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Pull Request Overview
This PR modernizes AlphaTims' README and Docker configuration to current standards. It improves the project's documentation structure and adds Docker publishing capabilities for better distribution and deployment workflows.
- Restructures README with improved navigation, installation instructions, and visual elements
- Updates Docker configuration for better security practices and modern Python base image
- Adds automated Docker image publishing workflow
Reviewed Changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| pyproject.toml | Updates project metadata including keywords ordering, URL structure, and repository references |
| README.md | Major restructuring with new logo section, improved installation guides, and reorganized content |
| Dockerfile | Modernizes Docker setup with security best practices and updated base image |
| CHANGELOG.md | Extracts historical changelog from README into dedicated file |
| .github/workflows/publish_docker_image.yml | Adds automated Docker image publishing workflow |
Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.
| "proteomics", | ||
| "bioinformatics", | ||
| "data indexing", | ||
| "AlphaPept", |
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The keywords list contains duplicate 'AlphaPept' entries. Line 22 has 'AlphaPept' and line 23 has 'AlphaPept ecosystem', which creates redundancy in the keywords.
README.md
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| * [**One-click GUI installation:**](#one-click-gui-installation) Choose this installation if you only want the GUI and/or keep things as simple as possible. | ||
| * [**Pip installation:**](#pip-installation) Choose this installation if you want to use AlphaTims as a Python package in an existing Python 3.8 environment (e.g. a Jupyter notebook). If needed, the GUI and CLI can be installed with pip as well. | ||
| * [**Developer installation:**](#developer-installation) Choose this installation if you are familiar with CLI tools, [conda](https://docs.conda.io/en/latest/) and Python. This installation allows access to all available features of AlphaTims and even allows to modify its source code directly. Generally, the developer version of AlphaTims outperforms the precompiled versions which makes this the installation of choice for high-throughput experiments. | ||
| * [**Docker installation:**](#docker-installation) Use this installation if you want to use a container based workflow. This is usefull to preserve a clean environment or when running multiple tools that might have conflicting dependencies. --> |
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There's a typo in 'usefull' which should be 'useful'. Also, there's a stray HTML comment closing tag '-->' at the end of the line.
| * [**Docker installation:**](#docker-installation) Use this installation if you want to use a container based workflow. This is usefull to preserve a clean environment or when running multiple tools that might have conflicting dependencies. --> | |
| * [**Docker installation:**](#docker-installation) Use this installation if you want to use a container based workflow. This is useful to preserve a clean environment or when running multiple tools that might have conflicting dependencies. |
README.md
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| This is indicated by a dialog telling you `“alphatims. ... .pkg” Not Opened`. | ||
| 1. Close this dialog by clicking `Done`. | ||
| 2. Choose `Apple menu` > `System Settings`, then `Privacy & Security` in the sidebar. (You may need to scroll down.) | ||
| 3. Go to `Security`, locate the line "alphadia.pkg was blocked to protect your Mac" then click `Open Anyway`. |
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The package name should be 'alphatims.pkg' not 'alphadia.pkg' to match the correct package being installed.
| 3. Go to `Security`, locate the line "alphadia.pkg was blocked to protect your Mac" then click `Open Anyway`. | |
| 3. Go to `Security`, locate the line "alphatims.pkg was blocked to protect your Mac" then click `Open Anyway`. |
Dockerfile
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| # to allow other host ports than 5006 | ||
| ENV BOKEH_ALLOW_WS_ORIGIN=localhost | ||
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| #USER alphatimsuser |
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The USER directive is commented out, which means the container will run as root. This violates security best practices. The container should run as the non-privileged 'alphatimsuser' that was created.
| #USER alphatimsuser | |
| USER alphatimsuser |
1 participant
Bringt Readme and Dockerfile to latest standard, adds Docker publishing workflow