]> git.arvados.org - arvados.git/log
arvados.git
2 weeks agoMerge branch '23009-multiselect-bug' into main. Closes #23009
Stephen Smith [Fri, 8 Aug 2025 15:35:23 +0000 (11:35 -0400)]
Merge branch '23009-multiselect-bug' into main. Closes #23009

Arvados-DCO-1.1-Signed-off-by: Stephen Smith <stephen@curii.com>

2 weeks agoMerge branch '23063-process-properties'
Lisa Knox [Thu, 7 Aug 2025 19:11:48 +0000 (15:11 -0400)]
Merge branch '23063-process-properties'

closes #23063

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

2 weeks ago23063: added component test 23063-process-properties
Lisa Knox [Thu, 7 Aug 2025 17:15:08 +0000 (13:15 -0400)]
23063: added component test

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

2 weeks ago23063: combined property chip generation to eliminate duplicate code
Lisa Knox [Thu, 7 Aug 2025 14:53:58 +0000 (10:53 -0400)]
23063: combined property chip generation to eliminate duplicate code

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

2 weeks agoMerge branch '20311-pep-517-builds'
Brett Smith [Wed, 6 Aug 2025 13:45:48 +0000 (09:45 -0400)]
Merge branch '20311-pep-517-builds'

Closes #20311, #23082.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

2 weeks agoMerge branch '23010-installer-jammy-pg-fix'. Closes #23010
Lucas Di Pentima [Wed, 6 Aug 2025 13:44:29 +0000 (10:44 -0300)]
Merge branch '23010-installer-jammy-pg-fix'. Closes #23010

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

2 weeks agoMerge branch '23025-test-with-stdlib'
Tom Clegg [Wed, 6 Aug 2025 13:40:10 +0000 (09:40 -0400)]
Merge branch '23025-test-with-stdlib'

fixes #23025

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

2 weeks ago23010: Uses new pg-formula supporting Ubuntu 24.04 23010-installer-jammy-pg-fix
Lucas Di Pentima [Tue, 5 Aug 2025 21:50:45 +0000 (18:50 -0300)]
23010: Uses new pg-formula supporting Ubuntu 24.04

Also, avoid installing postgresql-contrib as it depends on the currently
supported PG version on each distro, eg: install postgresql-16 on Ubuntu
24.04 so both v15 and v16 get installed (because v15 is the one
requested by the installer) and that creates issues with service ports.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

2 weeks ago20311: Include CWL schemas in Python packages 20311-pep-517-builds
Brett Smith [Tue, 5 Aug 2025 21:09:58 +0000 (17:09 -0400)]
20311: Include CWL schemas in Python packages

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

2 weeks ago20311: Update setup.py invocation in `arvados-server install`
Brett Smith [Tue, 5 Aug 2025 21:08:55 +0000 (17:08 -0400)]
20311: Update setup.py invocation in `arvados-server install`

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

2 weeks ago22436: Remove arvados-package
Brett Smith [Tue, 5 Aug 2025 20:59:10 +0000 (16:59 -0400)]
22436: Remove arvados-package

Because Arvados is deployed with third-party software like nginx, a
configuration management tool like Salt or Ansible is better suited to
orchestrate the install compared to a distribution package. We are
focusing future development on the Ansible installer.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

2 weeks agoMerge branch '23023-published-ports-docs'
Tom Clegg [Tue, 5 Aug 2025 19:06:35 +0000 (15:06 -0400)]
Merge branch '23023-published-ports-docs'

fixes #23023

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

2 weeks ago23023: Emphasize container request vs. running container difference.
Tom Clegg [Tue, 5 Aug 2025 19:05:36 +0000 (15:05 -0400)]
23023: Emphasize container request vs. running container difference.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

2 weeks ago23025: Comment (lack of) reason why integration test uses curl. 23025-test-with-stdlib
Tom Clegg [Tue, 5 Aug 2025 14:28:09 +0000 (10:28 -0400)]
23025: Comment (lack of) reason why integration test uses curl.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

