Prepare release 0.75.31

mvdbeek · mvdbeek · commit bb7f5244d23e · 2025-06-23T16:17:19.000-04:00
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -6,8 +6,45 @@ History
 .. to_doc
 
 ---------------------
-0.75.31.dev0
----------------------
+0.75.31 (2025-06-23)
+---------------------
+
+* Don't pollute working directory with tools.yaml file (thanks to
+  `@mvdbeek`_). `Pull Request 1554`_
+* Add ruff and isort to `make format` and tox, add pre-commit config (thanks
+  to `@mvdbeek`_). `Pull Request 1552`_
+* Make ``no_dependency_resolution`` and ``simultaneous_upload`` global options
+  (thanks to `@mvdbeek`_). `Pull Request 1553`_
+* Add flag to export invocation from run command (thanks to `@mvdbeek`_).
+  `Pull Request 1551`_
+* Load default job metrics (thanks to `@mvdbeek`_). `Pull Request 1548`_
+* Drop unnecessary autogen in cmd_slurm_init (thanks to `@mvdbeek`_). `Pull
+  Request 1549`_
+* Terminate polling if we can't advance invocation (thanks to `@mvdbeek`_).
+  `Pull Request 1547`_
+* Don't do preload in managed instance (thanks to `@mvdbeek`_). `Pull Request
+  1546`_
+* Add a slurm_init command (thanks to `@jmchilton`_). `Pull Request 1543`_
+* Add missing module to pyproject.toml (thanks to `@mvdbeek`_). `Pull Request
+  1545`_
+* Add the option to download the outputs of a completed workflow run (thanks
+  to `@Smeds`_). `Pull Request 1532`_
+* update shed categories (thanks to `@bgruening`_). `Pull Request 1539`_
+* cmd to export an existing invocations as an archive for storage or later
+  import (thanks to `@Smeds`_). `Pull Request 1534`_
+* Bump requirements for galaxy packages to 25.0 (thanks to
+  `@ahmedhamidawan`_). `Pull Request 1542`_
+* Print job errors in workflow invocation as they occur (thanks to
+  `@mvdbeek`_). `Pull Request 1540`_
+* Enable celery tasks (thanks to `@mvdbeek`_). `Pull Request 1541`_
+* add file extension to downloaded output (thanks to `@Smeds`_). `Pull Request
+  1531`_
+* Workflow progress bar (thanks to `@jmchilton`_). `Pull Request 1510`_
+* Fix job handler setup (thanks to `@mvdbeek`_). `Pull Request 1538`_
+* Overhaul Galaxy job config handling (thanks to `@jmchilton`_). `Pull Request
+  1506`_
+* create provided output_directory if it doesn't exist (thanks to `@Smeds`_).
+  `Pull Request 1526`_
 
 ---------------------
 0.75.30 (2025-05-07)
@@ -2210,6 +2247,27 @@ History
   tools - and more experimental features involving Docker and Homebrew. 7d07782_
 
