diff --git a/HISTORY.rst b/HISTORY.rst index d044368fb..fe376e000 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -5,6 +5,26 @@ History .. to_doc +--------------------- +0.75.3 (2022-11-30) +--------------------- + +* Mount test data dir read-only in docker (thanks to `@mvdbeek`_). `Pull + Request 1327`_ +* Add traceback to report template (thanks to `@bernt-matthias`_). `Pull + Request 1332`_ +* Add indent and sort_keys to tool_test_json (thanks to `@simonbray`_). `Pull + Request 1330`_ +* Fix ``planemo shed_test`` (thanks to `@mvdbeek`_). `Pull Request 1329`_ +* Add h5py dependency, required for comparing h5 files (thanks to + `@mvdbeek`_). `Pull Request 1326`_ +* Update GitHub action versions (thanks to `@nsoranzo`_). `Pull Request 1322`_ +* Fix "glone" typo in error message (thanks to `@bernt-matthias`_). `Pull + Request 1325`_ +* Type annotation for input staging-related code (thanks to `@nsoranzo`_). + `Pull Request 1320`_ +* Add creator dockstore (thanks to `@lldelisle`_). `Pull Request 1314`_ + --------------------- 0.75.2 (2022-11-02) --------------------- @@ -1898,6 +1918,15 @@ History tools - and more experimental features involving Docker and Homebrew. 7d07782_ .. github_links +.. _Pull Request 1327: https://github.com/galaxyproject/planemo/pull/1327 +.. _Pull Request 1332: https://github.com/galaxyproject/planemo/pull/1332 +.. _Pull Request 1330: https://github.com/galaxyproject/planemo/pull/1330 +.. _Pull Request 1329: https://github.com/galaxyproject/planemo/pull/1329 +.. _Pull Request 1326: https://github.com/galaxyproject/planemo/pull/1326 +.. _Pull Request 1322: https://github.com/galaxyproject/planemo/pull/1322 +.. _Pull Request 1325: https://github.com/galaxyproject/planemo/pull/1325 +.. _Pull Request 1320: https://github.com/galaxyproject/planemo/pull/1320 +.. _Pull Request 1314: https://github.com/galaxyproject/planemo/pull/1314 .. _Pull Request 1313: https://github.com/galaxyproject/planemo/pull/1313 .. _Pull Request 1312: https://github.com/galaxyproject/planemo/pull/1312 .. _Pull Request 1310: https://github.com/galaxyproject/planemo/pull/1310 diff --git a/docs/commands/autoupdate.rst b/docs/commands/autoupdate.rst index 959d7688f..58a4e5ec4 100644 --- a/docs/commands/autoupdate.rst +++ b/docs/commands/autoupdate.rst @@ -57,7 +57,7 @@ Auto-update tool requirements by checking against Conda and updating if newer ve --test_timeout INTEGER Maximum runtime of a single test in seconds. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.7|3.8|3.9] + --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be diff --git a/docs/commands/ci_setup.rst b/docs/commands/ci_setup.rst index 4489c5f62..f893a275b 100644 --- a/docs/commands/ci_setup.rst +++ b/docs/commands/ci_setup.rst @@ -22,7 +22,7 @@ Useful for populating a CI cache. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.7|3.8|3.9] + --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be diff --git a/docs/commands/run.rst b/docs/commands/run.rst index ec4f17ed9..3e4b94545 100644 --- a/docs/commands/run.rst +++ b/docs/commands/run.rst @@ -23,7 +23,7 @@ Planemo command for running tools and jobs. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.7|3.8|3.9] + --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be @@ -183,7 +183,8 @@ Planemo command for running tools and jobs. flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. - --docker_extra_volume PATH Extra path to mount if --engine docker. + --docker_extra_volume PATH Extra path to mount if --engine docker or + `--biocontainers` or `--docker`. --ignore_dependency_problems When installing shed repositories for workflows, ignore dependency issues. These likely indicate a problem but in some cases diff --git a/docs/commands/serve.rst b/docs/commands/serve.rst index 1dcbfb2f4..6adbac4fe 100644 --- a/docs/commands/serve.rst +++ b/docs/commands/serve.rst @@ -39,7 +39,7 @@ Galaxy instance. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.7|3.8|3.9] + --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be @@ -104,7 +104,8 @@ Galaxy instance. flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. - --docker_extra_volume PATH Extra path to mount if --engine docker. + --docker_extra_volume PATH Extra path to mount if --engine docker or + `--biocontainers` or `--docker`. --test_data DIRECTORY test-data directory to for specified tool(s). --tool_data_table PATH tool_data_table_conf.xml file to for specified tool(s). diff --git a/docs/commands/shed_serve.rst b/docs/commands/shed_serve.rst index c3dcacbee..155037c5f 100644 --- a/docs/commands/shed_serve.rst +++ b/docs/commands/shed_serve.rst @@ -47,7 +47,7 @@ logged into and explored interactively. mappings defined ~/.planemo.yml. