Merge pull request #1099 from nsoranzo/run_tests.sh_invocation_fix

Fix ``run_tests.sh`` invocation
galaxyproject · Nov 24, 2020 · 38227c1 · 38227c1
2 parents 1f9fdff + 730818c
commit 38227c1
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Showing 75 changed files with 807 additions and 90 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -5,7 +5,7 @@ jobs:
         tox-env:
           type: string
       docker:
-        - image: circleci/python:3.5-node
+        - image: circleci/python:3.6-node
       steps:
         - checkout
         - run: git submodule sync
@@ -19,7 +19,7 @@ workflows:
         matrix:
           parameters:
             tox-env:
-              - "py35-diagnostic-unit-servebasic-gx-dev"
-              - "py35-unit-nonredundant-noclientbuild-noshed-gx-2005"
-              - "py35-unit-nonredundant-noclientbuild-noshed-gx-dev"
-              - "py35-unit-nonredundant-noclientbuild-noshed"
+              - "py36-diagnostic-unit-servebasic-gx-dev"
+              - "py36-unit-nonredundant-noclientbuild-noshed-gx-2005"
+              - "py36-unit-nonredundant-noclientbuild-noshed-gx-dev"
+              - "py36-unit-nonredundant-noclientbuild-noshed"
diff --git a/.travis.yml b/.travis.yml
@@ -6,10 +6,6 @@ matrix:
       env: TOX_ENV=py37-lint_docstrings
     - python: 3.7
       env: TOX_ENV=py37-unit-diagnostic-serveshed
-    - python: 3.7
-      env: TOX_ENV=py37-unit-quick
-    - python: 3.7
-      env: TOX_ENV=py37-unit-nonredundant-noclientbuild-noshed-gx-2005
     - python: 3.7
       env: TOX_ENV=py37-unit-nonredundant-noclientbuild-noshed-gx-master
     - python: 3.7

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -106,7 +106,7 @@ Before you submit a pull request, check that it meets these guidelines:
 
 1. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring.
-2. The pull request should work for Python >=3.5. Check
+2. The pull request should work for Python >=3.6. Check
    https://travis-ci.org/galaxyproject/planemo/pull_requests
    and make sure that the tests pass for all supported Python versions.
 
@@ -118,7 +118,7 @@ To run a subset of tests::
     % make tox ENV=py37-unit ARGS='--tests tests/test_shed_upload.py'
 
 This will use Tox_ to run the specified tests using Python 3.7. ``ENV`` here
-can be used to specify different Python version (e.g. ``py35`` or
+can be used to specify different Python version (e.g. ``py36`` or
 ``py37``).
 
 Even more granularity is also possible by specifying specific test methods.::
@@ -148,16 +148,16 @@ Tox_ is a tool to automate testing across different Python versions. The
 testing environment. Planemo defines the following environments:
 
 ``py37-lint``
-    Lint the planemo code using Python 3.7..
+    Lint the planemo code using Python 3.7.
 
 ``py37-lint_docs``
     Lint the docs reStructuredText.
 
 ``py37-lint_docstrings``
     Lint the project Python docstrings (doesn't pass currently).
 
-``py35-unit-quick``
-    Run the fastest unit tests (with least external dependencies) on Python 3.5.
+``py36-unit-quick``
+    Run the fastest unit tests (with least external dependencies) on Python 3.6.
 
 ``py36-unit-nonredundant-noclientbuild-gx-2005``
     Run tests that are marked as targeting a Galaxy branch and test against Galaxy 20.05.