 .. github_links
+.. _Pull Request 1554: https://github.com/galaxyproject/planemo/pull/1554
+.. _Pull Request 1552: https://github.com/galaxyproject/planemo/pull/1552
+.. _Pull Request 1553: https://github.com/galaxyproject/planemo/pull/1553
+.. _Pull Request 1551: https://github.com/galaxyproject/planemo/pull/1551
+.. _Pull Request 1548: https://github.com/galaxyproject/planemo/pull/1548
+.. _Pull Request 1549: https://github.com/galaxyproject/planemo/pull/1549
+.. _Pull Request 1547: https://github.com/galaxyproject/planemo/pull/1547
+.. _Pull Request 1546: https://github.com/galaxyproject/planemo/pull/1546
+.. _Pull Request 1543: https://github.com/galaxyproject/planemo/pull/1543
+.. _Pull Request 1545: https://github.com/galaxyproject/planemo/pull/1545
+.. _Pull Request 1532: https://github.com/galaxyproject/planemo/pull/1532
+.. _Pull Request 1539: https://github.com/galaxyproject/planemo/pull/1539
+.. _Pull Request 1534: https://github.com/galaxyproject/planemo/pull/1534
+.. _Pull Request 1542: https://github.com/galaxyproject/planemo/pull/1542
+.. _Pull Request 1540: https://github.com/galaxyproject/planemo/pull/1540
+.. _Pull Request 1541: https://github.com/galaxyproject/planemo/pull/1541
+.. _Pull Request 1531: https://github.com/galaxyproject/planemo/pull/1531
+.. _Pull Request 1510: https://github.com/galaxyproject/planemo/pull/1510
+.. _Pull Request 1538: https://github.com/galaxyproject/planemo/pull/1538
+.. _Pull Request 1506: https://github.com/galaxyproject/planemo/pull/1506
+.. _Pull Request 1526: https://github.com/galaxyproject/planemo/pull/1526
 .. _Pull Request 1509: https://github.com/galaxyproject/planemo/pull/1509
 .. _Pull Request 1514: https://github.com/galaxyproject/planemo/pull/1514
 .. _Pull Request 1523: https://github.com/galaxyproject/planemo/pull/1523
@@ -3193,3 +3251,4 @@ History
 .. _@Smeds: https://github.com/Smeds
 .. _@jmchilton: https://github.com/jmchilton
 .. _@kostrykin: https://github.com/kostrykin
+.. _@ahmedhamidawan: https://github.com/ahmedhamidawan
diff --git a/docs/commands.rst b/docs/commands.rst
@@ -28,6 +28,9 @@ documentation describes these commands.
 .. include:: commands/docker_shell.rst
 .. include:: commands/dockstore_init.rst
 .. include:: commands/docs.rst
+.. include:: commands/invocation_download.rst
+.. include:: commands/invocation_export.rst
+.. include:: commands/job_config_init.rst
 .. include:: commands/lint.rst
 .. include:: commands/list_alias.rst
 .. include:: commands/list_invocations.rst
@@ -39,6 +42,7 @@ documentation describes these commands.
 .. include:: commands/open.rst
 .. include:: commands/profile_create.rst
 .. include:: commands/profile_delete.rst
+.. include:: commands/profile_job_config_init.rst
 .. include:: commands/profile_list.rst
 .. include:: commands/project_init.rst
 .. include:: commands/pull_request.rst
@@ -55,6 +59,7 @@ documentation describes these commands.
 .. include:: commands/shed_test.rst
 .. include:: commands/shed_update.rst
 .. include:: commands/shed_upload.rst
+.. include:: commands/slurm_init.rst
 .. include:: commands/syntax.rst
 .. include:: commands/test.rst
 .. include:: commands/test_reports.rst
@@ -69,4 +74,5 @@ documentation describes these commands.
 .. include:: commands/workflow_lint.rst
 .. include:: commands/workflow_test_init.rst
 .. include:: commands/workflow_test_on_invocation.rst
+.. include:: commands/workflow_track.rst
 .. include:: commands/workflow_upload.rst
diff --git a/docs/commands/autoupdate.rst b/docs/commands/autoupdate.rst
@@ -63,9 +63,10 @@ Auto-update tool requirements by checking against Conda and updating if newer ve
                                       output (see output reports for more complete
                                       summary). Set to 'none' to disable completely.
       --test_timeout INTEGER          Maximum runtime of a single test in seconds.
+      --fail_fast                     Stop on first job failure.
       --galaxy_root DIRECTORY         Root of development galaxy directory to
                                       execute command with.
-      --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
+      --galaxy_python_version [3|3.8|3.9|3.10|3.11|3.12]
                                       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
@@ -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|3.10|3.11]
+      --galaxy_python_version [3|3.8|3.9|3.10|3.11|3.12]
                                       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/config_init.rst b/docs/commands/config_init.rst
@@ -19,6 +19,7 @@ Helps initialize global configuration (in home directory) for Planemo.
 **Options**::
 
 
+      --open           Open the file in your default editor after creation.
       --template TEXT
       --help           Show this message and exit.
     
diff --git a/docs/commands/dockstore_init.rst b/docs/commands/dockstore_init.rst
@@ -26,5 +26,6 @@ https://docs.dockstore.org/en/develop/getting-started/dockstore-workflows.html.
 