2 weeks ago23025: Update stale comment and options struct name.
Tom Clegg [Tue, 5 Aug 2025 14:24:06 +0000 (10:24 -0400)]
23025: Update stale comment and options struct name.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

2 weeks agoRestart Docker after updating daemon.json
Brett Smith [Mon, 4 Aug 2025 19:33:32 +0000 (15:33 -0400)]
Restart Docker after updating daemon.json

This was not in the original version of the code because it was written
to build cloud compute images where we just needed to write the right
configuration. Now that it supports single-node installs and maybe more
in the future, we need to make sure services get new state. No issue #.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

2 weeks ago23025: Fix double redirect.
Tom Clegg [Mon, 4 Aug 2025 17:59:57 +0000 (13:59 -0400)]
23025: Fix double redirect.

Previous code did not use the query token to look up the container, so
the first request would fail the container lookup and send a 303
moving the token to a cookie, and the resulting second request would
succeed at the container lookup only to find the container UUID does
not match the client's cookie, and send another 303 to clear site
data.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

2 weeks ago23025: Convert curl-based test to stdlib.
Tom Clegg [Mon, 4 Aug 2025 18:08:21 +0000 (14:08 -0400)]
23025: Convert curl-based test to stdlib.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

2 weeks ago20311: Remove deprecated setup.py invocations
Brett Smith [Mon, 4 Aug 2025 01:47:10 +0000 (21:47 -0400)]
20311: Remove deprecated setup.py invocations

This is possible now that we define pyproject.toml for all our Python
modules. I'm not bothering with `arvados-server install` and `arvbox`
since they're both slated for removal in Arvados 3.2.0.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

2 weeks ago20311: Remove unused get-package-version script
Brett Smith [Mon, 4 Aug 2025 00:48:17 +0000 (20:48 -0400)]
20311: Remove unused get-package-version script

In addition to not having references in the repository, it was never
updated to remove the `development-` prefix following
b81baa970ca14b1ace4b9f0dc2ea0eae8330e788.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

2 weeks ago20311: Update Python packages for PEP 517
Brett Smith [Mon, 4 Aug 2025 00:39:16 +0000 (20:39 -0400)]
20311: Update Python packages for PEP 517

This moves as much build information as possible into `pyproject.toml`,
only using `setup.py` for dynamic metadata.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

2 weeks ago20311: Generate _version.py from a setuptools subcommand
Brett Smith [Fri, 1 Aug 2025 21:24:14 +0000 (17:24 -0400)]
20311: Generate _version.py from a setuptools subcommand

This restructures arvados_version.py so that metadata generation happens
in a dedicated class (useful for other build tooling like
build_docker_image.py) and then it provides a setuptools subcommand to
write _version.py where needed. This provides cleaner separation of
concerns and gives us a better base to build more tooling from.

As part of this change, we take care to no longer install tests as part
of the wheel we build. We shouldn't have been doing this anyway, and now
it's required for the tests to run as expected.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

3 weeks ago20311: Remove sys.path manipulation from run_test_server.py
Brett Smith [Fri, 1 Aug 2025 21:21:32 +0000 (17:21 -0400)]
20311: Remove sys.path manipulation from run_test_server.py

This has been obsolete since run-tests.sh started installing the PySDK
to its virtualenv as part of `install env`, and that's a better approach
since it also covers dependencies, etc.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

3 weeks ago20311: Add test command for cluster-activity Docker image
Brett Smith [Fri, 1 Aug 2025 04:13:29 +0000 (00:13 -0400)]
20311: Add test command for cluster-activity Docker image

Sure it's lightweight, but it's better than nothing.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

3 weeks ago20311: Remove calculate_python_sdk_cwl_package_versions
Brett Smith [Fri, 1 Aug 2025 04:08:16 +0000 (00:08 -0400)]
20311: Remove calculate_python_sdk_cwl_package_versions

