| Age | Commit message (Expand) | Author |
|---|
| 2024-09-23 | Add section on setting up virtuoso locally....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Update docs to use default virtuoso ports....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Update docs on how to use SPARQL default ports....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Update docs to highlight sparql conf params in SECRETS file....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-18 | Update docs with extra conf vars for updating virtuoso....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-12 | rqtl_wrapper: minor fixes | Pjotr Prins |
| 2024-09-12 | README | Pjotr Prins |
| 2023-12-19 | README: Replace pylint and mypy CI badges with all-tests CI badge. | Arun Isaac |
| 2023-09-05 | Update instructions on how to run pylint...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-08-14 | auth: Remove documentation...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.
| Frederick Muriuki Muriithi |
| 2023-05-26 | Document CLI Utility Commands...Document some CLI utility commands useful for development and for supporting
the operation of the GN3 app.
| Frederick Muriuki Muriithi |
| 2023-05-25 | Script to assign existing data to publicly-visible resources...A script to assign existing data not assigned to any group to publicly-visible
resources.
| Frederick Muriuki Muriithi |
| 2023-05-23 | Document how to log out information in GN3 | Frederick Muriuki Muriithi |
| 2023-03-23 | Docs: Add a note on how the configuration system works. | Frederick Muriuki Muriithi |
| 2023-03-13 | Add 'ON UPDATE/DELETE' clauses to foreign keys. | Frederick Muriuki Muriithi |
| 2023-03-13 | auth: cURL: Add some docs on using cURL | Frederick Muriuki Muriithi |
| 2023-03-08 | Replace Bcrypt with Argon2 for better security....Bcrypt is now somewhat vulnerable to offline cracking, so we move our password
hashing over to Argon2.
| Frederick Muriuki Muriithi |
| 2023-01-25 | Some comments | Pjotr Prins |
| 2023-01-24 | docs: Add information on running the OAuth2 server without HTTPS | Frederick Muriuki Muriithi |
| 2022-12-23 | Update how to set configurations in README | zsloan |
| 2022-12-23 | Add a couple necessary environment variables | zsloan |
| 2022-12-22 | auth: implement OAuth2 flow....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
oauth2_auth_flow | Frederick Muriuki Muriithi |
| 2022-11-13 | Documentation: Explain how to run migrations...* .gitignore: ignore all yoyo configuration files
* README.md: Update documentation
* yoyo.auth.ini: stop tracking the yoyo configuration file.
| Frederick Muriuki Muriithi |
| 2022-11-03 | Initialise the Auth(entic|oris)ation packages...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
| Frederick Muriuki Muriithi |
| 2022-10-08 | README: a note on design | Pjotr Prins |
| 2022-09-06 | Update link to continuous deployment....* README.md: Update link to continuous deployment.
| Arun Isaac |
| 2022-07-29 | New script to run sample correlations...* 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
| Frederick Muriuki Muriithi |
| 2022-06-20 | Update README: export env variables explicitly | Frederick Muriuki Muriithi |
| 2022-05-24 | New script to compute partial correlations...* 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.
| Frederick Muriuki Muriithi |
| 2022-05-05 | Link to continuous deployment in README....* README.md: Link to continuous deployment.
| Arun Isaac |
| 2022-03-18 | README: Update CI badge subdomain....The CI has been migrated from penguin2.genenetwork.org to ci.genenetwork.org.
* README.md: Update CI badge subdomain.
| Arun Isaac |
| 2022-03-12 | README: Replace "unit-test" instructions with "pytest" | BonfaceKilz |
| 2022-03-04 | Document basic partial correlations dependencies...* Document the things that the partial correlations feature depends on to work
| Frederick Muriuki Muriithi |
| 2022-02-02 | Revert "Use guix shell shortcut with guix.scm file"...This reverts commit f676c291967f8a81836b73c5a5dcd3c65e02552c.
| BonfaceKilz |
| 2022-01-27 | Use guix shell shortcut with guix.scm file | jgart |
| 2022-01-24 | README: Add pylint and mypy CI badges....We now have separate CI jobs for the pylint and mypy tests.
* README.md: Add pylint and mypy CI badges.
| Arun Isaac |
| 2022-01-21 | README: Update link to CI badge....The CI has been moved to penguin2, and this is accompanied by a URI change.
* README.md: Update link to CI badge.
| Arun Isaac |
| 2022-01-01 | guix_deploy | Pjotr Prins |
| 2021-12-09 | README: Link CI badge to CI status page....* README.md: Link CI badge to CI status page.
| Arun Isaac |
| 2021-12-09 | README: Add CI badge....* README.md: Add CI badge.
| Arun Isaac |
| 2021-11-19 | Replace guix environment with guix shell....* README.md, guix.scm: Replace guix environment with guix shell.
| Arun Isaac |
| 2021-11-11 | Disuse absolute paths to guix....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.
| Arun Isaac |
| 2021-11-11 | Disuse GUIX_PACKAGE_PATH....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.
| Arun Isaac |
| 2021-08-31 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into heatmap_gener... | Muriithi Frederick Muriuki |
| 2021-08-30 | Update documentation on genotype files...* Provide documentation on downloading and using the genotype files.
| Muriithi Frederick Muriuki |
| 2021-08-30 | Fix issues with traits file format...* 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.
| Muriithi Frederick Muriuki |
| 2021-08-30 | Document acquired knowledge on `rust-qtlreaper`...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.
| Muriithi Frederick Muriuki |
| 2021-08-28 | README: updated install instructions | Pjotr Prins |
| 2021-08-28 | Add explanation of using a guix profile | Pjotr Prins |
| 2021-08-07 | Add gunicorn support for production | Pjotr Prins |
