docs: improve README setup clarity and Docker instructions

[incursio-xd]

Fixes documentation issues in README.md.

Changes:

• Standardized Docker commands to use modern docker compose syntax
• Added Python prerequisite clarification
• Improved .env security note to avoid accidental token commits
• Minor setup clarity improvements

These are small documentation fixes with no functional changes.
Related to: #174

Summary by CodeRabbit

Release Notes

• Documentation
  • Improved README clarity with standardized wording and better overall organization.
  • Expanded prerequisites section with specific Python version requirements and dependencies.
  • Enhanced local setup instructions with clearer step-by-step guidance for users.
  • Clarified Docker deployment workflow with detailed build and launch instructions.
  • Added important security guidance for properly handling GitHub tokens in Docker setups.

[coderabbitai]

📝 Walkthrough

Walkthrough

README.md documentation updates standardizing and expanding content across multiple sections. Changes include refined wording, expanded "Run Locally" prerequisites, clarified Docker setup with two-Dockerfile explanation, explicit command examples, security notes, and updated references formatting.

Changes

Cohort / File(s)	Summary
Documentation Updates README.md	Standardized wording and capitalization; expanded "Run Locally" with new Prerequisites subsection (Python 3.9+, pip); reordered setup steps; reworked Docker instructions with two-Dockerfile descriptions, explicit docker/docker-compose commands, port mapping examples, and GitHub token security note; updated references with PMID formatting.

Possibly related PRs

• update Readme (Several way to run app) #267: Related README.md expansion covering "Run Locally" and Docker sections with similar two-Dockerfile explanation, explicit commands, and security considerations.

Suggested reviewers

• t0mdavid-m

Poem

🐰 The README hops with clarity so bright,
Prerequisites listed, Docker paths right,
Two Dockerfile friends now dance in the fold,
With tokens kept safe and port secrets told,
Documentation magic, a rabbit's delight! ✨

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately describes the main changes: documentation improvements to README setup clarity and Docker instructions, which aligns with the actual file modifications.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

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• Create PR with unit tests
• Post copyable unit tests in a comment

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[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@README.md`:
- Around line 92-94: Update the three fenced code blocks in README that
currently lack language specifiers: add "env" (or "text") to the block
containing GITHUB_TOKEN (the block showing GITHUB_TOKEN=<your-github-token>),
add "text" (or "console") to the Docker build output block (the block showing
"[+] Running 2/2 ... Built / Started"), and add "text" (or "console") to the
docker compose ps output block (the block showing "CONTAINER ID   IMAGE ...
4abe0603e521 ..."); ensure each opening triple-backtick includes the chosen
language label (e.g., ```env, ```text) so markdownlint MD040 is satisfied.

[coderabbitai]

⚠️ Potential issue | 🟡 Minor

Add language specifiers to the three fenced code blocks flagged by markdownlint (MD040).

Three code blocks are missing language identifiers, which triggers markdownlint rule MD040 in CI:

• Line 92: .env contents → use `env or `text
• Line 109: Docker build output → use `text or `console
• Line 116: docker compose ps output → use `text or `console

📝 Proposed fix

-   ```
+   ```env
    GITHUB_TOKEN=<your-github-token>
    ```

-   ```
+   ```text
    [+] Running 2/2
     ✔ openms-streamlit-template            Built
     ✔ Container openms-streamlit-template  Started
    ```

-   ```
+   ```text
    CONTAINER ID   IMAGE  ...
    4abe0603e521   ...
    ```

Also applies to: 109-113, 116-119

🧰 Tools

🪛 markdownlint-cli2 (0.21.0)

[warning] 92-92: Fenced code blocks should have a language specified

(MD040, fenced-code-language)

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@README.md` around lines 92 - 94, Update the three fenced code blocks in
README that currently lack language specifiers: add "env" (or "text") to the
block containing GITHUB_TOKEN (the block showing
GITHUB_TOKEN=<your-github-token>), add "text" (or "console") to the Docker build
output block (the block showing "[+] Running 2/2 ... Built / Started"), and add
"text" (or "console") to the docker compose ps output block (the block showing
"CONTAINER ID   IMAGE ... 4abe0603e521 ..."); ensure each opening
triple-backtick includes the chosen language label (e.g., ```env, ```text) so
markdownlint MD040 is satisfied.

[t0mdavid-m]

This is a huge diff that does not really change much. Could you reopen a PR that fixes the numbering issues? The rest of the doc changes seem unnecessary to me. Especially, we do not need to show expected docker output.