| Age | Commit message (Expand) | Author |
|---|
| 2024-06-19 | Replace tabs with white spaces....* genenetwork-development.scm: Run "M-x untabify".
| Munyoki Kilyungi |
| 2024-06-19 | Move xapian re-indexing checks into the indexing script....Let the python xapian indexing script check the checksums, instead of using a
G-expression. This approach is simpler and more understandable; it is also
more versatile and allows easier modification.
* genenetwork-development.scm (build-xapian-index-cron-gexp): Use the indexing
script to compare checksums. If the checksums changed, queue the
genenetwork3-build-xapian-index laminar job.
Co-authored-by: John Nduli <rookie101@jnduli.co.ke>
| Munyoki Kilyungi |
| 2024-06-17 | Configure CI for guile-lapack....* genenetwork-development.scm (guile-lapack-project): New variable.
(operating-system)[services]{forge-service-type}: Add
guile-lapack-project.
| Arun Isaac |
| 2024-06-17 | Configure CI for guile-gsl....* genenetwork-development.scm (guile-gsl-project): New variable.
(operating-system)[services]{forge-service-type}: Add
guile-gsl-project.
| Arun Isaac |
| 2024-05-02 | Mount llm-db-path into genenetwork3 container....* genenetwork-development.scm (genenetwork-shepherd-services): Mount
llm-db-path into genenetwork3 container.
| Arun Isaac |
| 2024-04-28 | Add llm-db-path for CD....genenetwork-development.scm (<genenetwork-configuration>)[llm-db-path]:
New field.
(genenetwork3-cd-gexp): Configure LLM_DB_PATH in gn3.conf.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Alexander_Kabui |
| 2024-04-26 | gn-auth: Use new entry-point script. | Frederick Muriuki Muriithi |
| 2024-04-26 | Set up SSL keys for CI/CD for gn2 and gn-auth | Frederick Muriuki Muriithi |
| 2024-04-26 | gn-auth: Update repository URL | Frederick Muriuki Muriithi |
| 2024-03-11 | Infer profile from guix executable used to build container....Not everyone has GUIX_PROFILE set in their environment. Inferring the
profile from the guix executable is more reliable.
* genenetwork-development.scm (channels-scm-gexp): Infer profile from
guix executable used to build container.
| Arun Isaac |
| 2024-03-06 | Move CI/CD configurations from ENVVARS into a file. | Frederick Muriuki Muriithi |
| 2024-03-05 | Pass on the request scheme to GN2 app...This is useful to enable building URIs with the correct scheme in the
application. These URIs are important when redirection to and from
external services such as the gn-auth service.
| Frederick Muriuki Muriithi |
| 2024-02-29 | Bump copyright year for Fred....* genenetwork-development.scm: Bump copyright year for Fred.
| Arun Isaac |
| 2024-02-29 | Do not hard-code GN_AUTH_SECRETS....*
genenetwork-development.scm (<genenetwork-configuration>)[gn-auth-secrets]:
New field.
* genenetwork-development.scm (gn-auth-cd-gexp): Set GN_AUTH_SECRTS
from gn-auth-secrets of <genenetwork-configuration> object.
(operating-system)[services]{genenetwork-service-type}: Set
gn-auth-secrets.
| Arun Isaac |
| 2024-02-28 | Set up correct secrets file for gn-auth | Frederick Muriuki Muriithi |
| 2024-02-16 | Run genenetwork auth CD with 8 workers....* genenetwork-development.scm (gn-auth-cd-gexp): Run with 8 workers.
| Arun Isaac |
| 2024-02-16 | Run genenetwork3 CD with 8 workers....* genenetwork-development.scm (genenetwork3-cd-gexp): Run with 8
workers.
| Arun Isaac |
| 2024-01-29 | Update module path in launch of mechanical-rob....With the reorganisation of the modules, and a change in the startup of
genenetwork2, the way mechanical-rob is launched has also
changed. This commit updates the launch command.
* genenetwork-development.scm (genenetwork-projects): Update module
path in launch of mechanical-rob CI job.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2024-01-18 | Configure CI for guile-lmdb....* genenetwork-development.scm (guile-lmdb-project): New variable.
