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.

1 files changed, 2 insertions, 1 deletions

diff --git a/.guix/pyhegp-package.scm b/.guix/pyhegp-package.scm
index cf132c5..6778e38 100644
--- a/.guix/pyhegp-package.scm
+++ b/.guix/pyhegp-package.scm
@@ -20,7 +20,7 @@
   #:use-module ((gnu packages check) #:select (python-hypothesis-next))
   #:use-module ((gnu packages check) #:select (python-pytest) #:prefix guix:)
   #:use-module ((gnu packages python-build) #:select (python-flit-core))
-  #:use-module ((gnu packages python-science) #:select (python-scipy))
+  #:use-module ((gnu packages python-science) #:select (python-pandas python-scipy))
   #:use-module ((gnu packages python-xyz) #:select (python-click python-numpy))
   #:use-module (guix build-system pyproject)
   #:use-module (guix gexp)
@@ -53,6 +53,7 @@
     (propagated-inputs
      (list python-click
            python-numpy
+           python-pandas
            python-scipy))
     (home-page "https://github.com/encryption4genetics/pyhegp")
     (synopsis "Homomorphic encryption of genotypes and phenotypes")