Prepare 0.60.0 (#936)

Prepare 0.60.0
galaxyproject · May 31, 2019 · 1664d28 · 1664d28
2 parents 929e5a4 + 555b5ac
commit 1664d28
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diff --git a/HISTORY.rst b/HISTORY.rst
@@ -6,11 +6,15 @@ History
 .. to_doc
 
 ---------------------
-0.60.0.dev0
+0.60.0 (2019-05-31)
 ---------------------
 
-
-
+* Return validation error if doi is empty `Pull Request 937`_
+* Add junit as test reporter (thanks to `@selten`_). `Pull Request 935`_
+* Update galaxy.xsd for new python 3 compatibility attribute (thanks to `@martenson`_). `Pull Request
+  931`_
+* Documentation: add a little warning for <param ... multiple="true"> (thanks to
+  `@bernt-matthias`_). `Pull Request 930`_
 
 ---------------------
 0.59.0 (2019-05-09)
@@ -1474,6 +1478,10 @@ History
   tools - and more experimental features involving Docker and Homebrew. 7d07782_
 
 .. github_links
+.. _Pull Request 937: https://github.com/galaxyproject/planemo/pull/937
+.. _Pull Request 935: https://github.com/galaxyproject/planemo/pull/935
+.. _Pull Request 931: https://github.com/galaxyproject/planemo/pull/931
+.. _Pull Request 930: https://github.com/galaxyproject/planemo/pull/930
 .. _Pull Request 913: https://github.com/galaxyproject/planemo/pull/913
 .. _Pull Request 917: https://github.com/galaxyproject/planemo/pull/917
 .. _Pull Request 921: https://github.com/galaxyproject/planemo/pull/921
@@ -2110,3 +2118,4 @@ History
 .. _@bernt-matthias: https://github.com/bernt-matthias
 .. _@katrinleinweber: https://github.com/katrinleinweber
 .. _@bebatut: https://github.com/bebatut
+.. _@selten: https://github.com/selten
diff --git a/cwl-runner/setup.py b/cwl-runner/setup.py
@@ -1,11 +1,8 @@
 #!/usr/bin/env python
 
 import os
-import sys
-import setuptools.command.egg_info as egg_info_cmd
-import shutil
 
-from setuptools import setup, find_packages
+from setuptools import setup
 
 SETUP_DIR = os.path.dirname(__file__)
 README = os.path.join(SETUP_DIR, 'README')
@@ -25,5 +22,4 @@
           'planemo'
         ],
       scripts=scripts,
-      zip_safe=True
-)
+      zip_safe=True)
diff --git a/docs/commands/bioc_tool_init.rst b/docs/commands/bioc_tool_init.rst
@@ -18,7 +18,7 @@ Generate a bioconductor tool outline from supplied arguments.
 
       -i, --id TEXT             Short identifier for new tool (no whitespace)
       -f, --force               Overwrite existing tool if present.
-      -t, --tool PATH           Output path for new tool (default is <id>.xml)
+      -t, --tool FILE           Output path for new tool (default is <id>.xml)
       -n, --name TEXT           Name for new R/Bioconductor tool (user facing).
       -d, --description TEXT    Short description for new tool (user facing)
       -c, --command TEXT        Command potentially including cheetah variables

diff --git a/docs/commands/brew.rst b/docs/commands/brew.rst
@@ -24,6 +24,6 @@ until a more permanent project home is setup.
 **Options**::
 
 
-      --brew PATH  Homebrew 'brew' executable to use.
+      --brew FILE  Homebrew 'brew' executable to use.
       --help       Show this message and exit.
     
diff --git a/docs/commands/brew_env.rst b/docs/commands/brew_env.rst
@@ -41,7 +41,7 @@ sourced.
 **Options**::
 
 
-      --brew PATH     Homebrew 'brew' executable to use.
+      --brew FILE     Homebrew 'brew' executable to use.
       --skip_install  Skip installation - only source requirements already
                       available.
       --shell

diff --git a/docs/commands/ci_find_repos.rst b/docs/commands/ci_find_repos.rst
@@ -21,7 +21,7 @@ file.
 
