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We no longer commit the built images into the git repository.
Committing build artifacts into the repository is never good practice.
And, linking to CI build artifacts is also more automatic and
seamless.
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This is so that we don't end up with long Guix store hashes in the
output filename when these images are built on CI using the Guix
computed-file.
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* doc/file-formats.md (File formats)[key file]: New section.
* pyhegp/serialization.py: Import numpy.
(read_key, write_key): New functions.
* pyhegp/pyhegp.py: Import write_key from pyhegp.serialization.
(encrypt): Use write_key.
* tests/test_serialization.py: Import arrays and array_shapes from
hypothesis.extra.numpy; approx from pytest; read_key and write_key
from pyhegp.serialization.
(test_read_write_key_are_inverses): New test.
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* README.md (How to use): Indent down into "Joint/federated analysis
with many data owners" section.
[Simple data sharing]: New section.
* doc/generate-images.sh: Add simple workflow.
* doc/workflow.png: Rename to doc/joint-workflow.png.
* doc/workflow.uml: Rename to doc/joint-workflow.uml.
* doc/simple-workflow.png, doc/simple-workflow.uml: New files.
* tests/test_pyhegp.py: Import pytest.
(test_simple_workflow): New test.
* test-data/genotype.tsv: New file.
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* 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.
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* pyhegp/serialization.py (read_summary, write_summary): Use tab as
the delimiter.
* doc/file-formats.md (File formats)[summary file]: Update
documentation.
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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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* doc/file-formats.md, pyhegp/serialization.py,
tests/test_serialization.py: New files.
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