pathmorph 0.2.1

Invertible directory structure transformations with schema-driven path remapping

pathmorph

Invertible directory structure transformations.

pathmorph lets you remap a directory layout to a different schema and restore the original at any time — with zero external state beyond a small JSON manifest embedded in the packed directory.

It is designed to be:

• Composable — fits naturally into shell pipelines and Makefiles
• Reproducible — the manifest is a ground-truth record of every file move
• Format-agnostic — schemas can be written in YAML, TOML, or JSON
• Dependency-light — confuk, omegaconf, rich, typer; nothing heavier

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Motivation

Pipeline tools tend to emit outputs in machine-friendly directory structures: short IDs, flat hierarchies, terse filenames. Collaborators often expect something different: descriptive names, nested grouping, human-readable paths.

pathmorph lets you have both. Define the mapping as a schema, pack when you need the human layout, unpack when you need the original back.

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Installation

pip install pathmorph

# Optional: faster hashing for large directories
pip install pathmorph[xxhash]

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Quickstart

1. Write a schema (my_schema.yaml/toml/json):

schema:
  name: human_v1
  description: "Friendly layout for collaborators"
  fallback: passthrough   # or: omit/cram

  rules:
    - pattern: "runs/(?P<exp>[^/]+)/(?P<variant>[^/]+)/scores\\.tsv"
      target:  "experiments/{exp}/candidates/{variant}/developability_scores.tsv"

    - pattern: "runs/(?P<exp>[^/]+)/(?P<variant>[^/]+)/(?P<rest>.+)"
      target:  "experiments/{exp}/candidates/{variant}/{rest}"

Each rule is a Python re full-match pattern with named capture groups. The target is a format string that references those groups via {name}.

Rules are evaluated in order — the first match wins.

fallback controls what happens when no rule matches:

• passthrough — file is copied as-is (default)
• omit — file is skipped entirely
• cram – file is crammed into the subdirectory path specified in the crampath variable in the schema

You can also use symlinks that match against a pre-existing rule via its id:

[[schema.rules]]
id      = "scores"          # optional id — required if referenced by a symlink rule
pattern = 'runs/(?P<exp>[^/]+)/(?P<variant>[^/]+)/scores\.tsv'
target  = "experiments/{exp}/candidates/{variant}/scores.tsv"

[[schema.rules]]
symlink = "scores"          # references the rule above by id
target  = "latest/{exp}/{variant}/scores.tsv"

[!note] TOML/YAML/JSON schema files are supported

There are three implicit variables always available in target:

Variable	Value for outputs/o01/o01_docked_result.txt
{__name__}	o01_docked_result.txt
{__stem__}	o01_docked_result
{__suffix__}	.txt

And you can leverage confuk/omegaconf's variable interpolation to avoid repeating RegEx patterns:

exp_pattern = '(?P<exp>exp\d+[^/]+)'
variant_pattern = '(?P<variant>v\d+[^/]+)'

[[schema.rules]]
pattern = 'runs/${exp_pattern}/${variant_pattern}/scores\.tsv'
target  = "experiments/{exp}/candidates/{variant}/scores.tsv"

[[schema.rules]]
pattern = 'runs/${exp_pattern}/${variant_pattern}/logs'
target  = "experiments/{exp}/candidates/{variant}/Reports"

2. Preview the mapping (dry-run, no filesystem changes):

pathmorph diff ./pipeline_output -s my_schema.yaml

3. Pack into the human layout:

pathmorph pack ./pipeline_output -d ./for_collaborators -s my_schema.yaml

This copies files (non-destructive by default) and writes ./for_collaborators/.pathmorph_manifest.json.

4. Restore the original layout:

pathmorph unpack ./for_collaborators ./restored_original

5. Verify integrity:

pathmorph verify ./for_collaborators

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Command reference

pack

pathmorph pack SRCS -d/--dst DST -s/--schema SCHEMA [OPTIONS]

Options:
  --move                   Move files instead of copying
  --handle-existing        abort | skip | overwrite
                           (prompts interactively if omitted)
  --hash ALGO              sha256 (default), sha1, md5, blake2b,
                           xxh64, xxh128, xxh3_64, xxh3_128

unpack

pathmorph unpack PACKED_DIR DST [OPTIONS]

Options:
  --move                   Move files instead of copying
  --handle-existing        abort | skip | overwrite

diff

pathmorph diff SRCS -s/--schema SCHEMA [OPTIONS]

Options:
  --show-passthrough / --hide-passthrough   (default: show)

verify

pathmorph verify PACKED_DIR

Exit code 0 on success, 1 if any file fails.

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Schema formats

pathmorph accepts any format supported by confuk: .yaml, .yml, .toml, .json.

See examples/ for the same schema in YAML and TOML.

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Manifest

A packed directory is self-describing. The manifest at .pathmorph_manifest.json records:

{
  "version": 1,
  "schema_name": "human_v1",
  "schema_description": "...",
  "packed_at": "2026-04-29T...",
  "algorithm": "sha256",
  "entries": [
    {
      "original": "runs/exp_001/A/scores.tsv",
      "packed":   "experiments/exp_001/candidates/A/developability_scores.tsv",
      "hash":     "abc123...",
      "algorithm": "sha256"
    }
  ]
}

unpack uses the entry table directly — it does not re-evaluate schema rules. This means the manifest is a durable, schema-version-independent record: even if you later change the schema, existing packed directories remain unpackable.

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Using as a library

from pathlib import Path
from pathmorph import pack, unpack, verify, diff
from pathmorph.schemas import Schema
from pathmorph.collision import CollisionStrategy

schema = Schema.from_file(Path("my_schema.yaml"))

# Dry-run
records = diff(Path("./pipeline_output"), schema)

# Pack
result = pack(
    Path("./pipeline_output"),
    Path("./for_collaborators"),
    schema=schema,
    collision=CollisionStrategy.SKIP,
    hash_algorithm="sha256",
)

# Verify
verify_result = verify(Path("./for_collaborators"))
assert verify_result.passed

# Restore
unpack(Path("./for_collaborators"), Path("./restored"))

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Development

git clone https://github.com/yourusername/pathmorph
cd pathmorph
pip install -e ".[dev]"
pytest

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License

MIT