After #21389 nothing calls this.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

3 weeks ago20311: Make discovery pydoc build a subcommand
Brett Smith [Thu, 31 Jul 2025 14:22:41 +0000 (10:22 -0400)]
20311: Make discovery pydoc build a subcommand

The removed comment is no longer a concern now that we consistently use
`pip install`, and this makes it easier to further extend the build
process for PEP 517.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

3 weeks ago20311: Fix return value of get_output_mapping
Brett Smith [Thu, 31 Jul 2025 14:18:50 +0000 (10:18 -0400)]
20311: Fix return value of get_output_mapping

Per the docs, the keys are outputs and the values are string paths
relative to the project root.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

3 weeks ago20311: Fix return value of get_source_files
Brett Smith [Thu, 31 Jul 2025 14:18:25 +0000 (10:18 -0400)]
20311: Fix return value of get_source_files

On a closer reading of the docs, it's supposed to be relative to the
project root.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

3 weeks agoMerge branch '23044-web-services-routing'
Tom Clegg [Fri, 1 Aug 2025 18:23:30 +0000 (14:23 -0400)]
Merge branch '23044-web-services-routing'

fixes #23044

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 weeks agoMerge branch '23062-disable-wf-linking'
Tom Clegg [Fri, 1 Aug 2025 18:22:12 +0000 (14:22 -0400)]
Merge branch '23062-disable-wf-linking'

closes #23062

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 weeks ago23023: Update API docs about published_ports. 23023-published-ports-docs
Tom Clegg [Fri, 1 Aug 2025 18:09:33 +0000 (14:09 -0400)]
23023: Update API docs about published_ports.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 weeks ago23044: Check `docker info` before running tests that need docker. 23044-web-services-routing
Tom Clegg [Fri, 1 Aug 2025 15:59:51 +0000 (11:59 -0400)]
23044: Check `docker info` before running tests that need docker.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 weeks ago23044: Merge branch 'main' into 23044-web-services-routing
Tom Clegg [Fri, 1 Aug 2025 15:52:12 +0000 (11:52 -0400)]
23044: Merge branch 'main' into 23044-web-services-routing

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 weeks agoMerge branch '23077-remove-keepclient'
Brett Smith [Fri, 1 Aug 2025 15:15:31 +0000 (11:15 -0400)]
Merge branch '23077-remove-keepclient'

From <https://github.com/arvados/arvados/pull/298>.
Closes #23077.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

3 weeks agoUpdate tests to work without KeepClient 23077-remove-keepclient
krzysztof [Fri, 1 Aug 2025 15:02:02 +0000 (11:02 -0400)]
Update tests to work without KeepClient

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

3 weeks agoRemove KeepClient API
krzysztof [Tue, 15 Apr 2025 12:46:50 +0000 (14:46 +0200)]
Remove KeepClient API

Arvados-DCO-1.1-Signed-off-by: Krzysztof Majewski <majewski.kielce@gmail.com>

3 weeks agoRemove KeepClient API
Brett Smith [Tue, 29 Jul 2025 14:04:15 +0000 (10:04 -0400)]
Remove KeepClient API

Arvados-DCO-1.1-Signed-off-by: Krzysztof Majewski <majewski.kielce@gmail.com>

3 weeks agoUpdate Keep Web API Client URL Builder
krzysztof [Tue, 8 Apr 2025 09:08:03 +0000 (11:08 +0200)]
Update Keep Web API Client URL Builder

Arvados-DCO-1.1-Signed-off-by: Krzysztof Majewski <majewski.kielce@gmail.com>

3 weeks ago23062: Hide/disable workflow>collection linking until 23057. 23062-disable-wf-linking
Tom Clegg [Fri, 1 Aug 2025 02:58:00 +0000 (22:58 -0400)]
23062: Hide/disable workflow>collection linking until 23057.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 weeks ago23044: Switch to docker to bypass singularity+sudo limitation.
Tom Clegg [Thu, 31 Jul 2025 14:25:25 +0000 (10:25 -0400)]
23044: Switch to docker to bypass singularity+sudo limitation.

singularity+sudo only works with passwordless sudo.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 weeks ago23044: Pass ARVADOS_TEST_PRIVESC through in test cluster.
Tom Clegg [Thu, 31 Jul 2025 14:09:48 +0000 (10:09 -0400)]
23044: Pass ARVADOS_TEST_PRIVESC through in test cluster.