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.7|3.8|3.9] + --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be @@ -112,7 +112,8 @@ logged into and explored interactively. flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. - --docker_extra_volume PATH Extra path to mount if --engine docker. + --docker_extra_volume PATH Extra path to mount if --engine docker or + `--biocontainers` or `--docker`. --test_data DIRECTORY test-data directory to for specified tool(s). --tool_data_table PATH tool_data_table_conf.xml file to for specified tool(s). diff --git a/docs/commands/shed_test.rst b/docs/commands/shed_test.rst index bbd3f4046..12d5d26b3 100644 --- a/docs/commands/shed_test.rst +++ b/docs/commands/shed_test.rst @@ -19,8 +19,6 @@ specified shed, find published artifacts (tools and dependencies) corresponding to command-line arguments and ``.shed.yml`` file(s), install these artifacts, and run the tool tests for these commands. -This command requires the target to be version 15.07 or newer. - **Options**:: @@ -48,7 +46,7 @@ This command requires the target to be version 15.07 or newer. mappings defined ~/.planemo.yml. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.7|3.8|3.9] + --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be @@ -97,6 +95,79 @@ This command requires the target to be version 15.07 or newer. --tool_data_path DIRECTORY Directory where data used by tools is located. Required if tests are run in docker and should make use of external reference data. + --test_data DIRECTORY test-data directory to for specified tool(s). + --tool_data_table PATH tool_data_table_conf.xml file to for specified + tool(s). + --dependency_resolvers_config_file FILE + Dependency resolver configuration for Galaxy + to target. + --brew_dependency_resolution Configure Galaxy to use plain brew dependency + resolution. + --shed_dependency_resolution Configure Galaxy to use brewed Tool Shed + dependency resolution. + --no_dependency_resolution Configure Galaxy with no dependency resolvers. + --conda_prefix DIRECTORY Conda prefix to use for conda dependency + commands. + --conda_exec FILE Location of conda executable. + --conda_channels, --conda_ensure_channels TEXT + Ensure conda is configured with specified + comma separated list of channels. + --conda_use_local Use locally built packages while building + Conda environments. + --conda_dependency_resolution Configure Galaxy to use only conda for + dependency resolution. + --conda_auto_install / --no_conda_auto_install + Conda dependency resolution for Galaxy will + attempt to install requested but missing + packages. + --conda_auto_init / --no_conda_auto_init + Conda dependency resolution for Galaxy will + auto install conda itself using miniconda if + not availabe on conda_prefix. + --simultaneous_uploads / --no_simultaneous_uploads + When uploading files to Galaxy for tool or + workflow tests or runs, upload multiple files + simultaneously without waiting for the + previous file upload to complete. + --check_uploads_ok / --no_check_uploads_ok + When uploading files to Galaxy for tool or + workflow tests or runs, check that the history + is in an 'ok' state before beginning tool or + workflow execution. + --profile TEXT Name of profile (created with the + profile_create command) to use with this + command. + --postgres Use postgres database type. + --database_type [postgres|postgres_docker|sqlite|auto] + Type of database to use for profile - 'auto', + 'sqlite', 'postgres', and 'postgres_docker' + are available options. Use postgres to use an + existing postgres server you user can access + without a password via the psql command. Use + postgres_docker to have Planemo manage a + docker container running postgres. Data with + postgres_docker is not yet persisted past when + you restart the docker container launched by + Planemo so be careful with this option. + --postgres_psql_path TEXT Name or or path to postgres client binary + (psql). + --postgres_database_user TEXT Postgres username for managed development + databases. + --postgres_database_host TEXT Postgres host name for managed development + databases. + --postgres_database_port TEXT Postgres port for managed development + databases. + --file_path DIRECTORY Location for files created by Galaxy (e.g. + database/files). + --database_connection TEXT Database connection string to use for Galaxy. + --shed_tool_conf TEXT Location of shed tools conf file for Galaxy. + --shed_tool_path TEXT Location of shed tools directory for Galaxy. + --galaxy_single_user / --no_galaxy_single_user + By default Planemo will configure Galaxy to + run in single-user mode where there is just + one user and this user is automatically logged + it. Use --no_galaxy_single_user to prevent + Galaxy from running this way. --update_test_data Update test-data directory with job outputs (normally written to directory --job_output_files if specified.) diff --git a/docs/commands/test.rst b/docs/commands/test.rst index 948904706..71ff8ae44 100644 --- a/docs/commands/test.rst +++ b/docs/commands/test.rst @@ -53,7 +53,7 @@ please careful and do not try this against production Galaxy instances. generated traffic. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.7|3.8|3.9] + --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be @@ -216,7 +216,8 @@ please careful and do not try this against production Galaxy instances. flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. - --docker_extra_volume PATH Extra path to mount if --engine docker. + --docker_extra_volume PATH Extra path to mount if --engine docker or + `--biocontainers` or `--docker`. --ignore_dependency_problems When installing shed repositories for workflows, ignore dependency issues. These likely indicate a problem but in some cases diff --git a/docs/commands/training_generate_from_wf.rst b/docs/commands/training_generate_from_wf.rst index 8c58f15b8..246f6fef2 100644 --- a/docs/commands/training_generate_from_wf.rst +++ b/docs/commands/training_generate_from_wf.rst @@ -28,7 +28,7 @@ Create tutorial skeleton from workflow. --workflow_id TEXT ID of the workflow on the Galaxy instance --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.7|3.8|3.9] + --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be @@ -93,7 +93,8 @@ Create tutorial skeleton from workflow. flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. - --docker_extra_volume PATH Extra path to mount if --engine docker. + --docker_extra_volume PATH Extra path to mount if --engine docker or + `--biocontainers` or `--docker`. --test_data DIRECTORY test-data directory to for specified tool(s). --tool_data_table PATH tool_data_table_conf.xml file to for specified tool(s). diff --git a/docs/commands/training_init.rst b/docs/commands/training_init.rst index 2b168f124..8d1b6edde 100644 --- a/docs/commands/training_init.rst +++ b/docs/commands/training_init.rst @@ -38,7 +38,7 @@ Build training template from workflow. Zenodo extension and Galaxy datatypes --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.7|3.8|3.9] + --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be @@ -103,7 +103,8 @@ Build training template from workflow. flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. - --docker_extra_volume PATH Extra path to mount if --engine docker. + --docker_extra_volume PATH Extra path to mount if --engine docker or + `--biocontainers` or `--docker`. --test_data DIRECTORY test-data directory to for specified tool(s). --tool_data_table PATH tool_data_table_conf.xml file to for specified tool(s). diff --git a/docs/commands/upload_data.rst b/docs/commands/upload_data.rst index ec0177ac2..20662a01e 100644 --- a/docs/commands/upload_data.rst +++ b/docs/commands/upload_data.rst @@ -33,7 +33,7 @@ the already completed data upload. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.7|3.8|3.9] + --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be diff --git a/docs/commands/workflow_convert.rst b/docs/commands/workflow_convert.rst index 5cf4ff713..8b6af43d0 100644 --- a/docs/commands/workflow_convert.rst +++ b/docs/commands/workflow_convert.rst @@ -20,7 +20,7 @@ Convert Format 2 workflows to native Galaxy workflows, and vice-versa. -o, --output FILE --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.7|3.8|3.9] + --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be @@ -85,7 +85,8 @@ Convert Format 2 workflows to native Galaxy workflows, and vice-versa. flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. - --docker_extra_volume PATH Extra path to mount if --engine docker. + --docker_extra_volume PATH Extra path to mount if --engine docker or + `--biocontainers` or `--docker`. --test_data DIRECTORY test-data directory to for specified tool(s). --tool_data_table PATH tool_data_table_conf.xml file to for specified tool(s). diff --git a/docs/commands/workflow_edit.rst b/docs/commands/workflow_edit.rst index a9935ef91..1afb0efc8 100644 --- a/docs/commands/workflow_edit.rst +++ b/docs/commands/workflow_edit.rst @@ -18,7 +18,7 @@ Open a synchronized Galaxy workflow editor. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_python_version [3|3.7|3.8|3.9] + --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11] Python version to start Galaxy under --extra_tools PATH Extra tool sources to include in Galaxy's tool panel (file or directory). These will not be @@ -83,7 +83,8 @@ Open a synchronized Galaxy workflow editor. flavor used if engine type is specified as ``docker-galaxy``. Defaults to quay.io/bgruening/galaxy. - --docker_extra_volume PATH Extra path to mount if --engine docker. + --docker_extra_volume PATH Extra path to mount if --engine docker or + `--biocontainers` or `--docker`. --test_data DIRECTORY test-data directory to for specified tool(s). --tool_data_table PATH tool_data_table_conf.xml file to for specified tool(s). diff --git a/planemo/__init__.py b/planemo/__init__.py index 44bdfb511..00114c5eb 100644 --- a/planemo/__init__.py +++ b/planemo/__init__.py @@ -1,4 +1,4 @@ -__version__ = "0.75.2" +__version__ = "0.75.3" PROJECT_NAME = "planemo"