diff --git a/docs/commands.rst b/docs/commands.rst
@@ -18,14 +18,18 @@ documentation describes these commands.
 .. include:: commands/conda_search.rst
 .. include:: commands/config_init.rst
 .. include:: commands/container_register.rst
+.. include:: commands/create_alias.rst
 .. include:: commands/database_create.rst
 .. include:: commands/database_delete.rst
 .. include:: commands/database_list.rst
+.. include:: commands/delete_alias.rst
 .. include:: commands/docker_build.rst
 .. include:: commands/docker_shell.rst
 .. include:: commands/dockstore_init.rst
 .. include:: commands/docs.rst
 .. include:: commands/lint.rst
+.. include:: commands/list_alias.rst
+.. include:: commands/list_invocations.rst
 .. include:: commands/list_repos.rst
 .. include:: commands/merge_test_reports.rst
 .. include:: commands/mull.rst
@@ -62,4 +66,5 @@ documentation describes these commands.
 .. include:: commands/workflow_edit.rst
 .. include:: commands/workflow_job_init.rst
 .. include:: commands/workflow_lint.rst
-.. include:: commands/workflow_test_init.rst
+.. include:: commands/workflow_test_init.rst
+.. include:: commands/workflow_upload.rst
diff --git a/docs/commands/ci_find_repos.rst b/docs/commands/ci_find_repos.rst
@@ -14,8 +14,8 @@ This section is auto-generated from the help text for the planemo command
 
 Find all shed repositories in one or more directories.
 
-Currently, a shed repository is considered a directory with a .shed.yml
-file.
+Currently, a repository is considered any directory with a .shed.yml
+or .dockstore.yml file.
 
 **Options**::
 
@@ -25,9 +25,11 @@ file.
       --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.
+    
       --chunk INTEGER                 When output is split into --chunk_count
                                       groups, output the group 0-indexedby this
                                       option.
+    
       --output TEXT                   File to output to, or - for standard output.
       --help                          Show this message and exit.
     
diff --git a/docs/commands/ci_find_tools.rst b/docs/commands/ci_find_tools.rst
@@ -25,11 +25,14 @@ operations over for continuous integration operations.
       --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.
+    
       --chunk INTEGER                 When output is split into --chunk_count
                                       groups, output the group 0-indexedby this
                                       option.
+    
       --output TEXT                   File to output to, or - for standard output.
       --group_tools                   Group tools of the same repository on a single
                                       line.
+    
       --help                          Show this message and exit.
     
diff --git a/docs/commands/clone.rst b/docs/commands/clone.rst
@@ -27,8 +27,9 @@ repository to allow a subsequent pull request to fix a problem with bwa.
     $ git commit -m "Fix bwa problem."
     $ planemo pull_request -m "Fix bwa problem."
 
-These changes do require that a github username and password are
-specified in ~/.planemo.yml.
+These changes do require that a github access token is
+specified in ~/.planemo.yml. An access token can be generated by going
+to https://github.com/settings/tokens.
 
 **Options**::
 

diff --git a/docs/commands/conda_build.rst b/docs/commands/conda_build.rst
@@ -18,12 +18,15 @@ Perform conda build with Planemo's conda.
 
       --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                       commands.
+    
       --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
                                       comma separated list of channels.
+    
       --conda_use_local               Use locally built packages while building
                                       Conda environments.
+    
       --help                          Show this message and exit.
     
diff --git a/docs/commands/conda_env.rst b/docs/commands/conda_env.rst
@@ -32,12 +32,15 @@ tool.
 
       --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                       commands.
+    
       --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
                                       comma separated list of channels.
+    
       --conda_use_local               Use locally built packages while building
                                       Conda environments.
+    
       --help                          Show this message and exit.
     
diff --git a/docs/commands/conda_init.rst b/docs/commands/conda_init.rst
@@ -29,12 +29,15 @@ if Conda is already installed.
 
       --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                       commands.
+    
       --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
                                       comma separated list of channels.
+    
       --conda_use_local               Use locally built packages while building
                                       Conda environments.
+    
       --help                          Show this message and exit.
     
diff --git a/docs/commands/conda_install.rst b/docs/commands/conda_install.rst
@@ -18,24 +18,30 @@ Install conda packages for tool requirements.
 