My intent was to enable the use of sudo in integration tests with
{RuntimeEngine: singularity}.  This still doesn't work with
non-passwordless sudo, but at least it tries to use sudo when so
configured, and logs something in stderr.txt if it fails.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 weeks ago23044: Enable use of crunch-run gateway with loopback driver.
Tom Clegg [Thu, 24 Jul 2025 17:51:51 +0000 (13:51 -0400)]
23044: Enable use of crunch-run gateway with loopback driver.

Normally a gateway address of 127.0.0.1:* means crunch-run couldn't
figure out its external IP address, but in the case of the loopback
driver, it's correct.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 weeks ago23044: Fix gateway usage when instance address contains :port.
Tom Clegg [Thu, 24 Jul 2025 14:28:08 +0000 (10:28 -0400)]
23044: Fix gateway usage when instance address contains :port.

e.g., when the SSH server runs on a port other than 22.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 weeks ago23009: Add test for data epxlorer filter+select+clear filter+select all 23009-multiselect-bug
Stephen Smith [Wed, 30 Jul 2025 15:00:01 +0000 (11:00 -0400)]
23009: Add test for data epxlorer filter+select+clear filter+select all

Arvados-DCO-1.1-Signed-off-by: Stephen Smith <stephen@curii.com>

3 weeks agoMerge branch 'pr311-upgrade-thor'
Brett Smith [Tue, 29 Jul 2025 15:01:37 +0000 (11:01 -0400)]
Merge branch 'pr311-upgrade-thor'

See <https://github.com/arvados/arvados/pull/311>.
No issue #.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

3 weeks agoBump thor from 1.3.2 to 1.4.0 in /services/api pr311-upgrade-thor
dependabot[bot] [Wed, 23 Jul 2025 20:39:33 +0000 (20:39 +0000)]
Bump thor from 1.3.2 to 1.4.0 in /services/api

Bumps [thor](https://github.com/rails/thor) from 1.3.2 to 1.4.0.
- [Release notes](https://github.com/rails/thor/releases)
- [Commits](https://github.com/rails/thor/compare/v1.3.2...v1.4.0)

---
updated-dependencies:
- dependency-name: thor
  dependency-version: 1.4.0
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

3 weeks ago21389: Add test command
Brett Smith [Tue, 29 Jul 2025 13:40:59 +0000 (09:40 -0400)]
21389: Add test command

This was in the code at some point. I guess I lost it while writing
version 2 of the branch. Refs #21389.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

3 weeks ago23064: Fix README typo
Brett Smith [Tue, 29 Jul 2025 13:27:39 +0000 (09:27 -0400)]
23064: Fix README typo

Refs #23064.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

3 weeks ago23009: Don't skip initialization of checkedList when not empty
Stephen Smith [Tue, 29 Jul 2025 13:01:21 +0000 (09:01 -0400)]
23009: Don't skip initialization of checkedList when not empty

Arvados-DCO-1.1-Signed-off-by: Stephen Smith <stephen@curii.com>

3 weeks ago23063: commented out failing out-of-scope test
Lisa Knox [Mon, 28 Jul 2025 18:42:33 +0000 (14:42 -0400)]
23063: commented out failing out-of-scope test

* created #23080 to address it

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

3 weeks ago23063: added property tag test
Lisa Knox [Mon, 28 Jul 2025 15:15:25 +0000 (11:15 -0400)]
23063: added property tag test

