| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2024-01-09 | Add "=" before --load-path argument value....guix requires "=" between argument names and values.
* production-deploy.sh: Add "=" before --load-path argument value.
| Arun Isaac |
| 2024-01-09 | genenetwork: Increase gunicorn timeout for genenetwork3....* genenetwork/services/genenetwork.scm (genenetwork-gunicorn-apps):
Increase gunicorn timeout for genenetwork3 to 1200 seconds.
| 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 |
| 2024-01-03 | Add GeneNetwork service to production container....* production.scm: Import (genenetwork services genenetwork), (forge
acme), (forge nginx) and (forge socket). Import shepherd from (gnu
packages admin).
(operating-system)[sudoers-file]: Allow acme user to restart nginx.
(services): Add forge-nginx, acme and genenetwork services.
| Arun Isaac |
| 2024-01-03 | Add GeneNetwork service....* genenetwork/services/genenetwork.scm: New file.
| 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 |
| 2023-12-30 | Do not auto-upgrade mysql databases in production....* production.scm (operating-system)[services]{mysql-service-type}: Set
auto-upgrade? to #f.
| 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 | Add documentation on connecting to container. | 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 |
| 2023-10-05 | Mount git repositories read-write....* genenetwork-development-deploy.sh: Mount /home/git/public read-write
into the container.
| 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 |
| 2023-10-04 | Import gn-auth from (gn packages genenetwork)....* genenetwork-development.scm: Import gn-auth from (gn packages
genenetwork) instead of from (gn-auth) or elsewhere.
| Arun Isaac |
| 2023-10-04 | Import python-mypy from (gnu packages python)....* genenetwork-development.scm: Import python-mypy from (gnu packages
python) instead of (gn packages python).
| Arun Isaac |
| 2023-10-04 | Use switch-symlinks from (guix build utils)....switch-symlinks was recently moved from (guix utils) to (guix build
utils). It can now be safely used in build-side code.
* genenetwork-development.scm (install-laminar-template-gexp): Use
switch-symlinks from (guix build utils).
| Arun Isaac |
| 2023-09-28 | Use upstream mypy....* genenetwork-development.scm: Replace python-mypy-0.981 import with
upstream version.
(genenetwork3-mypy, genenetwork-projects): Replace python-mypy-0.981
with upstream version.
Acked-by: Arun Isaac <arunisaac@systemreboot.net>
| Munyoki Kilyungi |
| 2023-09-27 | Revert "Set the envvar in the gexp"...This reverts commit 416bf833737b23e86756b68e0cb162529bbd2665.
| Frederick Muriuki Muriithi |
| 2023-09-27 | Revert "Expose configurations directory to pola-wrapper."...This reverts commit 5ec4b45702cba430b8da47949f37317527cf05a6.
| Frederick Muriuki Muriithi |
| 2023-09-27 | Revert "Expose config file to pola-wrapper"...This reverts commit d12e7e45883df361ab4f78055c8112ded2e896ca.
| Frederick Muriuki Muriithi |
| 2023-09-20 | Expose config file to pola-wrapper | Frederick Muriuki Muriithi |
| 2023-09-20 | Expose configurations directory to pola-wrapper. | Frederick Muriuki Muriithi |
| 2023-09-20 | Set the envvar in the gexp | Frederick Muriuki Muriithi |
