """
 
-
 from setuptools import setup, find_packages
 
 setup(