 
       --exclude PATH                  Paths to exclude.
-      --exclude_from PATH             File of paths to exclude.
+      --exclude_from FILE             File of paths to exclude.
       --changed_in_commit_range TEXT  Exclude paths unchanged in git commit range.
       --chunk_count INTEGER           Split output into chunks of this many item and
                                       print --chunk such group.

diff --git a/docs/commands/ci_find_tools.rst b/docs/commands/ci_find_tools.rst
@@ -21,7 +21,7 @@ operations over for continuous integration operations.
 
 
       --exclude PATH                  Paths to exclude.
-      --exclude_from PATH             File of paths to exclude.
+      --exclude_from FILE             File of paths to exclude.
       --changed_in_commit_range TEXT  Exclude paths unchanged in git commit range.
       --chunk_count INTEGER           Split output into chunks of this many item and
                                       print --chunk such group.

diff --git a/docs/commands/conda_build.rst b/docs/commands/conda_build.rst
@@ -18,7 +18,7 @@ Perform conda build with Planemo's conda.
 
       --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                       commands.
-      --conda_exec PATH               Location of conda executable.
+      --conda_exec FILE               Location of conda executable.
       --conda_debug                   Enable more verbose conda logging.
       --conda_channels, --conda_ensure_channels TEXT
                                       Ensure conda is configured with specified

diff --git a/docs/commands/conda_env.rst b/docs/commands/conda_env.rst
@@ -32,7 +32,7 @@ tool.
 
       --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                       commands.
-      --conda_exec PATH               Location of conda executable.
+      --conda_exec FILE               Location of conda executable.
       --conda_debug                   Enable more verbose conda logging.
       --conda_channels, --conda_ensure_channels TEXT
                                       Ensure conda is configured with specified

diff --git a/docs/commands/conda_init.rst b/docs/commands/conda_init.rst
@@ -29,7 +29,7 @@ if Conda is already installed.
 
       --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                       commands.
-      --conda_exec PATH               Location of conda executable.
+      --conda_exec FILE               Location of conda executable.
       --conda_debug                   Enable more verbose conda logging.
       --conda_channels, --conda_ensure_channels TEXT
                                       Ensure conda is configured with specified

diff --git a/docs/commands/conda_install.rst b/docs/commands/conda_install.rst
@@ -20,7 +20,7 @@ Install conda packages for tool requirements.
                                       subdirectories.
       --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                       commands.
-      --conda_exec PATH               Location of conda executable.
+      --conda_exec FILE               Location of conda executable.
       --conda_debug                   Enable more verbose conda logging.
       --conda_channels, --conda_ensure_channels TEXT
                                       Ensure conda is configured with specified

diff --git a/docs/commands/conda_search.rst b/docs/commands/conda_search.rst
@@ -21,7 +21,7 @@ Implicitly adds channels Planemo is configured with.
 
       --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                       commands.
-      --conda_exec PATH               Location of conda executable.
+      --conda_exec FILE               Location of conda executable.
       --conda_debug                   Enable more verbose conda logging.
       --conda_channels, --conda_ensure_channels TEXT
                                       Ensure conda is configured with specified

diff --git a/docs/commands/container_register.rst b/docs/commands/container_register.rst
@@ -30,7 +30,7 @@ so that a container can be created and registered for these tools.
                                       namespace biocontainers.
       --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                       commands.
-      --conda_exec PATH               Location of conda executable.
+      --conda_exec FILE               Location of conda executable.
       --conda_debug                   Enable more verbose conda logging.
       --conda_channels, --conda_ensure_channels TEXT
                                       Ensure conda is configured with specified

