From cc8aa3049806fefcba3ea7552b1d8159640d0408 Mon Sep 17 00:00:00 2001 From: Zach Sherman <19153455+zssherman@users.noreply.github.com> Date: Tue, 9 Sep 2025 12:06:16 -0500 Subject: [PATCH 1/4] Create codeql.yml --- .github/workflows/codeql.yml | 77 ++++++++++++++++++++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 .github/workflows/codeql.yml diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml new file mode 100644 index 0000000..419e004 --- /dev/null +++ b/.github/workflows/codeql.yml @@ -0,0 +1,77 @@ +# For most projects, this workflow file will not need changing; you simply need +# to commit it to your repository. +# +# You may wish to alter this file to override the set of languages analyzed, +# or to provide custom queries or build logic. +# +# ******** NOTE ******** +# We have attempted to detect the languages in your repository. Please check +# the `language` matrix defined below to confirm you have the correct set of +# supported CodeQL languages. +# +name: "CodeQL" + +on: + push: + branches: [ "main" ] + pull_request: + # The branches below must be a subset of the branches above + branches: [ "main" ] + schedule: + - cron: '39 13 * * 2' + +jobs: + analyze: + name: Analyze + runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }} + timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }} + permissions: + actions: read + contents: read + security-events: write + + strategy: + fail-fast: false + matrix: + language: ['python' ] + # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby', 'swift' ] + # Use only 'java' to analyze code written in Java, Kotlin or both + # Use only 'javascript' to analyze code written in JavaScript, TypeScript or both + # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support + + steps: + - name: Checkout repository + uses: actions/checkout@v5 + + # Initializes the CodeQL tools for scanning. + - name: Initialize CodeQL + uses: github/codeql-action/init@v3 + with: + languages: ${{ matrix.language }} + # If you wish to specify custom queries, you can do so here or in a config file. + # By default, queries listed here will override any specified in a config file. + # Prefix the list here with "+" to use these queries and those in the config file. + + # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs + # queries: security-extended,security-and-quality + + + # Autobuild attempts to build any compiled languages (C/C++, C#, Go, or Java). + # If this step fails, then you should remove it and run the build manually (see below) + - name: Autobuild + uses: github/codeql-action/autobuild@v3 + + # ℹī¸ Command-line programs to run using the OS shell. + # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun + + # If the Autobuild fails above, remove it and uncomment the following three lines. + # modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance. + + # - run: | + # echo "Run, Build Application using script" + # ./location_of_script_within_repo/buildscript.sh + + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v3 + with: + category: "/language:${{matrix.language}}" From 62c8684e9ed8559155066ae0b020b95f9dde0916 Mon Sep 17 00:00:00 2001 From: zssherman Date: Tue, 9 Sep 2025 12:12:20 -0500 Subject: [PATCH 2/4] MNT: Fix for PEP8 issues. --- .github/workflows/codeql-analysis.yml | 74 --------------------------- .github/workflows/codeql.yml | 63 +++++++++++------------ 2 files changed, 31 insertions(+), 106 deletions(-) delete mode 100644 .github/workflows/codeql-analysis.yml diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml deleted file mode 100644 index deb5a3e..0000000 --- a/.github/workflows/codeql-analysis.yml +++ /dev/null @@ -1,74 +0,0 @@ -# For most projects, this workflow file will not need changing; you simply need -# to commit it to your repository. -# -# You may wish to alter this file to override the set of languages analyzed, -# or to provide custom queries or build logic. -# -# ******** NOTE ******** -# We have attempted to detect the languages in your repository. Please check -# the `language` matrix defined below to confirm you have the correct set of -# supported CodeQL languages. -# -name: "CodeQL" - -on: - push: - branches: [main] - pull_request: - # The branches below must be a subset of the branches above - branches: [main] - schedule: - - cron: "37 14 * * 4" - -concurrency: - group: ${{ github.workflow }}-${{ github.ref }} - cancel-in-progress: true - -jobs: - analyze: - name: Analyze - runs-on: ubuntu-latest - permissions: - actions: read - contents: read - security-events: write - - strategy: - fail-fast: false - matrix: - language: ["python"] - # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ] - # Learn more about CodeQL language support at https://git.io/codeql-language-support - - steps: - - name: Checkout repository - uses: actions/checkout@v5 - - # Initializes the CodeQL tools for scanning. - - name: Initialize CodeQL - uses: github/codeql-action/init@v3 - with: - languages: ${{ matrix.language }} - # If you wish to specify custom queries, you can do so here or in a config file. - # By default, queries listed here will override any specified in a config file. - # Prefix the list here with "+" to use these queries and those in the config file. - # queries: ./path/to/local/query, your-org/your-repo/queries@main - - # Autobuild attempts to build any compiled