From bcdb235949c06db07172b0c6355a0059436b86fb Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Mon, 4 Aug 2025 12:52:39 +0100
Subject: Standardize file formats in the likeness of plink files.

* pyhegp/pyhegp.py: Import pandas.
(summary, pool, encrypt, cat): Use pandas data frames and new data
format.
* pyhegp/serialization.py: Import csv and pandas.
(Summary)[mean, std]: Delete fields.
[data]: New field.
(read_summary, write_summary, read_genotype, write_genotype): Use
pandas data frames and new data format.
* tests/test_serialization.py: Import column, columns and data_frames
from hypothesis.extra.pandas; pandas; negate from pyhegp.utils. Do not
import hypothesis.extra.numpy and approx from pytest.
(tabless_printable_ascii_text, chromosome_column, position_column,
reference_column, sample_names): New variables.
(summaries, genotype_reserved_column_name_p, genotype_frames): New
functions.
(test_read_write_summary_are_inverses): Use pandas data frames and new
data format.
(test_read_write_genotype_are_inverses): Use pandas for testing.
* doc/file-formats.md (File formats)[summary file]: Describe new
standard.
[genotype file]: New section.
* .guix/pyhegp-package.scm (pyhegp-package): Import python-pandas
from (gnu packages python-science).
(python-pyhegp)[propagated-inputs]: Add python-pandas.
* pyproject.toml (dependencies): Add pandas.
---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

(limited to 'pyproject.toml')

diff --git a/pyproject.toml b/pyproject.toml
index c0a6ab2..636a56d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -18,6 +18,7 @@ license = {file = "COPYING"}
 dependencies = [
   "click",
   "numpy",
+  "pandas",
   "scipy"
 ]
 
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cgit 1.4.1