diff --git a/docs/commands/run.rst b/docs/commands/run.rst
@@ -63,7 +63,7 @@ Planemo command for running tools and jobs.
       --mulled_containers, --biocontainers
                                       Test tools against mulled containers (forces
                                       --docker).
-      --job_config_file PATH          Job configuration file for Galaxy to target.
+      --job_config_file FILE          Job configuration file for Galaxy to target.
       --tool_dependency_dir DIRECTORY
                                       Tool dependency dir for Galaxy to target.
       --port INTEGER                  Port to serve Galaxy on (default is 9090).
@@ -75,7 +75,7 @@ Planemo command for running tools and jobs.
       --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 PATH
+      --dependency_resolvers_config_file FILE
                                       Dependency resolver configuration for Galaxy
                                       to target.
       --brew_dependency_resolution    Configure Galaxy to use plain brew dependency
@@ -85,7 +85,7 @@ Planemo command for running tools and jobs.
       --no_dependency_resolution      Configure Galaxy with no dependency resolvers.
       --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                       commands.
-      --conda_exec PATH               Location of conda executable.
+      --conda_exec FILE               Location of conda executable.
       --conda_debug                   Enable more verbose conda logging.
       --conda_channels, --conda_ensure_channels TEXT
                                       Ensure conda is configured with specified
@@ -150,7 +150,7 @@ Planemo command for running tools and jobs.
                                       and if CWL support is merged into Galaxy.
       --output_directory, --outdir DIRECTORY
                                       Where to store outputs of a 'run' task.
-      --output_json PATH              Where to store JSON dictionary describing
+      --output_json FILE              Where to store JSON dictionary describing
                                       outputs of a 'run' task.
       --engine [galaxy|docker_galaxy|cwltool|toil|external_galaxy]
                                       Select an engine to run or test artifacts such

diff --git a/docs/commands/serve.rst b/docs/commands/serve.rst
@@ -79,7 +79,7 @@ Galaxy instance.
       --mulled_containers, --biocontainers
                                       Test tools against mulled containers (forces
                                       --docker).
-      --job_config_file PATH          Job configuration file for Galaxy to target.
+      --job_config_file FILE          Job configuration file for Galaxy to target.
       --tool_dependency_dir DIRECTORY
                                       Tool dependency dir for Galaxy to target.
       --port INTEGER                  Port to serve Galaxy on (default is 9090).
@@ -102,7 +102,7 @@ Galaxy instance.
       --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 PATH
+      --dependency_resolvers_config_file FILE
                                       Dependency resolver configuration for Galaxy
                                       to target.
       --brew_dependency_resolution    Configure Galaxy to use plain brew dependency
@@ -112,7 +112,7 @@ Galaxy instance.
       --no_dependency_resolution      Configure Galaxy with no dependency resolvers.
       --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                       commands.
-      --conda_exec PATH               Location of conda executable.
+      --conda_exec FILE               Location of conda executable.
       --conda_debug                   Enable more verbose conda logging.
       --conda_channels, --conda_ensure_channels TEXT
                                       Ensure conda is configured with specified
@@ -167,7 +167,7 @@ Galaxy instance.
                                       it. Use --no_galaxy_single_user to prevent
                                       Galaxy from running this way.
       --daemon                        Serve Galaxy process as a daemon.
-      --pid_file PATH                 Location of pid file is executed with
+      --pid_file FILE                 Location of pid file is executed with
                                       --daemon.
       --ignore_dependency_problems    When installing shed repositories for
                                       workflows, ignore dependency issues. These

