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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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The authentication/authorisation stuff is being moved to a separate
repository. This commit removes the documentation for how to run migrations
from this repository since it has been moved over to the new repository.
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Document some CLI utility commands useful for development and for supporting
the operation of the GN3 app.
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A script to assign existing data not assigned to any group to publicly-visible
resources.
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Bcrypt is now somewhat vulnerable to offline cracking, so we move our password
hashing over to Argon2.
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Add code to implement the OAuth2 flow.
* Add test fixtures for setting up users and OAuth2 clients
* Add tests for token generation with the "Password Grant" flow
* Fix some issues with test due to changes in the database connection's
row_factory
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* .gitignore: ignore all yoyo configuration files
* README.md: Update documentation
* yoyo.auth.ini: stop tracking the yoyo configuration file.
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Initialise the authentication/authorisation system packages and set up the
initial database migrations to set up the system.
* README.md: Add documentation on migrations
* gn3/auth/__init__.py: init package
* gn3/auth/authentication/__init__.py: init package
* gn3/auth/authorisation/__init__.py: init package
* gn3/migrations.py: provide migration utilities
* migrations/auth/20221103_01_js9ub-initialise-the-auth-entic-oris-ation-database.py:
new migration
* tests/unit/auth/test_init_database.py: test new migration applies and rolls
back as expected
* tests/unit/conftest.py: fixtures for unit tests
* yoyo.auth.ini: basic configuration for yoyo-migration for auth system
migrations
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* README.md: Update link to continuous deployment.
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* README.md: update mypy's invocation
* scripts/argparse_actions.py: new file - implement custom FileCheck action
for argparse
* scripts/sample_correlations.py: new file - implement new script to run
sample correlations in an external process
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* Add a new script to compute the partial correlations against:
- a select list of traits, or
- an entire dataset
depending on the specified subcommand. This new script is meant to supercede
the `scripts/partial_correlations.py` script.
* Fix the check for errors
* Reorganise the order of arguments for the
`partial_correlations_with_target_traits` function: move the `method`
argument before the `target_trait_names` argument so that the common
arguments in the partial correlation computation functions share the same
order.
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* README.md: Link to continuous deployment.
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The CI has been migrated from penguin2.genenetwork.org to ci.genenetwork.org.
* README.md: Update CI badge subdomain.
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* Document the things that the partial correlations feature depends on to work
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This reverts commit f676c291967f8a81836b73c5a5dcd3c65e02552c.
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We now have separate CI jobs for the pylint and mypy tests.
* README.md: Add pylint and mypy CI badges.
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The CI has been moved to penguin2, and this is accompanied by a URI change.
* README.md: Update link to CI badge.
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* README.md: Link CI badge to CI status page.
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* README.md: Add CI badge.
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* README.md, guix.scm: Replace guix environment with guix shell.
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It is safe to assume that the user has correctly set up guix in their PATH.
* README.md: Disuse absolute paths to guix in command invocations.
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guix-bioinformatics is a Guix channel that is set up by `guix pull'. There is
no need to specify it explicitly using GUIX_PACKAGE_PATH.
* README.md: Do not explicitly set GUIX_PACKAGE_PATH for any command.
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heatmap_generation
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* Provide documentation on downloading and using the genotype files.
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* README.md: update header: Traits ==> Trait
* gn3/computations/qtlreaper.py: update header: Traits ==> Trait
* qtlfilesexport.py: Choose only BXD strains
Rename the first column header from "Traits" to "Trait" to correspond with
what `rust-qtlreaper` expects.
Choose only the BXD strains for the proof-of-concept example - this helped
bring out the fact that the traits file SHOULD NOT contain a strain column
for a strain that does not exist in the genotype file in consideration.
If the traits file has a strain column which does not exist in the genotype
file, then `rust-qtlreaper` fails with a panic, since, from what I can tell,
it tries to get a value from the genotype file for the non-existent strain,
which results to a `None` type. Subsequent attempts at running an operation
on the `None` type lead to the panic.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/heatmaps/heatmaps.py: document format of the traits file
To assist future developers, and development of the system, this commit
documents some of the hard-won knowledge about the operation of the system
to ease future development of the system.
The documentation, if good, might also help with future onboarding of new
developers to the system.
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