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2023-12-19Use guix-channel-job-gexp for genenetwork3 pylint and mypy CI jobs.Arun Isaac
* 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.
2023-12-19Delete unused genenetwork3-unit-tests variable.Arun Isaac
* genenetwork-development.scm (genenetwork3-unit-tests): Delete variable.
2023-12-19Remove qc-project.Arun Isaac
* genenetwork-development.scm (qc-project): Delete variable. (operating-system)[services]{forge-service-type}: Unlist qc-project.
2023-12-19Rebuild xapian index every hour.Arun Isaac
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.
2023-12-19Trigger xapian index rebuild conditionally.Arun Isaac
* 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.
2023-11-13Allow http transport for proxied appFrederick Muriuki Muriithi
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.
2023-11-13GN Secrets: Set up secrets files for GN2 and GN3Frederick Muriuki Muriithi
2023-11-10auth: define setting for CI/CD auth.Frederick Muriuki Muriithi
2023-11-10Add documentation on connecting to container.Frederick Muriuki Muriithi
2023-11-10Update domain for CD auth service.Frederick Muriuki Muriithi
2023-11-02Secrets: Add instance folder to pola-wrapper.Frederick Muriuki Muriithi
2023-11-02SECRETS: Fix secrets path.Frederick Muriuki Muriithi
2023-11-02Secrets: Setup gn-auth instance path to find the secrets.Frederick Muriuki Muriithi
2023-11-02gn-auth: restart GN2 also after any changes to gn-auth.Frederick Muriuki Muriithi
2023-11-02gn-auth: Remove automated migrations.Frederick Muriuki Muriithi
2023-10-28Do not use upstream Guix in CI jobs.Arun Isaac
* genenetwork-development.scm (genenetwork-projects): Remove default upstream Guix channels.
2023-10-05Fix guix-bioinformatics path in project definition.Arun Isaac
* genenetwork-development.scm (guix-bioinformatics-project)[repository]: Fix path.
2023-10-05Fix typo in comment about cloning the latest gn-auth repository.Arun Isaac
* genenetwork-development.scm (gn-auth-migrations-laminar): Fix typo in comment.
2023-10-05Construct yoyo.ini using guile-ini.Arun Isaac
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.
2023-10-05Mount git repositories read-write.Arun Isaac
* genenetwork-development-deploy.sh: Mount /home/git/public read-write into the container.
2023-10-04Use guix-bioinformatics repository on tux02.Arun Isaac
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.
2023-10-04Import gn-auth from (gn packages genenetwork).Arun Isaac
* genenetwork-development.scm: Import gn-auth from (gn packages genenetwork) instead of from (gn-auth) or elsewhere.
2023-10-04Import python-mypy from (gnu packages python).Arun Isaac
* genenetwork-development.scm: Import python-mypy from (gnu packages python) instead of (gn packages python).
2023-10-04Use switch-symlinks from (guix build utils).Arun Isaac
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).
2023-09-28Use upstream mypy.Munyoki Kilyungi
* 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>
2023-09-27Revert "Set the envvar in the gexp"Frederick Muriuki Muriithi
This reverts commit 416bf833737b23e86756b68e0cb162529bbd2665.
2023-09-27Revert "Expose configurations directory to pola-wrapper."Frederick Muriuki Muriithi
This reverts commit 5ec4b45702cba430b8da47949f37317527cf05a6.
2023-09-27Revert "Expose config file to pola-wrapper"Frederick Muriuki Muriithi
This reverts commit d12e7e45883df361ab4f78055c8112ded2e896ca.
2023-09-20Expose config file to pola-wrapperFrederick Muriuki Muriithi
2023-09-20Expose configurations directory to pola-wrapper.Frederick Muriuki Muriithi
2023-09-20Set the envvar in the gexpFrederick Muriuki Muriithi
2023-09-20Pass "secrets" configurations to GN2Frederick Muriuki Muriithi
We need to pass in secrets to the running applications. This commit does it for GeneNetwork2.
2023-09-19Use appropriate mypy for Python3.10Frederick Muriuki Muriithi
2023-09-19Add missing `gn-auth-repository` configurationFrederick Muriuki Muriithi
2023-09-16Add CI/CD definitions for gn-authFrederick Muriuki Muriithi
2023-09-11sed /s/dump-genenetwork/transform-genenetwork/g.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-11sed /s/dump-genenetwork/transform-genenetwork/g.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-11Update the repo-url for transforming genenetwork databases.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Use correct name for python-mypyMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Update arguments to pylintMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Use mypy defined in guix-bioinformaticsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-04Use self-hosted git repoMunyoki Kilyungi
2023-09-04Use self-hosted GN repositoryMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-12Add link to git repoPjotr Prins
2023-08-10Set up cgit service.Arun Isaac
* genenetwork-development.scm: Import (forge cgit). (operating-system)[services]: Add cgit service. * genenetwork-development-deploy.sh: Expose cgit repository directory.
2023-08-10Switch to the forge-nginx and ACME services.Arun Isaac
* 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.
2023-08-10Add nginx package with the ssl_preread module.Arun Isaac
* nginx-preread.scm, nginx-preread-deploy.sh: New files.
2023-07-27README: Remove references to penguin2.Arun Isaac
penguin2 is no more. We now use tux02 for development. * README.org: Change references to penguin2 to tux02.
2023-07-27Revert "README: host names"Arun Isaac
This reverts commit fc65c2a2c056ee9f313631da6e5f93adec277dd5.
2023-07-19Use tissue from guix-forge.Arun Isaac
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.
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-15 01:46:24 +0000