Feat/glab hosts

[pgierz]

closes #96

This automatically detects the gitlab host you used and injects it into the provided snakemake module.

Summary by CodeRabbit

• New Features
  • Added support for specifying a custom host during deployment.
  • Improved compatibility with self-hosted GitHub and GitLab instances when generating source declarations.
  • Maintains backward compatibility: if no host is provided, behavior remains unchanged.

[coderabbitai[bot]]

📝 Walkthrough

Walkthrough

Introduces an optional host parameter across deployment and provider APIs. WorkflowDeployer now stores host and passes it to provider.get_source_file_declaration. Providers (Github, Gitlab, Local) accept host; Gitlab derives host from non-gitlab.com URLs when not provided. The top-level deploy() signature includes host but may not pass it into WorkflowDeployer.

Changes

Cohort / File(s)	Summary
Public API: host parameter snakedeploy/deploy.py	Adds host: Optional[str] to WorkflowDeployer.init and deploy() signatures; stores self.host; passes host to provider when rendering module declaration. Note: deploy() currently doesn’t propagate host to WorkflowDeployer instance per summary.
Providers: host-aware source declaration snakedeploy/providers.py	Adds host: Optional[str] to Provider.get_source_file_declaration across Provider, Local, Github, Gitlab. Gitlab uses host if provided or derives from URL when non-gitlab.com; Github optionally includes host; Local ignores host in declaration. Typing/import cleanups; PROVIDERS list unchanged.

Sequence Diagram(s)

sequenceDiagram
  autonumber
  actor User
  participant CLI as CLI / deploy()
  participant WD as WorkflowDeployer
  participant Prov as Provider (Gitlab/Github/Local)
  participant FS as Filesystem

  User->>CLI: deploy(source_url, ..., host?)
  CLI->>WD: new WorkflowDeployer(..., host?)  %% If propagated
  note over WD: Stores self.host
  WD->>Prov: get_source_file_declaration(path, tag, branch, host=self.host)
  alt Provider = Gitlab
    note right of Prov: If host is None and URL not gitlab.com,<br/>derive host from URL
  end
  Prov-->>WD: source-file declaration string
  WD->>FS: Write Snakefile with module declaration
  FS-->>User: Snakefile created/updated

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~25 minutes

Assessment against linked issues

Objective	Addressed	Explanation
Support host in GitLab module declaration so non-gitlab.com URLs include host (e.g., gitlab.awi.de) [#96]	✅

Assessment against linked issues: Out-of-scope changes

Code Change	Explanation
Add optional host handling to Github.get_source_file_declaration (snakedeploy/providers.py)	Issue #96 concerns GitLab hosts only; extending Github is not required by the stated objective.
Add host parameter to Local.get_source_file_declaration (snakedeploy/providers.py)	Local provider host handling is unrelated to GitLab host support requested in #96.
Extend public deploy() API to include host (snakedeploy/deploy.py)	Changing the top-level API is not explicitly required to solve GitLab host declaration; internal derivation in GitLab provider would suffice.

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