 
       --publish / --no_publish  Set publish attribute to true in .dockstore.yml file
+      --open                    Open the file in your default editor after creation.
       --help                    Show this message and exit.
     
diff --git a/docs/commands/run.rst b/docs/commands/run.rst
@@ -8,7 +8,7 @@ This section is auto-generated from the help text for the planemo command
 
 **Usage**::
 
-    planemo run [OPTIONS] RUNNABLE_PATH_OR_ID JOB_PATH
+    planemo run [OPTIONS] RUNNABLE_PATH_OR_ID JOB_PATH model store format
 
 **Help**
 
@@ -22,7 +22,7 @@ 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|3.10|3.11]
+      --galaxy_python_version [3|3.8|3.9|3.10|3.11|3.12]
                                       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
@@ -177,6 +177,8 @@ Planemo command for running tools and jobs.
                                       After tool or workflow runs are complete,
                                       download the output files to the location
                                       specified by --output_directory.
+      --export_invocation PATH        Export workflow invocation as archive to
+                                      specified path.
       --engine [galaxy|docker_galaxy|cwltool|toil|external_galaxy]
                                       Select an engine to run or test artifacts such
                                       as tools and workflows. Defaults to a local
@@ -253,7 +255,6 @@ Planemo command for running tools and jobs.
                                       output (see output reports for more complete
                                       summary). Set to 'none' to disable completely.
       --test_timeout INTEGER          Maximum runtime of a single test in seconds.
-      --no_early_termination          Wait until all jobs terminate, even if some
-                                      jobs have failed
+      --fail_fast                     Stop on first job failure.
       --help                          Show this message and exit.
     
diff --git 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|3.10|3.11]
+      --galaxy_python_version [3|3.8|3.9|3.10|3.11|3.12]
                                       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/shed_init.rst b/docs/commands/shed_init.rst
@@ -29,7 +29,7 @@ to manage repositories in a Galaxy Tool Shed.
       --remote_repository_url TEXT    Specify repository remote_repository_url for
                                       .shed.yml.
       --homepage_url TEXT             Specify repository homepage_url for .shed.yml.
-      --category [Assembly|Astronomy|ChIP-seq|Climate Analysis|CLIP-seq|Combinatorial Selections|Computational chemistry|Constructive Solid Geometry|Convert Formats|Data Export|Data Managers|Data Source|Ecology|Entomology|Epigenetics|Fasta Manipulation|Fastq Manipulation|Flow Cytometry Analysis|Genome annotation|Genome editing|Genome-Wide Association Study|Genomic Interval Operations|Geo Science|GIS|Graphics|Imaging|InteractiveTools|Machine Learning|Materials science|Metabolomics|Metagenomics|Micro-array Analysis|Molecular Dynamics|Muon spectroscopy|Nanopore|Next Gen Mappers|NLP|Ontology Manipulation|Phylogenetics|Proteomics|RNA|SAM|Sequence Analysis|Single Cell|Spatial Omics|Statistics|Structural Materials Analysis|Synthetic Biology|Systems Biology|Text Manipulation|Tool Dependency Packages|Tool Generators|Transcriptomics|Variant Analysis|Visualization|Web Services]
+      --category [Assembly|Astronomy|ChIP-seq|Climate Analysis|CLIP-seq|Combinatorial Selections|Computational chemistry|Constructive Solid Geometry|Convert Formats|Data Export|Data Managers|Data Source|Ecology|Entomology|Epigenetics|Fasta Manipulation|Fastq Manipulation|Flow Cytometry Analysis|Genome annotation|Genome editing|Genome-Wide Association Study|Genomic Interval Operations|Geo Science|GIS|Graphics|Imaging|Interactive Tools|Machine Learning|Materials science|Metabolomics|Metagenomics|Micro-array Analysis|Molecular Dynamics|Muon spectroscopy|Nanopore|Natural Language Processing|Next Gen Mappers|Ontology Manipulation|Phylogenetics|Proteomics|RNA|SAM|Sequence Analysis|Single Cell|Spatial Omics|Statistics|Structural Materials Analysis|Synthetic Biology|Systems Biology|Text Manipulation|Tool Dependency Packages|Tool Generators|Transcriptomics|Variant Analysis|Visualization|Web Services]
                                       Specify repository category for .shed.yml (may
                                       specify multiple).
       --owner TEXT                    Tool Shed repository owner (username).
diff --git 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|3.10|3.11]
+      --galaxy_python_version [3|3.8|3.9|3.10|3.11|3.12]
                                       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/shed_test.rst b/docs/commands/shed_test.rst
@@ -46,7 +46,7 @@ install these artifacts, and run the tool tests for these commands.
                                       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|3.10|3.11]
+      --galaxy_python_version [3|3.8|3.9|3.10|3.11|3.12]
                                       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
@@ -207,7 +207,16 @@ install these artifacts, and run the tool tests for these commands.
                                       output (see output reports for more complete
                                       summary). Set to 'none' to disable completely.
       --test_timeout INTEGER          Maximum runtime of a single test in seconds.
+      --fail_fast                     Stop on first job failure.
       --skip_dependencies             Do not install shed dependencies as part of
                                       repository installation.
       --help                          Show this message and exit.
+    /Users/mvandenb/src/planemo/.venv/lib/python3.13/site-packages/click/core.py:1193: UserWarning: The parameter --fail_fast is used more than once. Remove its duplicate as parameters should be unique.
+      parser = self.make_parser(ctx)
+    /Users/mvandenb/src/planemo/.venv/lib/python3.13/site-packages/click/core.py:1186: UserWarning: The parameter --fail_fast is used more than once. Remove its duplicate as parameters should be unique.
+      self.parse_args(ctx, args)
+    /Users/mvandenb/src/planemo/.venv/lib/python3.13/site-packages/click/core.py:1002: UserWarning: The parameter --fail_fast is used more than once. Remove its duplicate as parameters should be unique.
+      pieces = self.collect_usage_pieces(ctx)
+    /Users/mvandenb/src/planemo/.venv/lib/python3.13/site-packages/click/core.py:1104: UserWarning: The parameter --fail_fast is used more than once. Remove its duplicate as parameters should be unique.
+      self.format_options(ctx, formatter)
     