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

3 weeks ago23063: filtered cwl-input and cwl_output from overview display
Lisa Knox [Mon, 28 Jul 2025 13:37:59 +0000 (09:37 -0400)]
23063: filtered cwl-input and cwl_output from overview display

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

4 weeks agoMerge branch '22831-zip-download-rebase2' into main. Closes #22831
Stephen Smith [Fri, 25 Jul 2025 14:36:47 +0000 (10:36 -0400)]
Merge branch '22831-zip-download-rebase2' into main. Closes #22831

Arvados-DCO-1.1-Signed-off-by: Stephen Smith <stephen@curii.com>

4 weeks agoMerge branch '23006-cwl-integration-pytests'
Brett Smith [Thu, 24 Jul 2025 15:30:07 +0000 (11:30 -0400)]
Merge branch '23006-cwl-integration-pytests'

Refs #23006.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks agoMerge branch '21389-update-docker-jobs'
Brett Smith [Thu, 24 Jul 2025 15:03:28 +0000 (11:03 -0400)]
Merge branch '21389-update-docker-jobs'

Refs #21389.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks ago23044: Fix unchecked proxy error.
Tom Clegg [Thu, 24 Jul 2025 13:45:20 +0000 (09:45 -0400)]
23044: Fix unchecked proxy error.

Was returning 200 OK with empty body when unable to reach container
gateway.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 weeks agoRun `bundle install` for multi_json
Brett Smith [Thu, 24 Jul 2025 00:01:17 +0000 (20:01 -0400)]
Run `bundle install` for multi_json

Should've been included in the previous commit. I thought this would be
a noop because we already had an indirect dependency on
`multi_json (1.15.0)`, but I guess (to its credit) bundler does check
everything. No issue #.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks agoPin multi_json for Ruby 2.7 compatibility
Brett Smith [Wed, 23 Jul 2025 20:37:21 +0000 (16:37 -0400)]
Pin multi_json for Ruby 2.7 compatibility

The usual story. No issue #.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks agoFix type of Docker daemon DNS configuration
Brett Smith [Wed, 23 Jul 2025 20:21:34 +0000 (16:21 -0400)]
Fix type of Docker daemon DNS configuration

Sorry, I forgot that we have an Ansible string that needs to become a
JSON list. No issue #.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks ago23044: Add integration test for ContainerWebServices.
Tom Clegg [Wed, 23 Jul 2025 20:07:26 +0000 (16:07 -0400)]
23044: Add integration test for ContainerWebServices.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 weeks agoOnly set Docker data-root for cloud compute nodes
Brett Smith [Wed, 23 Jul 2025 19:58:28 +0000 (15:58 -0400)]
Only set Docker data-root for cloud compute nodes

b6d8d5665243578986cefc5c3fec850d6cf25b05 could cause single-node
installs to configure Docker with a data root at /tmp/docker-data, which
is probably not what people want. Instead set this in
build-compute-image.yml, and introduce a system to extend the Docker
daemon.json selectively. No issue #.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks agoRemove stale sdk/java paths from .gitignore
Brett Smith [Wed, 23 Jul 2025 19:17:02 +0000 (15:17 -0400)]
Remove stale sdk/java paths from .gitignore

Note these were for Java SDK v1, not v2 that now lives in contrib.
No issue #.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks agoMerge branch '23064-contrib'
Brett Smith [Wed, 23 Jul 2025 19:15:49 +0000 (15:15 -0400)]
Merge branch '23064-contrib'

Refs #23064.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks agoDo not chown/chmod /etc/arvados
Brett Smith [Wed, 23 Jul 2025 19:14:17 +0000 (15:14 -0400)]
Do not chown/chmod /etc/arvados

On dedicated compute nodes this is unlikely to exist and no big deal,
but on single-node installs the admin may choose to change the
ownership (especially group) of this directory. Remove those specifiers
to avoid interfering with that. Ansible's defaults should be fine for
a newly-created directory. No issue #.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks agoConfigure Docker when installing it with crunch-dispatch-local
Brett Smith [Wed, 23 Jul 2025 19:12:35 +0000 (15:12 -0400)]
Configure Docker when installing it with crunch-dispatch-local

