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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,93 @@ | ||
| # 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: | ||
| branches: [ "main" ] | ||
| schedule: | ||
| - cron: '23 2 * * 6' | ||
|
|
||
| jobs: | ||
| analyze: | ||
| name: Analyze (${{ matrix.language }}) | ||
| # Runner size impacts CodeQL analysis time. To learn more, please see: | ||
| # - https://gh.io/recommended-hardware-resources-for-running-codeql | ||
| # - https://gh.io/supported-runners-and-hardware-resources | ||
| # - https://gh.io/using-larger-runners (GitHub.com only) | ||
| # Consider using larger runners or machines with greater resources for possible analysis time improvements. | ||
| runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }} | ||
| timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }} | ||
| permissions: | ||
| # required for all workflows | ||
| security-events: write | ||
|
|
||
| # required to fetch internal or private CodeQL packs | ||
| packages: read | ||
|
|
||
| # only required for workflows in private repositories | ||
| actions: read | ||
| contents: read | ||
|
|
||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| include: | ||
| - language: python | ||
| build-mode: none | ||
| # CodeQL supports the following values keywords for 'language': 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift' | ||
| # Use `c-cpp` to analyze code written in C, C++ or both | ||
| # Use 'java-kotlin' to analyze code written in Java, Kotlin or both | ||
| # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both | ||
| # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis, | ||
| # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning. | ||
| # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how | ||
| # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages | ||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
|
|
||
| # Initializes the CodeQL tools for scanning. | ||
| - name: Initialize CodeQL | ||
| uses: github/codeql-action/init@v3 | ||
| with: | ||
| languages: ${{ matrix.language }} | ||
| build-mode: ${{ matrix.build-mode }} | ||
| # If you wish to specify custom queries, you can do so here or in a config file. | ||
| # By default, queries listed here will override any specified in a config file. | ||
| # Prefix the list here with "+" to use these queries and those in the config file. | ||
|
|
||
| # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs | ||
| # queries: security-extended,security-and-quality | ||
|
|
||
| # If the analyze step fails for one of the languages you are analyzing with | ||
| # "We were unable to automatically build your code", modify the matrix above | ||
| # to set the build mode to "manual" for that language. Then modify this step | ||
| # to build your code. | ||
| # ℹ️ Command-line programs to run using the OS shell. | ||
| # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun | ||
| - if: matrix.build-mode == 'manual' | ||
| shell: bash | ||
| run: | | ||
| echo 'If you are using a "manual" build mode for one or more of the' \ | ||
| 'languages you are analyzing, replace this with the commands to build' \ | ||
| 'your code, for example:' | ||
| echo ' make bootstrap' | ||
| echo ' make release' | ||
| exit 1 | ||
| - name: Perform CodeQL Analysis | ||
| uses: github/codeql-action/analyze@v3 | ||
| with: | ||
| category: "/language:${{matrix.language}}" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| # This workflows will upload a Python Package using Twine when a release is created | ||
| # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries | ||
|
|
||
| name: tests | ||
|
|
||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| - npe2 | ||
| tags: | ||
| - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10 | ||
| pull_request: | ||
| branches: | ||
| - main | ||
| - npe2 | ||
| workflow_dispatch: | ||
|
|
||
| env: | ||
| OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }} | ||
|
|
||
| jobs: | ||
|
|
||
| deploy: | ||
| # this will run when you have tagged a commit, starting with "v*" | ||
| # and requires that you have put your twine API key in your | ||
| # github secrets (see readme for details) | ||
| needs: [ test ] | ||
| runs-on: ubuntu-latest | ||
| if: contains(github.ref, 'tags') | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Set up Python | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: "3.x" | ||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install -U setuptools setuptools_scm wheel twine build | ||
| - name: Build and publish | ||
| env: | ||
| TWINE_USERNAME: __token__ | ||
| TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }} | ||
| run: | | ||
| git tag | ||
| python -m build . | ||
| twine upload dist/* |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,11 +1,11 @@ | ||
| [metadata] | ||
| name = napari-chatgpt | ||
| version = v2024.3.13.3 | ||
| version = v2024.5.15 | ||
| description = A napari plugin to process and analyse images with chatGPT. | ||
| long_description = file: README.md | ||
| long_description_content_type = text/markdown | ||
| url = https://github.com/royerlab/napari-chatgpt | ||
| author = Loic A. Royer | ||
| author = Loic A. Royer and contributors | ||
| author_email = [email protected] | ||
| license = BSD-3-Clause | ||
| license_files = LICENSE | ||
|
|
@@ -36,9 +36,11 @@ install_requires = | |
| scikit-image | ||
| qtpy | ||
| QtAwesome | ||
| langchain==0.1.11 | ||
| langchain-openai==0.0.8 | ||
| openai==1.13.3 | ||
| langchain==0.2.0rc2 | ||
| langchain-community==0.2.0rc1 | ||
| langchain-openai==0.1.6 | ||
| langchain-anthropic==0.1.11 | ||
| openai==1.29.0 | ||
| anthropic | ||
| fastapi | ||
| uvicorn | ||
|
|
@@ -52,7 +54,7 @@ install_requires = | |
| xarray | ||
| arbol | ||
| playwright | ||
| duckduckgo_search | ||
| duckduckgo_search==5.3.0b4 | ||
| ome-zarr | ||
| transformers | ||
| cryptography | ||
|
|
@@ -64,6 +66,9 @@ install_requires = | |
| jedi | ||
| black | ||
|
|
||
| # needed because lxml has spun out this code out of its main repo: | ||
| lxml_html_clean | ||
|
|
||
|
|
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| python_requires = >=3.9 | ||
| include_package_data = True | ||
|
|
@@ -90,6 +95,5 @@ testing = | |
| napari | ||
| pyqt5 | ||
|
|
||
|
|
||
| [options.package_data] | ||
| * = *.yaml | ||
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