       -r, --recursive                 Recursively perform command for
                                       subdirectories.
+    
       --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                       commands.
+    
       --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
                                       comma separated list of channels.
+    
       --conda_use_local               Use locally built packages while building
                                       Conda environments.
+    
       --global                        Install Conda dependencies globally instead of
                                       in requirement specific environments packaged
                                       for tools. If the Conda bin directory is on
                                       your PATH, tools may still use binaries but
                                       this is more designed for interactive testing
                                       and debugging.
+    
       --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.
+    
       --help                          Show this message and exit.
     
diff --git a/docs/commands/conda_lint.rst b/docs/commands/conda_lint.rst
@@ -25,5 +25,6 @@ https://github.com/ContinuumIO/anaconda-verify.
       --fail_level [warn|error]
       -r, --recursive                 Recursively perform command for nested conda
                                       directories.
+    
       --help                          Show this message and exit.
     
diff --git a/docs/commands/conda_search.rst b/docs/commands/conda_search.rst
@@ -21,12 +21,15 @@ Implicitly adds channels Planemo is configured with.
 
       --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                       commands.
+    
       --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
                                       comma separated list of channels.
+    
       --conda_use_local               Use locally built packages while building
                                       Conda environments.
+    
       --help                          Show this message and exit.
     
diff --git a/docs/commands/container_register.rst b/docs/commands/container_register.rst
@@ -24,28 +24,37 @@ so that a container can be created and registered for these tools.
 
       -r, --recursive                 Recursively perform command for
                                       subdirectories.
+    
       --mulled_namespace TEXT         Build a mulled image with the specified
                                       namespace - defaults to biocontainers. Galaxy
                                       currently only recognizes images with the
                                       namespace biocontainers.
+    
       --conda_prefix DIRECTORY        Conda prefix to use for conda dependency
                                       commands.
+    
       --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
                                       comma separated list of channels.
+    
       --conda_use_local               Use locally built packages while building
                                       Conda environments.
+    
       --output_directory DIRECTORY    Container registration directory (defaults to
                                       ~/.planemo/multi-package-containers.
+    
       -m, --message TEXT              Commit and pull request message template for
                                       registration interactions.
+    
       --pull_request / --no_pull_request
                                       Fork and create a pull request against
                                       BioContainers/multi-package-containers for
                                       these changes.
+    
       --force_push / --no_force_push  Force push branch for pull request in case it
                                       already exists.
+    
       --help                          Show this message and exit.
     
diff --git a/docs/commands/create_alias.rst b/docs/commands/create_alias.rst
@@ -0,0 +1,26 @@
+
+``create_alias`` command
+======================================
+
+This section is auto-generated from the help text for the planemo command
+``create_alias``. This help message can be generated with ``planemo create_alias
+--help``.
+
+**Usage**::
+
+    planemo create_alias [OPTIONS] OBJ
+
+**Help**
+
+
+Add an alias for a path or a workflow or dataset ID. Aliases are associated with a particular planemo profile.
+
+**Options**::
+
+
+      --alias TEXT    Name of an alias.
+      --profile TEXT  Name of profile (created with the profile_create command) to
+                      use with this command.  [required]
+    
+      --help          Show this message and exit.
+    
diff --git a/docs/commands/database_create.rst b/docs/commands/database_create.rst
@@ -69,21 +69,29 @@ be set by setting up a file ``~/.pgpass`` file with the following contents.
                                       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.
+    
       --docker_cmd TEXT               Command used to launch docker (defaults to
                                       docker).
+    
       --docker_sudo / --no_docker_sudo
                                       Flag to use sudo when running docker.
       --docker_host TEXT              Docker host to target when executing docker
                                       commands (defaults to localhost).
+    
       --docker_sudo_cmd TEXT          sudo command to use when --docker_sudo is
                                       enabled (defaults to sudo).
+    
       --help                          Show this message and exit.
     
diff --git a/docs/commands/database_delete.rst b/docs/commands/database_delete.rst
@@ -69,21 +69,29 @@ be set by setting up a file ``~/.pgpass`` file with the following contents.
                                       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.
+    
       --docker_cmd TEXT               Command used to launch docker (defaults to
                                       docker).
+    
       --docker_sudo / --no_docker_sudo
                                       Flag to use sudo when running docker.
       --docker_host TEXT              Docker host to target when executing docker
                                       commands (defaults to localhost).
+    
       --docker_sudo_cmd TEXT          sudo command to use when --docker_sudo is
                                       enabled (defaults to sudo).
+    
       --help                          Show this message and exit.