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Merge pull request #1099 from nsoranzo/run_tests.sh_invocation_fix
Fix ``run_tests.sh`` invocation
2 parents 1f9fdff + 730818c commit 38227c1

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‎.circleci/config.yml

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tox-env:
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type: string
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docker:
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- image: circleci/python:3.5-node
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- image: circleci/python:3.6-node
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steps:
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- checkout
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- run: git submodule sync
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matrix:
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parameters:
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tox-env:
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- "py35-diagnostic-unit-servebasic-gx-dev"
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- "py35-unit-nonredundant-noclientbuild-noshed-gx-2005"
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- "py35-unit-nonredundant-noclientbuild-noshed-gx-dev"
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- "py35-unit-nonredundant-noclientbuild-noshed"
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- "py36-diagnostic-unit-servebasic-gx-dev"
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- "py36-unit-nonredundant-noclientbuild-noshed-gx-2005"
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- "py36-unit-nonredundant-noclientbuild-noshed-gx-dev"
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- "py36-unit-nonredundant-noclientbuild-noshed"

‎.travis.yml

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env: TOX_ENV=py37-lint_docstrings
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- python: 3.7
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env: TOX_ENV=py37-unit-diagnostic-serveshed
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- python: 3.7
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env: TOX_ENV=py37-unit-quick
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- python: 3.7
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env: TOX_ENV=py37-unit-nonredundant-noclientbuild-noshed-gx-2005
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- python: 3.7
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env: TOX_ENV=py37-unit-nonredundant-noclientbuild-noshed-gx-master
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- python: 3.7

‎CONTRIBUTING.rst

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@@ -106,7 +106,7 @@ Before you submit a pull request, check that it meets these guidelines:
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1. If the pull request adds functionality, the docs should be updated. Put
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your new functionality into a function with a docstring.
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2. The pull request should work for Python >=3.5. Check
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2. The pull request should work for Python >=3.6. Check
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https://travis-ci.org/galaxyproject/planemo/pull_requests
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and make sure that the tests pass for all supported Python versions.
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% make tox ENV=py37-unit ARGS='--tests tests/test_shed_upload.py'
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This will use Tox_ to run the specified tests using Python 3.7. ``ENV`` here
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can be used to specify different Python version (e.g. ``py35`` or
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can be used to specify different Python version (e.g. ``py36`` or
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``py37``).
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Even more granularity is also possible by specifying specific test methods.::
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testing environment. Planemo defines the following environments:
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``py37-lint``
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Lint the planemo code using Python 3.7..
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Lint the planemo code using Python 3.7.
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``py37-lint_docs``
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Lint the docs reStructuredText.
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``py37-lint_docstrings``
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Lint the project Python docstrings (doesn't pass currently).
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``py35-unit-quick``
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Run the fastest unit tests (with least external dependencies) on Python 3.5.
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``py36-unit-quick``
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Run the fastest unit tests (with least external dependencies) on Python 3.6.
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``py36-unit-nonredundant-noclientbuild-gx-2005``
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Run tests that are marked as targeting a Galaxy branch and test against Galaxy 20.05.

‎docs/commands.rst

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.. include:: commands/conda_search.rst
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.. include:: commands/config_init.rst
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.. include:: commands/container_register.rst
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.. include:: commands/create_alias.rst
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.. include:: commands/database_create.rst
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.. include:: commands/database_delete.rst
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.. include:: commands/database_list.rst
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.. include:: commands/delete_alias.rst
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.. include:: commands/docker_build.rst
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.. include:: commands/docker_shell.rst
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.. include:: commands/dockstore_init.rst
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.. include:: commands/docs.rst
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.. include:: commands/lint.rst
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.. include:: commands/list_alias.rst
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.. include:: commands/list_invocations.rst
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.. include:: commands/list_repos.rst
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.. include:: commands/merge_test_reports.rst
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.. include:: commands/mull.rst
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.. include:: commands/workflow_edit.rst
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.. include:: commands/workflow_job_init.rst
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.. include:: commands/workflow_lint.rst
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.. include:: commands/workflow_test_init.rst
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.. include:: commands/workflow_test_init.rst
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.. include:: commands/workflow_upload.rst

‎docs/commands/ci_find_repos.rst

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Find all shed repositories in one or more directories.
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Currently, a shed repository is considered a directory with a .shed.yml
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file.
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Currently, a repository is considered any directory with a .shed.yml
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or .dockstore.yml file.
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**Options**::
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--changed_in_commit_range TEXT Exclude paths unchanged in git commit range.
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--chunk_count INTEGER Split output into chunks of this many item and
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print --chunk such group.
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--chunk INTEGER When output is split into --chunk_count
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groups, output the group 0-indexedby this
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option.
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--output TEXT File to output to, or - for standard output.
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--help Show this message and exit.
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‎docs/commands/ci_find_tools.rst

