Milab-6720: fix tsv separator, fix anarci version

[erohinaelena]

Greptile Summary

The PR fixes server-side TSV profiling, restores ANARCI execution in containerized deployments, and migrates three companion software packages to environment-aware builds.

• Separator — the delimiter used to parse tabular fields; workflow arguments now carry stable names such as tab and comma, which the profiler resolves to characters locally.
• Column profile — whole-file evidence describing headers, value types, and likely amino-acid columns; its invocation now avoids tab-character corruption across shell-based runners.
• Software descriptor — metadata describing executable artifacts, commands, images, and entrypoints; software builds now use block-tools software build so local and remote variants include the expected container artifacts.
• ANARCI — the numbering executable used to derive receptor framework and CDR regions; its package moves from 0.0.3 to 1.0.1 so the descriptor records the micromamba container entrypoint.
• Build location — the local or remote destination selected through PL_BUILD_LOCATION; it replaces the legacy PL_PKG_DEV role in root scripts and Turbo cache inputs.
• Package scripts for column profiling, spreadsheet conversion, and region annotation now use Block Tools and portable shx file operations.

Confidence Score: 5/5

The PR appears safe to merge; the changed separator, software-build, and ANARCI dependency paths remain aligned with their current callers and runtime contracts.

The profiler receives a delimiter matching every supported prepared-file representation, the software packages use the repository’s environment-aware build flow, and no concrete incompatibility was found in the ANARCI upgrade.

Important Files Changed

Filename	Overview
software/column-profile/src/main.py	Adds validated named-separator resolution while preserving support for direct single-character delimiters.
workflow/src/prerun.tpl.tengo	Passes comma or tab according to the prepared file extension, keeping CSV, TSV, and converted XLSX profiling aligned.
workflow/src/profile-columns.tpl.tengo	Documents and forwards the named-separator contract to the profiling executable.
software/column-profile/package.json	Migrates software building and packing from package-builder to Block Tools with portable file operations.
software/region-annotation/package.json	Migrates the two-entrypoint region-annotation package to the environment-aware Block Tools build path.
software/xlsx-to-csv/package.json	Migrates spreadsheet-converter software builds and packaging to Block Tools.
pnpm-workspace.yaml	Upgrades the shared ANARCI software package to 1.0.1, whose descriptor records the required container entrypoint.
package.json	Removes obsolete PL_PKG_DEV settings from root test and local-build commands in favor of the existing PL_BUILD_* contract.
turbo.json	Removes the obsolete build-cache input while retaining the environment variables used by Block Tools.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  Input[CSV, TSV, or XLSX] --> Prepare[Prepare readable table]
  Prepare --> Select[Choose named separator]
  Select --> Profile[Resolve name and profile columns]
  Profile --> Mapping[Mapping setup]
  Mapping --> Import[Import records]
  Import --> ANARCI[ANARCI 1.0.1 with recorded entrypoint]
  ANARCI --> Regions[FR and CDR annotation]
  BuildEnv[PL_BUILD variant and location] --> BlockTools[Block Tools software build]
  BlockTools --> Profile
  BlockTools --> ANARCI

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_{Reviews (1): Last reviewed commit: "MILAB-6720: move to software-anarci 1.0...." | Re-trigger Greptile}

Context used (5)

• Context used - Terms is a types in codebase. Provide the list of ... (source)
• Knowledge Base — Column profiling tool
• Knowledge Base — Workflow orchestration and preparation
• Knowledge Base — Import processing tools
• Knowledge Base — Region annotation tool