| Age | Commit message (Expand) | Author |
|---|---|---|
| 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 |
| 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 |
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