From 9ab37dc81f6478a180159fc53e280a7a6b16cf23 Mon Sep 17 00:00:00 2001 From: "clara.bayley" Date: Wed, 4 Sep 2024 14:17:49 +0200 Subject: [PATCH 1/3] fix: Security vulnerability --- .github/workflows/CI.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 34380e159..4276177a4 100644 --- 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/ From 54bb0fa76172579ab0140f084c94aba1109ff4cf Mon Sep 17 00:00:00 2001 From: "clara.bayley" Date: Wed, 4 Sep 2024 14:28:28 +0200 Subject: [PATCH 2/3] fix: fix sphinx dependencies after sphinx version 8 --- ci_environment.yaml | 4 +++- requirements.txt | 2 ++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/ci_environment.yaml b/ci_environment.yaml index 1faba7c85..024cd9f8a 100644 --- 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/requirements.txt b/requirements.txt index d9ec4e1f1..cb9817f4d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,6 +3,8 @@ sphinx furo sphinx_copybutton sphinxcontrib-bibtex +sphinxcontrib-applehelp +sphinxcontrib-htmlhelp breathe numpy scipy From b6210eb2904c7c3f66597e8a7ad3f0299cd01f46 Mon Sep 17 00:00:00 2001 From: "clara.bayley" Date: Wed, 4 Sep 2024 14:32:09 +0200 Subject: [PATCH 3/3] chore: formatting --- docs/source/conf.py | 1 - examples/bubble3d/bubble3d.py | 1 - examples/bubble3d/yac_bubble_data_reader.py | 1 - examples/fromfile/src/gen_input_thermo.py | 1 - examples/fromfile/src/plot_output_thermo.py | 1 - pySD/initsuperdropsbinary_src/__init__.py | 1 - pySD/thermobinary_src/create_thermodynamics.py | 1 - pySD/writebinary.py | 1 - setup.py | 1 - 9 files changed, 9 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 75b147deb..17110ce18 100644 --- 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 index 6bd119ae1..75fbbf31f 100644 --- 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 index dd4d66456..c73280a1d 100755 --- 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 index e8c0d2c68..4d957de57 100644 --- 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 index 1ad427a95..3b5536a0d 100644 --- 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 index 9b87b6265..d12ed05f9 100644 --- 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 index 238eac7f7..57f12fe4a 100644 --- 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 index e572c4f9a..069657554 100644 --- a/pySD/writebinary.py +++ b/pySD/writebinary.py @@ -18,7 +18,6 @@ File Description: """ - import numpy as np import struct diff --git a/setup.py b/setup.py index 44a59631f..eb566bc79 100644 --- a/setup.py +++ b/setup.py @@ -15,7 +15,6 @@ Copyright (c) 2023 MPI-M, Clara Bayley """ - from setuptools import setup, find_packages setup(