languages (C/C++, C#, or Java). - # If this step fails, then you should remove it and run the build manually (see below) - - name: Autobuild - uses: github/codeql-action/autobuild@v3 - - # ℹī¸ Command-line programs to run using the OS shell. - # 📚 https://git.io/JvXDl - - # ✏ī¸ If the Autobuild fails above, remove it and uncomment the following three lines - # and modify them (or add more) to build your code if your project - # uses a compiled language - - #- run: | - # make bootstrap - # make release - - - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v3 diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index 419e004..867407e 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -13,12 +13,12 @@ name: "CodeQL" on: push: - branches: [ "main" ] + branches: ["main"] pull_request: # The branches below must be a subset of the branches above - branches: [ "main" ] + branches: ["main"] schedule: - - cron: '39 13 * * 2' + - cron: "39 13 * * 2" jobs: analyze: @@ -33,45 +33,44 @@ jobs: strategy: fail-fast: false matrix: - language: ['python' ] + language: ["python"] # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby', 'swift' ] # Use only 'java' to analyze code written in Java, Kotlin or both # Use only 'javascript' to analyze code written in JavaScript, TypeScript or both # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support steps: - - name: Checkout repository - uses: actions/checkout@v5 + - name: Checkout repository + uses: actions/checkout@v5 - # Initializes the CodeQL tools for scanning. - - name: Initialize CodeQL - uses: github/codeql-action/init@v3 - with: - languages: ${{ matrix.language }} - # If you wish to specify custom queries, you can do so here or in a config file. - # By default, queries listed here will override any specified in a config file. - # Prefix the list here with "+" to use these queries and those in the config file. + # Initializes the CodeQL tools for scanning. + - name: Initialize CodeQL + uses: github/codeql-action/init@v3 + with: + languages: ${{ matrix.language }} + # If you wish to specify custom queries, you can do so here or in a config file. + # By default, queries listed here will override any specified in a config file. + # Prefix the list here with "+" to use these queries and those in the config file. - # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs - # queries: security-extended,security-and-quality + # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs + # queries: security-extended,security-and-quality + # Autobuild attempts to build any compiled languages (C/C++, C#, Go, or Java). + # If this step fails, then you should remove it and run the build manually (see below) + - name: Autobuild + uses: github/codeql-action/autobuild@v3 - # Autobuild attempts to build any compiled languages (C/C++, C#, Go, or Java). - # If this step fails, then you should remove it and run the build manually (see below) - - name: Autobuild - uses: github/codeql-action/autobuild@v3 + # ℹī¸ Command-line programs to run using the OS shell. + # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun - # ℹī¸ Command-line programs to run using the OS shell. - # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun + # If the Autobuild fails above, remove it and uncomment the following three lines. + # modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance. - # If the Autobuild fails above, remove it and uncomment the following three lines. - # modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance. + # - run: | + # echo "Run, Build Application using script" + # ./location_of_script_within_repo/buildscript.sh - # - run: | - # echo "Run, Build Application using script" - # ./location_of_script_within_repo/buildscript.sh - - - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v3 - with: - category: "/language:${{matrix.language}}" + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v3 + with: + category: "/language:${{matrix.language}}" From 5f1ab5f93565de7258e634eda55be19415cb6ed8 Mon Sep 17 00:00:00 2001 From: zssherman Date: Tue, 9 Sep 2025 12:29:36 -0500 Subject: [PATCH 3/4] CI: Update conda-forge as only option. --- continuous_integration/environment_actions.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/continuous_integration/environment_actions.yml b/continuous_integration/environment_actions.yml index 1effadc..bb0a6d1 100644 --- a/continuous_integration/environment_actions.yml +++ b/continuous_integration/environment_actions.yml @@ -2,7 +2,6 @@ name: radtraq_env channels: - conda-forge - - defaults dependencies: - act-atmos - numpy From ab76bb3e116a86c0982d69cf7744786611f497b7 Mon Sep 17 00:00:00 2001 From: zssherman Date: Tue, 9 Sep 2025 12:36:33 -0500 Subject: [PATCH 4/4] FIX: Update backend to fix memory issues. --- radtraq/tests/test_plotting.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/radtraq/tests/test_plotting.py b/radtraq/tests/test_plotting.py index 399a19d..ac3173f 100644 --- a/radtraq/tests/test_plotting.py +++ b/radtraq/tests/test_plotting.py @@ -1,3 +1,4 @@ +import matplotlib import matplotlib.pyplot as plt import numpy as np import pytest @@ -9,6 +10,8 @@ from radtraq.plotting.corner_reflector import plot_cr_raster from radtraq.plotting.self_consistency import plot_self_consistency +matplotlib.use('Agg') + @pytest.mark.mpl_image_compare(tolerance=10) def test_plotting():