(operating-system)[services]{forge-service-type}: Add
guile-lmdb-project.
| Arun Isaac |
| 2024-01-18 | Fix channel name on transform-genenetwork-database channel....*
genenetwork-development.scm (transform-genenetwork-database-project):
Fix channel name.
| Arun Isaac |
| 2024-01-08 | Increase gunicorn timeout for genenetwork3....* genenetwork-development.scm (genenetwork3-cd-gexp): Increase
gunicorn timeout to 1200 seconds.
* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Add TODO note to increase gunicorn timeout to 1200 seconds.
| Arun Isaac |
| 2024-01-05 | Set ownership and permissions on secret files....* genenetwork-development.scm (genenetwork-activation): Set ownership
and permissions on secret files.
* genenetwork-development-deploy.sh: Share /etc/genenetwork/conf
instead of merely exposing it.
| Arun Isaac |
| 2024-01-05 | Abstract out gn2/gn3 secrets as configuration fields....*
genenetwork-development.scm (<genenetwork-configuration>)[gn2-secrets,
gn3-secrets]: New fields.
* genenetwork-development.scm (genenetwork2-cd-gexp): Use gn2-secrets
configuration field.
(genenetwork3-cd-gexp): Use gn3-secrets configuration field.
(operating-system)[services]: Set gn2-secrets and gn3-secrets fields
in genenetwork configuration.
| Arun Isaac |
| 2024-01-02 | Change path to default genenetwork2 settings file....The default settings file in the genenetwork2 code base has been moved
from etc/default_settings.py to gn2/default_settings.py. Adapt.
* genenetwork-development.scm (genenetwork-projects,
genenetwork2-cd-gexp): Change path to default genenetwork2 settings
file.
| Arun Isaac |
| 2023-12-30 | Delete unused qc-tests and qc-project....Somehow this code, that was deleted in
aaf6750858e061e5f5740fb1edbc49b68b3c4717, was added back in
93ff9ed6fd9f2ca15cf6a8930eae26c9f5c65450.
* genenetwork-development.scm (qc-tests, qc-project): Delete
variables.
| Arun Isaac |
| 2023-12-30 | Separate out guix-bioinformatics job that builds all packages....We split guix-bioinformatics into two jobs—one that only does a `guix
pull' and another that does a `guix pull' and builds all
packages. This allows us to catch failures in `guix pull'
separately. The job that builds all packages is practically always
bound to fail.
* genenetwork-development.scm (guix-bioinformatics-project): Split
guix-bioinformatics job into guix-bioinformatics and
guix-bioinformatics-all-packages jobs.
| Arun Isaac |
| 2023-12-21 | Simple gn-guile system container builds | Pjotr Prins |
| 2023-12-20 | Use local gn-transform-databases git repository....*
genenetwork-development.scm (transform-genenetwork-database-project)[repository]:
Set to local gn-transform-databases git repository.
[ci-jobs-trigger]: Do not use webhook. Reset to default.
| Arun Isaac |
| 2023-12-20 | Use guix-channel-job-gexp for gn-transform-databases CI job....* genenetwork-development.scm: Import (guix ci).
(transform-genenetwork-database-tests): Delete variable.
(%default-guix-channel-with-substitutes): New variable.
(transform-genenetwork-database-project): Use guix-channel-job-gexp
for transform-genenetwork-database-tests CI job.
* genenetwork/development-helper.scm: Delete file.
| Arun Isaac |
| 2023-12-19 | Delete unused qc-tests variable....* genenetwork-development.scm (qc-tests): Delete variable.
* genenetwork/development-helper.scm (asdf-test-gexp): Delete
function.
| Arun Isaac |
| 2023-12-19 | Use guix-channel-job-gexp for gn-auth pylint and mypy CI jobs....* genenetwork-development.scm (genenetwork3-tests): Delete function.
(gn-auth-pylint): Delete variable.
(genenetwork-projects): Build only the gn-auth variable in the gn-auth
CI job. Combine gn-auth-mypy and gn-auth-pylint CI jobs into a
gn-auth-all-tests job that uses guix-channel-job-gexp.
