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* doc/workflow.uml, doc/workflow.png, doc/generate-images.sh: New
files.
* README.md (How to use): New section.
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* README.md (Install development version): New section.
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* pyhegp/pyhegp.py (cat): New function.
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* pyhegp/pyhegp.py (encrypt): Only output key to file optionally.
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* pyhegp/pyhegp.py (encrypt): Use File instead of Path for options.
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Prefixed options are easier to follow than the order of positional
arguments.
* pyhegp/pyhegp.py (encrypt): Turn summary, key and ciphertext
arguments into options.
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* pyhegp/pyhegp.py: Import read_genotype from pyhegp.serialization.
(read_genotype): Move to pyhegp.serialization.
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* pyhegp/pyhegp.py (hegp_encrypt): Standardize before encryption.
(hegp_decrypt): Unstandardize after decryption.
(encrypt): Pass in mean and standard deviation from summary file to
hegp_encrypt.
* tests/test_pyhegp.py (test_hegp_encryption_decryption_are_inverses):
Pass in mean and standard deviation to hegp_encrypt.
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* pyhegp/pyhegp.py (standardize): Standardize using mean and standard
deviation, instead of the minor allele frequency.
(unstandardize): New function.
* tests/test_pyhegp.py: Import standardize and unstandardize from
pyhegp.pyhegp.
(no_column_zero_standard_deviation): New function.
(test_standardize_unstandardize_are_inverses): New test.
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* pyhegp/pyhegp.py: Import namedtuple from collections, and
read_summary from pyhegp.serialization.
(Stats): New type.
(pool_stats, pool): New functions.
* tests/test_pyhegp.py: Import Stats and pool_stats from
pyhegp.pyhegp.
(test_pool_stats): New test.
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* pyhegp/pyhegp.py: Import Summary and write_summary from
pyhegp.serialization.
(summary): New function.
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* doc/file-formats.md, pyhegp/serialization.py,
tests/test_serialization.py: New files.
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Decryption does not make much sense with HEGP. And, the added
complexity of standardization makes it even less attractive.
* pyhegp/pyhegp.py (decrypt): Delete function.
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* .guix/pyhegp-package.scm: Import python-pytest with guix: prefix.
(python-pytest): New variable.
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It may be better to sample a smaller set of matrices finely than a
large set of matrices coarsely.
* tests/test_pyhegp.py (test_hegp_encryption_decryption_are_inverses):
Use default array shapes testing encryption/decryption.
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* tests/test_pyhegp.py (test_hegp_encryption_decryption_are_inverses):
Reduce maximum matrix size to 100.
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* pyhegp/__init__.py: New file.
* pyhegp.py: Move to pyhegp/pyhegp.py.
* test_pyhegp.py: Move to tests/test_pyhegp.py. Import from
pyhegp.pyhegp instead of from pyhegp.
* pyproject.toml (project.scripts)[pyhegp]: Switch to
pyhegp.pyhegp:main.
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* guix.scm: Import python-hypothesis-next instead of
python-hypothesis.
(python-pyhegp)[native-inputs]: Replace python-hypothesis with
python-hypothesis-next.
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* guix.scm: Link to .guix/pyhegp-package.scm instead of
.guix/pyhegp-project.scm.
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* pyhegp.py (read_genotype): Remove obsolete commented out code.
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* .guix-channel: New file.
* guix.scm: Move to ...
* .guix/pyhegp-package.scm: ... here as its own module.
* guix.scm: Link to .guix/pyhegp-package.scm.
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* test_pyhegp.py: New file.
* README.md (Run tests): New section.
* guix.scm: Import python-hypothesis from (gnu packages check).
(python-pyhegp)[arguments]: Enable tests.
[native-inputs]: Add python-hypothesis.
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* README.md: Add missing preposition "in".
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