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Feat: Publish new PubMed MCP server (#41)
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‎pubmed-mcp-server/.actor/actor.json‎

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{
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"actorSpecification": 1,
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"name": "pubmed-mcp-server",
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"title": "PubMed MCP server",
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"description": "A server implementing the Model Context Protocol (MCP) for accessing and processing PubMed biomedical literature data.",
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"version": "0.0",
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"buildTag": "latest",
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"usesStandbyMode": true,
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"meta": {
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"templateId": "python-mcp-server"
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},
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"dockerfile": "../Dockerfile",
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"webServerMcpPath": "/mcp"
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}

‎pubmed-mcp-server/.actor/pay_per_event.json‎

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{
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"actor-start": {
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"eventTitle": "MCP server startup",
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"eventDescription": "Initial fee for starting the MCP Server Actor",
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"eventPriceUsd": 0.1
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},
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"searchPubmedKeywords": {
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"eventTitle": "PubMed keyword search",
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"eventDescription": "Fee for searching PubMed articles by keywords.",
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"eventPriceUsd": 0.0001
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},
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"searchPubmedAdvanced": {
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"eventTitle": "PubMed advanced search",
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"eventDescription": "Fee for advanced search on PubMed articles.",
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"eventPriceUsd": 0.0002
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},
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"getPubmedArticleMetadata": {
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"eventTitle": "Get PubMed article metadata",
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"eventDescription": "Fee for retrieving metadata for a PubMed article.",
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"eventPriceUsd": 0.00005
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},
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"downloadPubmedPdf": {
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"eventTitle": "Download PubMed article PDF",
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"eventDescription": "Fee for downloading a PubMed article PDF.",
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"eventPriceUsd": 0.0005
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},
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"deepPaperAnalysis": {
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"eventTitle": "Deep analysis of PubMed paper",
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"eventDescription": "Fee for running deep analysis on a PubMed paper.",
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"eventPriceUsd": 0.001
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}
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}

‎pubmed-mcp-server/.gitignore‎

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.mise.toml
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.nvim.lua
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storage
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# The rest is copied from https://github.com/github/gitignore/blob/main/Python.gitignore
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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.python-version
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/latest/usage/project/#working-with-version-control
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.pdm.toml
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.pdm-python
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.pdm-build/
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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.idea/
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# Visual Studio Code
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# Ignores the folder created by VS Code when changing workspace settings, doing debugger
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# configuration, etc. Can be commented out to share Workspace Settings within a team
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.vscode
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# Zed editor
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# Ignores the folder created when setting Project Settings in the Zed editor. Can be commented out
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# to share Project Settings within a team
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.zed
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# Added by Apify CLI
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node_modules

‎pubmed-mcp-server/.ruff.toml‎

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exclude = ["PubMed-MCP-Server/*"]
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‎pubmed-mcp-server/Dockerfile‎

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# First, specify the base Docker image.
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# You can see the Docker images from Apify at https://hub.docker.com/r/apify/.
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# You can also use any other image from Docker Hub.
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FROM apify/actor-python:3.13
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# Second, copy just requirements.txt into the Actor image,
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# since it should be the only file that affects the dependency installation in the next step,
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# in order to speed up the build.
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COPY requirements.txt ./
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# Install the packages specified in requirements.txt,
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# print the installed Python version, pip version,
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# and all installed packages with their versions for debugging.
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RUN echo "Python version:" \
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&& python --version \
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&& echo "Pip version:" \
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&& pip --version \
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&& echo "Installing dependencies:" \
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&& pip install -r requirements.txt \
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&& echo "All installed Python packages:" \
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&& pip freeze
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# Next, copy the remaining files and directories with the source code.
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# Since we do this after installing the dependencies, quick builds will be really fast
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# for most source file changes.
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COPY . ./
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# Use compileall to ensure the runnability of the Actor Python code.
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RUN python3 -m compileall -q src/
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# Specify how to launch the source code of your Actor.
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# By default, the "python3 -m ." command is run.
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CMD ["python3", "-m", "src"]

‎pubmed-mcp-server/PubMed-MCP-Server/.gitignore‎

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# Python-generated files
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__pycache__/
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*.py[oc]
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build/
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dist/
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wheels/
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*.egg-info
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# Virtual environments
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.venv

‎pubmed-mcp-server/PubMed-MCP-Server/Dockerfile‎

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# Generated by https://smithery.ai. See: https://smithery.ai/docs/config#dockerfile
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FROM python:3.10-alpine
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# Install necessary system dependencies
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RUN apk add --no-cache gcc musl-dev linux-headers
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WORKDIR /app
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# Copy the entire repository to the container
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COPY . .
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# Install Python dependencies
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RUN pip install --no-cache-dir -r requirements.txt
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# Expose ports if needed (not required for stdio transport)
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CMD ["python", "pubmed_server.py"]

‎pubmed-mcp-server/PubMed-MCP-Server/LICENSE‎

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MIT License
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Copyright (c) 2025 JackKuo666
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

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