* genenetwork/development-helper.scm (genenetwork-lint-gexp): Delete
function.
| Arun Isaac |
| 2023-12-19 | Use guix-channel-job-gexp for genenetwork3 pylint and mypy CI jobs....* genenetwork-development.scm (genenetwork3-mypy,
genenetwork3-pylint): Delete variables.
(genenetwork-projects): Build only genenetwork3 variable in
genenetwork3 CI job. Combine genenetwork3-mypy and genenetwork3-pylint
CI jobs into a genenetwork3-all-tests job that uses
guix-channel-job-gexp.
* genenetwork/development-helper.scm (genenetwork3-lint-gexp): Delete
function.
| Arun Isaac |
| 2023-12-19 | Delete unused genenetwork3-unit-tests variable....* genenetwork-development.scm (genenetwork3-unit-tests): Delete
variable.
| Arun Isaac |
| 2023-12-19 | Remove qc-project....* genenetwork-development.scm (qc-project): Delete variable.
(operating-system)[services]{forge-service-type}: Unlist qc-project.
| Arun Isaac |
| 2023-12-19 | Rebuild xapian index every hour....The xapian index rebuild cron job runs every hour, but doesn't
actually rebuild the index unless the MySQL database has changed since
the previous index rebuild.
* genenetwork-development.scm (operating-system): Run xapian index
rebuild job every hour.
| Arun Isaac |
| 2023-12-19 | Trigger xapian index rebuild conditionally....* genenetwork-development.scm: Import mariadb from (gnu packages
databases). Import guile-dsv and guile-xapian from (gnu packages
guile-xyz).
(build-xapian-index-cron-gexp): New variable.
(operating-system)[services]: Use build-xapian-index-cron-gexp.
| Arun Isaac |
| 2023-11-13 | Allow http transport for proxied app...The application is behind a proxy and is running as http, therefore,
to allow the redirects within the application and responses to work,
we need to enable the http transport for the application.
| Frederick Muriuki Muriithi |
| 2023-11-13 | GN Secrets: Set up secrets files for GN2 and GN3 | Frederick Muriuki Muriithi |
| 2023-11-10 | auth: define setting for CI/CD auth. | Frederick Muriuki Muriithi |
| 2023-11-10 | Update domain for CD auth service. | Frederick Muriuki Muriithi |
| 2023-11-02 | Secrets: Add instance folder to pola-wrapper. | Frederick Muriuki Muriithi |
| 2023-11-02 | SECRETS: Fix secrets path. | Frederick Muriuki Muriithi |
| 2023-11-02 | Secrets: Setup gn-auth instance path to find the secrets. | Frederick Muriuki Muriithi |
| 2023-11-02 | gn-auth: restart GN2 also after any changes to gn-auth. | Frederick Muriuki Muriithi |
| 2023-11-02 | gn-auth: Remove automated migrations. | Frederick Muriuki Muriithi |
| 2023-10-28 | Do not use upstream Guix in CI jobs....* genenetwork-development.scm (genenetwork-projects): Remove default
upstream Guix channels.
| Arun Isaac |
| 2023-10-05 | Fix guix-bioinformatics path in project definition....*
genenetwork-development.scm (guix-bioinformatics-project)[repository]:
Fix path.
| Arun Isaac |
| 2023-10-05 | Fix typo in comment about cloning the latest gn-auth repository....* genenetwork-development.scm (gn-auth-migrations-laminar): Fix typo
in comment.
| Arun Isaac |
| 2023-10-05 | Construct yoyo.ini using guile-ini....Constructing INI files from S-expressions instead of using string
substitutions is a little nicer.
* genenetwork-development.scm (gn-auth-migrations-yoyo-ini-gexp): New
function.
(gn-auth-migrations): Use gn-auth-migrations-yoyo-ini-gexp.
| Arun Isaac |
| 2023-10-04 | Use guix-bioinformatics repository on tux02....The guix-bioinformatics repository is now on tux02. There is no
webhook to listen for. So, use it directly as a local repository.
*
genenetwork-development.scm (guix-bioinformatics-project)[repository]:
Use local repository on tux02.
| Arun Isaac |