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|ChIP-seq|Combinatorial Selections|Computational chemistry|Constructive Solid Geometry|Convert Formats|Epigenetics|Data Export|Data Managers|Data Source|Fasta Manipulation|Fastq Manipulation|Flow Cytometry Analysis|Genome-Wide Association Study|Genomic Interval Operations|Graphics|Imaging|Metabolomics|Metagenomics|Micro-array Analysis|Next Gen Mappers|NLP|Ontology Manipulation|Phylogenetics|Proteomics|RNA|SAM|Sequence Analysis|Statistics|Systems Biology|Text Manipulation|Tool Dependency Packages|Tool Generators|Transcriptomics|Variant Analysis|Visualization|Web Services]
+      --category [Assembly|ChIP-seq|Combinatorial Selections|Computational chemistry|Constructive Solid Geometry|Convert Formats|Data Export|Data Managers|Data Source|Entomology|Epigenetics|Fasta Manipulation|Fastq Manipulation|Flow Cytometry Analysis|Genome annotation|Genome editing|Genome-Wide Association Study|Genomic Interval Operations|Graphics|Imaging|Machine Learning|Metabolomics|Metagenomics|Micro-array Analysis|Molecular Dynamics|Next Gen Mappers|NLP|Ontology Manipulation|Phylogenetics|Proteomics|RNA|SAM|Sequence Analysis|Statistics|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
@@ -87,7 +87,7 @@ logged into and explored interactively.
       --mulled_containers, --biocontainers
                                       Test tools against mulled containers (forces
                                       --docker).
-      --job_config_file PATH          Job configuration file for Galaxy to target.
+      --job_config_file FILE          Job configuration file for Galaxy to target.
       --tool_dependency_dir DIRECTORY
                                       Tool dependency dir for Galaxy to target.
       --port INTEGER                  Port to serve Galaxy on (default is 9090).
@@ -99,7 +99,7 @@ logged into and explored interactively.
       --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 PATH
+      --dependency_resolvers_config_file FILE
                                       Dependency resolver configuration for Galaxy
                                       to target.
       --brew_dependency_resolution    Configure Galaxy to use plain brew dependency
@@ -109,7 +109,7 @@ logged into and explored interactively.
       --no_dependency_resolution      Configure Galaxy with no dependency resolvers.
       --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                       commands.
-      --conda_exec PATH               Location of conda executable.
+      --conda_exec FILE               Location of conda executable.
       --conda_debug                   Enable more verbose conda logging.
       --conda_channels, --conda_ensure_channels TEXT
                                       Ensure conda is configured with specified
@@ -163,7 +163,7 @@ logged into and explored interactively.
                                       one user and this user is automatically logged
                                       it. Use --no_galaxy_single_user to prevent
                                       Galaxy from running this way.
-      --pid_file PATH                 Location of pid file is executed with
+      --pid_file FILE                 Location of pid file is executed with
                                       --daemon.
       --daemon                        Serve Galaxy process as a daemon.
       --skip_dependencies             Do not install shed dependencies as part of

diff --git a/docs/commands/shed_test.rst b/docs/commands/shed_test.rst
@@ -88,7 +88,7 @@ This command requires the target to be version 15.07 or newer.
       --mulled_containers, --biocontainers
                                       Test tools against mulled containers (forces
                                       --docker).
-      --job_config_file PATH          Job configuration file for Galaxy to target.
+      --job_config_file FILE          Job configuration file for Galaxy to target.
       --tool_dependency_dir DIRECTORY
                                       Tool dependency dir for Galaxy to target.
       --update_test_data              Update test-data directory with job outputs
@@ -106,8 +106,10 @@ This command requires the target to be version 15.07 or newer.
                                       in CI)
       --test_output_markdown PATH     Output test report (Markdown style - for
                                       humans & computers)
-      --test_output_xunit PATH        Output test report (xUnit style - for
-                                      computers).
+      --test_output_xunit PATH        Output test report (xunit style - for CI
+                                      systems
+      --test_output_junit PATH        Output test report (jUnit style - for CI
+                                      systems
       --test_output_json PATH         Output test report (planemo json) defaults to
                                       tool_test_output.json.
       --job_output_files DIRECTORY    Write job outputs to specified directory.

diff --git a/docs/commands/shed_upload.rst b/docs/commands/shed_upload.rst
@@ -63,7 +63,7 @@ metadata (to handle metadata changes in ``.shed.yml`` files).
                                    populated by the shed would be updated.)
       --tar_only                   Produce tar file for upload but do not publish to
                                    a tool shed.
-      --tar PATH                   Specify a pre-existing tar file instead of
+      --tar FILE                   Specify a pre-existing tar file instead of
                                    automatically building one as part of this
                                    command.
       --help                       Show this message and exit.