In order for crunch-dispatch-local to work, the local node needs to be
configured like any other compute node. Most of this is already done via
the dependency on arvados_compute, but that does not configure Docker
services, that's the job of compute_docker. Pull that in when necessary.
No issue #.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks agoMerge branch 'main' of public.ts.curii.com:arvados into 22831-zip-download-rebase2 22831-zip-download-rebase2
Stephen Smith [Wed, 23 Jul 2025 18:11:27 +0000 (14:11 -0400)]
Merge branch 'main' of public.ts.curii.com:arvados into 22831-zip-download-rebase2

Arvados-DCO-1.1-Signed-off-by: Stephen Smith <stephen@curii.com>

4 weeks ago22831: Reword collection download all to clarify behavior when in subfolders
Stephen Smith [Wed, 23 Jul 2025 18:08:16 +0000 (14:08 -0400)]
22831: Reword collection download all to clarify behavior when in subfolders

Arvados-DCO-1.1-Signed-off-by: Stephen Smith <stephen@curii.com>

4 weeks agoMerge Python .gitignore files into top level
Brett Smith [Wed, 23 Jul 2025 13:32:13 +0000 (09:32 -0400)]
Merge Python .gitignore files into top level

At least in my development environment, the symlinks generally don't
work and confuse tools. Most of the temporary-type files are already
covered by patterns in .gitignore, so the easiest fix from here is just
to ignore the full build and dist paths. No issue #.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks agoAnchor .gitignore full paths
Brett Smith [Wed, 23 Jul 2025 13:29:39 +0000 (09:29 -0400)]
Anchor .gitignore full paths

No issue #.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks agoMake .gitignore directories explicit
Brett Smith [Wed, 23 Jul 2025 13:28:18 +0000 (09:28 -0400)]
Make .gitignore directories explicit

No issue #.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks agoAdd pidfiles to .gitignore
Brett Smith [Wed, 23 Jul 2025 13:25:23 +0000 (09:25 -0400)]
Add pidfiles to .gitignore

No issue #.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks agoAdd more binstubs directories to gitignore
Brett Smith [Wed, 23 Jul 2025 13:22:54 +0000 (09:22 -0400)]
Add more binstubs directories to gitignore

No issue #.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks ago23064: Start contrib directory 23064-contrib
Brett Smith [Wed, 23 Jul 2025 01:56:09 +0000 (21:56 -0400)]
23064: Start contrib directory

The goal of this directory is to help users better understand what
components are "core" Arvados vs. additional tools and to give us a
place to start building more of the latter.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks ago22831: Fix flaky test
Stephen Smith [Tue, 22 Jul 2025 16:21:44 +0000 (12:21 -0400)]
22831: Fix flaky test

Arvados-DCO-1.1-Signed-off-by: Stephen Smith <stephen@curii.com>

4 weeks ago22831: Try to fix flaky test
Stephen Smith [Tue, 22 Jul 2025 15:21:31 +0000 (11:21 -0400)]
22831: Try to fix flaky test

Arvados-DCO-1.1-Signed-off-by: Stephen Smith <stephen@curii.com>

4 weeks ago22817: Remove Java SDK Docker test scripts
Brett Smith [Tue, 22 Jul 2025 15:16:41 +0000 (11:16 -0400)]
22817: Remove Java SDK Docker test scripts

These were used by previous Jenkins configuration. Our current nodes are
sure to have Gradle, so we have eliminated the need for this indirection.
Closes #22817.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks ago23044: De-dup ContainerWebServices routing logic.
Tom Clegg [Tue, 22 Jul 2025 15:03:15 +0000 (11:03 -0400)]
23044: De-dup ContainerWebServices routing logic.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 weeks ago22831: Add tests for zipfile download requests
Stephen Smith [Mon, 21 Jul 2025 23:14:47 +0000 (19:14 -0400)]
22831: Add tests for zipfile download requests