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--changed_in_commit_range TEXT Exclude paths unchanged in git commit range.
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--chunk_count INTEGER Split output into chunks of this many item and
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print --chunk such group.
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--chunk INTEGER When output is split into --chunk_count
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groups, output the group 0-indexedby this
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option.
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--output TEXT File to output to, or - for standard output.
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--group_tools Group tools of the same repository on a single
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line.
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--help Show this message and exit.
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‎docs/commands/clone.rst

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$ git commit -m "Fix bwa problem."
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$ planemo pull_request -m "Fix bwa problem."
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These changes do require that a github username and password are
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specified in ~/.planemo.yml.
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These changes do require that a github access token is
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specified in ~/.planemo.yml. An access token can be generated by going
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to https://github.com/settings/tokens.
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**Options**::
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‎docs/commands/conda_build.rst

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--conda_prefix DIRECTORY Conda prefix to use for conda dependency
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commands.
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--conda_exec FILE Location of conda executable.
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--conda_debug Enable more verbose conda logging.
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--conda_channels, --conda_ensure_channels TEXT
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comma separated list of channels.
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--conda_use_local Use locally built packages while building
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Conda environments.
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--help Show this message and exit.
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‎docs/commands/conda_env.rst

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--conda_prefix DIRECTORY Conda prefix to use for conda dependency
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commands.
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--conda_exec FILE Location of conda executable.
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--conda_debug Enable more verbose conda logging.
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--conda_channels, --conda_ensure_channels TEXT
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comma separated list of channels.
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--conda_use_local Use locally built packages while building
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--help Show this message and exit.
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‎docs/commands/conda_init.rst

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--conda_prefix DIRECTORY Conda prefix to use for conda dependency
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--conda_exec FILE Location of conda executable.
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--conda_debug Enable more verbose conda logging.
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--conda_channels, --conda_ensure_channels TEXT
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comma separated list of channels.
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--conda_use_local Use locally built packages while building
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--help Show this message and exit.
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‎docs/commands/conda_install.rst

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-r, --recursive Recursively perform command for
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--conda_prefix DIRECTORY Conda prefix to use for conda dependency
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commands.
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--conda_exec FILE Location of conda executable.
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--conda_debug Enable more verbose conda logging.
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--conda_channels, --conda_ensure_channels TEXT
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comma separated list of channels.
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--conda_use_local Use locally built packages while building
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--global Install Conda dependencies globally instead of
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in requirement specific environments packaged
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for tools. If the Conda bin directory is on
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your PATH, tools may still use binaries but
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this is more designed for interactive testing
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and debugging.
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--conda_auto_init / --no_conda_auto_init
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Conda dependency resolution for Galaxy will
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auto install conda itself using miniconda if
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--help Show this message and exit.
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‎docs/commands/conda_lint.rst

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--fail_level [warn|error]
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-r, --recursive Recursively perform command for nested conda
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directories.
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--help Show this message and exit.
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‎docs/commands/conda_search.rst

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--conda_prefix DIRECTORY Conda prefix to use for conda dependency
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commands.
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--conda_exec FILE Location of conda executable.
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--conda_debug Enable more verbose conda logging.
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--conda_channels, --conda_ensure_channels TEXT
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comma separated list of channels.
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--conda_use_local Use locally built packages while building
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--help Show this message and exit.
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‎docs/commands/container_register.rst

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-r, --recursive Recursively perform command for
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--mulled_namespace TEXT Build a mulled image with the specified
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namespace - defaults to biocontainers. Galaxy
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currently only recognizes images with the
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namespace biocontainers.
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--conda_prefix DIRECTORY Conda prefix to use for conda dependency
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commands.
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--conda_exec FILE Location of conda executable.
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--conda_debug Enable more verbose conda logging.
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--conda_channels, --conda_ensure_channels TEXT
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--conda_use_local Use locally built packages while building
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--output_directory DIRECTORY Container registration directory (defaults to
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‎docs/commands/create_alias.rst

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``create_alias`` command
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======================================
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This section is auto-generated from the help text for the planemo command
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``create_alias``. This help message can be generated with ``planemo create_alias
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--help``.
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**Usage**::
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planemo create_alias [OPTIONS] OBJ
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**Help**
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Add an alias for a path or a workflow or dataset ID. Aliases are associated with a particular planemo profile.
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**Options**::
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--alias TEXT Name of an alias.
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--profile TEXT Name of profile (created with the profile_create command) to
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‎docs/commands/database_create.rst

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--postgres_psql_path TEXT Name or or path to postgres client binary
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--postgres_database_user TEXT Postgres username for managed development
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--postgres_database_host TEXT Postgres host name for managed development
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--postgres_database_port TEXT Postgres port for managed development
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--docker_host TEXT Docker host to target when executing docker
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--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
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‎docs/commands/database_delete.rst

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--postgres_psql_path TEXT Name or or path to postgres client binary
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--postgres_database_user TEXT Postgres username for managed development
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databases.
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--postgres_database_host TEXT Postgres host name for managed development
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--postgres_database_port TEXT Postgres port for managed development
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--docker_cmd TEXT Command used to launch docker (defaults to
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docker).
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--docker_host TEXT Docker host to target when executing docker
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commands (defaults to localhost).
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--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
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--help Show this message and exit.
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