| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2023-09-20 | Pass "secrets" configurations to GN2...We need to pass in secrets to the running applications. This commit
does it for GeneNetwork2.
| Frederick Muriuki Muriithi |
| 2023-09-19 | Use appropriate mypy for Python3.10 | Frederick Muriuki Muriithi |
| 2023-09-19 | Add missing `gn-auth-repository` configuration | Frederick Muriuki Muriithi |
| 2023-09-16 | Add CI/CD definitions for gn-auth | Frederick Muriuki Muriithi |
| 2023-09-11 | sed /s/dump-genenetwork/transform-genenetwork/g....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-11 | sed /s/dump-genenetwork/transform-genenetwork/g....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-11 | Update the repo-url for transforming genenetwork databases....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Use correct name for python-mypy...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Update arguments to pylint...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Use mypy defined in guix-bioinformatics...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-04 | Use self-hosted git repo | Munyoki Kilyungi |
| 2023-09-04 | Use self-hosted GN repository...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-08-12 | Add link to git repo | Pjotr Prins |
| 2023-08-10 | Set up cgit service....* genenetwork-development.scm: Import (forge cgit).
(operating-system)[services]: Add cgit service.
* genenetwork-development-deploy.sh: Expose cgit repository directory.
| Arun Isaac |
| 2023-08-10 | Switch to the forge-nginx and ACME services....* genenetwork-development.scm: Import only nginx-server-configuration
and nginx-location-configuration from (gnu services
web). Import (forge acme) and (forge nginx).
(development-server-reverse-proxy-server-block,
laminar-reverse-proxy-server-block,
tissue-reverse-proxy-server-block): Remove listen argument.
(operating-system)[sudoers-file]: Permit the acme user to restart
nginx.
[services]: Replace nginx service with a forge-nginx service. Add ACME
service.
* genenetwork-development-deploy.sh: Share /var/lib/acme.
| Arun Isaac |
| 2023-08-10 | Add nginx package with the ssl_preread module....* nginx-preread.scm, nginx-preread-deploy.sh: New files.
| Arun Isaac |
| 2023-07-27 | README: Remove references to penguin2....penguin2 is no more. We now use tux02 for development.
* README.org: Change references to penguin2 to tux02.
| Arun Isaac |
| 2023-07-27 | Revert "README: host names"...This reverts commit fc65c2a2c056ee9f313631da6e5f93adec277dd5.
| Arun Isaac |
| 2023-07-19 | Use tissue from guix-forge....The libgit2 patch is now in guix-forge. So, we don't have to repeat it
here.
* genenetwork-development.scm (libgit2-1.3, guile-git-for-tissue,
tissue): Delete variables.
(operating-system)[services]: Do not specify package for tissue
service.
| Arun Isaac |
| 2023-07-19 | Disable verbose build logs for guix-bioinformatics job....* genenetwork-development.scm (guix-bioinformatics-project): Disable
verbose build logs.
| Arun Isaac |
| 2023-07-19 | Use guix-channel-job-gexp for genenetwork3 tests....* genenetwork-development.scm (genenetwork-projects): Use
guix-channel-job-gexp for genenetwork3 tests.
| Arun Isaac |
| 2023-07-19 | Add guix-bioinformatics CI job....* genenetwork-development.scm (guix-channel-job-gexp): New function.
(guix-bioinformatics-project): New variable.
(operating-system)[services]: Add guix-bioinformatics-project to
forge-service-type.
| Arun Isaac |
| 2023-07-11 | README: host names | Pjotr Prins |
| 2023-07-11 | Revert "Disable tests"...This reverts commit 37fa3c11908d7aada419be296ebef67415de3bc9.
| Munyoki Kilyungi |
| 2023-07-10 | Add a troubleshooting subsection to README | Munyoki Kilyungi |
| 2023-07-10 | Revert "Fix genotype file path"...This reverts commit ecd97bc513323459898b34db45fda6c9edd7ca22.
| Munyoki Kilyungi |
| 2023-07-10 | Fix genotype file path | Munyoki Kilyungi |
| 2023-07-10 | Disable tests...Rob is giving a demo, so disable tests and fix them later.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-10 | Basic mail/opensmtpd service added | Pjotr Prins |
| 2023-06-26 | Add virtuoso allowed dirs | Munyoki Kilyungi |
| 2023-06-15 | Increase threshold for number-of-buffers and maximum-dirty-buffers....* genenetwork-development.scm,
public-sparql.scm (operating-system)[services]<virtuoso-service>: Set
number-of-buffers and maximum-dirty-buffers.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Munyoki Kilyungi |
| 2023-06-15 | Add links to README....* README.org (GeneNetwork development container): Link to
guix-bioinformatics and guix-forge channels.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Munyoki Kilyungi |
| 2023-06-08 | Share auth-db-path with genenetwork3-pola-wrapper....* genenetwork-development.scm (genenetwork-shepherd-services): Share
auth-db-path with genenetwork3-pola-wrapper.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2023-06-06 | Set AUTH_DB, not AUTH_DB_PATH....genenetwork3 expects AUTH_DB, not AUTH_DB_PATH.
* genenetwork-development.scm (genenetwork3-cd-gexp): Set AUTH_DB, not
AUTH_DB_PATH.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2023-05-31 | Do not create xapian build directory....* genenetwork-development.scm (build-xapian-index-gexp): Do not create
xapian build directory.
| Arun Isaac |
| 2023-05-31 | Use an absolute GN_SERVER_URL....A relative GN_SERVER_URL sometimes leads to issues when code (in
libraries e.g. requests and the like) cannot expand the URI since it
does not have context about the running server.
* genenetwork-development.scm (genenetwork2-cd-gexp): Use an absolute
GN_SERVER_URL.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2023-05-31 | Add trailing slash to GN_SERVER_URL....Without the trailing slash, the urllib.parse.urljoin function produces
the wrong endpoint.
* genenetwork-development.scm (genenetwork2-cd-gexp): Add trailing
slash to GN_SERVER_URL.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
| 2023-05-22 | Document getting a shell into container...For some tasks (e.g. debugging the xapian index build), we need to
manually queue the job, which means we need a shell into the
container.
Getting a shell using the default command displayed actually fails
with:
nsenter: failed to execute /bin/bash: No such file or directory
so we need to provide the correct path to bash, and optionally,
initialise the shell to setup the correct paths.
| Frederick Muriuki Muriithi |
| 2023-05-05 | Run migrations after tests and before restarting genenetwork3....Add a CI job that applies the auth database migrations. This job is
run after the genenetwork3 tests have passed but before genenetwork3
is restarted.
* genenetwork-development-deploy.sh: Share
/export/data/genenetwork-sqlite.
* genenetwork-development.scm: Import yoyo-migrations from (gnu
packages databases).
(<genenetwork-configuration>)[auth-db-path]: New field.
(genenetwork3-auth-migrations-genenetwork,
genenetwork3-auth-migrations-laminar, genenetwork-activation): New
functions.
(genenetwork-projects): Add genenetwork3-auth-migrations CI
job. Trigger this job after genenetwork3 tests.
(genenetwork3-cd-gexp): Configure AUTH_DB_PATH in gn3.conf.
(genenetwork-service-type): Extend activation-service-type with
genenetwork-activation.
(operating-system)[sudoers-file]: Permit the laminar user to run auth
database migrations as the genenetwork user.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Frederick Muriuki Muriithi |