Arvados-DCO-1.1-Signed-off-by: Stephen Smith <stephen@curii.com>

4 weeks ago22831: Add zipfile download dialog tests
Stephen Smith [Mon, 21 Jul 2025 16:16:44 +0000 (12:16 -0400)]
22831: Add zipfile download dialog tests

Arvados-DCO-1.1-Signed-off-by: Stephen Smith <stephen@curii.com>

4 weeks ago23006: Hardcode runner image inside arvbox 23006-cwl-integration-pytests
Brett Smith [Sun, 20 Jul 2025 17:47:24 +0000 (13:47 -0400)]
23006: Hardcode runner image inside arvbox

It is already a known limitation that arvbox can't build its own
arvados/jobs image because it runs Singularity. This pins it to a
known-good version while we work on transitioning away from arvbox.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks ago23006: Port CWL conformance+integration tests to pytest
Brett Smith [Mon, 21 Jul 2025 20:56:44 +0000 (16:56 -0400)]
23006: Port CWL conformance+integration tests to pytest

This removes arvados_tests.sh, simplifies test_with_arvbox.sh, and sets
the stage to remove it as well.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks ago21389: Unify Python Docker images 21389-update-docker-jobs
Brett Smith [Mon, 21 Jul 2025 20:37:38 +0000 (16:37 -0400)]
21389: Unify Python Docker images

Fundamentally these images all build a Docker image with a Python
virtualenv. There are minor details in how they go about it, but none of
them have any real consequence for the final built image. We can use the
same code to build all these images and just parametrize it in the build
context.

* Port build-dev-docker-jobs-image.sh to Python (build_docker_image.py).
  This makes it easier to share code between them; provides better
  argument parsing; gives us a better base to build from; and makes
  sense for build tooling that works so much with Python.

* Update the Dockerfile to use a two-stage build. It still builds a
  virtualenv with wheels provided by the build script, but a two-stage
  build keeps image sizes in line with what we had with the package-based
  approach, which is appropriate for an image that gets distributed as
  widely as arvados/jobs.

* Synchronize everything on bookworm-slim.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

4 weeks ago21389: Remove Docker image build from test_with_arvbox
Brett Smith [Mon, 21 Jul 2025 20:34:18 +0000 (16:34 -0400)]
21389: Remove Docker image build from test_with_arvbox

This code has been noop for a while: arvbox doesn't include Docker, it
uses Singularity, to avoid the usual Docker-in-Docker problems. Since
there's no way it can work, we should stop maintaining it.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

5 weeks ago21389: Add requirements.txt files to build
Brett Smith [Thu, 17 Jul 2025 18:29:05 +0000 (14:29 -0400)]
21389: Add requirements.txt files to build

This makes it easier for different build tools to install all their
dependencies and keep them all consistent.

With this change, I have chosen to flatten the distinction between "env"
and "deps" in run-tests.sh. It's already a little shaky, and it didn't
seem worth splitting out two files to keep it going.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

5 weeks agoMerge branch '19378-test-fix'
Lisa Knox [Fri, 18 Jul 2025 16:20:42 +0000 (12:20 -0400)]
Merge branch '19378-test-fix'

closes #19378

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

5 weeks ago19378: fixed collection test that was overwritten in merge 19378-test-fix
Lisa Knox [Fri, 18 Jul 2025 14:16:45 +0000 (10:16 -0400)]
19378: fixed collection test that was overwritten in merge

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

5 weeks agoMerge branch '19378-folder-upload'
Lisa Knox [Thu, 17 Jul 2025 17:37:01 +0000 (13:37 -0400)]
Merge branch '19378-folder-upload'

closes #19378

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

5 weeks ago19378: added unit test for getMinNecessaryPaths 19378-folder-upload
Lisa Knox [Wed, 16 Jul 2025 18:55:13 +0000 (14:55 -0400)]
19378: added unit test for getMinNecessaryPaths

