Create release 0.75.21

galaxyproject · Feb 8, 2024 · aacd70c · aacd70c
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,4 +1,4 @@
-__version__ = "0.75.20"
+__version__ = "0.75.21"
 
 
 PROJECT_NAME = "planemo"