diff --git 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|3.10|3.11]
+      --galaxy_python_version [3|3.8|3.9|3.10|3.11|3.12]
                                       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
@@ -214,6 +214,7 @@ please careful and do not try this against production Galaxy instances.
                                       output (see output reports for more complete
                                       summary). Set to 'none' to disable completely.
       --test_timeout INTEGER          Maximum runtime of a single test in seconds.
+      --fail_fast                     Stop on first job failure.
       --engine [galaxy|docker_galaxy|cwltool|toil|external_galaxy]
                                       Select an engine to run or test artifacts such
                                       as tools and workflows. Defaults to a local
diff --git 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|3.10|3.11]
+      --galaxy_python_version [3|3.8|3.9|3.10|3.11|3.12]
                                       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/training_init.rst b/docs/commands/training_init.rst
@@ -36,7 +36,7 @@ Build training template from workflow.
       --zenodo_link TEXT              Zenodo URL with the input data
       --galaxy_root DIRECTORY         Root of development galaxy directory to
                                       execute command with.
-      --galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
+      --galaxy_python_version [3|3.8|3.9|3.10|3.11|3.12]
                                       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/upload_data.rst b/docs/commands/upload_data.rst
@@ -32,7 +32,7 @@ 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|3.10|3.11]
+      --galaxy_python_version [3|3.8|3.9|3.10|3.11|3.12]
                                       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
@@ -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|3.10|3.11]
+      --galaxy_python_version [3|3.8|3.9|3.10|3.11|3.12]
                                       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_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|3.10|3.11]
+      --galaxy_python_version [3|3.8|3.9|3.10|3.11|3.12]
                                       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/planemo.commands.rst b/docs/planemo.commands.rst
diff --git a/docs/planemo.galaxy.rst b/docs/planemo.galaxy.rst
diff --git a/planemo/__init__.py b/planemo/__init__.py

Original file line number	Diff line number	Diff line change
`@@ -26,5 +26,6 @@ https://docs.dockstore.org/en/develop/getting-started/dockstore-workflows.html.`
`26`	`26`
`27`	`27`
`28`	`28`	`--publish / --no_publish Set publish attribute to true in .dockstore.yml file`
	`29`	`+ --open Open the file in your default editor after creation.`
`29`	`30`	`--help Show this message and exit.`
`30`	`31`