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

5 weeks ago19378: updated createDirectory unit test
Lisa Knox [Wed, 16 Jul 2025 18:31:00 +0000 (14:31 -0400)]
19378: updated createDirectory unit test

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

5 weeks ago19378: added empty path check in uploadFiles
Lisa Knox [Wed, 16 Jul 2025 18:16:38 +0000 (14:16 -0400)]
19378: added empty path check in uploadFiles

* Now d&d works if both file and folder are dropped

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

5 weeks ago19378: Added warning that empty folders will be ignored in upload
Lisa Knox [Wed, 16 Jul 2025 17:40:35 +0000 (13:40 -0400)]
19378: Added warning that empty folders will be ignored in upload

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

5 weeks ago19378: all dirs now created with a single call
Lisa Knox [Wed, 16 Jul 2025 15:30:30 +0000 (11:30 -0400)]
19378: all dirs now created with a single call

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

5 weeks ago19378: fixed getMinNecessaryPaths
Lisa Knox [Wed, 16 Jul 2025 15:03:39 +0000 (11:03 -0400)]
19378:  fixed getMinNecessaryPaths

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

5 weeks ago19378: creating multiple folders in one update now only bumps the version by one
Lisa Knox [Wed, 16 Jul 2025 13:32:42 +0000 (09:32 -0400)]
19378: creating multiple folders in one update now only bumps the version by one

Arvados-DCO-1.1-Signed-off-by: Lisa Knox <lisa.knox@curii.com>

5 weeks ago23044: Add external service container port routing to handler
Brett Smith [Tue, 15 Jul 2025 18:40:48 +0000 (14:40 -0400)]
23044: Add external service container port routing to handler

This is an initial pass to address the bug in refs #23044.
This might not be the right solution, but it seems to at least get
things functioning, and it's self-contained so it's easy to replace
later as desired.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

5 weeks agoMerge branch '23041-fuse3'
Brett Smith [Tue, 15 Jul 2025 14:40:34 +0000 (10:40 -0400)]
Merge branch '23041-fuse3'

Closes #23041, #23042.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

5 weeks ago23041: Refine Ansible's strategy for installing FUSE 23041-fuse3
Brett Smith [Tue, 15 Jul 2025 13:18:25 +0000 (09:18 -0400)]
23041: Refine Ansible's strategy for installing FUSE

`/etc/fuse.conf` could be provided by either `fuse` or `fuse3`. If it
already exists, don't install a package, to avoid messing with the
administrator's selections. If it doesn't, install `fuse3` to get the
most modern version. All of our supported distributions have this except
maybe Ubuntu 20.04, where we're not going to run the Ansible installer
anyway.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

5 weeks ago23033: Remove fuse dependency from arvados-client
Brett Smith [Mon, 14 Jul 2025 16:03:04 +0000 (12:03 -0400)]
23033: Remove fuse dependency from arvados-client

The arv-mount dependency notes it is there because arv-mount can
sometimes call FUSE command line tools. As best I can tell, this is not
true for arvados-client. Declaring the library dependency is more
accurate. Refs #23033.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

5 weeks ago23033: Add libfuse2 dependency to arvados-client
Brett Smith [Mon, 14 Jul 2025 16:02:02 +0000 (12:02 -0400)]
23033: Add libfuse2 dependency to arvados-client

This is basically commit 9a68b3ef3bcfae2c8d064b573230870bfad1d19b
with the same rationale, just applied to arvados-client instead of
arv-mount. Refs #23033.

Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith@curii.com>

6 weeks agoMerge branch '22945-ansible-secrets-nolog'. Closes #22945
Lucas Di Pentima [Fri, 11 Jul 2025 20:52:58 +0000 (17:52 -0300)]
Merge branch '22945-ansible-secrets-nolog'. Closes #22945

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>