From aacd70c15222a791af8e7869ec9f6489d54ed5a1 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Thu, 8 Feb 2024 15:48:58 +0100 Subject: [PATCH] Create release 0.75.21 --- HISTORY.rst | 11 +++++++++++ docs/commands/autoupdate.rst | 2 ++ docs/commands/ci_setup.rst | 2 ++ docs/commands/database_create.rst | 2 ++ docs/commands/database_delete.rst | 2 ++ docs/commands/database_list.rst | 2 ++ docs/commands/profile_create.rst | 2 ++ docs/commands/profile_delete.rst | 2 ++ docs/commands/run.rst | 2 ++ docs/commands/serve.rst | 2 ++ docs/commands/shed_serve.rst | 2 ++ docs/commands/shed_test.rst | 2 ++ docs/commands/test.rst | 2 ++ docs/commands/training_generate_from_wf.rst | 2 ++ docs/commands/training_init.rst | 2 ++ docs/commands/upload_data.rst | 2 ++ docs/commands/workflow_convert.rst | 2 ++ docs/commands/workflow_edit.rst | 2 ++ planemo/__init__.py | 2 +- 19 files changed, 46 insertions(+), 1 deletion(-) diff --git a/HISTORY.rst b/HISTORY.rst index 1ff227290..9f3a13ca5 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -5,6 +5,14 @@ History .. to_doc +--------------------- +0.75.21 (2024-02-01) +--------------------- +* Add option to pass extra arguments to `docker run` (thanks to `@bernt-matthias`_). `Pull Request 1428`_ +* Fix workflow_edit (thanks to `@mvdbeek`_). `Pull Request 1427`_ +* Update to black 2024 stable style (thanks to `@nsoranzo`_). `Pull Request + 1425`_ + --------------------- 0.75.20 (2024-01-30) --------------------- @@ -2082,6 +2090,9 @@ History tools - and more experimental features involving Docker and Homebrew. 7d07782_ .. github_links +.. _Pull Request 1428: https://github.com/galaxyproject/planemo/pull/1428 +.. _Pull Request 1427: https://github.com/galaxyproject/planemo/pull/1427 +.. _Pull Request 1425: https://github.com/galaxyproject/planemo/pull/1425 .. _Pull Request 1424: https://github.com/galaxyproject/planemo/pull/1424 .. _Pull Request 1422: https://github.com/galaxyproject/planemo/pull/1422 .. _Pull Request 1419: https://github.com/galaxyproject/planemo/pull/1419 diff --git a/docs/commands/autoupdate.rst b/docs/commands/autoupdate.rst index 9ed8e5ef4..dbe30d3d1 100644 --- a/docs/commands/autoupdate.rst +++ b/docs/commands/autoupdate.rst @@ -98,6 +98,8 @@ Auto-update tool requirements by checking against Conda and updating if newer ve commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless diff --git a/docs/commands/ci_setup.rst b/docs/commands/ci_setup.rst index 90224a40d..f4783af48 100644 --- a/docs/commands/ci_setup.rst +++ b/docs/commands/ci_setup.rst @@ -58,6 +58,8 @@ Useful for populating a CI cache. commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless diff --git a/docs/commands/database_create.rst b/docs/commands/database_create.rst index 30bdb6c19..433dd563b 100644 --- a/docs/commands/database_create.rst +++ b/docs/commands/database_create.rst @@ -85,5 +85,7 @@ be set by setting up a file ``~/.pgpass`` file with the following contents. commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --help Show this message and exit. diff --git a/docs/commands/database_delete.rst b/docs/commands/database_delete.rst index 3bbc8edde..be460a0e3 100644 --- a/docs/commands/database_delete.rst +++ b/docs/commands/database_delete.rst @@ -85,5 +85,7 @@ be set by setting up a file ``~/.pgpass`` file with the following contents. commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --help Show this message and exit. diff --git a/docs/commands/database_list.rst b/docs/commands/database_list.rst index 0627d3598..689a3a4f8 100644 --- a/docs/commands/database_list.rst +++ b/docs/commands/database_list.rst @@ -85,5 +85,7 @@ be set by setting up a file ``~/.pgpass`` file with the following contents. commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --help Show this message and exit. diff --git a/docs/commands/profile_create.rst b/docs/commands/profile_create.rst index 83e5a223b..a9f8e51a5 100644 --- a/docs/commands/profile_create.rst +++ b/docs/commands/profile_create.rst @@ -49,6 +49,8 @@ Create a profile. commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --galaxy_url