Test updates: stabler debup hash and cli integration coverage

[rugeli]

Problem

follow-up to #419, closes #460

Solution

• added _normalize_for_hashing to sort lists whose element order is not meaningful (e.g. "interior": ["A", "B", "C"], "interior": [ {"object": "green_sphere", "count": 5}, "outer_sphere"] ), while leaving order-sensitive lists(vectors, colors, etc.) unchanged.
• added integration tests in test_pack_cli.py
• refactored aws tests to write temporary files to tmp_path instead of the working dir

One note: this change can alter hash values for recipes that have lists, so re-run the same recipe after this merge may hash differently. Shouldn't cause issues, but worth noting so we can keep an eye on database tidiness.

Type of change

• Refactor (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)

[github-actions]

Packing analysis report

Analysis for packing results located at cellpack/tests/outputs/test_spheres/spheresSST

Ingredient name	Encapsulating radius	Average number packed
ext_A	25	236.0

Packing image

Distance analysis

Expected minimum distance: 50.00
Actual minimum distance: 50.01

Ingredient key	Pairwise distance distribution
ext_A

[rugeli]

a bit out of scope but a simple change, switched tests to write via tmp_path so they leave no trace like test_file.txt in the repo root

[rugeli]

similar to tmp_path in aws tests, we don't want test files written inside the repo, so we change directory to tmp_path with monkeypatch.chdir()

[Copilot]

Pull request overview

This PR strengthens recipe deduplication by normalizing recipe JSON prior to hashing (so semantically equivalent recipes hash the same), and adds/updates tests to cover both the hashing behavior and the CLI workflow.

Changes:

• Add DataDoc._normalize_for_hashing() and update generate_hash() to canonicalize order-insensitive lists while preserving positional numeric lists.
• Add integration tests for cellpack/bin/pack.py covering recipe path input, recipe dict input, and default config behavior.
• Refactor AWS handler tests to write temporary files under tmp_path instead of the working directory.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.

File	Description
cellpack/autopack/DBRecipeHandler.py	Implements normalization logic to produce stable dedup hashes across semantically equivalent JSON.
cellpack/tests/test_data_doc.py	Adds test cases that assert hash stability across dict key order and order-insensitive list permutations.
cellpack/tests/test_pack_cli.py	Introduces CLI integration tests covering recipe-as-path, recipe-as-dict, and default config flows.
cellpack/tests/test_aws_handler.py	Updates tests to use tmp_path for safer cross-platform temp file handling.

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[Copilot]

recipe_data is a module-level dict that gets passed into pack() (directly or via json.dumps). RecipeLoader mutates the input dict when recipe is a dict (it reuses nested references and later replaces objects[*]["representations"]/partners with class instances), so test order can become flaky (e.g., json.dumps(recipe_data) can fail after another test runs). Use a per-test fresh recipe dict (e.g., a pytest fixture returning a new dict or copy.deepcopy(recipe_data) at call sites) before writing/packing.

[meganrm]

looks good, thanks for all the tests

[mogres]

Very clever solution using ._is_positional!! Looks good to me and thanks for adding tests (and fixing the test file issue)!