TEXT Remote Galaxy URL to use with external Galaxy engine. --galaxy_user_key TEXT User key to use with external Galaxy engine. diff --git a/docs/commands/profile_delete.rst b/docs/commands/profile_delete.rst index bc778e4a3..17bdc0aad 100644 --- a/docs/commands/profile_delete.rst +++ b/docs/commands/profile_delete.rst @@ -44,5 +44,7 @@ Delete a profile. commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --help Show this message and exit. diff --git a/docs/commands/run.rst b/docs/commands/run.rst index 7e77725ad..94c1b4bee 100644 --- a/docs/commands/run.rst +++ b/docs/commands/run.rst @@ -59,6 +59,8 @@ Planemo command for running tools and jobs. commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless diff --git a/docs/commands/serve.rst b/docs/commands/serve.rst index 7f781ad3d..a7277c94e 100644 --- a/docs/commands/serve.rst +++ b/docs/commands/serve.rst @@ -75,6 +75,8 @@ Galaxy instance. commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless diff --git a/docs/commands/shed_serve.rst b/docs/commands/shed_serve.rst index 155a48469..37dd01f3a 100644 --- a/docs/commands/shed_serve.rst +++ b/docs/commands/shed_serve.rst @@ -83,6 +83,8 @@ logged into and explored interactively. commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless diff --git a/docs/commands/shed_test.rst b/docs/commands/shed_test.rst index d401d8179..ad2078f47 100644 --- a/docs/commands/shed_test.rst +++ b/docs/commands/shed_test.rst @@ -82,6 +82,8 @@ install these artifacts, and run the tool tests for these commands. commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless diff --git a/docs/commands/test.rst b/docs/commands/test.rst index 024a2843d..618c63a5d 100644 --- a/docs/commands/test.rst +++ b/docs/commands/test.rst @@ -89,6 +89,8 @@ please careful and do not try this against production Galaxy instances. commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless diff --git a/docs/commands/training_generate_from_wf.rst b/docs/commands/training_generate_from_wf.rst index 671f3024c..ac1426afd 100644 --- a/docs/commands/training_generate_from_wf.rst +++ b/docs/commands/training_generate_from_wf.rst @@ -64,6 +64,8 @@ Create tutorial skeleton from workflow. commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless diff --git a/docs/commands/training_init.rst b/docs/commands/training_init.rst index 0eb952963..704111d81 100644 --- a/docs/commands/training_init.rst +++ b/docs/commands/training_init.rst @@ -72,6 +72,8 @@ Build training template from workflow. commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless diff --git a/docs/commands/upload_data.rst b/docs/commands/upload_data.rst index b0cd08834..4d9bd81bb 100644 --- a/docs/commands/upload_data.rst +++ b/docs/commands/upload_data.rst @@ -69,6 +69,8 @@ the already completed data upload. commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless diff --git a/docs/commands/workflow_convert.rst b/docs/commands/workflow_convert.rst index e9987c476..94aa34b02 100644 --- a/docs/commands/workflow_convert.rst +++ b/docs/commands/workflow_convert.rst @@ -56,6 +56,8 @@ Convert Format 2 workflows to native Galaxy workflows, and vice-versa. commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless diff --git a/docs/commands/workflow_edit.rst b/docs/commands/workflow_edit.rst index ec728155f..af3201e11 100644 --- a/docs/commands/workflow_edit.rst +++ b/docs/commands/workflow_edit.rst @@ -54,6 +54,8 @@ Open a synchronized Galaxy workflow editor. commands (defaults to localhost). --docker_sudo_cmd TEXT sudo command to use when --docker_sudo is enabled (defaults to sudo). + --docker_run_extra_arguments TEXT + Extra arguments to pass to docker run. --mulled_containers, --biocontainers Test tools against mulled containers (forces --docker). Disables conda resolution unless diff --git a/planemo/__init__.py b/planemo/__init__.py index c7c074da6..cd3700e50 100644 --- a/planemo/__init__.py +++ b/planemo/__init__.py @@ -1,4 +1,4 @@ -__version__ = "0.75.20" +__version__ = "0.75.21" PROJECT_NAME = "planemo"